RPS-BLAST 2.2.16 [Mar-25-2007]
Database: 40scop73nmM
9549 sequences; 1,678,726 total letters
Searching..................................................done
Query= ABO50796.1 dred0 ABO50796.1 GIB00494CH01 "RNA polymerase,
sigma-24 subunit, ECF subfamily"
(200 letters)
Score E
Sequences producing significant alignments: (bits) Value
1or7A2 [a.177.1.1] RNA POLYMERASE SIGMA-E FACTOR A:-1 -- 111 94 2e-22
1h3lA [a.177.1.1] RNA POLYMERASE SIGMA FACTOR 86 5e-20
1iw7F3 [a.177.1.1] RNA POLYMERASE SIGMA-70 SUBUNIT F:74 -- 257 85 5e-20
1z77A2 [a.121.1.1] TRANSCRIPTIONAL REGULATOR (TETR FAMILY) A:76 ... 83 2e-19
1rp3A3 [a.177.1.1] RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA) A... 80 2e-18
1k78A1 [a.4.1.5] PAIRED BOX PROTEIN PAX5 A:19 -- 81 52 5e-10
1p4wA [a.4.6.2] RCSB 51 1e-09
1yioA1 [a.4.6.2] RESPONSE REGULATORY PROTEIN A:131 -- 200 50 2e-09
1ku3A [a.4.13.2] SIGMA FACTOR SIGA 50 2e-09
1iw7F2 [a.4.13.2] RNA POLYMERASE SIGMA-70 SUBUNIT F:319 -- 423 50 3e-09
1aw8.1 [b.52.2.1] L-ASPARTATE-ALPHA-DECARBOXYLASE A:- -- - B:- -- - 44 1e-07
1sigA [a.177.1.1] RNA POLYMERASE PRIMARY SIGMA FACTOR 44 1e-07
1rp3A2 [a.4.13.2] RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA) A:... 44 2e-07
1fseA [a.4.6.2] GERE 43 4e-07
1tc3C [a.4.1.2] PROTEIN (TC3 TRANSPOSASE) 41 1e-06
1h0mA1 [a.4.6.2] TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR A:170 --... 40 2e-06
1or7A1 [a.4.13.2] RNA POLYMERASE SIGMA-E FACTOR A:120 -- 187 40 3e-06
1c9bA2 [a.74.1.2] GENERAL TRANSCRIPTION FACTOR IIB A:208 -- 316 39 5e-06
2dk5A1 [a.4.5.85] DNA-DIRECTED RNA POLYMERASE III 39 KDA A:8 -- 85 39 6e-06
1pdnC [a.4.1.5] PROTEIN (PRD PAIRED) 32 5e-04
1a04A1 [a.4.6.2] NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL... 32 6e-04
1fseF [a.4.6.2] GERE 32 7e-04
1resA [a.4.1.2] GAMMA DELTA-RESOLVASE 32 8e-04
>1or7A2 [a.177.1.1] RNA POLYMERASE SIGMA-E FACTOR A:-1 -- 111
Length = 113
Score = 93.8 bits (233), Expect = 2e-22
Identities = 44/93 (47%), Positives = 63/93 (67%), Gaps = 1/93 (1%)
Query: 2 PLEDQLLVERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALP 61
L DQ+LVER +KGD++AF LV Y++KV ++ R + + D D+ Q+AFIK Y+AL
Sbjct: 6 QLTDQVLVERVQKGDQKAFNLLVVRYQHKVASLVSRYVPSG-DVPDVVQEAFIKAYRALD 64
Query: 62 NFRGDSSFSTWIYHITVNVCRDELRKRQRRPTV 94
+FRGDS+F TW+Y I VN ++ L + RRP
Sbjct: 65 SFRGDSAFYTWLYRIAVNTAKNYLVAQGRRPPS 97
>1h3lA [a.177.1.1] RNA POLYMERASE SIGMA FACTOR
Length = 75
Score = 85.6 bits (212), Expect = 5e-20
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 10 ERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALPNFRGDSSF 69
ERS + +R+A E L ++Y + A R+ N ADA DL Q+ + K Y + FR ++
Sbjct: 4 ERSARFERDALEFLDQMY-----SAALRMTRNPADAEDLVQETYAKAYASFHQFREGTNL 58
Query: 70 STWIYHITVNVCRDELR 86
W+Y I N + R
Sbjct: 59 KAWLYRILTNTFINSYR 75
>1iw7F3 [a.177.1.1] RNA POLYMERASE SIGMA-70 SUBUNIT F:74 -- 257
Length = 184
Score = 85.5 bits (211), Expect = 5e-20
