Query psy2180
Match_columns 129
No_of_seqs 98 out of 138
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 18:19:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2180.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2180hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00292 PAX: 'Paired box' dom 100.0 8E-41 1.7E-45 251.0 -0.3 94 14-110 1-114 (125)
2 KOG3517|consensus 100.0 8.3E-38 1.8E-42 261.4 3.8 94 14-110 4-117 (334)
3 KOG3862|consensus 100.0 2.5E-36 5.3E-41 253.4 3.3 100 8-110 3-122 (327)
4 KOG0849|consensus 99.9 6.5E-26 1.4E-30 191.4 2.0 92 16-110 1-113 (354)
5 cd00131 PAX Paired Box domain 99.8 4.1E-20 9E-25 136.4 3.5 98 14-114 1-118 (128)
6 smart00351 PAX Paired Box doma 99.7 1.2E-17 2.5E-22 122.4 3.6 93 14-109 1-113 (125)
7 PF13384 HTH_23: Homeodomain-l 93.5 0.025 5.4E-07 34.4 0.3 34 33-66 4-45 (50)
8 PF12759 HTH_Tnp_IS1: InsA C-t 89.2 0.3 6.4E-06 31.8 1.9 25 33-57 8-32 (46)
9 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 88.4 0.16 3.4E-06 33.2 0.2 36 27-62 1-40 (50)
10 PF01710 HTH_Tnp_IS630: Transp 84.6 0.67 1.4E-05 33.5 1.9 64 32-99 4-81 (119)
11 PF13551 HTH_29: Winged helix- 83.8 0.28 6.1E-06 33.1 -0.4 31 36-66 1-40 (112)
12 PF02796 HTH_7: Helix-turn-hel 78.3 0.87 1.9E-05 27.9 0.5 25 33-57 8-32 (45)
13 PF06056 Terminase_5: Putative 77.2 1.4 3.1E-05 29.0 1.3 24 35-58 2-25 (58)
14 COG3415 Transposase and inacti 75.3 2.4 5.1E-05 32.6 2.2 47 28-74 2-58 (138)
15 PF13518 HTH_28: Helix-turn-he 74.6 1 2.2E-05 27.0 0.0 31 36-66 2-40 (52)
16 KOG0400|consensus 69.7 2.5 5.5E-05 33.4 1.3 26 32-57 30-55 (151)
17 PF13936 HTH_38: Helix-turn-he 67.7 2 4.3E-05 26.3 0.3 29 29-57 3-31 (44)
18 PF04218 CENP-B_N: CENP-B N-te 65.0 5.3 0.00012 25.4 1.9 29 29-57 5-33 (53)
19 cd00569 HTH_Hin_like Helix-tur 64.2 7.6 0.00016 19.4 2.1 27 31-57 6-32 (42)
20 PF08069 Ribosomal_S13_N: Ribo 62.3 2.7 5.9E-05 28.5 0.2 26 32-57 30-55 (60)
21 PRK11303 DNA-binding transcrip 59.4 11 0.00024 29.5 3.2 32 26-57 21-57 (328)
22 PRK10727 DNA-binding transcrip 58.1 12 0.00027 29.7 3.3 31 27-57 23-55 (343)
23 PF13072 DUF3936: Protein of u 55.9 5.5 0.00012 25.1 0.7 10 90-101 16-25 (38)
24 smart00421 HTH_LUXR helix_turn 55.6 11 0.00023 21.8 1.9 26 31-57 4-29 (58)
25 TIGR02417 fruct_sucro_rep D-fr 55.6 15 0.00033 28.8 3.3 31 27-57 21-56 (327)
26 PRK10423 transcriptional repre 48.4 23 0.0005 27.6 3.3 31 27-57 20-52 (327)
27 PRK10141 DNA-binding transcrip 45.2 13 0.00029 27.5 1.4 28 30-57 12-41 (117)
28 PRK14987 gluconate operon tran 45.1 28 0.0006 27.5 3.3 35 22-57 23-59 (331)
29 PRK12794 flaF flagellar biosyn 44.5 22 0.00047 26.7 2.5 21 26-46 67-87 (122)
30 PRK12793 flaF flagellar biosyn 44.0 22 0.00048 26.5 2.5 23 26-48 65-87 (115)
31 PRK10703 DNA-binding transcrip 43.8 29 0.00064 27.4 3.3 28 30-57 27-55 (341)
32 PRK10339 DNA-binding transcrip 43.0 29 0.00062 27.4 3.1 29 27-56 23-55 (327)
33 PRK10401 DNA-binding transcrip 42.4 32 0.0007 27.4 3.4 28 30-57 27-55 (346)
34 COG1609 PurR Transcriptional r 42.2 30 0.00064 28.7 3.2 36 22-57 18-54 (333)
35 PRK09526 lacI lac repressor; R 41.2 33 0.00072 27.0 3.2 35 23-57 24-59 (342)
36 COG4405 Uncharacterized protei 40.8 13 0.00029 29.2 0.9 53 77-129 3-60 (140)
37 TIGR01481 ccpA catabolite cont 40.5 35 0.00077 26.7 3.3 31 27-57 23-55 (329)
38 PF07309 FlaF: Flagellar prote 39.9 28 0.00061 25.6 2.5 20 26-45 64-83 (113)
39 PF01022 HTH_5: Bacterial regu 38.0 16 0.00035 22.1 0.8 25 33-57 1-26 (47)
40 PLN00061 photosystem II protei 37.9 10 0.00022 30.1 -0.2 27 16-42 116-145 (150)
41 PRK08561 rps15p 30S ribosomal 37.4 25 0.00055 27.8 2.0 26 32-57 30-55 (151)
42 cd01392 HTH_LacI Helix-turn-he 35.7 52 0.0011 19.4 2.8 31 26-56 18-50 (52)
43 COG1710 Uncharacterized protei 32.8 46 0.001 26.1 2.7 32 27-58 88-121 (139)
44 PHA00738 putative HTH transcri 32.6 27 0.00058 26.2 1.4 27 31-57 9-37 (108)
45 PRK09492 treR trehalose repres 32.0 30 0.00065 26.9 1.7 37 21-57 21-58 (315)
46 PTZ00072 40S ribosomal protein 31.9 33 0.00072 27.2 1.9 26 32-57 27-52 (148)
47 TIGR03044 PS_II_psb27 photosys 28.6 24 0.00053 27.5 0.6 26 16-41 96-123 (135)
48 PRK10014 DNA-binding transcrip 26.7 83 0.0018 24.8 3.3 28 30-57 32-60 (342)
49 PRK00964 tetrahydromethanopter 26.6 13 0.00029 31.0 -1.2 58 35-95 87-165 (225)
50 KOG3862|consensus 26.4 13 0.00027 32.7 -1.5 41 17-57 102-142 (327)
51 PRK11041 DNA-binding transcrip 26.0 73 0.0016 24.5 2.8 27 31-57 4-31 (309)
52 PF01527 HTH_Tnp_1: Transposas 25.7 26 0.00057 22.3 0.3 29 30-58 6-35 (76)
53 PF00356 LacI: Bacterial regul 25.4 72 0.0016 19.9 2.2 26 24-49 19-45 (46)
54 cd06171 Sigma70_r4 Sigma70, re 24.2 70 0.0015 17.7 1.9 27 31-57 11-37 (55)
55 PF00196 GerE: Bacterial regul 23.2 46 0.00099 20.6 1.0 22 36-57 8-29 (58)
56 PF13542 HTH_Tnp_ISL3: Helix-t 23.2 50 0.0011 19.7 1.2 30 28-57 9-38 (52)
57 cd06170 LuxR_C_like C-terminal 22.6 78 0.0017 18.3 1.9 22 36-57 5-26 (57)
58 PF12840 HTH_20: Helix-turn-he 22.4 29 0.00062 21.8 -0.0 27 31-57 7-35 (61)
59 smart00354 HTH_LACI helix_turn 22.0 63 0.0014 21.0 1.6 35 23-57 19-54 (70)
60 PF13326 PSII_Pbs27: Photosyst 21.5 22 0.00048 27.4 -0.8 26 16-41 108-136 (145)
61 PF12926 MOZART2: Mitotic-spin 20.6 1.7E+02 0.0036 21.4 3.6 38 28-65 38-78 (88)
62 PF01119 DNA_mis_repair: DNA m 20.6 44 0.00095 23.7 0.6 22 23-44 43-65 (119)
No 1
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=100.00 E-value=8e-41 Score=250.98 Aligned_cols=94 Identities=39% Similarity=0.725 Sum_probs=75.9
Q ss_pred CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc-----------
Q psy2180 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT----------- 74 (129)
Q Consensus 14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~----------- 74 (129)
|++++|||||+|+||||||.++|++||||+++|+|||||||+|+ ||.||++|||+.|++++
T Consensus 1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v 80 (125)
T PF00292_consen 1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEV 80 (125)
