Query psy3393
Match_columns 433
No_of_seqs 139 out of 202
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 23:51:19 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3393.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3393hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2252|consensus 100.0 6.8E-45 1.5E-49 375.0 21.7 304 76-433 62-405 (558)
2 PF02376 CUT: CUT domain; Int 100.0 1.1E-32 2.3E-37 227.4 6.7 82 350-431 4-86 (87)
3 KOG3755|consensus 96.0 0.0042 9E-08 67.7 2.7 71 359-429 377-448 (769)
4 PF04814 HNF-1_N: Hepatocyte n 92.7 0.16 3.4E-06 48.4 4.6 58 354-414 113-170 (180)
5 PRK09726 antitoxin HipB; Provi 92.7 0.45 9.7E-06 38.9 6.6 63 353-421 6-68 (88)
6 smart00530 HTH_XRE Helix-turn- 91.9 0.42 9.1E-06 31.8 4.7 52 364-421 2-53 (56)
7 PF13443 HTH_26: Cro/C1-type H 90.7 0.49 1.1E-05 35.5 4.5 54 363-422 1-55 (63)
8 TIGR03070 couple_hipB transcri 90.3 0.41 9E-06 34.3 3.6 38 359-397 2-39 (58)
9 PRK09706 transcriptional repre 89.7 1 2.2E-05 39.2 6.2 40 356-396 2-41 (135)
10 PF01381 HTH_3: Helix-turn-hel 89.0 0.82 1.8E-05 33.2 4.4 51 364-420 1-51 (55)
11 PF12844 HTH_19: Helix-turn-he 88.9 1.1 2.5E-05 33.6 5.2 55 362-422 2-56 (64)
12 cd00093 HTH_XRE Helix-turn-hel 87.6 1.8 3.9E-05 28.9 5.2 54 362-421 2-55 (58)
13 PHA01976 helix-turn-helix prot 87.3 0.67 1.4E-05 35.1 3.1 58 359-422 2-59 (67)
14 PF13560 HTH_31: Helix-turn-he 85.9 1.9 4E-05 32.9 5.0 62 359-425 1-62 (64)
15 smart00352 POU Found in Pit-Oc 84.7 1.7 3.6E-05 36.4 4.5 39 357-395 9-52 (75)
16 PF13744 HTH_37: Helix-turn-he 83.4 1.2 2.6E-05 35.9 3.1 36 359-395 18-53 (80)
17 TIGR02607 antidote_HigA addict 83.2 4.4 9.5E-05 31.4 6.0 56 360-421 5-61 (78)
18 PRK09943 DNA-binding transcrip 81.9 4.3 9.4E-05 36.8 6.4 58 357-421 5-63 (185)
19 PRK13890 conjugal transfer pro 80.9 1.8 3.9E-05 37.9 3.4 74 358-432 4-80 (120)
20 KOG3755|consensus 79.9 2.2 4.8E-05 47.4 4.4 72 358-429 498-571 (769)
21 TIGR03830 CxxCG_CxxCG_HTH puta 75.4 3.2 6.9E-05 35.0 3.3 35 362-397 68-102 (127)
22 COG5606 Uncharacterized conser 69.4 4.7 0.0001 35.0 3.0 37 359-396 28-64 (91)
23 PRK10072 putative transcriptio 68.9 5.2 0.00011 34.3 3.1 52 361-420 35-87 (96)
24 COG2944 Predicted transcriptio 66.2 5.8 0.00013 35.0 2.9 30 362-392 47-76 (104)
25 PRK08154 anaerobic benzoate ca 64.1 20 0.00043 35.6 6.5 80 350-431 20-120 (309)
26 PRK13355 bifunctional HTH-doma 63.4 14 0.00031 38.6 5.7 58 359-421 3-64 (517)
27 KOG2252|consensus 63.1 3.2 6.9E-05 45.5 0.9 55 355-419 1-56 (558)
28 PHA00542 putative Cro-like pro 62.4 11 0.00025 30.7 3.8 50 363-413 22-74 (82)
29 PRK06424 transcription factor; 60.9 11 0.00023 34.6 3.7 58 358-421 83-140 (144)
30 TIGR00270 conserved hypothetic 51.1 19 0.00042 33.2 3.7 59 359-423 69-127 (154)
31 PRK08359 transcription factor; 49.8 25 0.00055 33.4 4.4 59 359-423 85-143 (176)
32 PRK04140 hypothetical protein; 47.0 40 0.00088 34.6 5.6 55 361-421 128-182 (317)
33 COG3313 Predicted Fe-S protein 45.9 17 0.00036 30.7 2.3 18 413-430 32-49 (74)
34 PRK10856 cytoskeletal protein 44.3 73 0.0016 32.7 7.0 66 359-427 14-82 (331)
35 PF08667 BetR: BetR domain; I 41.1 36 0.00078 31.7 3.9 61 357-422 3-66 (147)
36 PF07022 Phage_CI_repr: Bacter 36.9 24 0.00052 27.6 1.8 56 360-418 2-59 (66)
37 PF13601 HTH_34: Winged helix 36.6 13 0.00028 30.4 0.2 24 395-418 53-77 (80)
38 TIGR02612 mob_myst_A mobile my 35.7 36 0.00079 31.4 3.0 34 362-396 28-61 (150)
39 PF13945 NST1: Salt tolerance 30.4 24 0.00051 34.1 1.0 18 415-432 110-127 (190)
40 smart00875 BACK BTB And C-term 29.6 1.2E+02 0.0026 23.5 4.7 73 356-431 12-84 (101)
41 TIGR00180 parB_part ParB-like 29.5 1.4E+02 0.0029 27.6 5.7 76 352-428 100-183 (187)
42 PF06945 DUF1289: Protein of u 29.3 45 0.00098 25.5 2.2 18 413-430 27-44 (51)
43 PF08519 RFC1: Replication fac 24.1 26 0.00056 32.3 0.0 50 360-415 104-154 (155)
44 TIGR02684 dnstrm_HI1420 probab 23.7 93 0.002 26.3 3.3 56 356-419 29-84 (89)
45 TIGR02147 Fsuc_second hypothet 23.6 3.3E+02 0.0072 27.4 7.6 78 351-428 4-96 (271)
46 cd03562 CID CID (CTD-Interacti 22.2 2.2E+02 0.0048 23.8 5.3 67 356-431 34-103 (114)
47 TIGR03764 ICE_PFGI_1_parB inte 22.1 85 0.0018 31.7 3.2 45 353-397 111-165 (258)
48 PF06778 Chlor_dismutase: Chlo 21.6 18 0.0004 34.5 -1.5 20 412-431 111-130 (193)
49 TIGR01637 phage_arpU phage tra 21.1 1.1E+02 0.0023 26.5 3.3 75 353-427 3-88 (132)
50 smart00354 HTH_LACI helix_turn 20.8 87 0.0019 24.5 2.4 23 375-398 3-25 (70)
51 cd03036 ArsC_like Arsenate Red 20.5 2.4E+02 0.0051 24.0 5.1 16 359-374 10-25 (111)
52 COG2522 Predicted transcriptio 20.5 1.3E+02 0.0028 27.2 3.7 36 363-399 13-48 (119)
53 PRK02866 cyanate hydratase; Va 20.4 1.4E+02 0.0031 27.9 4.0 63 356-424 2-64 (147)
No 1
>KOG2252|consensus
Probab=100.00 E-value=6.8e-45 Score=375.00 Aligned_cols=304 Identities=42% Similarity=0.498 Sum_probs=211.8
Q ss_pred cCcCCCCCCCCccccchhhcccC----cccc-----cC--CCCCccccccccCCCCCCCCCCCCCCccccCCCCCCCCCc
Q psy3393 76 EILSPGKISPSGISVSVASIMDS----SEFR-----NL--HAEPTYQTLTNVNGRLSPPGYSPSSSYATLTPLQPLPPIS 144 (433)
Q Consensus 76 ~~~~~~~~~~~~~~~~mas~ld~----~d~r-----~~--~~~~~~~tlts~~~~~sppg~s~sssYtTLTPLQpLPPIS 144 (433)
-++++...+-..+...||..++. +++. +. .+.|+++++.+.|+. +++|++.++.|++++|+++.||||
