Query psy16493
Match_columns 151
No_of_seqs 132 out of 236
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 22:42:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16493hhsearch_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 1E-61 2.2E-66 372.5 5.7 116 25-141 1-125 (125)
2 KOG3517|consensus 100.0 3.1E-61 6.8E-66 410.2 7.0 123 25-148 4-135 (334)
3 KOG3862|consensus 100.0 3.2E-55 7E-60 374.9 7.2 126 24-150 8-142 (327)
4 KOG0849|consensus 100.0 4.3E-39 9.4E-44 278.4 6.1 122 27-149 1-132 (354)
5 cd00131 PAX Paired Box domain 100.0 3.1E-29 6.7E-34 189.8 8.3 119 25-144 1-128 (128)
6 smart00351 PAX Paired Box doma 99.9 7.6E-27 1.7E-31 175.3 8.4 116 25-141 1-125 (125)
7 PF13551 HTH_29: Winged helix- 97.5 0.00028 6.1E-09 49.3 5.9 88 51-142 9-110 (112)
8 PF13565 HTH_32: Homeodomain-l 96.6 0.0052 1.1E-07 41.2 4.9 67 71-140 2-77 (77)
9 PF01710 HTH_Tnp_IS630: Transp 94.0 0.17 3.7E-06 37.6 5.7 85 43-143 4-95 (119)
10 PF13011 LZ_Tnp_IS481: leucine 92.9 0.16 3.4E-06 37.4 3.8 64 41-105 8-84 (85)
11 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 91.3 0.13 2.9E-06 34.4 1.7 37 39-76 2-42 (50)
12 COG3415 Transposase and inacti 89.2 0.86 1.9E-05 35.9 4.9 93 39-142 2-109 (138)
13 PF13384 HTH_23: Homeodomain-l 86.8 0.31 6.7E-06 30.2 0.9 31 51-82 15-45 (50)
14 KOG3862|consensus 83.3 0.26 5.7E-06 43.7 -0.8 53 24-77 98-154 (327)
15 cd00569 HTH_Hin_like Helix-tur 78.9 1.9 4E-05 22.4 1.9 24 51-75 19-42 (42)
16 PF13936 HTH_38: Helix-turn-he 78.2 0.76 1.6E-05 28.9 0.2 38 39-77 2-43 (44)
17 PF13072 DUF3936: Protein of u 76.3 1.4 3E-05 28.4 1.0 10 112-121 16-25 (38)
18 PF01022 HTH_5: Bacterial regu 75.2 0.82 1.8E-05 28.7 -0.2 39 44-83 1-44 (47)
19 PRK10141 DNA-binding transcrip 63.4 8 0.00017 29.4 2.9 61 41-102 12-83 (117)
20 PF07508 Recombinase: Recombin 61.0 18 0.00039 24.8 4.2 48 95-144 5-53 (102)
21 PF06755 DUF1219: Protein of u 54.7 8.9 0.00019 29.9 1.8 34 29-62 30-65 (114)
22 PF06413 Neugrin: Neugrin; In 49.7 23 0.00049 29.9 3.7 50 86-144 5-54 (225)
23 PF01325 Fe_dep_repress: Iron 49.3 5 0.00011 26.8 -0.2 30 52-82 21-50 (60)
24 PLN00061 photosystem II protei 48.9 8.1 0.00017 31.4 0.8 26 26-51 115-143 (150)
25 PLN00064 photosystem II protei 48.0 7.6 0.00016 32.0 0.6 30 25-54 123-155 (166)
26 PF12802 MarR_2: MarR family; 46.2 4.9 0.00011 25.4 -0.6 29 54-83 22-50 (62)
27 TIGR02417 fruct_sucro_rep D-fr 45.4 16 0.00035 29.5 2.1 29 37-65 20-57 (327)
28 PF00356 LacI: Bacterial regul 44.4 35 0.00076 21.9 3.2 37 57-105 3-39 (46)
29 PF10788 DUF2603: Protein of u 42.7 20 0.00044 28.6 2.2 26 83-111 108-133 (137)
30 PF04545 Sigma70_r4: Sigma-70, 41.6 16 0.00036 22.6 1.3 35 42-77 5-43 (50)
31 PRK10727 DNA-binding transcrip 41.1 21 0.00046 29.2 2.2 29 37-65 22-56 (343)
32 PF13412 HTH_24: Winged helix- 40.5 11 0.00024 23.1 0.4 31 52-83 16-46 (48)
33 cd01392 HTH_LacI Helix-turn-he 40.0 14 0.0003 22.6 0.7 18 58-76 2-19 (52)
34 cd00090 HTH_ARSR Arsenical Res 39.7 19 0.00041 22.1 1.4 32 52-84 19-50 (78)
35 PHA00738 putative HTH transcri 38.5 14 0.0003 28.5 0.7 41 43-84 10-56 (108)
36 smart00550 Zalpha Z-DNA-bindin 38.2 15 0.00032 24.8 0.7 31 53-84 22-52 (68)
37 PRK11303 DNA-binding transcrip 37.1 27 0.00059 28.1 2.2 28 37-64 21-57 (328)
38 PF13326 PSII_Pbs27: Photosyst 35.0 15 0.00032 29.0 0.4 26 26-51 107-135 (145)
39 PF13518 HTH_28: Helix-turn-he 34.6 17 0.00037 22.1 0.5 37 51-89 10-46 (52)
40 TIGR03044 PS_II_psb27 photosys 33.4 19 0.00041 28.7 0.7 29 25-53 94-124 (135)
41 TIGR01529 argR_whole arginine 30.9 64 0.0014 25.1 3.3 41 98-143 5-45 (146)
42 PF04218 CENP-B_N: CENP-B N-te 29.0 40 0.00087 21.9 1.6 35 41-76 6-44 (53)
43 PRK10423 transcriptional repre 28.7 49 0.0011 26.6 2.4 28 37-64 19-52 (327)
44 PF06056 Terminase_5: Putative 28.0 34 0.00075 22.9 1.2 28 51-79 11-38 (58)
45 PRK09526 lacI lac repressor; R 27.6 47 0.001 27.0 2.1 28 38-65 27-60 (342)
46 KOG0400|consensus 26.5 23 0.0005 28.7 0.1 64 43-111 30-113 (151)
47 COG1609 PurR Transcriptional r 26.4 50 0.0011 28.1 2.1 29 37-65 21-55 (333)
48 TIGR01481 ccpA catabolite cont 26.1 53 0.0011 26.5 2.2 29 37-65 22-56 (329)
49 PRK04140 hypothetical protein; 26.0 75 0.0016 28.1 3.2 41 33-76 120-161 (317)
50 PHA01976 helix-turn-helix prot 25.9 47 0.001 21.3 1.5 25 51-76 13-37 (67)
51 smart00529 HTH_DTXR Helix-turn 25.1 27 0.00059 23.8 0.3 48 55-103 1-50 (96)
52 PRK14987 gluconate operon tran 24.9 63 0.0014 26.2 2.4 27 38-64 27-59 (331)
53 PRK10339 DNA-binding transcrip 24.8 58 0.0013 26.5 2.2 27 37-64 22-56 (327)
54 cd06171 Sigma70_r4 Sigma70, re 24.6 47 0.001 19.0 1.2 28 51-79 24-51 (55)
55 PRK10401 DNA-binding transcrip 24.4 57 0.0012 26.8 2.1 28 38-65 23-56 (346)