T ss_dssp S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCH
T ss_pred CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHH
Confidence 68999999999999999999999999999999999999999998 89999999999999885
Q ss_pred -ccccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180 75 -STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD 110 (129)
Q Consensus 75 -s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~ 110 (129)
.+|++| |++||+||+|| |||+|++|++|+.+++
T Consensus 81 ~~~I~~~-k~enP~ifawE--iR~~L~~~gvc~~~~~ 114 (125)
T PF00292_consen 81 VEKIEQY-KRENPTIFAWE--IRDRLIADGVCDRSNV 114 (125)
T ss_dssp HHHHHHH-HHH-TTS-HHH--HHHHHHHTTSS-TTTS
T ss_pred HHHHHHH-HhcCCCcchHH--HHHHHHHcCCCCCCCC
Confidence 248999 99999999999 9999999999999885
No 2
>KOG3517|consensus
Probab=100.00 E-value=8.3e-38 Score=261.36 Aligned_cols=94 Identities=41% Similarity=0.656 Sum_probs=88.2
Q ss_pred CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCcccccccc-c--------
Q psy2180 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFTS-T-------- 76 (129)
Q Consensus 14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~s-~-------- 76 (129)
..+.||||||+|+||||||.+.|-|||||++.|+|||||||||+ ||.||.|||||-|+|++. +
T Consensus 4 ~~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~V 83 (334)
T KOG3517|consen 4 SYGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKV 83 (334)
T ss_pred cccchhhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhH
Confidence 45799999999999999999999999999999999999999999 899999999999999962 1
Q ss_pred ---ccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180 77 ---GAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD 110 (129)
Q Consensus 77 ---Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~ 110 (129)
|++| ||++|.||||| |||||++||+||..|.
T Consensus 84 V~~IR~~-Kq~DPGIFAWE--IRDRLlsdgiCDk~Nv 117 (334)
T KOG3517|consen 84 VKYIRSL-KQRDPGIFAWE--IRDRLLSDGICDKYNV 117 (334)
T ss_pred HHHHHHh-hccCCceeeeh--hhhhhhhcccccccCC
Confidence 8888 99999999999 9999999999999883
No 3
>KOG3862|consensus
Probab=100.00 E-value=2.5e-36 Score=253.39 Aligned_cols=100 Identities=42% Similarity=0.731 Sum_probs=92.9
Q ss_pred eeeecCCCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc-----
Q psy2180 8 FGCSAAGHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT----- 74 (129)
Q Consensus 8 ~~~~~~~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~----- 74 (129)
+.+...||++||||||+|+||||||+..|++||||+++|+|||||||||+ ||-||+|||||.|+.++
T Consensus 3 ~~s~~~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~K 82 (327)
T KOG3862|consen 3 HNSIHSGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPK 82 (327)
T ss_pred ccCCCCCccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccc
Confidence 45567899999999999999999999999999999999999999999998 89999999999888875
Q ss_pred -------ccccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180 75 -------STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD 110 (129)
Q Consensus 75 -------s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~ 110 (129)
.+|+.| |++||+||||| |||+|+.|++|++|+.
T Consensus 83 vAtp~Vvk~i~~~-k~~n~~mfawe--iR~~l~~~~ic~~d~v 122 (327)
T KOG3862|consen 83 VATPKVVKKIALY-KRQNPTMFAWE--IRDRLLAEPICDNDTV 122 (327)
T ss_pred cccchHHHHHHHH-hhcCcchhhhh--hhhhhhcccccCCCCC
Confidence 348899 99999999999 9999999999999983
No 4
>KOG0849|consensus
Probab=99.91 E-value=6.5e-26 Score=191.39 Aligned_cols=92 Identities=40% Similarity=0.708 Sum_probs=86.8
Q ss_pred CCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc-------------
Q psy2180 16 SGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT------------- 74 (129)
Q Consensus 16 ~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~------------- 74 (129)
+.+|||||+|+||+|||.+.|++|+||++.|+|||+||++|. ||+||++|||+.|..++
T Consensus 1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~ 80 (354)
T KOG0849|consen 1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVE 80 (354)
T ss_pred CCcccCCcccccCCCCCCchhhccccccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhH
Confidence 479999999999999999999999999999999999999998 89999999999999885
Q ss_pred ccccccccccCCcchhhhhhhhhhhhhcccCCCCch
Q psy2180 75 STGAPYRTQRDRRSWNWRTLARDPVISRASCRSPTD 110 (129)
Q Consensus 75 s~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~ 110 (129)
..|++| |++||.+|+|| |||+|+.+++|+++|.
T Consensus 81 ~~i~~~-k~~~P~~~~~~--ir~~l~~~~~~~~~t~ 113 (354)
T KOG0849|consen 81 AKIEQY-KRENPAMFAWE--IRDQLLHEGLCTQATL 113 (354)
T ss_pred HHHHHH-HhcCCcccchh--hhhcccCcccccCCCC
Confidence 348889 99999999999 9999999999999863
No 5
>cd00131 PAX Paired Box domain
Probab=99.79 E-value=4.1e-20 Score=136.45 Aligned_cols=98 Identities=44% Similarity=0.726 Sum_probs=86.1
Q ss_pred CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc----cc-----
Q psy2180 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT----ST----- 76 (129)
Q Consensus 14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~----s~----- 76 (129)
|++++|||||+|.+|+||+.++|++||+|++.|+.+.+||++++ ++.||.++|++.|+..+ .+
T Consensus 1 ~~~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~ 80 (128)
T cd00131 1 GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEV 80 (128)
T ss_pred CCccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHH
Confidence 57899999999999999999999999999999999999999998 79999999999988653 11
Q ss_pred ---ccccccccCCcchhhhhhhhhhhhhcccCCCCchhhhh
Q psy2180 77 ---GAPYRTQRDRRSWNWRTLARDPVISRASCRSPTDVCRK 114 (129)
Q Consensus 77 ---Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~~v~~~ 114 (129)
|..+ .++||.++.|| |+|.|..+|+|.+++.|+.+
T Consensus 81 ~~~i~~~-v~~~p~~Tl~E--l~~~L~~~gv~~~~~~~s~s 118 (128)
T cd00131 81 VKKIEIY-KQENPGMFAWE--IRDRLLQEGVCDKSNVPSVS 118 (128)
T ss_pred HHHHHHH-HHHCCCCCHHH--HHHHHHHcCCcccCCCCCHH
Confidence 4444 67899999999 99999999999976666553
No 6
>smart00351 PAX Paired Box domain.