T Consensus 62 ~~~~~~~~~~~~~~~~m~~~~~~~~~gs~~~~~~~~p~~s~a~p~~~~~~s~~e~-~~~~~~~~~l~~s~~~~~~~p~~s 140 (558)
T KOG2252|consen 62 ALSSAEPRSVWPADQNMAHPLDSGLLGSSVPSEFKEPELSLASPLVPTIKSSCES-SSSGSGASSLSASLAPHQPSPPIS 140 (558)
T ss_pred ccCccccccccchhhcccccccccccCCCccccccCcccccccCcccccccCcCC-CCcccccccccccccccCCCCCCc
Confidence 44555555555677888988884 4554 11 234899999887775 488999999999999999999999
Q ss_pred cccccccCCC----------------CCCcccc-eeeeecccccc-cCCCCC-cCcc-CCCCCCCCCC----CCCCCccc
Q psy3393 145 TMSDKFAYGH----------------TGNVTGS-FTVMQNNIGLG-INSHYT-YDKI-QMSPPQHYSP----NNGLSTIV 200 (433)
Q Consensus 145 TvSDKF~~~H----------------~gnvsGs-Ftlmr~~~gL~-~n~~Y~-y~k~-~m~~p~~~sp----~~gl~~~~ 200 (433)
+++|+|+++| .|+|.|+ ||+|++.+|+. ++++|. |..+ .+.+ .++| .+|++.++
T Consensus 141 ~ts~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~t~~~~~~g~tt~~~ly~~~~~~~~~~~--~~ap~~~~~n~i~q~~ 218 (558)
T KOG2252|consen 141 TTSDYGTSPHRVHSPRGESTSHNQRAAGYVSGPSFTLMLPENGLTTENNLYSRSPDTGSQSQ--SLAPNAVTTNGISQLD 218 (558)
T ss_pred cccccccCCCcccccccccCCcCccccccccCCcccccccCCCCCcCccccccccccccccc--cccccccccccccccc
Confidence 9999998531 4889988 99999999998 999997 6433 3443 2442 36888888
Q ss_pred ccccCCCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCCcCCCCCCcccccccCCCCcc
Q psy3393 201 ITQENSPLSPQSTYSQNGL--NSPQKSLSPNSYDSPYNQRDLVDRSVLGGGSQSPTLSPNEGSLHSSPTTLVTNFQGAAT 278 (433)
Q Consensus 201 ~~q~~sp~s~~~~y~~~g~--~~~~k~~~~~~~e~~~~~~~~~~r~~~~~~~hsp~ls~~~~~~h~~~~~l~~~~~~~~~ 278 (433)
+.++..+ .|...+. --.+|+.+|..|..+... +.-+ ....|+... .+-..+++
T Consensus 219 ~~~~s~~-----s~~~pla~~~~t~k~~sP~~f~~~~~~--~~~~---------------~~~q~~~~~---~~~~~a~~ 273 (558)
T KOG2252|consen 219 NGELSQG-----SVSDPLARAILTQKGRSPFIFLDDVAA--YQVP---------------VPAQHSITI---CGSPQAVT 273 (558)
T ss_pred chhhccC-----CCCchhhhhhccccccCCccccccccc--cccC---------------Ccccccccc---CCCccccc
Confidence 8775433 3333332 123466677667665431 1111 112233211 11223668
Q ss_pred ccCCCCccccCCCccccCCCCCCCccccccccccCCCCCCCccchhhhhhccccccccccCCCCcccc--CCCCCCCccC
Q psy3393 279 IPTMNGITTITPHTVVVSPQTSPQHSLISNQLQRSDSPGPPKIISQQTATLTLKTVTPTNAVVGAVSL--GNSGELEEIN 356 (433)
Q Consensus 279 ~~~lNg~~~~~~~~~~~s~~~~~~~~~l~~~~~~~~~~~~~~~~~q~~~~~~~~~~~~~~~s~~~~~~--~~i~d~~~ID 356 (433)
++++|+..+.+++.+..+..+.+ +... .++.. ..+++++..+ .++++.++||
T Consensus 274 ~~~~~s~~~~~ps~~~~s~~~e~---~s~~-----------------~~p~~------~~sss~~~~~~~~~~~d~eeld 327 (558)
T KOG2252|consen 274 PSTPNSLEPSKPSGHKSSVKQEA---LSEI-----------------DQPKG------ISSSSDSHSNRKEESGDDEELD 327 (558)
T ss_pred cCCCCCccccCCCCccccccccc---cccc-----------------cCCCC------CCccccccccchhhcCCcceec
Confidence 88899886444432211111111 0000 00000 0111122222 3588999999
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHHHH-HHHHHHhcC
Q psy3393 357 TKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQR-MSALRLAGN 433 (433)
Q Consensus 357 TKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEdeR-meILRl~~c 433 (433)
||+||+||+.+||+|+|+|++||++|||||||||||||||||||+|||+|||+|+||||||+.|+++| |.+||+++|
T Consensus 328 Tkeia~rI~~eLk~~sIpQaiFAervLcRSQGTLSDLLrnPKPW~klKsGRetFrRM~~WL~eP~~~r~m~~L~~~a~ 405 (558)
T KOG2252|consen 328 TKEIAQRIKAELKRYSIPQAIFAERVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMANWLEEPEFQRLMSALRKKAC 405 (558)
T ss_pred HHHHHHHHHHHHhhcCCcHHHHHHHHhhcccchHHHHhhCCCchhhhccccHHHHHHHHHhcCHHHHHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999 999999987
No 2
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=99.97 E-value=1.1e-32 Score=227.45 Aligned_cols=82 Identities=56% Similarity=0.917 Sum_probs=75.5
Q ss_pred CCCCccCHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCccccc-chhHHHHHHHhhcCCCHHHHHHHH
Q psy3393 350 GELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK-SGRETFRRMWKWLQEPEFQRMSAL 428 (433)
Q Consensus 350 ~d~~~IDTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLk-sGRE~YiRMyNWLqlPEdeRmeIL 428 (433)
.+.++|||++||++|++||++++|+|++||++|||||||||||||++||||++|+ +||++|+||||||++++++|++||
T Consensus 4 ~~~~~ldT~~I~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~PKpW~~L~~~gre~y~RM~nWL~~~e~~r~~i~ 83 (87)
T PF02376_consen 4 ENSEYLDTKEIARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLRKPKPWNKLKPKGREPYIRMYNWLSLPEEERMEIL 83 (87)
T ss_dssp HHCSSS-HHHHHHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHHSCCTTCHHHHHHHHHHHHHHHHHCSTHHHHHHHH
T ss_pred cccCccCHHHHHHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhCCCCCHHHcCccccHHHHHHHHHhcCCHHHHHHHH
Confidence 4568999999999999999999999999999999999999999999999999999 999999999999999999999999
Q ss_pred HHh
Q psy3393 429 RLA 431 (433)
Q Consensus 429 Rl~ 431 (433)
++.
T Consensus 84 ~~~ 86 (87)
T PF02376_consen 84 KME 86 (87)
T ss_dssp HHH
T ss_pred hcc
Confidence 974
No 3
>KOG3755|consensus
Probab=95.98 E-value=0.0042 Score=67.68 Aligned_cols=71 Identities=32% Similarity=0.393 Sum_probs=65.2
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCccccc-chhHHHHHHHhhcCCCHHHHHHHHH
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK-SGRETFRRMWKWLQEPEFQRMSALR 429 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLk-sGRE~YiRMyNWLqlPEdeRmeILR 429 (433)
+|-++|+.++++.+++|.+||..-+||.||.+++++|.-.+=..+. +--..-+-|.|+|.+||-||-.|..