56 PF08535 KorB: KorB domain; I 24.1 32 0.0007 24.2 0.5 27 52-79 2-28 (93)
57 TIGR02944 suf_reg_Xantho FeS a 24.1 32 0.0007 25.2 0.5 30 54-84 26-55 (130)
58 PF15311 HYLS1_C: Hydrolethalu 23.9 58 0.0013 24.3 1.8 27 97-123 19-55 (89)
59 cd07498 Peptidases_S8_15 Pepti 23.6 93 0.002 24.5 3.1 31 91-121 211-241 (242)
60 smart00540 LEM in nuclear memb 23.1 99 0.0022 20.1 2.6 35 113-150 9-43 (44)
61 smart00347 HTH_MARR helix_turn 22.9 30 0.00065 22.9 0.2 31 53-84 24-54 (101)
62 cd08637 DNA_pol_A_pol_I_C Poly 22.8 1.9E+02 0.0041 25.6 5.2 105 3-124 153-266 (377)
63 PRK11920 rirA iron-responsive 22.6 43 0.00094 25.9 1.0 47 54-101 25-83 (153)
64 PRK02919 oxaloacetate decarbox 22.5 1.7E+02 0.0037 21.2 4.0 42 65-107 29-81 (82)
65 PF01381 HTH_3: Helix-turn-hel 22.5 1.7E+02 0.0037 17.8 3.6 26 51-77 7-32 (55)
66 PRK06474 hypothetical protein; 22.3 46 0.001 26.5 1.1 38 42-79 8-52 (178)
67 PF03734 YkuD: L,D-transpeptid 21.9 23 0.00049 25.3 -0.6 7 66-72 117-123 (144)
68 cd08638 DNA_pol_A_theta DNA po 21.8 1.7E+02 0.0037 25.9 4.7 105 3-124 142-255 (373)
69 smart00421 HTH_LUXR helix_turn 21.3 72 0.0016 18.7 1.6 28 51-79 16-43 (58)
70 COG0749 PolA DNA polymerase I 21.1 2.9E+02 0.0064 26.8 6.3 123 3-142 366-502 (593)
71 cd00093 HTH_XRE Helix-turn-hel 21.0 71 0.0015 17.8 1.5 25 51-76 10-34 (58)
72 PF03333 PapB: Adhesin biosynt 20.9 1.1E+02 0.0023 22.7 2.8 63 7-75 22-88 (91)
73 COG1376 ErfK Uncharacterized p 20.7 29 0.00062 27.9 -0.4 7 66-72 201-207 (232)
74 smart00482 POLAc DNA polymeras 20.4 1.7E+02 0.0037 23.5 4.1 104 3-123 16-128 (206)
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=1e-61 Score=372.45 Aligned_cols=116 Identities=45% Similarity=0.652 Sum_probs=91.7
Q ss_pred ccchhhhhcccccCCCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhhcc-----CCCccCCCCCcccChH
Q psy16493 25 LIGSLRELYALAASQQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGTLR-----PPGLIGGSKPKVATPA 95 (151)
Q Consensus 25 ~~~~vNqLGg~f~nGRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r~r-----~pG~IGGSKPkvatp~ 95 (151)
+++++|||||+|+||||||+++|+|| ++|+|||||||+|.| |||||||||+||+ .||+|||||||++||+
T Consensus 1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~V-s~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~ 79 (125)
T PF00292_consen 1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRV-SHGCVSKILSRYRETGSIRPGPIGGSKPRVATPE 79 (125)
T ss_dssp S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT---HHHHHHHHHHHHHHS-SS----S----SSS-HC
T ss_pred CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHcc-chhHHHHHHHHHHHhcccCcccccCCCCCCCChH
Confidence 58999999999999999999999998 789999999999985 9999999999987 6999999999999999
Q ss_pred HHHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHHh
Q psy16493 96 VVSKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIEE 141 (151)
Q Consensus 96 V~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRilR 141 (151)
|+++|++||+|||+||||||||+|++||+|+++++|||||||||||
T Consensus 80 v~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~PsvssInRilr 125 (125)
T PF00292_consen 80 VVEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSVSSINRILR 125 (125)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--HHHHHHHHH
T ss_pred HHHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCHHHHHHhhC
Confidence 9999999999999999999999999999999999999999999997
No 2
>KOG3517|consensus
Probab=100.00 E-value=3.1e-61 Score=410.25 Aligned_cols=123 Identities=35% Similarity=0.549 Sum_probs=117.8
Q ss_pred ccchhhhhcccccCCCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhhccC-----CCccCCCCCcccChH
Q psy16493 25 LIGSLRELYALAASQQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGTLRP-----PGLIGGSKPKVATPA 95 (151)
Q Consensus 25 ~~~~vNqLGg~f~nGRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r~r~-----pG~IGGSKPkvatp~ 95 (151)
..|.|||||||||||||||+.+|.|| +.|+|||||||||+| |||||||||.||.+ ||+||||||||+||.
T Consensus 4 ~~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrv-SHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~ 82 (334)
T KOG3517|consen 4 SYGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRV-SHGCVSKILARYNETGSILPGAIGGSKPRVTTPK 82 (334)
T ss_pred cccchhhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhh-ccchHHHHHHHhccCCcccccccCCCCCccCChh
Confidence 45799999999999999999999999 789999999999995 99999999999874 899999999999999
Q ss_pred HHHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHHhhhhcccc
Q psy16493 96 VVSKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIEEIKYSTLR 148 (151)
Q Consensus 96 V~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRilR~k~~~~~ 148 (151)
||+.|.+||+..|+|||||||||||+|||||+.||||||||+||||||++.+.