Probab=99.69 E-value=1.2e-17 Score=122.40 Aligned_cols=93 Identities=47% Similarity=0.813 Sum_probs=82.6
Q ss_pred CCCCCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCccccccc----c------
Q psy2180 14 GHSGINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFT----S------ 75 (129)
Q Consensus 14 ~~~~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~----s------ 75 (129)
+++++|||||+|++|+|++.+.|.+||.++..|....+||++++ ++.||.++|++.|+..+ .
T Consensus 1 ~~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~ 80 (125)
T smart00351 1 GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKV 80 (125)
T ss_pred CCCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHH
Confidence 47899999999999999999999999999999999999999998 69999999999886443 1
Q ss_pred --cccccccccCCcchhhhhhhhhhhhhcccCCCCc
Q psy2180 76 --TGAPYRTQRDRRSWNWRTLARDPVISRASCRSPT 109 (129)
Q Consensus 76 --~Ia~y~K~~np~~faWE~~IRd~Li~e~~C~~~~ 109 (129)
.|..+ .++||.++.|| |++.|..+|+|..++
T Consensus 81 ~~~I~~~-~~~~p~~t~~e--l~~~L~~~gv~~~~~ 113 (125)
T smart00351 81 VKKIADY-KQENPGIFAWE--IRDRLLSEGVCDKDN 113 (125)
T ss_pred HHHHHHH-HHHCCCCCHHH--HHHHHHHcCCCcCCC
Confidence 25556 78899999999 999999999999544
No 7
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.47 E-value=0.025 Score=34.39 Aligned_cols=34 Identities=21% Similarity=0.365 Sum_probs=19.1
Q ss_pred hHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccC
Q psy2180 33 DSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRG 66 (129)
Q Consensus 33 ~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tG 66 (129)
...|..||+|..+|...-+||+.|+ +++||.+.|
T Consensus 4 ~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 4 EERRAQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp ------HHHHHHHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred hhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 4578999999999999999999998 689998877
No 8
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=89.21 E-value=0.3 Score=31.80 Aligned_cols=25 Identities=28% Similarity=0.433 Sum_probs=22.7
Q ss_pred hHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 33 DSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 33 ~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
+...++||||+..|+---|+||-|.
T Consensus 8 pgikeqIvema~nG~GiRdtaRvL~ 32 (46)
T PF12759_consen 8 PGIKEQIVEMAFNGSGIRDTARVLK 32 (46)
T ss_pred ccHHHHHHHHHhcCCcchhhHhHhc
Confidence 3578899999999999999999998
No 9
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=88.42 E-value=0.16 Score=33.22 Aligned_cols=36 Identities=28% Similarity=0.431 Sum_probs=26.2
Q ss_pred CCCCCChHHHHHHHHHHhcCCCCCchhhhhh----cccCC
Q psy2180 27 NGRPLPDSTRQKIVELAHSGARPCDISRTCS----AVRRP 62 (129)
Q Consensus 27 nGrPLp~~~R~kIVELa~~GvRPcdISR~L~----IL~Ry 62 (129)
.|.+|.+.+|.+|.-|.+.|+.-.+||+++. .+++|
T Consensus 1 RG~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~Ir~y 40 (50)
T PF11427_consen 1 RGKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCIRRY 40 (50)
T ss_dssp -S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHH
T ss_pred CCCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHHHHH
Confidence 3789999999999999999999999999997 56655
No 10
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=84.56 E-value=0.67 Score=33.51 Aligned_cols=64 Identities=6% Similarity=0.035 Sum_probs=49.8
Q ss_pred ChHHHHHHHHHHhcCCCCCchhhhhh--------cccCCCccCCcccccccc-c-----ccccccccCCcchhhhhhhhh
Q psy2180 32 PDSTRQKIVELAHSGARPCDISRTCS--------AVRRPATRGSTSWAAFTS-T-----GAPYRTQRDRRSWNWRTLARD 97 (129)
Q Consensus 32 p~~~R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tGS~~p~a~~s-~-----Ia~y~K~~np~~faWE~~IRd 97 (129)
+.+.|++||+....|....++|+... -+. ..++|++.+..-+. + +..+ =++||.+..+| |.+
T Consensus 4 S~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~Kid~~~L~~~-v~~~pd~tl~E--la~ 79 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRKKIDRDELKAL-VEENPDATLRE--LAE 79 (119)
T ss_pred CHHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHH-hcccccccccccccccccHHHHHHH-HHHCCCcCHHH--HHH
Confidence 67899999999999999999999988 255 56788887766543 3 3344 35579999999 877
Q ss_pred hh
Q psy2180 98 PV 99 (129)
Q Consensus 98 ~L 99 (129)
+|
T Consensus 80 ~l 81 (119)
T PF01710_consen 80 RL 81 (119)
T ss_pred Hc
Confidence 76
No 11
>PF13551 HTH_29: Winged helix-turn helix
Probab=83.76 E-value=0.28 Score=33.07 Aligned_cols=31 Identities=26% Similarity=0.369 Sum_probs=27.8
Q ss_pred HHHHHHHHhcCCC-CCchhhhhh--------cccCCCccC
Q psy2180 36 RQKIVELAHSGAR-PCDISRTCS--------AVRRPATRG 66 (129)
Q Consensus 36 R~kIVELa~~GvR-PcdISR~L~--------IL~Ry~~tG 66 (129)
|.+||.|+.+|+. +.+||+.++ .+++|.++|
T Consensus 1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 6789999999995 999999998 588888888
No 12
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=78.29 E-value=0.87 Score=27.86 Aligned_cols=25 Identities=20% Similarity=0.295 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 33 DSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 33 ~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
++....|++|...|+...+||+.+.