T Consensus 377 ~~~qQv~d~~~rl~~sqav~gr~~~N~~q~~~s~~~raE~~~~s~s~sll~~~~a~~N~~~~Pe~e~dsi~~ 448 (769)
T KOG3755|consen 377 PIYQQVRDELKRLDESQAVFGRVAFNRTQGLLSEILRAEEDPHSASQSLLVNLRAMQNFLILPEPERDSIYQ 448 (769)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhhccccchhcccccchHHHHHHHHHHHhhhcCCccccccccc
Confidence 7899999999999999999999999999999999999888877776 6777888899999999999988863
No 4
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=92.75 E-value=0.16 Score=48.39 Aligned_cols=58 Identities=24% Similarity=0.253 Sum_probs=39.6
Q ss_pred ccCHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHH
Q psy3393 354 EINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMW 414 (433)
Q Consensus 354 ~IDTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMy 414 (433)
.-|...|++.||..|..++|+|+.-++.. |+||..||.-|++=-|-+. .-|..|-|+|
T Consensus 113 r~D~~~VkeeIK~fl~~h~IsQ~~V~q~T-GisQS~lSq~L~kGt~Mk~--qKR~alY~Wy 170 (180)
T PF04814_consen 113 RRDPWRVKEEIKAFLQQHNISQREVVQVT-GISQSHLSQHLNKGTPMKE--QKRRALYRWY 170 (180)
T ss_dssp TS-HHHHHHHHHHHHHHCT--CHHHHHHH-T--HHHHHHHHCTB----H--HHHHHHHHHH
T ss_pred hhCHHHHHHHHHHHHHHcCCcHHHHHHHh-hhhHHHHHHHHHcCCCccH--HHHHHHHHHH
Confidence 34999999999999999999999999877 9999999999965433222 3455555554
No 5
>PRK09726 antitoxin HipB; Provisional
Probab=92.65 E-value=0.45 Score=38.86 Aligned_cols=63 Identities=19% Similarity=0.249 Sum_probs=49.8
Q ss_pred CccCHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCH
Q psy3393 353 EEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPE 421 (433)
Q Consensus 353 ~~IDTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPE 421 (433)
...+.++|..+|++.+++.+++|+.||+++ |+++.||+.+.+... .-..+.+.++-+.|..+.
T Consensus 6 ~~~~~~~l~~~lk~~R~~~gltq~elA~~~-gvs~~tis~~e~g~~-----~ps~~~l~~ia~~lgv~~ 68 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQNGWTQSELAKKI-GIKQATISNFENNPD-----NTTLTTFFKILQSLELSM 68 (88)
T ss_pred cccCHHHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHCCCC-----CCCHHHHHHHHHHcCCCc
Confidence 456789999999999999999999999975 699999999999642 123445666667776653
No 6
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=91.89 E-value=0.42 Score=31.82 Aligned_cols=52 Identities=19% Similarity=0.170 Sum_probs=41.2
Q ss_pred HHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCH
Q psy3393 364 ISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPE 421 (433)
Q Consensus 364 IkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPE 421 (433)
|+..++..+++++.||+.+ ++++.+++.+++..... ..+...++..+|..+.
T Consensus 2 i~~~~~~~~~s~~~la~~~-~i~~~~i~~~~~~~~~~-----~~~~~~~i~~~~~~~~ 53 (56)
T smart00530 2 LKELREEKGLTQEELAEKL-GVSRSTLSRIENGKRKP-----SLETLKKLAKALGVSL 53 (56)
T ss_pred HHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHCCCCCC-----CHHHHHHHHHHhCCCh
Confidence 5677888999999999875 89999999998865422 5566778888887764
No 7
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=90.72 E-value=0.49 Score=35.46 Aligned_cols=54 Identities=20% Similarity=0.175 Sum_probs=35.2
Q ss_pred HHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCC-CCcccccchhHHHHHHHhhcCCCHH
Q psy3393 363 RISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNP-KPWSKLKSGRETFRRMWKWLQEPEF 422 (433)
Q Consensus 363 rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnP-KPW~kLksGRE~YiRMyNWLqlPEd 422 (433)
+|+++|++.+++|..||+. .|+++.||+.+++.. ..| .-+...++-..|..+-+
T Consensus 1 ~L~~~m~~~~it~~~La~~-~gis~~tl~~~~~~~~~~~-----~~~~l~~ia~~l~~~~~ 55 (63)
T PF13443_consen 1 KLKELMAERGITQKDLARK-TGISRSTLSRILNGKPSNP-----SLDTLEKIAKALNCSPE 55 (63)
T ss_dssp HHHHHHHHTT--HHHHHHH-HT--HHHHHHHHTTT----------HHHHHHHHHHHT--HH
T ss_pred CHHHHHHHcCCCHHHHHHH-HCcCHHHHHHHHhcccccc-----cHHHHHHHHHHcCCCHH
Confidence 5899999999999999975 599999999999976 233 23556666666665543
No 8
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=90.27 E-value=0.41 Score=34.30 Aligned_cols=38 Identities=16% Similarity=0.111 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCC
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNP 397 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnP 397 (433)
++.++|++..++.+++|..||++ +|+++.+|+.+.+.-
T Consensus 2 ~~~~~l~~~r~~~gltq~~lA~~-~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 2 QIGMLVRARRKALGLTQADLADL-AGVGLRFIRDVENGK 39 (58)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHH-hCCCHHHHHHHHCCC
Confidence 47889999999999999999976 579999999999754
No 9
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=89.73 E-value=1 Score=39.19 Aligned_cols=40 Identities=28% Similarity=0.284 Sum_probs=35.9
Q ss_pred CHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcC
Q psy3393 356 NTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRN 396 (433)
Q Consensus 356 DTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrn 396 (433)
+-+.|.++|++.+++.+++|..||+.+ |+++.||+.+.+.
T Consensus 2 ~~~~~g~rlk~~R~~~gltq~~lA~~~-gvs~~~is~~E~g 41 (135)
T PRK09706 2 KNLTLGQRIRYRRKQLKLSQRSLAKAV-KVSHVSISQWERD 41 (135)
T ss_pred chhhHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHcC
Confidence 456789999999999999999999965 8999999999875
No 10
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=89.02 E-value=0.82 Score=33.24 Aligned_cols=51 Identities=20% Similarity=0.176 Sum_probs=35.3
Q ss_pred HHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCC
Q psy3393 364 ISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEP 420 (433)
Q Consensus 364 IkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlP 420 (433)
|++.++..+++|+.||+.+- +++.||+.+++.-+.. .-+.-.++-+-|..+
T Consensus 1 ik~~r~~~gls~~~la~~~g-is~~~i~~~~~g~~~~-----~~~~~~~ia~~l~~~ 51 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLG-ISRSTISRIENGKRNP-----SLDTLKKIAKALGVS 51 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHT-S-HHHHHHHHTTSSTS-----BHHHHHHHHHHHTSE
T ss_pred CHHHHHHcCCCHHHHHHHhC-CCcchhHHHhcCCCCC-----CHHHHHHHHHHHCCC
Confidence 67889999999999999876 9999999999983322 223444444444444
No 11
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=88.87 E-value=1.1 Score=33.57 Aligned_cols=55 Identities=16% Similarity=0.145 Sum_probs=38.0
Q ss_pred HHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHH
Q psy3393 362 QRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEF 422 (433)
Q Consensus 362 ~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEd 422 (433)
++||+.++..+++|..||+ .++.++++|+.+.+.-+. -..+.+.++-.-+.++.+
T Consensus 2 ~~lk~~r~~~~lt~~~~a~-~~~i~~~~i~~~e~g~~~-----~~~~~l~~i~~~~~v~~~ 56 (64)
T PF12844_consen 2 ERLKELREEKGLTQKDLAE-KLGISRSTISKIENGKRK-----PSVSTLKKIAEALGVSLD 56 (64)
T ss_dssp HHHHHHHHHCT--HHHHHH-HHTS-HHHHHHHHTTSS-------BHHHHHHHHHHHTS-HH
T ss_pred HHHHHHHHHcCCCHHHHHH-HHCcCHHHHHHHHCCCcC-----CCHHHHHHHHHHhCCCHH
Confidence 6899999999999999999 678899999999987331 124455666666665544
No 12
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=87.65 E-value=1.8 Score=28.92 Aligned_cols=54 Identities=22% Similarity=0.249 Sum_probs=39.2
Q ss_pred HHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCH
Q psy3393 362 QRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPE 421 (433)
Q Consensus 362 ~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPE 421 (433)
+.|+..+.+.++++..||+. +++++++|+.+++.-+ .-..+...++...+.++.