T Consensus 83 VV~~IR~~Kq~DPGIFAWEIRDRLlsdgiCDk~NvPSVSSISRILRNKiGsLa 135 (334)
T KOG3517|consen 83 VVKYIRSLKQRDPGIFAWEIRDRLLSDGICDKYNVPSVSSISRILRNKIGSLA 135 (334)
T ss_pred HHHHHHHhhccCCceeeehhhhhhhhcccccccCCcchHHHHHHHHhhhcccc
Confidence 99999999999999999999999999999999999999999999999988764
No 3
>KOG3862|consensus
Probab=100.00 E-value=3.2e-55 Score=374.89 Aligned_cols=126 Identities=41% Similarity=0.620 Sum_probs=120.5
Q ss_pred cccchhhhhcccccCCCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhhcc-----CCCccCCCCCcccCh
Q psy16493 24 KLIGSLRELYALAASQQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGTLR-----PPGLIGGSKPKVATP 94 (151)
Q Consensus 24 ~~~~~vNqLGg~f~nGRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r~r-----~pG~IGGSKPkvatp 94 (151)
.+||||||||||||||||||+.+|++| |.|+|||||||||+| |||||||||+||. .||+|||||||||||
T Consensus 8 ~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~v-ShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp 86 (327)
T KOG3862|consen 8 SGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRV-SHGCVSKILGRYYETGSIRPGVIGGSKPKVATP 86 (327)
T ss_pred CCccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhh-ccCCchhHHHHHHHhcCcccCCCCCCccccccc
Confidence 489999999999999999999999999 899999999999995 9999999999876 499999999999999
Q ss_pred HHHHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHHhhhhcccccC
Q psy16493 95 AVVSKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIEEIKYSTLRKG 150 (151)
Q Consensus 95 ~V~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRilR~k~~~~~~g 150 (151)
.|+++|..||++||+||||||||+|+.+++|+.+++|||||||||+|++..+.-+|
T Consensus 87 ~Vvk~i~~~k~~n~~mfaweiR~~l~~~~ic~~d~vpsVssinri~r~~~~~~~~~ 142 (327)
T KOG3862|consen 87 KVVKKIALYKRQNPTMFAWEIRDRLLAEPICDNDTVPSVSSINRIIRTKVQQKQLG 142 (327)
T ss_pred hHHHHHHHHhhcCcchhhhhhhhhhhcccccCCCCCchHHHHHHHHHHhhhhcccC
Confidence 99999999999999999999999999999999999999999999999998876555
No 4
>KOG0849|consensus
Probab=100.00 E-value=4.3e-39 Score=278.37 Aligned_cols=122 Identities=36% Similarity=0.531 Sum_probs=115.0
Q ss_pred chhhhhcccccCCCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhhcc-----CCCccCCCCCc-ccChHH
Q psy16493 27 GSLRELYALAASQQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGTLR-----PPGLIGGSKPK-VATPAV 96 (151)
Q Consensus 27 ~~vNqLGg~f~nGRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r~r-----~pG~IGGSKPk-vatp~V 96 (151)
+++|||||+|+||||||+++|++| +.|.|||+|+|+|.| |||||||||+||. .||.|||+||+ ++||+|
T Consensus 1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~v-s~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~ 79 (354)
T KOG0849|consen 1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKV-SHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEV 79 (354)
T ss_pred CCcccCCcccccCCCCCCchhhccccccccccCcccchhhhhh-hhHHHHhhhcccccccccccccccccccCCCCCchh
Confidence 579999999999999999999998 789999999999995 9999999999886 37889999999 999999
Q ss_pred HHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHHhhhhccccc
Q psy16493 97 VSKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIEEIKYSTLRK 149 (151)
Q Consensus 97 ~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRilR~k~~~~~~ 149 (151)
+.+|++||++||+||+||||++|+.+++|+..++||+++|+|++|+.....-+
T Consensus 80 ~~~i~~~k~~~P~~~~~~ir~~l~~~~~~~~~t~Ps~ssi~r~~r~~~~~~d~ 132 (354)
T KOG0849|consen 80 EAKIEQYKRENPAMFAWEIRDQLLHEGLCTQATLPSVSSINRVLRNGALGKDQ 132 (354)
T ss_pred HHHHHHHHhcCCcccchhhhhcccCcccccCCCCCChhhhhHHhhcccccccc
Confidence 99999999999999999999999999999999999999999999998765543
No 5
>cd00131 PAX Paired Box domain
Probab=99.96 E-value=3.1e-29 Score=189.76 Aligned_cols=119 Identities=40% Similarity=0.587 Sum_probs=111.5
Q ss_pred ccchhhhhcccccCCCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhhcc-----CCCccCCCCCcccChH
Q psy16493 25 LIGSLRELYALAASQQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGTLR-----PPGLIGGSKPKVATPA 95 (151)
Q Consensus 25 ~~~~vNqLGg~f~nGRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r~r-----~pG~IGGSKPkvatp~ 95 (151)
+++++|||||+|+||+||+.+.|++| +.|..+.+||+++.| |.+||+|++.+|+ .|...||.+|+..+++
T Consensus 1 ~~~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~V-s~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~ 79 (128)
T cd00131 1 GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRV-SHGCVSKILNRYYETGSIRPGAIGGSKPRVATPE 79 (128)
T ss_pred CCccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCc-CHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHH
Confidence 46899999999999999999999998 789999999999985 9999999999887 3677789899999999
Q ss_pred HHHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHHhhhh
Q psy16493 96 VVSKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIEEIKY 144 (151)
Q Consensus 96 V~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRilR~k~ 144 (151)
.+..|+.+..+||.+++|||+++|..+|+|.+++.||+|+|+|+|++|+
T Consensus 80 ~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~~ 128 (128)
T cd00131 80 VVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNKA 128 (128)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhcC
Confidence 9999999999999999999999999999999999999999999999874
No 6
>smart00351 PAX Paired Box domain.
Probab=99.94 E-value=7.6e-27 Score=175.29 Aligned_cols=116 Identities=43% Similarity=0.612 Sum_probs=108.7
Q ss_pred ccchhhhhcccccCCCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhhcc-----CCCccCCCCCcccChH
Q psy16493 25 LIGSLRELYALAASQQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGTLR-----PPGLIGGSKPKVATPA 95 (151)
Q Consensus 25 ~~~~vNqLGg~f~nGRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r~r-----~pG~IGGSKPkvatp~ 95 (151)
++.++|||||+|++|+||+.+.|++| +.|....+||+++.+ |..||+|++.+|+ .|...||.+|+..+++
T Consensus 1 ~~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gv-s~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~ 79 (125)
T smart00351 1 GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCV-SHGCVSKILGRYYETGSIRPGAIGGSKPKVATPK 79 (125)
T ss_pred CCCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCc-CHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHH
Confidence 36899999999999999999999998 689999999999985 9999999999886 3666788999999999
Q ss_pred HHHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHHh
Q psy16493 96 VVSKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIEE 141 (151)
Q Consensus 96 V~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRilR 141 (151)
.+..|+++..+||.+++|||++.|.++|+|...++||+|+|+|+||
T Consensus 80 ~~~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 80 VVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRILR 125 (125)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence 9999999999999999999999999999999999999999999996
No 7
>PF13551 HTH_29: Winged helix-turn helix
Probab=97.53 E-value=0.00028 Score=49.25 Aligned_cols=88 Identities=22% Similarity=0.243 Sum_probs=67.3
Q ss_pred HhhCC-ccchhhhhhhhhhhhhhhhhhhccCCC-------ccCCCCCcc-cChHHHHHHHHHhhhCCC-----cchHHHH
Q psy16493 51 RLLFR-HYDIAQHVLHQQQGAVSKLLGTLRPPG-------LIGGSKPKV-ATPAVVSKIEQYKRENPT-----IFAWEIR 116 (151)
Q Consensus 51 ~~GvR-pcdISrqL~vVSHGCVSKIL~r~r~pG-------~IGGSKPkv-atp~V~~kI~~yk~enP~-----iFaWEIR 116 (151)
.+|+. +.+|++.+.+ |..=|.+.+.+|+.-| .-++-+|+. .|++.++.|.++-.++|. ...=+++
T Consensus 9 ~~g~~~~~~ia~~lg~-s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~ 87 (112)
T PF13551_consen 9 AEGVSTIAEIARRLGI-SRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELA 87 (112)
T ss_pred HcCCCcHHHHHHHHCc-CHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHH
Confidence 68994 9999999985 9999999999987444 112334554 799999999999999993 3445678
Q ss_pred hhhhhcCCCCCCCCCCCChhhHHHhh
Q psy16493 117 ERLISEDVGVNGLALQTPPRNAIEEI 142 (151)
Q Consensus 117 drLi~~gvC~~~~vPSVSSInRilR~ 142 (151)
+.|+++.. .--+|.++|.|+|+.