Identities = 16/92 (17%), Positives = 30/92 (32%), Gaps = 2/92 (2%)
Query: 1 MPLEDQLLVERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQAL 60
++ + A +HL+ V +IA + G DL Q+ + +A+
Sbjct: 92 SLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAV 151
Query: 61 PNFRGD--SSFSTWIYHITVNVCRDELRKRQR 90
F FST+ + + R
Sbjct: 152 EKFEYKRRFKFSTYATWWIRQAINRAIADQAR 183
>1z77A2 [a.121.1.1] TRANSCRIPTIONAL REGULATOR (TETR FAMILY) A:76 --
200
Length = 125
Score = 83.5 bits (206), Expect = 2e-19
Identities = 6/95 (6%), Positives = 28/95 (29%), Gaps = 2/95 (2%)
Query: 2 PLEDQLLVERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALP 61
+ + + +G R+ + + + + + A D+ ++ +K
Sbjct: 24 EADFLITLVSVDEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLXWFF 83
Query: 62 NFRGDSSFSTW--IYHITVNVCRDELRKRQRRPTV 94
+ + T+ + + + + +
Sbjct: 84 SGFEEVYLRTYQGKPELLKRDXNTLVEEVKVXLRI 118
>1rp3A3 [a.177.1.1] RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA)
A:0 -- 86
Length = 87
Score = 80.0 bits (197), Expect = 2e-18
Identities = 16/84 (19%), Positives = 28/84 (33%), Gaps = 5/84 (5%)
Query: 10 ERSKKGDREAFEHLVRLYENKVYTIAYRL---MGNHADASDLAQDAFIKIYQALPNFRGD 66
++ ++ E L+ Y V IA + + D DL I + +A+ N +
Sbjct: 2 MKNPYSNQIEREELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTE 61
Query: 67 --SSFSTWIYHITVNVCRDELRKR 88
+I D LR
Sbjct: 62 NPKRAEAYIKLRIKGAIYDYLRSL 85
>1k78A1 [a.4.1.5] PAIRED BOX PROTEIN PAX5 A:19 -- 81
Length = 63
Score = 52.1 bits (125), Expect = 5e-10
Identities = 13/56 (23%), Positives = 19/56 (33%)
Query: 126 ETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQAL 181
+ L D R+ IV Q + +I+ L S G V L R +
Sbjct: 3 NQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETG 58
>1p4wA [a.4.6.2] RCSB
Length = 87
Score = 50.7 bits (121), Expect = 1e-09
Identities = 16/81 (19%), Positives = 30/81 (37%), Gaps = 3/81 (3%)
Query: 118 PEEMLDRSETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRA 177
PE + E + LS E++ + + EIA+ L S+ T+ S+ A
Sbjct: 3 PESVAKLLEKISAGGYGDKRLSPKESEVLRLF-AEGFLVTEIAKKLNRSIKTISSQKKSA 61
Query: 178 RQALKEKISKQMELITPAKRL 198
L + + L+ +
Sbjct: 62 MMKL--GVDNDIALLNYLSSV 80
>1yioA1 [a.4.6.2] RESPONSE REGULATORY PROTEIN A:131 -- 200
Length = 70
Score = 50.2 bits (120), Expect = 2e-09
Identities = 15/64 (23%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 126 ETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKI 185
ETQ ++ ++L+ ++++ + I+ L ++IA LG + TVK Q L +
Sbjct: 1 ETQDQLEQLFSSLTGREQQVLQLT-IRGLMNKQIAGELGIAEVTVKVHRHNIMQKLNVRS 59
Query: 186 SKQM 189
+
Sbjct: 60 LANL 63
>1ku3A [a.4.13.2] SIGMA FACTOR SIGA
Length = 61
Score = 50.1 bits (120), Expect = 2e-09
Identities = 13/60 (21%), Positives = 28/60 (46%), Gaps = 4/60 (6%)
Query: 131 IQACLNTLSDDYREIIVMR----EIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKIS 186
++ L+ LS+ ++ MR + +E EE+ G + ++ ++A + LK S
Sbjct: 2 LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLKYHES 61