T Consensus 2 ~~l~~~~~~~~~s~~~~a~~-~~~~~~~v~~~~~g~~-----~~~~~~~~~i~~~~~~~~ 55 (58)
T cd00093 2 ERLKELRKEKGLTQEELAEK-LGVSRSTISRIENGKR-----NPSLETLEKLAKALGVSL 55 (58)
T ss_pred hHHHHHHHHcCCCHHHHHHH-HCCCHHHHHHHHcCCC-----CCCHHHHHHHHHHhCCCh
Confidence 45777888899999999976 6899999999888643 234445555666555543
No 13
>PHA01976 helix-turn-helix protein
Probab=87.33 E-value=0.67 Score=35.12 Aligned_cols=58 Identities=10% Similarity=0.041 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHH
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEF 422 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEd 422 (433)
.+.++|+...+..+++|..||+++ ++++.+|+.+.+.-. .-..+...++-+.|..+.+
T Consensus 2 ~~~~rl~~~R~~~glt~~~lA~~~-gvs~~~v~~~e~g~~-----~p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRA-GVRHSLIYDFEADKR-----LPNLKTLLRLADALGVTLD 59 (67)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHcCCC-----CCCHHHHHHHHHHHCcCHH
Confidence 368999999999999999999985 799999999876422 1123455566666665543
No 14
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=85.95 E-value=1.9 Score=32.85 Aligned_cols=62 Identities=31% Similarity=0.429 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHHHHH
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQRM 425 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEdeRm 425 (433)
++...|+++.++.+++|+.+|+. +|.++.+|+.+.+--.+ .-....+.++-.-|..+.+++.
T Consensus 1 ~lg~~lr~~R~~~gls~~~lA~~-~g~s~s~v~~iE~G~~~----~p~~~~l~~l~~~l~~~~~~~~ 62 (64)
T PF13560_consen 1 QLGRRLRRLRERAGLSQAQLADR-LGVSQSTVSRIERGRRP----RPSPDTLQRLARALGVPPDERA 62 (64)
T ss_dssp HHHHHHHHHHHCHTS-HHHHHHH-HTS-HHHHHHHHTTSSS----S-BHHHHHHHHHHTT--HHHHH
T ss_pred CHHHHHHHHHHHcCCCHHHHHHH-HCcCHHHHHHHHCCCCC----CCCHHHHHHHHHHHCcCHHHHc
Confidence 47789999999999999999986 57999999999984332 1133466777777777776654
No 15
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=84.75 E-value=1.7 Score=36.44 Aligned_cols=39 Identities=15% Similarity=0.077 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHhhhhc-----ccCchhhhhhc
Q psy3393 357 TKELAQRISAELKRYSIPQAIFAQRVLC-----RSQGTLSDLLR 395 (433)
Q Consensus 357 TKeIa~rIkewLkr~~IsQavFAekILg-----RSQGTLSDLLr 395 (433)
-+++++++++..+..+++|+-+|+.+=. .||.|||.+-+
T Consensus 9 le~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 9 LEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 3568999999999999999999999763 79999998544
No 16
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=83.43 E-value=1.2 Score=35.93 Aligned_cols=36 Identities=28% Similarity=0.192 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhc
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLR 395 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLr 395 (433)
+++..|+++++..+++|+..|+ .||.+|.+||+|++
T Consensus 18 ~l~~~i~~~~~~~~ltQ~e~A~-~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 18 QLMAAIRELREERGLTQAELAE-RLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHCCT--HHHHHH-HHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCHHHHHH-HHCCChhHHHHHHc
Confidence 5788899999999999999886 58999999999997
No 17
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=83.23 E-value=4.4 Score=31.36 Aligned_cols=56 Identities=16% Similarity=0.135 Sum_probs=40.9
Q ss_pred HHHHHH-HHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCH
Q psy3393 360 LAQRIS-AELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPE 421 (433)
Q Consensus 360 Ia~rIk-ewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPE 421 (433)
..++|+ ..+++.+++|..||+++ |+++.||+.+++..... ..+...++-+.|..+.
T Consensus 5 ~g~~i~~~~~~~~~~t~~~lA~~~-gis~~tis~~~~g~~~~-----~~~~~~~l~~~l~v~~ 61 (78)
T TIGR02607 5 PGEILREEFLEPLGLSIRALAKAL-GVSRSTLSRIVNGRRGI-----TADMALRLAKALGTSP 61 (78)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHcCCCCC-----CHHHHHHHHHHcCCCH
Confidence 457888 78999999999999875 68999999999865322 1234455656665554
No 18
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=81.87 E-value=4.3 Score=36.83 Aligned_cols=58 Identities=14% Similarity=0.130 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCC-CCcccccchhHHHHHHHhhcCCCH
Q psy3393 357 TKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNP-KPWSKLKSGRETFRRMWKWLQEPE 421 (433)
Q Consensus 357 TKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnP-KPW~kLksGRE~YiRMyNWLqlPE 421 (433)
+..|..+||+.+++.+++|+.+|++ +|+++++|+.+.+.- .| ..+...++-..|..+.
T Consensus 5 ~~~~g~~l~~~R~~~glt~~elA~~-~gis~~~is~~E~g~~~p------~~~~l~~ia~~l~v~~ 63 (185)
T PRK09943 5 GLAPGKRLSEIRQQQGLSQRRAAEL-SGLTHSAISTIEQDKVSP------AISTLQKLLKVYGLSL 63 (185)
T ss_pred hhHHHHHHHHHHHHcCCCHHHHHHH-HCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCH
Confidence 3458899999999999999999998 568999999999843 23 2445566666555554
No 19
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=80.91 E-value=1.8 Score=37.88 Aligned_cols=74 Identities=16% Similarity=0.130 Sum_probs=48.6
Q ss_pred HHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCC-C-ccccc-chhHHHHHHHhhcCCCHHHHHHHHHHhc
Q psy3393 358 KELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK-P-WSKLK-SGRETFRRMWKWLQEPEFQRMSALRLAG 432 (433)
Q Consensus 358 KeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPK-P-W~kLk-sGRE~YiRMyNWLqlPEdeRmeILRl~~ 432 (433)
+-+..+|++.+++.+++|..||++ +|+++.+++.+.+.-. | .+.|. -.+..=+.+.-|+...+++|.....++|
T Consensus 4 ~i~~~~l~~ll~~~Glsq~eLA~~-~Gis~~~is~iE~g~~~ps~~~l~kIa~aL~v~~~~L~~~~~~~~~~l~~la~ 80 (120)
T PRK13890 4 YIFFTNVLRLLDERHMTKKELSER-SGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLLLESTDLDKEALDALAG 80 (120)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHH-HCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHHhccCccCHHHHHHHcC
Confidence 346789999999999999999998 5699999999998543 1 12221 1222223334444446666665555544
No 20
>KOG3755|consensus
Probab=79.85 E-value=2.2 Score=47.44 Aligned_cols=72 Identities=26% Similarity=0.315 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCccccc-chhHHHHHH-HhhcCCCHHHHHHHHH
Q psy3393 358 KELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK-SGRETFRRM-WKWLQEPEFQRMSALR 429 (433)
Q Consensus 358 KeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLk-sGRE~YiRM-yNWLqlPEdeRmeILR 429 (433)
..|-+.|.+++++....|.+|++..-..+||+|-|++|.-+--+.+. .-+|.|.-| .-+++++-.+|-.|++
T Consensus 498 aa~~d~i~~em~d~~~eq~~~~k~~a~~~~g~~~el~r~~e~~~~~n~~~~EN~~~~~rh~~~l~q~er~a~~~ 571 (769)
T KOG3755|consen 498 AAIYDEIQQEMKDAKVEQALFAKVAAEKSQGWLCELLRWKECPSPENRTLWENYLHIIRHFLKLPQKERDAIYE 571 (769)
T ss_pred HHhhhHHHHHhHhhhhhhHHHHHHHhhCCCchHHHHHHhhhCCChhhhhhhhcchhHHHhhhccchhhhhHHHh
Confidence 44556899999999999999999999999999999999877777666 678887665 4578899999999885
No 21
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=75.44 E-value=3.2 Score=34.95 Aligned_cols=35 Identities=20% Similarity=0.170 Sum_probs=30.3
Q ss_pred HHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCC
Q psy3393 362 QRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNP 397 (433)
Q Consensus 362 ~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnP 397 (433)
.+|+.+++..+++|+.||+ +||.++.||+.+.+.-
T Consensus 68 ~~i~~~r~~~gltq~~lA~-~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 68 PEIRRIRKKLGLSQREAAE-LLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHCCC
Confidence 5788889999999999995 5689999999988754
No 22
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=69.43 E-value=4.7 Score=35.03 Aligned_cols=37 Identities=30% Similarity=0.344 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcC
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRN 396 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrn 396 (433)
+|...|+.|++.++..|+.-|+ +|+++|..+||+.+.