T Consensus 88 ~~l~~~~~---~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 88 EWLIEEEF---GIDVSPSTIRRILKR 110 (112)
T ss_pred HHHHHhcc---CccCCHHHHHHHHHH
Confidence 87866654 234799999999975
No 8
>PF13565 HTH_32: Homeodomain-like domain
Probab=96.61 E-value=0.0052 Score=41.18 Aligned_cols=67 Identities=24% Similarity=0.188 Sum_probs=48.9
Q ss_pred hhhhhhhccCCCcc---------CCCCCcccChHHHHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHH
Q psy16493 71 VSKLLGTLRPPGLI---------GGSKPKVATPAVVSKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIE 140 (151)
Q Consensus 71 VSKIL~r~r~pG~I---------GGSKPkvatp~V~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRil 140 (151)
|++.+.+|+.-|.- .+-+|+. ++++++.|.++..++|..-..+|.+.|..+.-..- -||.|.|+|+|
T Consensus 2 v~rw~~ry~~~G~~gL~~~~~~~~~Grp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~--~~S~~tv~R~L 77 (77)
T PF13565_consen 2 VYRWLKRYREEGLEGLKDRKRRPRPGRPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV--RVSRSTVYRIL 77 (77)
T ss_pred HHHHHHHHHhhCchhhhcccccCCCCCCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC--CccHhHHHHhC
Confidence 56677777643411 1124445 78999999999999999999999999988732221 57999999986
No 9
>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=94.01 E-value=0.17 Score=37.61 Aligned_cols=85 Identities=18% Similarity=0.103 Sum_probs=62.3
Q ss_pred chhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhhccCCCccCCCCCcccCh---HHHHHHHHHhhhCCCcchHHH
Q psy16493 43 ASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLIGGSKPKVATP---AVVSKIEQYKRENPTIFAWEI 115 (151)
Q Consensus 43 p~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~IGGSKPkvatp---~V~~kI~~yk~enP~iFaWEI 115 (151)
+.+.|+++ ..|....++|+...| |-.-|-..+.+.+ +| ..+|+.... + .+.+.++-.++|.+.-+||
T Consensus 4 S~DlR~rVl~~~~~g~s~~eaa~~F~V-S~~Tv~~W~k~~~-~G---~~~~k~r~~~Kid-~~~L~~~v~~~pd~tl~El 77 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGKSIREAAKRFGV-SRNTVYRWLKRKE-TG---DLEPKPRGRKKID-RDELKALVEENPDATLREL 77 (119)
T ss_pred CHHHHHHHHHHHHccchHHHHHHHhCc-HHHHHHHHHHhcc-cc---ccccccccccccc-HHHHHHHHHHCCCcCHHHH
Confidence 45789997 679999999999875 9889999888554 33 222222211 2 3457888889999999999
Q ss_pred HhhhhhcCCCCCCCCCCCChhhHHHhhh
Q psy16493 116 RERLISEDVGVNGLALQTPPRNAIEEIK 143 (151)
Q Consensus 116 RdrLi~~gvC~~~~vPSVSSInRilR~k 143 (151)
.++| || |.++|++.|+..
T Consensus 78 a~~l---~V-------s~~ti~~~Lkrl 95 (119)
T PF01710_consen 78 AERL---GV-------SPSTIWRALKRL 95 (119)
T ss_pred HHHc---CC-------CHHHHHHHHHHc
Confidence 9887 43 788999998643
No 10
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=92.89 E-value=0.16 Score=37.39 Aligned_cols=64 Identities=20% Similarity=0.213 Sum_probs=48.2
Q ss_pred CcchhhHHHH-----HhhCCccchhhhhhhhhhhhhhhhhhhccCCCccC----CCCCc----ccChHHHHHHHHHhh
Q psy16493 41 PLASLVNQQQ-----RLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLIG----GSKPK----VATPAVVSKIEQYKR 105 (151)
Q Consensus 41 PLp~~~R~ki-----~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~IG----GSKPk----vatp~V~~kI~~yk~ 105 (151)
+|...-|..+ ..|....+.++...| |.-|+.|-+.||+.-|.-| .|+|+ -+.+++|..|.+.++
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gV-S~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~~~I~~lRr 84 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGWPVAHAAAEFGV-SRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVERRIIELRR 84 (85)
T ss_pred CCCHHHHHHHHHHHHHcCCcHHHHHHHhCC-CHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHHHHHHHHhc
Confidence 4555555554 578999999999985 9999999999999544443 34555 456789999988875
No 11
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=91.33 E-value=0.13 Score=34.35 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=26.5
Q ss_pred CCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhh
Q psy16493 39 QQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLG 76 (151)
Q Consensus 39 GRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~ 76 (151)
|.+|.+.++-+| +.|+.-.+|||++.. |+-||.+.|.