T Consensus 8 ~~~~~~i~~l~~~G~si~~IA~~~g 32 (45)
T PF02796_consen 8 KEQIEEIKELYAEGMSIAEIAKQFG 32 (45)
T ss_dssp HCCHHHHHHHHHTT--HHHHHHHTT
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHC
Confidence 3356899999999999999999987
No 13
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=77.16 E-value=1.4 Score=28.96 Aligned_cols=24 Identities=13% Similarity=0.112 Sum_probs=22.0
Q ss_pred HHHHHHHHHhcCCCCCchhhhhhc
Q psy2180 35 TRQKIVELAHSGARPCDISRTCSA 58 (129)
Q Consensus 35 ~R~kIVELa~~GvRPcdISR~L~I 58 (129)
.|++..+|+..|.+|.+||+.|.+
T Consensus 2 ~k~~A~~LY~~G~~~~eIA~~Lg~ 25 (58)
T PF06056_consen 2 VKEQARSLYLQGWSIKEIAEELGV 25 (58)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCC
Confidence 588899999999999999999983
No 14
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=75.29 E-value=2.4 Score=32.60 Aligned_cols=47 Identities=17% Similarity=0.268 Sum_probs=39.3
Q ss_pred CCCCChHHHHHHHHHH-hcCCCCCchhhhhh--------cccCCCccCCc-cccccc
Q psy2180 28 GRPLPDSTRQKIVELA-HSGARPCDISRTCS--------AVRRPATRGST-SWAAFT 74 (129)
Q Consensus 28 GrPLp~~~R~kIVELa-~~GvRPcdISR~L~--------IL~Ry~~tGS~-~p~a~~ 74 (129)
.+|-..+.|.+++... ..|+.--+||..++ -++||.++|+. ++...+
T Consensus 2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~ 58 (138)
T COG3415 2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRK 58 (138)
T ss_pred CchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCC
Confidence 3577788999999988 77999999999998 38999999999 666554
No 15
>PF13518 HTH_28: Helix-turn-helix domain
Probab=74.63 E-value=1 Score=26.97 Aligned_cols=31 Identities=32% Similarity=0.418 Sum_probs=25.2
Q ss_pred HHHHHHHHhcCCCCCchhhhhh--------cccCCCccC
Q psy2180 36 RQKIVELAHSGARPCDISRTCS--------AVRRPATRG 66 (129)
Q Consensus 36 R~kIVELa~~GvRPcdISR~L~--------IL~Ry~~tG 66 (129)
|.+||+++.+|...-+||+.+. .+.+|.+.|
T Consensus 2 r~~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 2 RLQIVELYLEGESVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 6789999999999999999888 356666555
No 16
>KOG0400|consensus
Probab=69.75 E-value=2.5 Score=33.37 Aligned_cols=26 Identities=27% Similarity=0.469 Sum_probs=24.7
Q ss_pred ChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 32 PDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 32 p~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
+++...+|+.|+..|+.|++|.-.|+
T Consensus 30 ~ddvkeqI~K~akKGltpsqIGviLR 55 (151)
T KOG0400|consen 30 ADDVKEQIYKLAKKGLTPSQIGVILR 55 (151)
T ss_pred HHHHHHHHHHHHHcCCChhHceeeee
Confidence 78899999999999999999999888
No 17
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=67.74 E-value=2 Score=26.32 Aligned_cols=29 Identities=21% Similarity=0.319 Sum_probs=16.4
Q ss_pred CCCChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 29 RPLPDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 29 rPLp~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
..|..+.|..|-.|...|....+||+.|+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg 31 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGMSIREIAKRLG 31 (44)
T ss_dssp ---------HHHHHHCS---HHHHHHHTT
T ss_pred cchhhhHHHHHHHHHHcCCCHHHHHHHHC
Confidence 45788999999999999999999999997
No 18
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=64.99 E-value=5.3 Score=25.45 Aligned_cols=29 Identities=21% Similarity=0.331 Sum_probs=23.8
Q ss_pred CCCChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 29 RPLPDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 29 rPLp~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
+.|......+||+++..|....+||+.++
T Consensus 5 ~~LTl~eK~~iI~~~e~g~s~~~ia~~fg 33 (53)
T PF04218_consen 5 KSLTLEEKLEIIKRLEEGESKRDIAREFG 33 (53)
T ss_dssp SS--HHHHHHHHHHHHCTT-HHHHHHHHT
T ss_pred ccCCHHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 45788899999999999999999999987
No 19
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=64.19 E-value=7.6 Score=19.37 Aligned_cols=27 Identities=19% Similarity=0.262 Sum_probs=23.0
Q ss_pred CChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 31 LPDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 31 Lp~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
+++..+..|+++...|....+|++.+.
T Consensus 6 ~~~~~~~~i~~~~~~~~s~~~ia~~~~ 32 (42)
T cd00569 6 LTPEQIEEARRLLAAGESVAEIARRLG 32 (42)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHC
Confidence 467788899999999988889998876
No 20
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=62.29 E-value=2.7 Score=28.50 Aligned_cols=26 Identities=31% Similarity=0.515 Sum_probs=22.8
Q ss_pred ChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 32 PDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 32 p~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
+++.-..||+||+.|..|+.|--.||
T Consensus 30 ~~eVe~~I~klakkG~tpSqIG~iLR 55 (60)
T PF08069_consen 30 PEEVEELIVKLAKKGLTPSQIGVILR 55 (60)
T ss_dssp HHHHHHHHHHHCCTTHCHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCHHHhhhhhh
Confidence 57889999999999999999976665
No 21
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=59.40 E-value=11 Score=29.47 Aligned_cols=32 Identities=19% Similarity=0.432 Sum_probs=28.0
Q ss_pred cCCCC----CChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 26 VNGRP----LPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 26 ~nGrP----Lp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
.||++ +++++|+||.+.+++ |-+|...+|.|.
T Consensus 21 Ln~~~~~~~Vs~~tr~rV~~~a~elgY~pn~~a~~l~ 57 (328)
T PRK11303 21 INGKAKQYRVSDKTVEKVMAVVREHNYHPNAVAAGLR 57 (328)
T ss_pred HcCCCCCCCcCHHHHHHHHHHHHHhCCCCCHHHHHhh
Confidence 36665 899999999999987 999999999886
No 22
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=58.08 E-value=12 Score=29.68 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=27.0
Q ss_pred CCCC-CChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 27 NGRP-LPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 27 nGrP-Lp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
||++ +++++|+||.+-+.+ |-+|...||.|+
T Consensus 23 n~~~~Vs~~tr~rV~~~a~elgY~pn~~ar~l~ 55 (343)
T PRK10727 23 NNSPKASEASRLAVHSAMESLSYHPNANARALA 55 (343)
T ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCCHHHHhhh
Confidence 4444 899999999999988 999999999886
No 23
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=55.90 E-value=5.5 Score=25.09 Aligned_cols=10 Identities=20% Similarity=0.574 Sum_probs=8.4
Q ss_pred hhhhhhhhhhhh
Q psy2180 90 NWRTLARDPVIS 101 (129)
Q Consensus 90 aWE~~IRd~Li~ 101 (129)
||| ||.+|-.
T Consensus 16 AWe--Ir~~Lke 25 (38)
T PF13072_consen 16 AWE--IRAKLKE 25 (38)
T ss_pred HHH--HHHHHHH
Confidence 899 9999853
No 24
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=55.62 E-value=11 Score=21.83 Aligned_cols=26 Identities=19% Similarity=0.327 Sum_probs=21.8
Q ss_pred CChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 31 LPDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 31 Lp~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
|++..++ |+.|...|....+||..+.
T Consensus 4 l~~~e~~-i~~~~~~g~s~~eia~~l~ 29 (58)
T smart00421 4 LTPRERE-VLRLLAEGLTNKEIAERLG 29 (58)
T ss_pred CCHHHHH-HHHHHHcCCCHHHHHHHHC
Confidence 5666665 8999999999999999987
No 25
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=55.61 E-value=15 Score=28.83 Aligned_cols=31 Identities=16% Similarity=0.388 Sum_probs=27.5
Q ss_pred CCCC----CChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 27 NGRP----LPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 27 nGrP----Lp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
||++ +++++|+||.+-+.+ |-+|...+|.|+
T Consensus 21 n~~~~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~ 56 (327)
T TIGR02417 21 NGKAKEYRISQETVERVMAVVREQGYQPNIHAASLR 56 (327)
T ss_pred cCCCCCCccCHHHHHHHHHHHHHhCCCCCHHHHHhh
Confidence 5665 899999999999977 999999999886
No 26
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=48.42 E-value=23 Score=27.62 Aligned_cols=31 Identities=13% Similarity=0.253 Sum_probs=26.7
Q ss_pred CCCC-CChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 27 NGRP-LPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 27 nGrP-Lp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
||++ +++++|+||.+.+.+ |-.|..++|.|+
T Consensus 20 n~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~ 52 (327)
T PRK10423 20 NKDRFVSEAITAKVEAAIKELNYAPSALARSLK 52 (327)
T ss_pred CCCCCCCHHHHHHHHHHHHHHCCCccHHHHHHh
Confidence 4444 899999999999977 999999999886
No 27
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=45.19 E-value=13 Score=27.48 Aligned_cols=28 Identities=36% Similarity=0.469 Sum_probs=19.5
Q ss_pred CCChHHHHHHHHHHhc-C-CCCCchhhhhh
Q psy2180 30 PLPDSTRQKIVELAHS-G-ARPCDISRTCS 57 (129)
Q Consensus 30 PLp~~~R~kIVELa~~-G-vRPcdISR~L~ 57 (129)
-|++..|.+|+++... | +-.++|+..+.