T Consensus 28 ~l~~~i~~~i~q~~l~Q~qiae-~lgV~qprvS~l~~g 64 (91)
T COG5606 28 ALMMAIKQWIEQAALSQAQIAE-LLGVTQPRVSDLARG 64 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HhCCCCchHHHHHhc
Confidence 5677889999999999999886 689999999999873
No 23
>PRK10072 putative transcriptional regulator; Provisional
Probab=68.92 E-value=5.2 Score=34.34 Aligned_cols=52 Identities=17% Similarity=0.132 Sum_probs=36.9
Q ss_pred HHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCC-CcccccchhHHHHHHHhhcCCC
Q psy3393 361 AQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK-PWSKLKSGRETFRRMWKWLQEP 420 (433)
Q Consensus 361 a~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPK-PW~kLksGRE~YiRMyNWLqlP 420 (433)
..+|++..+..+++|..||+ +||++++||++..+.-. | ++ ..+++-++|+..
T Consensus 35 ~~eik~LR~~~glTQ~elA~-~lGvS~~TVs~WE~G~r~P-----~~--~~l~Ll~~L~~~ 87 (96)
T PRK10072 35 FTEFEQLRKGTGLKIDDFAR-VLGVSVAMVKEWESRRVKP-----SS--AELKLMRLIQAN 87 (96)
T ss_pred hHHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHcCCCCC-----CH--HHHHHHHHHhhC
Confidence 35688888999999999995 56799999998765311 1 11 235677888543
No 24
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=66.19 E-value=5.8 Score=35.04 Aligned_cols=30 Identities=27% Similarity=0.347 Sum_probs=26.4
Q ss_pred HHHHHHHHHcCCChHHHHhhhhcccCchhhh
Q psy3393 362 QRISAELKRYSIPQAIFAQRVLCRSQGTLSD 392 (433)
Q Consensus 362 ~rIkewLkr~~IsQavFAekILgRSQGTLSD 392 (433)
.+|+...+..+++|.+||. .||.|-+||++
T Consensus 47 ~eIk~iRe~~~lSQ~vFA~-~L~vs~~Tv~~ 76 (104)
T COG2944 47 TEIKAIREKLGLSQPVFAR-YLGVSVSTVRK 76 (104)
T ss_pred HHHHHHHHHhCCCHHHHHH-HHCCCHHHHHH
Confidence 5788888999999999995 68999999976
No 25
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=64.11 E-value=20 Score=35.58 Aligned_cols=80 Identities=16% Similarity=0.086 Sum_probs=52.6
Q ss_pred CCCCccCHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCC--Ccccc--------------c--c--hhHH
Q psy3393 350 GELEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK--PWSKL--------------K--S--GRET 409 (433)
Q Consensus 350 ~d~~~IDTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPK--PW~kL--------------k--s--GRE~ 409 (433)
.+...+. +.|.++|++..++.+++|+.+|++ +|+++.+++.+.+.-+ ..+.| - . .-.-
T Consensus 20 ~~~~~~~-~~~g~rl~~~R~~~gltq~~lA~~-~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~~l~~~~~~~~~~ 97 (309)
T PRK08154 20 AEEAPFL-AALGERVRTLRARRGMSRKVLAQA-SGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDVDTSSPD 97 (309)
T ss_pred cchHHHH-HHHHHHHHHHHHHcCCCHHHHHHH-HCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHHhCCCCCCChH
Confidence 4444444 669999999999999999999985 6789998888877421 11211 1 0 1112
Q ss_pred HHHHHhhc-CCCHHHHHHHHHHh
Q psy3393 410 FRRMWKWL-QEPEFQRMSALRLA 431 (433)
Q Consensus 410 YiRMyNWL-qlPEdeRmeILRl~ 431 (433)
+.++..|| +++++++..++.+.
T Consensus 98 ~~~l~~~l~~l~~~~~~~~~~~l 120 (309)
T PRK08154 98 WLLIRELLEQASPAQLARVRDAL 120 (309)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHH
Confidence 34555555 57777777776653
No 26
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=63.42 E-value=14 Score=38.58 Aligned_cols=58 Identities=14% Similarity=0.193 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhh----hcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCH
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRV----LCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPE 421 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekI----LgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPE 421 (433)
.+.++|+..+++.+++|..||+.. +++++++|+.+++.-. .-..+...++-.||+.+.
T Consensus 3 ~~~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~-----~p~~~~l~~la~~l~v~~ 64 (517)
T PRK13355 3 TFAERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKT-----GPRRDVLPFLAAILGVSE 64 (517)
T ss_pred hHHHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCC-----CCCHHHHHHHHHHhCcCH
Confidence 467899999999999999999997 5799999999887521 112234556666666654
No 27
>KOG2252|consensus
Probab=63.07 E-value=3.2 Score=45.49 Aligned_cols=55 Identities=24% Similarity=0.361 Sum_probs=49.6
Q ss_pred cCHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCccccc-chhHHHHHHHhhcCC
Q psy3393 355 INTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK-SGRETFRRMWKWLQE 419 (433)
Q Consensus 355 IDTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLk-sGRE~YiRMyNWLql 419 (433)
+||..+++.+++..-.++|+|+ ++ ..+|+|.+|.+|..++ .+|+.+.+.|-|...
T Consensus 1 ~~~~~~~~~~~~l~~~~~~~~~---------~~-~~se~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (558)
T KOG2252|consen 1 MNTQLTMEALKELHGAYGIGQR---------GP-SESELLAKPSPWGARRSKRREAQGLIYPPTSP 56 (558)
T ss_pred CchHHHHHHhhhhcccCCCCCC---------Cc-chhhhhcCCCccccccccccccccccCCCcCc
Confidence 4788899999999999999998 77 8999999999999999 799999999988754
No 28
>PHA00542 putative Cro-like protein
Probab=62.36 E-value=11 Score=30.72 Aligned_cols=50 Identities=18% Similarity=0.148 Sum_probs=36.5
Q ss_pred HHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCC---CCcccccchhHHHHHH
Q psy3393 363 RISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNP---KPWSKLKSGRETFRRM 413 (433)
Q Consensus 363 rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnP---KPW~kLksGRE~YiRM 413 (433)
++..+|+..+++|+.+|+ .+|+++.||+.+++.. -..+.+.+=.+.|.+.
T Consensus 22 ~l~~~l~~~glTq~elA~-~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~~~~ 74 (82)
T PHA00542 22 ELVCALIRAGWSQEQIAD-ATDVSQPTICRIYSGRHKDPRYSVVEKLRHLVLNL 74 (82)
T ss_pred HHHHHHHHCCCCHHHHHH-HHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHHHh
Confidence 566788999999999985 6799999999999754 2344454555555443
No 29
>PRK06424 transcription factor; Provisional
Probab=60.90 E-value=11 Score=34.64 Aligned_cols=58 Identities=19% Similarity=0.227 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCH
Q psy3393 358 KELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPE 421 (433)
Q Consensus 358 KeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPE 421 (433)
.++.++|+++++..+++|..+|+++ |.++.+|+.+.+.-. .-.-++..++-++|..+.