T Consensus 2 G~~Lt~~Eqaqid~m~qlG~s~~~isr~i~R-Sr~~Ir~yl~ 42 (50)
T PF11427_consen 2 GKTLTDAEQAQIDVMHQLGMSLREISRRIGR-SRTCIRRYLK 42 (50)
T ss_dssp S----HHHHHHHHHHHHTT--HHHHHHHHT---HHHHHHHHH
T ss_pred CCcCCHHHHHHHHHHHHhchhHHHHHHHhCc-cHHHHHHHhc
Confidence 789999999998 689999999999997 9999998874
No 12
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.22 E-value=0.86 Score=35.89 Aligned_cols=93 Identities=12% Similarity=0.185 Sum_probs=63.8
Q ss_pred CCCcchhhHHHH-----HhhCCccchhhhhhhhhhhhhhhhhhhccC-----CCccCCCCCcccChHHHHHH-HHHhhhC
Q psy16493 39 QQPLASLVNQQQ-----RLLFRHYDIAQHVLHQQQGAVSKLLGTLRP-----PGLIGGSKPKVATPAVVSKI-EQYKREN 107 (151)
Q Consensus 39 GRPLp~~~R~ki-----~~GvRpcdISrqL~vVSHGCVSKIL~r~r~-----pG~IGGSKPkvatp~V~~kI-~~yk~en 107 (151)
.+|..+..|+++ ..|.+-.+||..+.| |-+=|=+-++||++ |...||.+|+..+.+-++-+ +..+..+
T Consensus 2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gv-s~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~ 80 (138)
T COG3415 2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGV-SISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD 80 (138)
T ss_pred CchhhHHHHHHHHHHHHHcCccHHHHHHHhCc-cHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc
Confidence 367777888886 579999999999985 98888889999985 44558888987776644444 4444444
Q ss_pred CCcchHHHH---hhhh-hcCCCCCCCCCCCChhhHHHhh
Q psy16493 108 PTIFAWEIR---ERLI-SEDVGVNGLALQTPPRNAIEEI 142 (151)
Q Consensus 108 P~iFaWEIR---drLi-~~gvC~~~~vPSVSSInRilR~ 142 (151)
|+.. +.|- +-||= =+-+++.++|+.
T Consensus 81 -----wTl~~~~~~l~~e~gv~-----y~~~~v~~~l~~ 109 (138)
T COG3415 81 -----WTLKELVEELGLEFGVW-----YHASAVRRLLHE 109 (138)
T ss_pred -----chHHHHHHHHhhhcCeE-----EeHHHHHHHHHH
Confidence 7754 4433 45551 123477777764
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=86.79 E-value=0.31 Score=30.25 Aligned_cols=31 Identities=19% Similarity=0.233 Sum_probs=20.4
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhhhhccCCC
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPG 82 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG 82 (151)
..|....+||+.|.+ |..-|++++.+|++-|
T Consensus 15 ~~G~s~~~ia~~lgv-s~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 15 REGWSIREIAKRLGV-SRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHT--HHHHHHHHTS--HHHHHHHHT------
T ss_pred HCCCCHHHHHHHHCc-CHHHHHHHHHHccccc
Confidence 569999999999985 9999999999998644
No 14
>KOG3862|consensus
Probab=83.25 E-value=0.26 Score=43.70 Aligned_cols=53 Identities=9% Similarity=-0.011 Sum_probs=47.1
Q ss_pred cccchhhhhcccccCCCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhh
Q psy16493 24 KLIGSLRELYALAASQQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGT 77 (151)
Q Consensus 24 ~~~~~vNqLGg~f~nGRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r 77 (151)
+.....|-.+.-++-|+||.+..++++ ..++|--.|..|+.. +|+||||.|.+
T Consensus 98 ~n~~mfaweiR~~l~~~~ic~~d~vpsVssinri~r~~~~~~~~~~-~~s~vsk~l~~ 154 (327)
T KOG3862|consen 98 QNPTMFAWEIRDRLLAEPICDNDTVPSVSSINRIIRTKVQQKQLGI-THSCVTKVLAR 154 (327)
T ss_pred cCcchhhhhhhhhhhcccccCCCCCchHHHHHHHHHHhhhhcccCC-ccchhhccccC
Confidence 456677888899999999999999997 689999999999986 99999999965
No 15
>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=78.86 E-value=1.9 Score=22.44 Aligned_cols=24 Identities=13% Similarity=0.022 Sum_probs=19.4
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhh
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLL 75 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL 75 (151)
..|....+|++++.+ |...|++++
T Consensus 19 ~~~~s~~~ia~~~~i-s~~tv~~~~ 42 (42)
T cd00569 19 AAGESVAEIARRLGV-SRSTLYRYL 42 (42)
T ss_pred HcCCCHHHHHHHHCC-CHHHHHHhC
Confidence 568888899999975 888888764
No 16
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=78.17 E-value=0.76 Score=28.93 Aligned_cols=38 Identities=18% Similarity=0.114 Sum_probs=19.9
Q ss_pred CCCcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhh
Q psy16493 39 QQPLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGT 77 (151)
Q Consensus 39 GRPLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r 77 (151)
...|....|.+| ..|....+||++|.+ |+.=|++.|.|
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~-s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLGR-SRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT---HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHCc-CcHHHHHHHhc
Confidence 356788888888 579999999999985 99999988754
No 17
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=76.32 E-value=1.4 Score=28.41 Aligned_cols=10 Identities=60% Similarity=1.122 Sum_probs=8.6
Q ss_pred hHHHHhhhhh
Q psy16493 112 AWEIRERLIS 121 (151)
Q Consensus 112 aWEIRdrLi~ 121 (151)
|||||.+|-+
T Consensus 16 AWeIr~~Lke 25 (38)
T PF13072_consen 16 AWEIRAKLKE 25 (38)
T ss_pred HHHHHHHHHH
Confidence 8999999854
No 18
>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=75.21 E-value=0.82 Score=28.66 Aligned_cols=39 Identities=23% Similarity=0.206 Sum_probs=28.7
Q ss_pred hhhHHHH-----HhhCCccchhhhhhhhhhhhhhhhhhhccCCCc
Q psy16493 44 SLVNQQQ-----RLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPGL 83 (151)
Q Consensus 44 ~~~R~ki-----~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~ 83 (151)
+.+|.+| ......|||+..+.+ |.+-||+=|..++.-|.
T Consensus 1 d~~R~~Il~~L~~~~~~~~el~~~l~~-s~~~vs~hL~~L~~~gl 44 (47)
T PF01022_consen 1 DPTRLRILKLLSEGPLTVSELAEELGL-SQSTVSHHLKKLREAGL 44 (47)
T ss_dssp SHHHHHHHHHHTTSSEEHHHHHHHHTS--HHHHHHHHHHHHHTTS
T ss_pred CHHHHHHHHHHHhCCCchhhHHHhccc-cchHHHHHHHHHHHCcC
Confidence 3567776 334778999999985 99999999987765443
No 19
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=63.44 E-value=8 Score=29.40 Aligned_cols=61 Identities=18% Similarity=0.149 Sum_probs=42.5
Q ss_pred CcchhhHHHH-----H-hhCCccchhhhhhhhhhhhhhhhhhhccCCCcc-----CCCCCcccChHHHHHHHH
Q psy16493 41 PLASLVNQQQ-----R-LLFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLI-----GGSKPKVATPAVVSKIEQ 102 (151)
Q Consensus 41 PLp~~~R~ki-----~-~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~I-----GGSKPkvatp~V~~kI~~ 102 (151)
-|.+.+|.+| . .++..|||+.++.+ +..-||+=|.-+++-|.| |...-....|++.+.+..