>1iw7F2 [a.4.13.2] RNA POLYMERASE SIGMA-70 SUBUNIT F:319 -- 423
Length = 100
Score = 49.8 bits (119), Expect = 3e-09
Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 1/76 (1%)
Query: 114 NDPGPEEMLDRSETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSR 173
+ P P + +S ++ L+ LS+ ++ + EE+ G + ++
Sbjct: 19 HLPSPVDAATQSLLSEELEKALSKLSEREAMVL-KLRKGLIDGEEVGAFFGVTRERIRQI 77
Query: 174 LSRARQALKEKISKQM 189
++A + LK S+
Sbjct: 78 ENKALRKLKYHESRTR 93
>1aw8.1 [b.52.2.1] L-ASPARTATE-ALPHA-DECARBOXYLASE A:- -- - B:- --
-
Length = 115
Score = 44.5 bits (105), Expect = 1e-07
Identities = 12/76 (15%), Positives = 22/76 (28%), Gaps = 4/76 (5%)
Query: 21 EHLVR--LYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALPNFRGD--SSFSTWIYHI 76
+++ L+ KV G+ A D A I +A+ + FST+
Sbjct: 3 RTMLQGKLHRVKVTHADLHYEGSCAIDQDFLDAAGILENEAIDIWNVTNGKRFSTYAIAA 62
Query: 77 TVNVCRDELRKRQRRP 92
+
Sbjct: 63 ERGSRIISVNGAAAHC 78
>1sigA [a.177.1.1] RNA POLYMERASE PRIMARY SIGMA FACTOR
Length = 305
Score = 44.1 bits (104), Expect = 1e-07
Identities = 17/90 (18%), Positives = 33/90 (36%), Gaps = 5/90 (5%)
Query: 4 EDQLLVERSKKGDRE---AFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQAL 60
+ + + R G+ + A + +V V +IA + DL Q+ I + +A+
Sbjct: 216 QVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 275
Query: 61 PNF--RGDSSFSTWIYHITVNVCRDELRKR 88
F R FST+ + +
Sbjct: 276 DKFEYRRGYKFSTYATWWIRQAITRSIADQ 305
>1rp3A2 [a.4.13.2] RNA POLYMERASE SIGMA FACTOR SIGMA-28 (FLIA) A:164
-- 234
Length = 71
Score = 43.6 bits (102), Expect = 2e-07
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 118 PEEMLDRSETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRA 177
EE + + E ++ ++ L + + +I + +EL +E+A+IL S+ V ++A
Sbjct: 2 VEEEVIKRELTEKVKEAVSKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKA 61
Query: 178 RQALKEKI 185
+ L+E +
Sbjct: 62 LERLREML 69
>1fseA [a.4.6.2] GERE
Length = 67
Score = 42.8 bits (101), Expect = 4e-07
Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 135 LNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKISKQMELITP 194
L+ RE+ + +Q+ +EIA L S TV++ +S A Q L + + + +
Sbjct: 2 KPLLTKREREVFELL-VQDKTTKEIASELFISEKTVRNHISNAMQKL--GVKGRSQAVVE 58
Query: 195 AKRL 198
R+
Sbjct: 59 LLRM 62
>1tc3C [a.4.1.2] PROTEIN (TC3 TRANSPOSASE)
Length = 51
Score = 41.3 bits (97), Expect = 1e-06
Identities = 7/46 (15%), Positives = 18/46 (39%)
Query: 137 TLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALK 182
LSD R + + ++ ++ E++ + S ++ L
Sbjct: 5 ALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGT 50
>1h0mA1 [a.4.6.2] TRANSCRIPTIONAL ACTIVATOR PROTEIN TRAR A:170 --
234
Length = 65
Score = 40.1 bits (94), Expect = 2e-06
Identities = 12/62 (19%), Positives = 21/62 (33%), Gaps = 3/62 (4%)
Query: 137 TLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKISKQMELITPAK 196
L + EEIA++ G +V+ +L A + + + L A
Sbjct: 4 WLDPKEATYLRWI-AVGKTXEEIADVEGVKYNSVRVKLREAXKRF--DVRSKAHLTALAI 60