T Consensus 83 ~~~g~~Ir~lRe~~GLSQ~eLA~~i-Gvs~stIskiE~G~~-----~Ps~~~l~kLa~~Lgvsl 140 (144)
T PRK06424 83 EDYAELVKNARERLSMSQADLAAKI-FERKNVIASIERGDL-----LPDIKTARKLEKILGITL 140 (144)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHCCCC-----CCCHHHHHHHHHHhCCCC
Confidence 5688999999999999999999765 679999999887321 123445666666666553
No 30
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=51.09 E-value=19 Score=33.18 Aligned_cols=59 Identities=10% Similarity=0.143 Sum_probs=44.3
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHHH
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQ 423 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEde 423 (433)
++.++|++..++.+++|..||+++ +.++.+|+.+-+.- ..-..++..++-+.|..+-.+
T Consensus 69 ~~g~~Ir~~Re~~glSqeeLA~~l-gvs~s~IsriE~G~-----~~Ps~~~l~kLa~~Lgvsl~e 127 (154)
T TIGR00270 69 DYGIIIRREREKRGWSQEQLAKKI-QEKESLIKKIENAE-----IEPEPKVVEKLEKLLKIKLRE 127 (154)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHCCC-----CCCCHHHHHHHHHHhCCCHHH
Confidence 367889999999999999999975 69999999988631 122345667777777766554
No 31
>PRK08359 transcription factor; Validated
Probab=49.75 E-value=25 Score=33.42 Aligned_cols=59 Identities=7% Similarity=0.186 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHHH
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQ 423 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEde 423 (433)
++.++|++..++.+++|..+| ..+|+++.+|+.|=+ .+..-.-++-+|+-++|..+-.+
T Consensus 85 dy~~rIkeaRe~kglSQeeLA-~~lgvs~stI~~iE~-----G~~~Ps~~~l~kLak~l~VsL~e 143 (176)
T PRK08359 85 DYAERVYEAIQKSGLSYEELS-HEVGLSVNDLRRIAH-----GEYEPTIKEAKKLERYFKIKLIE 143 (176)
T ss_pred HHHHHHHHHHHHcCCCHHHHH-HHhCCCHHHHHHHHC-----CCcCCCHHHHHHHHHHhCCcccc
Confidence 566788888899999999999 568999999987743 33333456667777777776444
No 32
>PRK04140 hypothetical protein; Provisional
Probab=46.96 E-value=40 Score=34.60 Aligned_cols=55 Identities=13% Similarity=0.094 Sum_probs=40.2
Q ss_pred HHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCH
Q psy3393 361 AQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPE 421 (433)
Q Consensus 361 a~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPE 421 (433)
.++|++.+++.+++|..||+.+ |+|++|++.+.+.-.. --.+...++-++|..+.
T Consensus 128 GerLk~lRe~~GlSq~eLA~~l-GVSr~tIskyE~G~~~-----Ps~e~~~kLa~~Lgv~l 182 (317)
T PRK04140 128 GDVLREAREELGLSLGELASEL-GVSRRTISKYENGGMN-----ASIEVAIKLEEILDVPL 182 (317)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHcCCCC-----CCHHHHHHHHHHhCCCh
Confidence 5889999999999999999875 6999999999883110 12345555556665543
No 33
>COG3313 Predicted Fe-S protein [General function prediction only]
Probab=45.91 E-value=17 Score=30.68 Aligned_cols=18 Identities=28% Similarity=0.637 Sum_probs=16.1
Q ss_pred HHhhcCCCHHHHHHHHHH
Q psy3393 413 MWKWLQEPEFQRMSALRL 430 (433)
Q Consensus 413 MyNWLqlPEdeRmeILRl 430 (433)
+.||..|+++||.+||++
T Consensus 32 i~~W~~msd~Er~aVl~~ 49 (74)
T COG3313 32 IFNWSSMSDDERRAVLRL 49 (74)
T ss_pred HHHHhhCCHHHHHHHHHH
Confidence 459999999999999975
No 34
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=44.32 E-value=73 Score=32.66 Aligned_cols=66 Identities=18% Similarity=0.229 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCccccc---chhHHHHHHHhhcCCCHHHHHHH
Q psy3393 359 ELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK---SGRETFRRMWKWLQEPEFQRMSA 427 (433)
Q Consensus 359 eIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLk---sGRE~YiRMyNWLqlPEdeRmeI 427 (433)
.+-+++|+.+++.+++|..+|++ |++++++|++|.++- +..+. --|.+.+.+-++|.+++++=+..
T Consensus 14 ~~G~~Lr~aRe~~GlSq~~vA~~-l~l~~~~I~~iE~g~--~~~~~~~tf~RGyir~yA~~lgv~~~~L~~~ 82 (331)
T PRK10856 14 TTGERLRQAREQLGLTQQAVAER-LCLKVSTVRDIEEDK--APADLASTFLRGYIRSYARLVHIPEEELLPG 82 (331)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHH-HCCCHHHHHHHHCCC--CCCChhHHHHHHHHHHHHHHHCcCHHHHHHh
Confidence 47899999999999999999987 468999999999862 33222 23444555567999998764443
No 35
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=41.14 E-value=36 Score=31.70 Aligned_cols=61 Identities=21% Similarity=0.293 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHh---hhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHH
Q psy3393 357 TKELAQRISAELKRYSIPQAIFAQ---RVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEF 422 (433)
Q Consensus 357 TKeIa~rIkewLkr~~IsQavFAe---kILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEd 422 (433)
-..++.+|++.|++++|+++.-++ +||++++.+++.=|+--.+|.- +=-.++..++.++-+
T Consensus 3 ~~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl-----~EI~~Ia~~fgvS~d 66 (147)
T PF08667_consen 3 DQAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTL-----EEIKKIAKHFGVSPD 66 (147)
T ss_pred hHHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCH-----HHHHHHHHHhCcCHH
Confidence 346889999999999999976554 6899999999888887778863 122445566666644
No 36
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=36.92 E-value=24 Score=27.60 Aligned_cols=56 Identities=23% Similarity=0.214 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHcCCChHHHHhhhhcccCchhh-hhhcC-CCCcccccchhHHHHHHHhhcC
Q psy3393 360 LAQRISAELKRYSIPQAIFAQRVLCRSQGTLS-DLLRN-PKPWSKLKSGRETFRRMWKWLQ 418 (433)
Q Consensus 360 Ia~rIkewLkr~~IsQavFAekILgRSQGTLS-DLLrn-PKPW~kLksGRE~YiRMyNWLq 418 (433)
|.+||++.+... +|+.||+. ||+++.||+ ...++ --|-+.|..=-+.|--=.+||-
T Consensus 2 ~i~rl~~~~g~~--~~~~lA~~-lgis~st~s~~~~~r~~~P~~~l~~ia~~~gvsl~WLl 59 (66)
T PF07022_consen 2 VIERLKEALGVK--SDKELAER-LGISKSTLSNNWKKRGSIPAEWLIKIALETGVSLDWLL 59 (66)
T ss_dssp HHHHHHHHHT-S--SCHHHHCC-TT--HHHHH-HHHHSSS--HHHHHHHHHHH---HHHHH
T ss_pred HHHHHHHHhCCC--CHHHHHHH-hCcCHHHhhHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 445555554443 56799987 999999999 55554 3365555432223333346653
No 37
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=36.55 E-value=13 Score=30.43 Aligned_cols=24 Identities=42% Similarity=0.810 Sum_probs=19.5
Q ss_pred cCCCCccccc-chhHHHHHHHhhcC
Q psy3393 395 RNPKPWSKLK-SGRETFRRMWKWLQ 418 (433)
Q Consensus 395 rnPKPW~kLk-sGRE~YiRMyNWLq 418 (433)
++|+-|=+|+ +||+.|.+-.+||+
T Consensus 53 ~~p~t~~~lT~~Gr~~~~~~~~~L~ 77 (80)
T PF13601_consen 53 RRPRTWYSLTDKGREAFERYVAALR 77 (80)
T ss_dssp S--EEEEEE-HHHHHHHHHHHHHHH
T ss_pred CCCeEEEEECHHHHHHHHHHHHHHH
Confidence 5699999999 89999999999985
No 38
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=35.74 E-value=36 Score=31.37 Aligned_cols=34 Identities=21% Similarity=0.178 Sum_probs=30.9
Q ss_pred HHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcC
Q psy3393 362 QRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRN 396 (433)
Q Consensus 362 ~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrn 396 (433)
.+|+...+..+++|..+|++ +|+|+.+|+.+.+.
T Consensus 28 ~~Ir~~R~~lGmTq~eLAer-lGVS~~tIs~iE~G 61 (150)
T TIGR02612 28 GWVRAIRKALGMSGAQLAGR-LGVTPQRVEALEKS 61 (150)
T ss_pred HHHHHHHHHcCCCHHHHHHH-hCCCHHHHHHHHcC
Confidence 68999999999999999976 67999999999984
No 39
>PF13945 NST1: Salt tolerance down-regulator
Probab=30.39 E-value=24 Score=34.11 Aligned_cols=18 Identities=22% Similarity=0.326 Sum_probs=15.9
Q ss_pred hhcCCCHHHHHHHHHHhc
Q psy3393 415 KWLQEPEFQRMSALRLAG 432 (433)
Q Consensus 415 NWLqlPEdeRmeILRl~~ 432 (433)
=||.|.|+||.+++|+.+
T Consensus 110 FW~SL~eeERr~LVkIEK 127 (190)
T PF13945_consen 110 FWESLSEEERRSLVKIEK 127 (190)
T ss_pred HHHccCHHHHHHHHHhhH
Confidence 499999999999998764
No 40
>smart00875 BACK BTB And C-terminal Kelch. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues.