T Consensus 12 aLadptRl~IL~~L~~~~~~~v~ela~~l~l-sqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~ 83 (117)
T PRK10141 12 ILSDETRLGIVLLLRESGELCVCDLCTALDQ-SQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAK 83 (117)
T ss_pred HhCCHHHHHHHHHHHHcCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHH
Confidence 3678899998 2 24678999999985 999999999877766665 332222334556555655
No 20
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=60.98 E-value=18 Score=24.81 Aligned_cols=48 Identities=15% Similarity=0.035 Sum_probs=36.1
Q ss_pred HHHHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCC-CCChhhHHHhhhh
Q psy16493 95 AVVSKIEQYKRENPTIFAWEIRERLISEDVGVNGLAL-QTPPRNAIEEIKY 144 (151)
Q Consensus 95 ~V~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vP-SVSSInRilR~k~ 144 (151)
+++..|-++..+.-++ -+|-+.|-++|+=.....+ +.++|.+||+|..
T Consensus 5 ~vVr~if~~~~~g~s~--~~I~~~ln~~gi~~~~~~~W~~~~v~~iL~np~ 53 (102)
T PF07508_consen 5 EVVREIFELYLEGYSL--RQIARELNEKGIPTPRGKKWSKSTVRRILRNPA 53 (102)
T ss_pred HHHHHHHHHHHcCCCH--HHHHHHHHhcCCccccCCcccHHHHHHHHhhhh
Confidence 4666666665555444 7889999999996665666 8999999999865
No 21
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=54.69 E-value=8.9 Score=29.90 Aligned_cols=34 Identities=15% Similarity=0.209 Sum_probs=27.8
Q ss_pred hhhhcccccCCCCcchhhH--HHHHhhCCccchhhh
Q psy16493 29 LRELYALAASQQPLASLVN--QQQRLLFRHYDIAQH 62 (151)
Q Consensus 29 vNqLGg~f~nGRPLp~~~R--~ki~~GvRpcdISrq 62 (151)
+.|++|.-.|..||.++.= +.|..|++|+|----
T Consensus 30 L~~HYGLtLNDT~f~de~vI~~hidaGIs~~~AVN~ 65 (114)
T PF06755_consen 30 LEQHYGLTLNDTPFSDETVIQEHIDAGISPADAVNF 65 (114)
T ss_pred HHHhcCCccCCCccchHHHHHHHHHhCCCHHHHHHH
Confidence 5688999999999998754 557899999987443
No 22
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=49.72 E-value=23 Score=29.92 Aligned_cols=50 Identities=24% Similarity=0.352 Sum_probs=37.3
Q ss_pred CCCCcccChHHHHHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHHhhhh
Q psy16493 86 GSKPKVATPAVVSKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIEEIKY 144 (151)
Q Consensus 86 GSKPkvatp~V~~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRilR~k~ 144 (151)
|.-||.-|.+..+.|..++.++|..|.=+ +| +++ -.| |..+|-|||++|-
T Consensus 5 ~~p~k~Ls~~~~~~ir~L~~~~p~~~t~~---~L-ae~----F~v-spe~irrILkskw 54 (225)
T PF06413_consen 5 GNPPKKLSREAMEQIRYLHKEDPEEWTVE---RL-AES----FKV-SPEAIRRILKSKW 54 (225)
T ss_pred CCCCCCCCHHHHHHHHHHHHhCccccCHH---HH-Hhh----CCC-CHHHHHHHHhcCC
Confidence 55678899999999999999999986543 22 222 222 7789999999764
No 23
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=49.31 E-value=5 Score=26.85 Aligned_cols=30 Identities=27% Similarity=0.268 Sum_probs=24.5
Q ss_pred hhCCccchhhhhhhhhhhhhhhhhhhccCCC
Q psy16493 52 LLFRHYDIAQHVLHQQQGAVSKLLGTLRPPG 82 (151)
Q Consensus 52 ~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG 82 (151)
..+++-|||+.|.| |..-|++.|.++..-|
T Consensus 21 ~~v~~~~iA~~L~v-s~~tvt~ml~~L~~~G 50 (60)
T PF01325_consen 21 GPVRTKDIAERLGV-SPPTVTEMLKRLAEKG 50 (60)
T ss_dssp SSBBHHHHHHHHTS--HHHHHHHHHHHHHTT
T ss_pred CCccHHHHHHHHCC-ChHHHHHHHHHHHHCC
Confidence 46899999999985 9999999999876434
No 24
>PLN00061 photosystem II protein Psb27; Provisional
Probab=48.85 E-value=8.1 Score=31.36 Aligned_cols=26 Identities=19% Similarity=0.245 Sum_probs=22.2
Q ss_pred cchhhhhcccccC---CCCcchhhHHHHH
Q psy16493 26 IGSLRELYALAAS---QQPLASLVNQQQR 51 (151)
Q Consensus 26 ~~~vNqLGg~f~n---GRPLp~~~R~ki~ 51 (151)
+.-+|.|+|-|.+ -||||+.+|.||.
T Consensus 115 qtALnsLAghYssyGpnrPLPe~lK~Rll 143 (150)
T PLN00061 115 EKAIRSLASFYSKAGPSAPLPEDVKSEIL 143 (150)
T ss_pred HHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Confidence 4678999999865 5999999999984
No 25
>PLN00064 photosystem II protein Psb27; Provisional
Probab=47.99 E-value=7.6 Score=31.98 Aligned_cols=30 Identities=10% Similarity=0.081 Sum_probs=23.7
Q ss_pred ccchhhhhcccccC---CCCcchhhHHHHHhhC
Q psy16493 25 LIGSLRELYALAAS---QQPLASLVNQQQRLLF 54 (151)
Q Consensus 25 ~~~~vNqLGg~f~n---GRPLp~~~R~ki~~Gv 54 (151)
-..-+|+|-|-|.| -||||+..+.|+.+.+
T Consensus 123 MyTALNaLAGHY~SfgpnrPlPeKlK~RL~qE~ 155 (166)
T PLN00064 123 MYSALNAVSGHYISFGPTAPIPAKRKARILEEM 155 (166)
T ss_pred HHHHHHHHHHHhhccCCCCCCcHHHHHHHHHHH
Confidence 35678999999865 5999999999984433
No 26
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=46.23 E-value=4.9 Score=25.37 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=22.9
Q ss_pred CCccchhhhhhhhhhhhhhhhhhhccCCCc
Q psy16493 54 FRHYDIAQHVLHQQQGAVSKLLGTLRPPGL 83 (151)
Q Consensus 54 vRpcdISrqL~vVSHGCVSKIL~r~r~pG~ 83 (151)
+++.||++.+.+ +.+-||+++.++..-|.