Query: 197 RL 198
R
Sbjct: 61 RR 62
>1or7A1 [a.4.13.2] RNA POLYMERASE SIGMA-E FACTOR A:120 -- 187
Length = 68
Score = 39.7 bits (92), Expect = 3e-06
Identities = 25/64 (39%), Positives = 42/64 (65%)
Query: 121 MLDRSETQAMIQACLNTLSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQA 180
++ E + ++ + +L +D R I +RE+ L+YEEIA I+ C +GTV+SR+ RAR+A
Sbjct: 2 LMLSEELRQIVFRTIESLPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRAREA 61
Query: 181 LKEK 184
+ K
Sbjct: 62 IDNK 65
>1c9bA2 [a.74.1.2] GENERAL TRANSCRIPTION FACTOR IIB A:208 -- 316
Length = 109
Score = 39.1 bits (91), Expect = 5e-06
Identities = 8/45 (17%), Positives = 17/45 (37%)
Query: 156 YEEIAEILGCSLGTVKSRLSRARQALKEKISKQMELITPAKRLAK 200
+EI +I G + T++ + + TP +L +
Sbjct: 64 QKEIGDIAGVADVTIRQSYRLIYPRAPDLFPTDFKFDTPVDKLPQ 108
>2dk5A1 [a.4.5.85] DNA-DIRECTED RNA POLYMERASE III 39 KDA A:8 -- 85
Length = 78
Score = 38.7 bits (90), Expect = 6e-06
Identities = 2/49 (4%), Positives = 12/49 (24%), Gaps = 3/49 (6%)
Query: 131 IQACLNTLSDDYREIIVM---REIQELAYEEIAEILGCSLGTVKSRLSR 176
+ + + + + + + ++ L + L
Sbjct: 4 NAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKN 52
>1pdnC [a.4.1.5] PROTEIN (PRD PAIRED)
Length = 123
Score = 32.3 bits (73), Expect = 5e-04
Identities = 11/50 (22%), Positives = 19/50 (38%)
Query: 138 LSDDYREIIVMREIQELAYEEIAEILGCSLGTVKSRLSRARQALKEKISK 187
L ++ R IV + I+ L S G V L+R ++ +
Sbjct: 17 LPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 66
>1a04A1 [a.4.6.2] NITRATE/NITRITE RESPONSE REGULATOR PROTEIN NARL
A:150 -- 216
Length = 67
Score = 32.0 bits (73), Expect = 6e-04
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 135 LNTLSDDYREIIVMREI-QELAYEEIAEILGCSLGTVKSRLSRARQALKEK 184
+N L+ RE +++ I Q L + IA L + TVK + + +K K
Sbjct: 4 VNQLTP--RERDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 52
>1fseF [a.4.6.2] GERE
Length = 50
Score = 31.9 bits (73), Expect = 7e-04
Identities = 8/45 (17%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 154 LAYEEIAEILGCSLGTVKSRLSRARQALKEKISKQMELITPAKRL 198
L E V++ +S A Q L + + + + R+
Sbjct: 3 LTKREREVFELLVQDKVRNHISNAMQKL--GVKGRSQAVVELLRM 45
>1resA [a.4.1.2] GAMMA DELTA-RESOLVASE
Length = 43
Score = 31.6 bits (72), Expect = 8e-04
Identities = 6/35 (17%), Positives = 14/35 (40%), Gaps = 1/35 (2%)
Query: 143 REIIVMREIQE-LAYEEIAEILGCSLGTVKSRLSR 176
V+ Q+ L I++ + + TV ++
Sbjct: 7 DRDAVLNMWQQGLGASHISKTMNIARSTVYKVINE 41
Database: 40scop73nmM
Posted date: Nov 2, 2009 11:39 AM
Number of letters in database: 1,678,726
Number of sequences in database: 9549
Lambda K H
0.323 0.139 0.424
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9549
Number of Hits to DB: 10,724,593
Number of extensions: 748388
Number of successful extensions: 3292
Number of sequences better than 1.0e-03: 10
Number of HSP's gapped: 3165
Number of HSP's successfully gapped: 154
Length of database: 100,000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)