Probab=29.59 E-value=1.2e+02 Score=23.46 Aligned_cols=73 Identities=18% Similarity=0.201 Sum_probs=49.5
Q ss_pred CHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHHHHHHHHHHh
Q psy3393 356 NTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQRMSALRLA 431 (433)
Q Consensus 356 DTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEdeRmeILRl~ 431 (433)
+-+++.+.+.+++.++ ..+-.-.+-.+.++...+..||+..+-. ..+..++|.-.-+|++-...+|..+.++.
T Consensus 12 ~~~~L~~~~~~~i~~n-f~~~~~~~~f~~L~~~~l~~iL~~d~l~--v~~E~~v~~av~~W~~~~~~~~~~~~~ll 84 (101)
T smart00875 12 GLEELLEKALRFILKN-FLEVAQSEEFLELSLEQLLSLLSSDDLN--VPSEEEVFEAVLRWVKHDPERRRHLPELL 84 (101)
T ss_pred ChHHHHHHHHHHHHHH-HHHHhcCcHHhcCCHHHHHHHhCcccCC--CCCHHHHHHHHHHHHHCCHHHHHHHHHHH
Confidence 3456667777776654 3332222466788889999999986653 23578899999999998876665444443
No 41
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=29.48 E-value=1.4e+02 Score=27.62 Aligned_cols=76 Identities=20% Similarity=0.224 Sum_probs=55.2
Q ss_pred CCccCHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhc---CCCCcccc-cc----hhHHHHHHHhhcCCCHHH
Q psy3393 352 LEEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLR---NPKPWSKL-KS----GRETFRRMWKWLQEPEFQ 423 (433)
Q Consensus 352 ~~~IDTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLr---nPKPW~kL-ks----GRE~YiRMyNWLqlPEde 423 (433)
-..+...+.+..+++.+...+.+++..|+. ||+|+++|+.+|+ -|..+.++ .. .+..+.+...-++-.++.
T Consensus 100 r~~lt~~e~a~~~~~l~~~~g~s~~~iA~~-lg~s~~~V~r~l~l~~lp~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 178 (187)
T TIGR00180 100 REDLSPIEEAQAYKRLLEKFSMTQEDLAKK-IGKSRAHITNLLRLLKLPSEIQSAIPEASGLLSSGHARLLLALKKKPKL 178 (187)
T ss_pred ccCCCHHHHHHHHHHHHHHhCCCHHHHHHH-HCcCHHHHHHHHHHHcCCHHHHHHHHhccCCCcHHHHHHHHcCCCchHH
Confidence 357788889999999888889999998865 5899999998877 47777764 33 445555666666655555
Q ss_pred HHHHH
Q psy3393 424 RMSAL 428 (433)
Q Consensus 424 RmeIL 428 (433)
+++..
T Consensus 179 ~~~~~ 183 (187)
T TIGR00180 179 QELLA 183 (187)
T ss_pred HHHHH
Confidence 55544
No 42
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=29.33 E-value=45 Score=25.49 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=15.7
Q ss_pred HHhhcCCCHHHHHHHHHH
Q psy3393 413 MWKWLQEPEFQRMSALRL 430 (433)
Q Consensus 413 MyNWLqlPEdeRmeILRl 430 (433)
+.+|..+++++|.+||+.
T Consensus 27 I~~W~~~s~~er~~i~~~ 44 (51)
T PF06945_consen 27 IRDWKSMSDDERRAILAR 44 (51)
T ss_pred HHHHhhCCHHHHHHHHHH
Confidence 458999999999999964
No 43
>PF08519 RFC1: Replication factor RFC1 C terminal domain; InterPro: IPR013725 This is the C-terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo [, ]. ; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_A.
Probab=24.11 E-value=26 Score=32.26 Aligned_cols=50 Identities=12% Similarity=0.282 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCccccc-chhHHHHHHHh
Q psy3393 360 LAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLK-SGRETFRRMWK 415 (433)
Q Consensus 360 Ia~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLk-sGRE~YiRMyN 415 (433)
=++++.+.|..|++++.-| +.|.... ..-..+.+++++. +=|..|.|.||
T Consensus 104 ~v~~vi~~Md~Y~Ltred~-d~i~el~-----~~~~~~~~~~~i~tkvKaafTR~yN 154 (155)
T PF08519_consen 104 GVDEVIDLMDEYGLTREDW-DNIMELS-----KWPGKEDPLKKIDTKVKAAFTRAYN 154 (155)
T ss_dssp ---------------------------------------------------------
T ss_pred cHHHHHHHHHHhCCCHHHH-HHHHHhc-----cCCCCcccccCCcHHHHHHHHHHhc
Confidence 3456677788999999999 9988877 4556788999996 89999999998
No 44
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=23.68 E-value=93 Score=26.30 Aligned_cols=56 Identities=16% Similarity=0.127 Sum_probs=39.8
Q ss_pred CHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCC
Q psy3393 356 NTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQE 419 (433)
Q Consensus 356 DTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLql 419 (433)
+...|..+|++..+..+++| +|++ .|+++.||+.+.+... .-.-.++.|+-+-|.+
T Consensus 29 ~~~~~~~~l~~~r~~~glSq--LAe~-~GIs~stLs~iE~g~~-----~Ps~~tL~kI~~aLgi 84 (89)
T TIGR02684 29 DPAYIAHALGYIARARGMTQ--LARK-TGLSRESLYKALSGKG-----NPTFDTILKVTKALGL 84 (89)
T ss_pred CHHHHHHHHHHHHHHCChHH--HHHH-HCCCHHHHHHHHcCCC-----CCCHHHHHHHHHHcCC
Confidence 56678889999999999997 6665 5789999999998653 1133445555444443
No 45
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=23.62 E-value=3.3e+02 Score=27.38 Aligned_cols=78 Identities=18% Similarity=0.237 Sum_probs=57.0
Q ss_pred CCCccCHHHHHHHHHHHHHHcC--CChHHHHhhhhcccCchhhhhhcCCCCccc-----------cc-chhHHHHHHHhh
Q psy3393 351 ELEEINTKELAQRISAELKRYS--IPQAIFAQRVLCRSQGTLSDLLRNPKPWSK-----------LK-SGRETFRRMWKW 416 (433)
Q Consensus 351 d~~~IDTKeIa~rIkewLkr~~--IsQavFAekILgRSQGTLSDLLrnPKPW~k-----------Lk-sGRE~YiRMyNW 416 (433)
-.+|.|-.+.-++..+|.++.+ .+-+.||++.---+.+.|+++++--++-.. |. ..++.|.-|.++
T Consensus 4 I~eY~dYR~fl~d~ye~rk~~~p~fS~R~fa~~~G~ss~s~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E~~yF~~lV~f 83 (271)
T TIGR02147 4 IFEYTDYRKYLRDYYEERKKTDPAFSWRFFAEKAGFSSTSYLNDIIKGKKNLTKRMIPKFAEALGLDEKEAAYFEAMVNF 83 (271)
T ss_pred chhhhhHHHHHHHHHHHHhccCcCcCHHHHHHHhCCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 3567888888999999999876 999999987544445999999997765443 22 567788888777
Q ss_pred cCCC-HHHHHHHH
Q psy3393 417 LQEP-EFQRMSAL 428 (433)
Q Consensus 417 LqlP-EdeRmeIL 428 (433)
-+-. +.+|..++
T Consensus 84 ~~ak~~~~k~~~~ 96 (271)
T TIGR02147 84 GQAKTDTEKQQFF 96 (271)
T ss_pred hccCCHHHHHHHH
Confidence 7755 34555543
No 46
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=22.15 E-value=2.2e+02 Score=23.81 Aligned_cols=67 Identities=18% Similarity=0.201 Sum_probs=47.3
Q ss_pred CHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCC-CCccccc--chhHHHHHHHhhcCCCHHHHHHHHHHh
Q psy3393 356 NTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNP-KPWSKLK--SGRETFRRMWKWLQEPEFQRMSALRLA 431 (433)
Q Consensus 356 DTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnP-KPW~kLk--sGRE~YiRMyNWLqlPEdeRmeILRl~ 431 (433)
..++|++.|.+++++..-.|++.+=.+++ +|+++= ++....- ..-..|...|. +.+++.|..+.|+.