T Consensus 22 ~t~~~la~~l~~-~~~~vs~~v~~L~~~Gl 50 (62)
T PF12802_consen 22 LTQSELAERLGI-SKSTVSRIVKRLEKKGL 50 (62)
T ss_dssp EEHHHHHHHHTS--HHHHHHHHHHHHHTTS
T ss_pred cCHHHHHHHHCc-CHHHHHHHHHHHHHCCC
Confidence 788899999985 99999999988754443
No 27
>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=45.39 E-value=16 Score=29.53 Aligned_cols=29 Identities=3% Similarity=-0.055 Sum_probs=24.8
Q ss_pred cCCCC----cchhhHHHH-----HhhCCccchhhhhhh
Q psy16493 37 ASQQP----LASLVNQQQ-----RLLFRHYDIAQHVLH 65 (151)
Q Consensus 37 ~nGRP----Lp~~~R~ki-----~~GvRpcdISrqL~v 65 (151)
.||++ .+.++|+|| +.|.+|...+|.|+.
T Consensus 20 Ln~~~~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~ 57 (327)
T TIGR02417 20 INGKAKEYRISQETVERVMAVVREQGYQPNIHAASLRA 57 (327)
T ss_pred HcCCCCCCccCHHHHHHHHHHHHHhCCCCCHHHHHhhc
Confidence 47776 999999997 689999999998863
No 28
>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=44.42 E-value=35 Score=21.92 Aligned_cols=37 Identities=19% Similarity=0.169 Sum_probs=26.3
Q ss_pred cchhhhhhhhhhhhhhhhhhhccCCCccCCCCCcccChHHHHHHHHHhh
Q psy16493 57 YDIAQHVLHQQQGAVSKLLGTLRPPGLIGGSKPKVATPAVVSKIEQYKR 105 (151)
Q Consensus 57 cdISrqL~vVSHGCVSKIL~r~r~pG~IGGSKPkvatp~V~~kI~~yk~ 105 (151)
-|||+.+.+ |..=||++|+-- ....++..++|.+.-+
T Consensus 3 ~dIA~~agv-S~~TVSr~ln~~-----------~~vs~~tr~rI~~~a~ 39 (46)
T PF00356_consen 3 KDIAREAGV-SKSTVSRVLNGP-----------PRVSEETRERILEAAE 39 (46)
T ss_dssp HHHHHHHTS-SHHHHHHHHTTC-----------SSSTHHHHHHHHHHHH
T ss_pred HHHHHHHCc-CHHHHHHHHhCC-----------CCCCHHHHHHHHHHHH
Confidence 389999985 999999999732 2456666666665533
No 29
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=42.68 E-value=20 Score=28.57 Aligned_cols=26 Identities=31% Similarity=0.632 Sum_probs=22.1
Q ss_pred ccCCCCCcccChHHHHHHHHHhhhCCCcc
Q psy16493 83 LIGGSKPKVATPAVVSKIEQYKRENPTIF 111 (151)
Q Consensus 83 ~IGGSKPkvatp~V~~kI~~yk~enP~iF 111 (151)
.-+|++|...+-.+++.| |+++|..|
T Consensus 108 ~~~~~~~~id~~~lvk~I---Kk~HPNLF 133 (137)
T PF10788_consen 108 QKDGNLPNIDLDKLVKNI---KKEHPNLF 133 (137)
T ss_pred hcCCCcCCCCHHHHHHHH---HHhCCCee
Confidence 457889999888887777 99999988
No 30
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=41.61 E-value=16 Score=22.61 Aligned_cols=35 Identities=14% Similarity=0.066 Sum_probs=25.6
Q ss_pred cchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhhh
Q psy16493 42 LASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLGT 77 (151)
Q Consensus 42 Lp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~r 77 (151)
||+..|+=| -.|..-.|||..|.+ |.+-|++++.+
T Consensus 5 L~~~er~vi~~~y~~~~t~~eIa~~lg~-s~~~V~~~~~~ 43 (50)
T PF04545_consen 5 LPPREREVIRLRYFEGLTLEEIAERLGI-SRSTVRRILKR 43 (50)
T ss_dssp S-HHHHHHHHHHHTST-SHHHHHHHHTS-CHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCCHHHHHHHHCC-cHHHHHHHHHH
Confidence 555555444 468888999999985 99999999865
No 31
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=41.08 E-value=21 Score=29.22 Aligned_cols=29 Identities=10% Similarity=0.119 Sum_probs=24.3
Q ss_pred cCCCC-cchhhHHHH-----HhhCCccchhhhhhh
Q psy16493 37 ASQQP-LASLVNQQQ-----RLLFRHYDIAQHVLH 65 (151)
Q Consensus 37 ~nGRP-Lp~~~R~ki-----~~GvRpcdISrqL~v 65 (151)
.||++ ..+++|+|| +.|.+|.-.+|.|+.
T Consensus 22 Ln~~~~Vs~~tr~rV~~~a~elgY~pn~~ar~l~~ 56 (343)
T PRK10727 22 INNSPKASEASRLAVHSAMESLSYHPNANARALAQ 56 (343)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHhhhh
Confidence 36665 899999998 689999999998863
No 32
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=40.48 E-value=11 Score=23.13 Aligned_cols=31 Identities=19% Similarity=0.296 Sum_probs=23.3
Q ss_pred hhCCccchhhhhhhhhhhhhhhhhhhccCCCc
Q psy16493 52 LLFRHYDIAQHVLHQQQGAVSKLLGTLRPPGL 83 (151)
Q Consensus 52 ~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~ 83 (151)
.++..-|||+.+-+ |.+-|+++|..+..-|.
T Consensus 16 ~~~t~~ela~~~~i-s~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 16 PRITQKELAEKLGI-SRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp TTS-HHHHHHHHTS--HHHHHHHHHHHHHTTS
T ss_pred CCCCHHHHHHHhCC-CHHHHHHHHHHHHHCcC
Confidence 45888899999985 99999999988754444
No 33
>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=40.05 E-value=14 Score=22.65 Aligned_cols=18 Identities=33% Similarity=0.368 Sum_probs=15.7
Q ss_pred chhhhhhhhhhhhhhhhhh
Q psy16493 58 DIAQHVLHQQQGAVSKLLG 76 (151)
Q Consensus 58 dISrqL~vVSHGCVSKIL~ 76 (151)
||++.+.+ |...||++|.