T Consensus 12 aLadptRl~IL~~L~~~~~~~v~ela~~l~ 41 (117)
T PRK10141 12 ILSDETRLGIVLLLRESGELCVCDLCTALD 41 (117)
T ss_pred HhCCHHHHHHHHHHHHcCCcCHHHHHHHHC
Confidence 4788999999998864 2 34566655544
No 28
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=45.08 E-value=28 Score=27.49 Aligned_cols=35 Identities=17% Similarity=0.135 Sum_probs=28.2
Q ss_pred CCcCcCCCC-CChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 22 GGVYVNGRP-LPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 22 Gg~f~nGrP-Lp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
.+++ ||++ .++++|+||.+.+++ |-+|...|+.|+
T Consensus 23 SrvL-n~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~ 59 (331)
T PRK14987 23 SRFL-RNPEQVSVALRGKIAAALDELGYIPNRAPDILS 59 (331)
T ss_pred hhhh-CCCCCCCHHHHHHHHHHHHHhCCCccHHHHHHh
Confidence 3444 3444 799999999999988 899999999886
No 29
>PRK12794 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=44.50 E-value=22 Score=26.69 Aligned_cols=21 Identities=29% Similarity=0.322 Sum_probs=18.5
Q ss_pred cCCCCCChHHHHHHHHHHhcC
Q psy2180 26 VNGRPLPDSTRQKIVELAHSG 46 (129)
Q Consensus 26 ~nGrPLp~~~R~kIVELa~~G 46 (129)
-++.|||.++|..|+.|+..-
T Consensus 67 ~~~N~LP~eLRa~lisL~~fv 87 (122)
T PRK12794 67 DPDNPLPIELRARIFNLSLFV 87 (122)
T ss_pred CCCCCCCHHHHHHHHHHHHHH
Confidence 368999999999999999873
No 30
>PRK12793 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed
Probab=44.02 E-value=22 Score=26.52 Aligned_cols=23 Identities=13% Similarity=0.270 Sum_probs=19.4
Q ss_pred cCCCCCChHHHHHHHHHHhcCCC
Q psy2180 26 VNGRPLPDSTRQKIVELAHSGAR 48 (129)
Q Consensus 26 ~nGrPLp~~~R~kIVELa~~GvR 48 (129)
-+++|||.++|..|+.|+..-.+
T Consensus 65 ~p~N~LP~eLRa~lisL~~fv~k 87 (115)
T PRK12793 65 SPENALPEELRADLISIGLWVLK 87 (115)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHH
Confidence 46899999999999999877443
No 31
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=43.76 E-value=29 Score=27.37 Aligned_cols=28 Identities=14% Similarity=0.247 Sum_probs=25.4
Q ss_pred CCChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 30 PLPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 30 PLp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
.++.++|+||.+.+++ |-.|...++.|.
T Consensus 27 ~vs~~tr~~V~~~a~elgY~pn~~a~~l~ 55 (341)
T PRK10703 27 FVAEETRNAVWAAIKELHYSPSAVARSLK 55 (341)
T ss_pred CCCHHHHHHHHHHHHHHCCCcCHHHHHHh
Confidence 4899999999999987 999999999885
No 32
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=43.01 E-value=29 Score=27.43 Aligned_cols=29 Identities=24% Similarity=0.510 Sum_probs=23.7
Q ss_pred CCCC---CChHHHHHHHHHHhc-CCCCCchhhhh
Q psy2180 27 NGRP---LPDSTRQKIVELAHS-GARPCDISRTC 56 (129)
Q Consensus 27 nGrP---Lp~~~R~kIVELa~~-GvRPcdISR~L 56 (129)
||+| +++++|+||.+.+++ |-+|.. ++.+
T Consensus 23 n~~~~~~vs~~tr~rV~~~a~~lgY~pn~-~~~~ 55 (327)
T PRK10339 23 NDDPTLNVKEETKHRILEIAEKLEYKTSS-ARKL 55 (327)
T ss_pred cCCCCCCcCHHHHHHHHHHHHHhCCCCch-hhhh
Confidence 6776 799999999998876 999997 4444
No 33
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=42.38 E-value=32 Score=27.36 Aligned_cols=28 Identities=18% Similarity=0.335 Sum_probs=25.4
Q ss_pred CCChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 30 PLPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 30 PLp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
.+++++|+||++-+++ |-.|..++|.|+
T Consensus 27 ~Vs~~tr~kV~~~a~elgY~pn~~a~~l~ 55 (346)
T PRK10401 27 LVSADTREAVMKAVSELGYRPNANAQALA 55 (346)
T ss_pred CCCHHHHHHHHHHHHHHCCCCCHHHHHhh
Confidence 3799999999999977 999999999886
No 34
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=42.20 E-value=30 Score=28.68 Aligned_cols=36 Identities=22% Similarity=0.386 Sum_probs=29.3
Q ss_pred CCcCcCCCCCChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 22 GGVYVNGRPLPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 22 Gg~f~nGrPLp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
.+++.+.--++.++|+||.+.+++ |-+|...||.|+
T Consensus 18 Srvln~~~~Vs~eTr~kV~~a~~elgY~pN~~Ar~L~ 54 (333)
T COG1609 18 SRVLNGSPYVSEETREKVLAAIKELGYRPNAVARSLR 54 (333)
T ss_pred HHHHcCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence 344444445899999999998887 999999999997
No 35
>PRK09526 lacI lac repressor; Reviewed
Probab=41.18 E-value=33 Score=27.02 Aligned_cols=35 Identities=14% Similarity=0.191 Sum_probs=27.5
Q ss_pred CcCcCCCCCChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 23 GVYVNGRPLPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 23 g~f~nGrPLp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
+++.+...+++++|+||.+.+.+ |-.|..++|.|+
T Consensus 24 rvLn~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~ 59 (342)
T PRK09526 24 RVLNQASHVSAKTREKVEAAMAELNYVPNRVAQQLA 59 (342)
T ss_pred HHhcCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHhh
Confidence 34433334799999999999877 899999999886
No 36
>COG4405 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.76 E-value=13 Score=29.15 Aligned_cols=53 Identities=13% Similarity=0.196 Sum_probs=33.7
Q ss_pred ccccccccCCcch-hhhh----hhhhhhhhcccCCCCchhhhhhhhhHhCCCCCCCCC
Q psy2180 77 GAPYRTQRDRRSW-NWRT----LARDPVISRASCRSPTDVCRKFSAEQTGKRPNQSVG 129 (129)
Q Consensus 77 Ia~y~K~~np~~f-aWE~----~IRd~Li~e~~C~~~~~v~~~~~~~~~~~~~~~~~~ 129 (129)
++++.++.+|.+| +|+- -.-|.|+.-=.=---++-|+.+...++..-|=|++|
T Consensus 3 m~~~~~~k~~~~~~~Wafgd~~~~Ad~L~~lV~~G~KtaTcs~~~~y~e~~ep~p~vG 60 (140)
T COG4405 3 MWDKYKEKYPSTFGAWAFGDSPGLADELADLVLNGEKTATCSSLYSYDEDREPYPTVG 60 (140)
T ss_pred hHHHHHHhccchhcccccCCCccHHHHHHHHHHcCccceehhhhhhhhhcccCCCCCC
Confidence 3445477899999 6971 012444443333344566778888888878888876
No 37
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=40.48 E-value=35 Score=26.68 Aligned_cols=31 Identities=32% Similarity=0.616 Sum_probs=26.8
Q ss_pred CCCC-CChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 27 NGRP-LPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 27 nGrP-Lp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
||++ +++++|+||.+-+.+ |-+|...++.|+
T Consensus 23 n~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~ 55 (329)
T TIGR01481 23 NGNPNVKPATRKKVLEVIKRLDYRPNAVARGLA 55 (329)
T ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHh
Confidence 4444 799999999999988 999999999886
No 38
>PF07309 FlaF: Flagellar protein FlaF; InterPro: IPR010845 This family consists of several bacterial FlaF flagellar proteins. FlaF and FlaG are trans-acting, regulatory factors that modulate flagellin synthesis during flagellum biogenesis [].