T Consensus 34 ~a~~iv~~i~~~i~~~~~~~KL~~LYL~d-------sIvkn~~~~~~~~~~~~~~~~f~~~~~--~~~~~~r~kl~rl~ 103 (114)
T cd03562 34 HAKEIVEIIEKHIKKCPPEQKLPLLYLLD-------SIVKNVGRKYKEFFSEFLVPLFLDAYE--KVDEKTRKKLERLL 103 (114)
T ss_pred HHHHHHHHHHHHHHhCCcccchHHHHHHH-------HHHHHcccchHHHHHHHHHHHHHHHHH--hCCHHHHHHHHHHH
Confidence 45688888888888888888887777664 555542 2333332 23677877776 88999999999885
No 47
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=22.07 E-value=85 Score=31.74 Aligned_cols=45 Identities=22% Similarity=0.136 Sum_probs=31.9
Q ss_pred CccCHHHHHHH---HHHHHHH---cCCChHHHHhhhh----cccCchhhhhhcCC
Q psy3393 353 EEINTKELAQR---ISAELKR---YSIPQAIFAQRVL----CRSQGTLSDLLRNP 397 (433)
Q Consensus 353 ~~IDTKeIa~r---IkewLkr---~~IsQavFAekIL----gRSQGTLSDLLrnP 397 (433)
..++..|-|.- +++.+.+ .+++|+.+|+++- +++|.+++.+|+--
T Consensus 111 ~dLsfIE~A~~~~~l~~l~e~~~g~~ltq~ela~~lgk~g~~isrs~Isn~lrll 165 (258)
T TIGR03764 111 GDLTFIEKALGVQKARALYEKELGESLSQRELARRLSADGYPISQSHISRMGDTV 165 (258)
T ss_pred cCCCHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHhcccCCCCCHHHHHHHHHHH
Confidence 35556666655 4444445 6899999999984 56999999888743
No 48
>PF06778 Chlor_dismutase: Chlorite dismutase; InterPro: IPR010644 This family contains chlorite dismutase enzymes of bacterial and archaeal origin. This enzyme catalyses the disproportionation of chlorite into chloride and oxygen [, ]. Note that many family members are hypothetical proteins.; PDB: 2VXH_B 3NN4_A 3NN2_A 3NN3_D 3NN1_E 3QPI_A 3Q08_Q 3Q09_B 1T0T_V 1VDH_E ....
Probab=21.58 E-value=18 Score=34.52 Aligned_cols=20 Identities=15% Similarity=0.234 Sum_probs=15.1
Q ss_pred HHHhhcCCCHHHHHHHHHHh
Q psy3393 412 RMWKWLQEPEFQRMSALRLA 431 (433)
Q Consensus 412 RMyNWLqlPEdeRmeILRl~ 431 (433)
|-+||..+|.++|.+||+=.
T Consensus 111 K~~~Wy~Lp~~eR~~mm~eH 130 (193)
T PF06778_consen 111 KSREWYLLPFEERRRMMEEH 130 (193)
T ss_dssp E-HHHHHS-HHHHHHHHHHH
T ss_pred cCchhhcCCHHHHHHHHHHH
Confidence 33399999999999999743
No 49
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=21.14 E-value=1.1e+02 Score=26.49 Aligned_cols=75 Identities=16% Similarity=0.114 Sum_probs=41.5
Q ss_pred CccCHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCC-Ccccc------c--chhHHHHHHHhhc--CCCH
Q psy3393 353 EEINTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPK-PWSKL------K--SGRETFRRMWKWL--QEPE 421 (433)
Q Consensus 353 ~~IDTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPK-PW~kL------k--sGRE~YiRMyNWL--qlPE 421 (433)
.+||-++..+.+++.|+.+..=+.......+...-.+++.....+- ...+- . .-.+......+|+ .+++
T Consensus 3 p~ID~~kT~~~v~~~L~~y~~~~~~~~~~~~~~~sp~~~~~p~~~~~~~~~~~E~~~i~~i~a~~~~~~i~~ai~~~l~~ 82 (132)
T TIGR01637 3 PEIDEKKTRANVKRFLEDYRRLRRIAGRSLTPKLSPSLSLEPPSFTNEFHSKTEEAAIHNLDAEQEARAIVNAIVNQLDE 82 (132)
T ss_pred CcccHHHHHHHHHHHHHHHHHHHHHcCCcccCccCcccccCCCCCCCccCCHHHHHHHHHhHHHHHHHHHHHHHHHhCCH
Confidence 4678888889999999876555554444444433334444433221 01111 1 1223445677777 8888
Q ss_pred HHHHHH
Q psy3393 422 FQRMSA 427 (433)
Q Consensus 422 deRmeI 427 (433)
.+|.=|
T Consensus 83 ~~r~Il 88 (132)
T TIGR01637 83 ISRQIL 88 (132)
T ss_pred HHHHHH
Confidence 765433
No 50
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=20.85 E-value=87 Score=24.54 Aligned_cols=23 Identities=22% Similarity=0.081 Sum_probs=16.7
Q ss_pred hHHHHhhhhcccCchhhhhhcCCC
Q psy3393 375 QAIFAQRVLCRSQGTLSDLLRNPK 398 (433)
Q Consensus 375 QavFAekILgRSQGTLSDLLrnPK 398 (433)
++..|++ +|+|+.|||.+|++..
T Consensus 3 ~~~iA~~-~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 3 IKDVARL-AGVSKATVSRVLNGNG 25 (70)
T ss_pred HHHHHHH-HCCCHHHHHHHHCCCC
Confidence 3444443 4899999999999753
No 51
>cd03036 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine.
Probab=20.51 E-value=2.4e+02 Score=23.98 Aligned_cols=16 Identities=6% Similarity=0.080 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHcCCC
Q psy3393 359 ELAQRISAELKRYSIP 374 (433)
Q Consensus 359 eIa~rIkewLkr~~Is 374 (433)
.-|++.++||+.++|.
T Consensus 10 ~~c~ka~~~L~~~~i~ 25 (111)
T cd03036 10 STCRKAKKWLDEHGVD 25 (111)
T ss_pred HHHHHHHHHHHHcCCc
Confidence 3478889999998774
No 52
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=20.45 E-value=1.3e+02 Score=27.20 Aligned_cols=36 Identities=22% Similarity=0.268 Sum_probs=29.5
Q ss_pred HHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCC
Q psy3393 363 RISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKP 399 (433)
Q Consensus 363 rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKP 399 (433)
.+-.+|...+.+|.--| ++||+||..||.+|+-++.
T Consensus 13 ~lA~~L~eeG~Sq~~iA-~LLGltqaAVS~Yls~krg 48 (119)
T COG2522 13 LLAKELIEEGLSQYRIA-KLLGLTQAAVSQYLSGKRG 48 (119)
T ss_pred HHHHHHHHcCCcHHHHH-HHhCCCHHHHHHHHccCCc
Confidence 34455666699999887 5899999999999998887
No 53
>PRK02866 cyanate hydratase; Validated
Probab=20.44 E-value=1.4e+02 Score=27.89 Aligned_cols=63 Identities=19% Similarity=0.090 Sum_probs=48.8
Q ss_pred CHHHHHHHHHHHHHHcCCChHHHHhhhhcccCchhhhhhcCCCCcccccchhHHHHHHHhhcCCCHHHH
Q psy3393 356 NTKELAQRISAELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEPEFQR 424 (433)
Q Consensus 356 DTKeIa~rIkewLkr~~IsQavFAekILgRSQGTLSDLLrnPKPW~kLksGRE~YiRMyNWLqlPEdeR 424 (433)
+-.+++++|.+..++.+++++-.|+.| |+|+-++..++.-=..- -.+.-.++-.-|.++++..
T Consensus 2 ~~~~~~e~Ll~AK~~kGLTw~~IA~~i-G~S~v~vaaa~lGQ~~l-----s~e~A~kla~~LgL~~~~~ 64 (147)
T PRK02866 2 KREELTEKILAAKKEKGLTWADIAEAI-GLSEVWVTAALLGQMTL-----PAEEAEKVAELLGLDEDAV 64 (147)
T ss_pred CHHHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHhCCCCC-----CHHHHHHHHHHhCCCHHHH
Confidence 456889999999999999999999999 99999988888632211 3355566667778887644
Done!