Probab=39.91 E-value=28 Score=25.55 Aligned_cols=20 Identities=30% Similarity=0.542 Sum_probs=18.0
Q ss_pred cCCCCCChHHHHHHHHHHhc
Q psy2180 26 VNGRPLPDSTRQKIVELAHS 45 (129)
Q Consensus 26 ~nGrPLp~~~R~kIVELa~~ 45 (129)
-++.|||.++|..|+.|+..
T Consensus 64 ~~~n~LP~~LRa~LisL~~f 83 (113)
T PF07309_consen 64 SPDNPLPDELRANLISLGLF 83 (113)
T ss_pred CccCCCCHHHHHHHHHHHHH
Confidence 36889999999999999987
No 39
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=38.00 E-value=16 Score=22.12 Aligned_cols=25 Identities=24% Similarity=0.454 Sum_probs=18.9
Q ss_pred hHHHHHHHHHHhcCC-CCCchhhhhh
Q psy2180 33 DSTRQKIVELAHSGA-RPCDISRTCS 57 (129)
Q Consensus 33 ~~~R~kIVELa~~Gv-RPcdISR~L~ 57 (129)
+..|.+|+.+...|- ..|||++.+.
T Consensus 1 d~~R~~Il~~L~~~~~~~~el~~~l~ 26 (47)
T PF01022_consen 1 DPTRLRILKLLSEGPLTVSELAEELG 26 (47)
T ss_dssp SHHHHHHHHHHTTSSEEHHHHHHHHT
T ss_pred CHHHHHHHHHHHhCCCchhhHHHhcc
Confidence 357999999888865 4777777765
No 40
>PLN00061 photosystem II protein Psb27; Provisional
Probab=37.87 E-value=10 Score=30.11 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=21.6
Q ss_pred CCCcccCCcCcC---CCCCChHHHHHHHHH
Q psy2180 16 SGINQLGGVYVN---GRPLPDSTRQKIVEL 42 (129)
Q Consensus 16 ~~vNqLGg~f~n---GrPLp~~~R~kIVEL 42 (129)
..+|.|+|-|.+ -||||+.+|.+|.+-
T Consensus 116 tALnsLAghYssyGpnrPLPe~lK~Rll~E 145 (150)
T PLN00061 116 KAIRSLASFYSKAGPSAPLPEDVKSEILDD 145 (150)
T ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence 457888877764 499999999999864
No 41
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=37.37 E-value=25 Score=27.79 Aligned_cols=26 Identities=31% Similarity=0.460 Sum_probs=23.9
Q ss_pred ChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 32 PDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 32 p~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
+++.-..||+||+.|..|+.|--.|+
T Consensus 30 ~eeve~~I~~lakkG~~pSqIG~~LR 55 (151)
T PRK08561 30 PEEIEELVVELAKQGYSPSMIGIILR 55 (151)
T ss_pred HHHHHHHHHHHHHCCCCHHHhhhhHh
Confidence 67899999999999999999988887
No 42
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=35.74 E-value=52 Score=19.44 Aligned_cols=31 Identities=29% Similarity=0.613 Sum_probs=23.8
Q ss_pred cCCC-CCChHHHHHHHHHHhc-CCCCCchhhhh
Q psy2180 26 VNGR-PLPDSTRQKIVELAHS-GARPCDISRTC 56 (129)
Q Consensus 26 ~nGr-PLp~~~R~kIVELa~~-GvRPcdISR~L 56 (129)
.||. ......+.+|.+++.. |.+|...++.+
T Consensus 18 l~g~~~vs~~~~~~i~~~~~~l~~~~~~~~~~~ 50 (52)
T cd01392 18 LNGKPRVSEETRERVLAAAEELGYRPNAAARSL 50 (52)
T ss_pred HcCCCCCCHHHHHHHHHHHHHhCCCCCHHHHHh
Confidence 3455 4577899999999988 88888777654
No 43
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.76 E-value=46 Score=26.08 Aligned_cols=32 Identities=31% Similarity=0.502 Sum_probs=26.5
Q ss_pred CCCCC--ChHHHHHHHHHHhcCCCCCchhhhhhc
Q psy2180 27 NGRPL--PDSTRQKIVELAHSGARPCDISRTCSA 58 (129)
Q Consensus 27 nGrPL--p~~~R~kIVELa~~GvRPcdISR~L~I 58 (129)
.|||- .-.++..|=||+..|..|-+||+.|+|
T Consensus 88 rGrprkyd~~t~~~i~emlr~gk~preIsk~lGI 121 (139)
T COG1710 88 RGRPRKYDRNTLLRIREMLRNGKTPREISKDLGI 121 (139)
T ss_pred CCCCcccchhHHHHHHHHHHcCCCHHHHHHhhCC
Confidence 46664 444778999999999999999999984
No 44
>PHA00738 putative HTH transcription regulator
Probab=32.58 E-value=27 Score=26.24 Aligned_cols=27 Identities=30% Similarity=0.224 Sum_probs=18.5
Q ss_pred CChHHHHHHHHHHhcC--CCCCchhhhhh
Q psy2180 31 LPDSTRQKIVELAHSG--ARPCDISRTCS 57 (129)
Q Consensus 31 Lp~~~R~kIVELa~~G--vRPcdISR~L~ 57 (129)
.++..|.+||++...| +-.|+|+..+.
T Consensus 9 ~~dptRr~IL~lL~~~e~~~V~eLae~l~ 37 (108)
T PHA00738 9 RAKILRRKILELIAENYILSASLISHTLL 37 (108)
T ss_pred cCCHHHHHHHHHHHHcCCccHHHHHHhhC
Confidence 3678999999977664 44556665543
No 45
>PRK09492 treR trehalose repressor; Provisional
Probab=32.05 E-value=30 Score=26.90 Aligned_cols=37 Identities=19% Similarity=0.359 Sum_probs=29.0
Q ss_pred cCCcCcCCCCCChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 21 LGGVYVNGRPLPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 21 LGg~f~nGrPLp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
...++.|...+++++|+||.+.+.+ |-.|...+|.|+
T Consensus 21 VSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~ 58 (315)
T PRK09492 21 VSRVLNNESGVSEETRERVEAVINQHGFSPSKSARAMR 58 (315)
T ss_pred HhHHhCCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHhh
Confidence 3445544445799999999999977 889999998875
No 46
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=31.89 E-value=33 Score=27.16 Aligned_cols=26 Identities=23% Similarity=0.387 Sum_probs=23.4
Q ss_pred ChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 32 PDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 32 p~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
+++.-..|++||+.|..|++|--.|+
T Consensus 27 ~eeVe~~I~klaKkG~~pSqIG~iLR 52 (148)
T PTZ00072 27 SSEVEDQICKLAKKGLTPSQIGVILR 52 (148)
T ss_pred HHHHHHHHHHHHHCCCCHhHhhhhhh
Confidence 67789999999999999999987777
No 47
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=28.57 E-value=24 Score=27.46 Aligned_cols=26 Identities=31% Similarity=0.768 Sum_probs=20.1
Q ss_pred CCCcccCCcCcC--CCCCChHHHHHHHH
Q psy2180 16 SGINQLGGVYVN--GRPLPDSTRQKIVE 41 (129)
Q Consensus 16 ~~vNqLGg~f~n--GrPLp~~~R~kIVE 41 (129)
...|.|.|-|.+ -+|||+..+.+|.+
T Consensus 96 TALNsLAGHY~sy~~rPlPeklk~Rl~~ 123 (135)
T TIGR03044 96 TALNSLAGHYKSYANRPLPEKLKERLEK 123 (135)
T ss_pred HHHHHHHHHhccCCCCCCCHHHHHHHHH
Confidence 457888765543 59999999999874
No 48
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=26.70 E-value=83 Score=24.77 Aligned_cols=28 Identities=7% Similarity=0.094 Sum_probs=24.7
Q ss_pred CCChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 30 PLPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 30 PLp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
.++.++|+||.+.+++ |-.|...++.|+
T Consensus 32 ~vs~~tr~~V~~~a~elgY~p~~~a~~l~ 60 (342)
T PRK10014 32 RISTATGERVNQAIEELGFVRNRQASALR 60 (342)
T ss_pred CCCHHHHHHHHHHHHHhCCCcCHHHHhhc
Confidence 3799999999999977 999999998875
No 49
>PRK00964 tetrahydromethanopterin S-methyltransferase subunit A; Provisional
Probab=26.64 E-value=13 Score=31.05 Aligned_cols=58 Identities=21% Similarity=0.202 Sum_probs=38.8
Q ss_pred HHHHHHHHHhcCCCCCchhhhhh--------------cccCCCc-------cCCcccccccccccccccccCCcchhhhh
Q psy2180 35 TRQKIVELAHSGARPCDISRTCS--------------AVRRPAT-------RGSTSWAAFTSTGAPYRTQRDRRSWNWRT 93 (129)
Q Consensus 35 ~R~kIVELa~~GvRPcdISR~L~--------------IL~Ry~~-------tGS~~p~a~~s~Ia~y~K~~np~~faWE~ 93 (129)
.=|-++.|.+.|+. +=.|..+ -+.||++ .|.--+.++.++|+++ +.++|..|.||.
T Consensus 87 tGqsl~aL~~NGvd--~~grIiGa~GaiPfleNi~~~aV~rFq~qVeivd~i~~eD~~~I~a~I~ec-~~kdpga~~~~p 163 (225)
T PRK00964 87 TGQSLKALHENGVD--DDGRIIGAKGAIPFLENVPDEAVERFQEQIEIVDLIDTEDPGAITAKIKEC-IAKDPGAFDEEP 163 (225)
T ss_pred ccHHHHHHHHcCCC--CCCCCccCCCCCchhhcCCHHHHHHHHhheEEEeeecCCCHHHHHHHHHHH-HccCCCCCCCCC
Confidence 44778889999885 2222222 2444442 4566666667889999 888899999984
Q ss_pred hh
Q psy2180 94 LA 95 (129)
Q Consensus 94 ~I 95 (129)
++
T Consensus 164 ~~ 165 (225)
T PRK00964 164 MV 165 (225)
T ss_pred ce
Confidence 43
No 50
>KOG3862|consensus
Probab=26.44 E-value=13 Score=32.67 Aligned_cols=41 Identities=10% Similarity=-0.116 Sum_probs=37.3
Q ss_pred CCcccCCcCcCCCCCChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 17 GINQLGGVYVNGRPLPDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 17 ~vNqLGg~f~nGrPLp~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
..|-.++-++-++|+.+.+++++||....++|-.+|..++.
T Consensus 102 mfaweiR~~l~~~~ic~~d~vpsVssinri~r~~~~~~~~~ 142 (327)
T KOG3862|consen 102 MFAWEIRDRLLAEPICDNDTVPSVSSINRIIRTKVQQKQLG 142 (327)
T ss_pred hhhhhhhhhhhcccccCCCCCchHHHHHHHHHHhhhhcccC
Confidence 34566888899999999999999999999999999999998
No 51
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=26.02 E-value=73 Score=24.54 Aligned_cols=27 Identities=22% Similarity=0.418 Sum_probs=24.7
Q ss_pred CChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 31 LPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 31 Lp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
++.++|+||.+-+.+ |-+|...||.|+
T Consensus 4 Vs~~Tr~rV~~~a~elgY~pn~~a~~l~ 31 (309)
T PRK11041 4 VSQATRQRVEQAVLEVGYSPQSLGRNLK 31 (309)
T ss_pred CCHHHHHHHHHHHHHHCCCcCHHHHHhh
Confidence 688999999999966 999999999886
No 52
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=25.74 E-value=26 Score=22.30 Aligned_cols=29 Identities=14% Similarity=0.178 Sum_probs=23.1
Q ss_pred CCChHHHHHHHHHH-hcCCCCCchhhhhhc
Q psy2180 30 PLPDSTRQKIVELA-HSGARPCDISRTCSA 58 (129)
Q Consensus 30 PLp~~~R~kIVELa-~~GvRPcdISR~L~I 58 (129)
--+.+.+.+||+++ ..|....++|+.++|
T Consensus 6 ~ys~e~K~~~v~~~~~~g~sv~~va~~~gi 35 (76)
T PF01527_consen 6 RYSPEFKLQAVREYLESGESVSEVAREYGI 35 (76)
T ss_dssp ---HHHHHHHHHHHHHHHCHHHHHHHHHTS
T ss_pred CCCHHHHHHHHHHHHHCCCceEeeeccccc
Confidence 34678899999999 889999999999883
No 53
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=25.40 E-value=72 Score=19.94 Aligned_cols=26 Identities=35% Similarity=0.549 Sum_probs=18.6
Q ss_pred cCcCCCCCChHHHHHHHHHHhc-CCCC
Q psy2180 24 VYVNGRPLPDSTRQKIVELAHS-GARP 49 (129)
Q Consensus 24 ~f~nGrPLp~~~R~kIVELa~~-GvRP 49 (129)
++.+-..+++++|+||.+.+.+ |-+|
T Consensus 19 ~ln~~~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 19 VLNGPPRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp HHTTCSSSTHHHHHHHHHHHHHHTB-S
T ss_pred HHhCCCCCCHHHHHHHHHHHHHHCCCC
Confidence 3444456799999999999876 6555
No 54
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=24.24 E-value=70 Score=17.70 Aligned_cols=27 Identities=22% Similarity=0.268 Sum_probs=19.5
Q ss_pred CChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 31 LPDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 31 Lp~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
|++..|.-+..++.+|..+-+||..+.
T Consensus 11 l~~~~~~~~~~~~~~~~~~~~ia~~~~ 37 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEILG 37 (55)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHC
Confidence 456665555555569999999999886
No 55
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=23.22 E-value=46 Score=20.63 Aligned_cols=22 Identities=14% Similarity=0.252 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCCCCCchhhhhh
Q psy2180 36 RQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 36 R~kIVELa~~GvRPcdISR~L~ 57 (129)
-..|+++...|..+.+||+.|.
T Consensus 8 E~~vl~~l~~G~~~~eIA~~l~ 29 (58)
T PF00196_consen 8 ELEVLRLLAQGMSNKEIAEELG 29 (58)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHT
T ss_pred HHHHHHHHHhcCCcchhHHhcC
Confidence 3569999999999999999987
No 56
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=23.18 E-value=50 Score=19.72 Aligned_cols=30 Identities=17% Similarity=0.133 Sum_probs=24.2
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCchhhhhh
Q psy2180 28 GRPLPDSTRQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 28 GrPLp~~~R~kIVELa~~GvRPcdISR~L~ 57 (129)
+.......++.|++++....---+||+.++
T Consensus 9 ~~r~T~~~~~~i~~~~~~~~s~~~vA~~~~ 38 (52)
T PF13542_consen 9 YCRITKRLEQYILKLLRESRSFKDVARELG 38 (52)
T ss_pred CCcHHHHHHHHHHHHHhhcCCHHHHHHHHC
Confidence 344567789999999999977788999887
No 57
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=22.64 E-value=78 Score=18.26 Aligned_cols=22 Identities=14% Similarity=0.285 Sum_probs=18.3
Q ss_pred HHHHHHHHhcCCCCCchhhhhh
Q psy2180 36 RQKIVELAHSGARPCDISRTCS 57 (129)
Q Consensus 36 R~kIVELa~~GvRPcdISR~L~ 57 (129)
...|+.|...|...-+||..+.
T Consensus 5 e~~i~~~~~~~~s~~eia~~l~ 26 (57)
T cd06170 5 EREVLRLLAEGKTNKEIADILG 26 (57)
T ss_pred HHHHHHHHHcCCCHHHHHHHHC
Confidence 3448888889999999998886
No 58
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=22.42 E-value=29 Score=21.85 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=17.9
Q ss_pred CChHHHHHHHHHH--hcCCCCCchhhhhh
Q psy2180 31 LPDSTRQKIVELA--HSGARPCDISRTCS 57 (129)
Q Consensus 31 Lp~~~R~kIVELa--~~GvRPcdISR~L~ 57 (129)
|.+..|.+|+++. ..++...+||+.+.
T Consensus 7 L~~p~R~~Il~~L~~~~~~t~~ela~~l~ 35 (61)
T PF12840_consen 7 LSDPTRLRILRLLASNGPMTVSELAEELG 35 (61)
T ss_dssp HTSHHHHHHHHHHHHCSTBEHHHHHHHHT
T ss_pred hCCHHHHHHHHHHhcCCCCCHHHHHHHHC
Confidence 5678999999998 23444555555554
No 59
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=21.99 E-value=63 Score=21.00 Aligned_cols=35 Identities=20% Similarity=0.348 Sum_probs=25.7
Q ss_pred CcCcCCCCCChHHHHHHHHHHhc-CCCCCchhhhhh
Q psy2180 23 GVYVNGRPLPDSTRQKIVELAHS-GARPCDISRTCS 57 (129)
Q Consensus 23 g~f~nGrPLp~~~R~kIVELa~~-GvRPcdISR~L~ 57 (129)
.++.+-..+.++.|++|.+.+++ |-.|...++.+.
T Consensus 19 r~ln~~~~v~~~t~~~i~~~~~~~gy~~~~~~~~~~ 54 (70)
T smart00354 19 RVLNGNGRVSEETREKVLAAMEELGYIPNRVARSLK 54 (70)
T ss_pred HHHCCCCCCCHHHHHHHHHHHHHhCCCCCHHHHHHh
Confidence 33433345688999999999887 888888777654
No 60
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=21.47 E-value=22 Score=27.39 Aligned_cols=26 Identities=31% Similarity=0.819 Sum_probs=18.4
Q ss_pred CCCcccCCcCcC--CC-CCChHHHHHHHH
Q psy2180 16 SGINQLGGVYVN--GR-PLPDSTRQKIVE 41 (129)
Q Consensus 16 ~~vNqLGg~f~n--Gr-PLp~~~R~kIVE 41 (129)
..+|.|+|-|.. -+ |||...+.+|++
T Consensus 108 tAln~LaghY~s~g~raPlP~k~k~rll~ 136 (145)
T PF13326_consen 108 TALNALAGHYSSYGNRAPLPEKLKERLLK 136 (145)
T ss_dssp HHHHHHHHHCHHHTTS-S--HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHH
Confidence 357889887753 35 999999999985
No 61
>PF12926 MOZART2: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR024332 The MOZART2 family of proteins (also known as FAM128 and Mitotic-spindle organizing protein 2) operate as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBGCP nomenclature cannot be used for it. The exact function of MOZART2 is not clear [].
Probab=20.63 E-value=1.7e+02 Score=21.42 Aligned_cols=38 Identities=21% Similarity=0.253 Sum_probs=31.1
Q ss_pred CCCCChHHHHHHHHHHhcCCCCCchhhhhh---cccCCCcc
Q psy2180 28 GRPLPDSTRQKIVELAHSGARPCDISRTCS---AVRRPATR 65 (129)
Q Consensus 28 GrPLp~~~R~kIVELa~~GvRPcdISR~L~---IL~Ry~~t 65 (129)
|.++-++.=.-||||.+.++.|-.|-..|+ .-.++..+
T Consensus 38 Gv~~dp~VFriildLL~~nVsP~AI~qmLK~m~s~~~~~~~ 78 (88)
T PF12926_consen 38 GVPMDPEVFRIILDLLRLNVSPDAIFQMLKSMCSGSRLAST 78 (88)
T ss_pred CCCcChHHHHHHHHHHHcCCCHHHHHHHHHHHHcccccCcc
Confidence 557788899999999999999999999887 44555544
No 62
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=20.55 E-value=44 Score=23.70 Aligned_cols=22 Identities=32% Similarity=0.529 Sum_probs=15.0
Q ss_pred CcCcCCCCCChH-HHHHHHHHHh
Q psy2180 23 GVYVNGRPLPDS-TRQKIVELAH 44 (129)
Q Consensus 23 g~f~nGrPLp~~-~R~kIVELa~ 44 (129)
-+|+||||+-.. +.+.|-+.+.
T Consensus 43 ~ifVN~R~V~~~~l~~~I~~~y~ 65 (119)
T PF01119_consen 43 FIFVNGRPVENKALSKAINEAYR 65 (119)
T ss_dssp EEEETTEEE--HHHHHHHHHHHH
T ss_pred EEEeCCCeEeChHHHHHHHHHHh
Confidence 589999999655 6666666665
Done!