T Consensus 2 ~lA~~~gv-s~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGV-SVATVSRVLN 19 (52)
T ss_pred cHHHHHCc-CHHHHHHHHc
Confidence 78898875 9999999995
No 34
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=39.72 E-value=19 Score=22.05 Aligned_cols=32 Identities=25% Similarity=0.294 Sum_probs=24.5
Q ss_pred hhCCccchhhhhhhhhhhhhhhhhhhccCCCcc
Q psy16493 52 LLFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLI 84 (151)
Q Consensus 52 ~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~I 84 (151)
.++...||++.+.+ +.+.+++.|.++..-|.|
T Consensus 19 ~~~~~~ei~~~~~i-~~~~i~~~l~~L~~~g~i 50 (78)
T cd00090 19 GPLTVSELAERLGL-SQSTVSRHLKKLEEAGLV 50 (78)
T ss_pred CCcCHHHHHHHHCc-CHhHHHHHHHHHHHCCCe
Confidence 34777899999875 999999999887543443
No 35
>PHA00738 putative HTH transcription regulator
Probab=38.52 E-value=14 Score=28.46 Aligned_cols=41 Identities=20% Similarity=0.241 Sum_probs=31.7
Q ss_pred chhhHHHH----Hh--hCCccchhhhhhhhhhhhhhhhhhhccCCCcc
Q psy16493 43 ASLVNQQQ----RL--LFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLI 84 (151)
Q Consensus 43 p~~~R~ki----~~--GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~I 84 (151)
.+.+|.+| .. ..-.|||+..+-+ |+.-|||=|.-++.-|.|
T Consensus 10 ~dptRr~IL~lL~~~e~~~V~eLae~l~l-SQptVS~HLKvLreAGLV 56 (108)
T PHA00738 10 AKILRRKILELIAENYILSASLISHTLLL-SYTTVLRHLKILNEQGYI 56 (108)
T ss_pred CCHHHHHHHHHHHHcCCccHHHHHHhhCC-CHHHHHHHHHHHHHCCce
Confidence 46688888 23 3778899999985 999999999777655554
No 36
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=38.19 E-value=15 Score=24.84 Aligned_cols=31 Identities=16% Similarity=0.222 Sum_probs=25.6
Q ss_pred hCCccchhhhhhhhhhhhhhhhhhhccCCCcc
Q psy16493 53 LFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLI 84 (151)
Q Consensus 53 GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~I 84 (151)
|+..-|||.+|-+ +-..|.++|.++..-|.|
T Consensus 22 ~~ta~eLa~~lgl-~~~~v~r~L~~L~~~G~V 52 (68)
T smart00550 22 TSTALQLAKNLGL-PKKEVNRVLYSLEKKGKV 52 (68)
T ss_pred CcCHHHHHHHHCC-CHHHHHHHHHHHHHCCCE
Confidence 3899999999985 989999999887644544
No 37
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=37.08 E-value=27 Score=28.15 Aligned_cols=28 Identities=4% Similarity=0.045 Sum_probs=24.4
Q ss_pred cCCCC----cchhhHHHH-----HhhCCccchhhhhh
Q psy16493 37 ASQQP----LASLVNQQQ-----RLLFRHYDIAQHVL 64 (151)
Q Consensus 37 ~nGRP----Lp~~~R~ki-----~~GvRpcdISrqL~ 64 (151)
.||+| .+.++|+|| +.|.+|-..+|.|+
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 47876 999999998 68999999999885
No 38
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=35.00 E-value=15 Score=29.03 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=19.5
Q ss_pred cchhhhhcccccC--CC-CcchhhHHHHH
Q psy16493 26 IGSLRELYALAAS--QQ-PLASLVNQQQR 51 (151)
Q Consensus 26 ~~~vNqLGg~f~n--GR-PLp~~~R~ki~ 51 (151)
..-+|.|+|-|.+ -| |||...+.+|.
T Consensus 107 ~tAln~LaghY~s~g~raPlP~k~k~rll 135 (145)
T PF13326_consen 107 YTALNALAGHYSSYGNRAPLPEKLKERLL 135 (145)
T ss_dssp HHHHHHHHHHCHHHTTS-S--HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHHH
Confidence 4678999999854 46 99999999983
No 39
>PF13518 HTH_28: Helix-turn-helix domain
Probab=34.64 E-value=17 Score=22.09 Aligned_cols=37 Identities=24% Similarity=0.205 Sum_probs=28.8
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhhhhccCCCccCCCCC
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLIGGSKP 89 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~IGGSKP 89 (151)
..|...-+||+++.+ |+.-|...+.+|+.-| +-|.+|
T Consensus 10 ~~g~s~~~~a~~~gi-s~~tv~~w~~~y~~~G-~~~l~~ 46 (52)
T PF13518_consen 10 LEGESVREIAREFGI-SRSTVYRWIKRYREGG-IEGLKP 46 (52)
T ss_pred HcCCCHHHHHHHHCC-CHhHHHHHHHHHHhcC-HHHhcc
Confidence 568888899999986 9999999999998544 334443
No 40
>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=33.36 E-value=19 Score=28.75 Aligned_cols=29 Identities=17% Similarity=0.201 Sum_probs=23.2
Q ss_pred ccchhhhhcccccC--CCCcchhhHHHHHhh
Q psy16493 25 LIGSLRELYALAAS--QQPLASLVNQQQRLL 53 (151)
Q Consensus 25 ~~~~vNqLGg~f~n--GRPLp~~~R~ki~~G 53 (151)
-..-+|.|-|-|.+ -||||+..+.||.+.
T Consensus 94 m~TALNsLAGHY~sy~~rPlPeklk~Rl~~E 124 (135)
T TIGR03044 94 MQTALNSLAGHYKSYANRPLPEKLKERLEKE 124 (135)
T ss_pred HHHHHHHHHHHhccCCCCCCCHHHHHHHHHH
Confidence 35678999998865 699999999998443
No 41
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=30.92 E-value=64 Score=25.08 Aligned_cols=41 Identities=12% Similarity=0.021 Sum_probs=34.1
Q ss_pred HHHHHHhhhCCCcchHHHHhhhhhcCCCCCCCCCCCChhhHHHhhh
Q psy16493 98 SKIEQYKRENPTIFAWEIRERLISEDVGVNGLALQTPPRNAIEEIK 143 (151)
Q Consensus 98 ~kI~~yk~enP~iFaWEIRdrLi~~gvC~~~~vPSVSSInRilR~k 143 (151)
..|+++-.+++-.-+.||.++|-++|+. .|.+.|+|.|+..
T Consensus 5 ~~i~~Li~~~~i~tqeeL~~~L~~~G~~-----vsqaTIsRdL~el 45 (146)
T TIGR01529 5 ERIKEIITEEKISTQEELVALLKAEGIE-----VTQATVSRDLREL 45 (146)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHhCCC-----cCHHHHHHHHHHc
Confidence 3577778888888999999999999984 4789999998853
No 42
>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=28.98 E-value=40 Score=21.91 Aligned_cols=35 Identities=20% Similarity=0.059 Sum_probs=23.8
Q ss_pred CcchhhHHHH----HhhCCccchhhhhhhhhhhhhhhhhh
Q psy16493 41 PLASLVNQQQ----RLLFRHYDIAQHVLHQQQGAVSKLLG 76 (151)
Q Consensus 41 PLp~~~R~ki----~~GvRpcdISrqL~vVSHGCVSKIL~ 76 (151)
.|......+| +.|....+||+++-+ +..=|+.|+.
T Consensus 6 ~LTl~eK~~iI~~~e~g~s~~~ia~~fgv-~~sTv~~I~K 44 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEGESKRDIAREFGV-SRSTVSTILK 44 (53)
T ss_dssp S--HHHHHHHHHHHHCTT-HHHHHHHHT---CCHHHHHHH
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHhCC-CHHHHHHHHH
Confidence 3455555554 689999999999985 9999999984
No 43
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=28.71 E-value=49 Score=26.60 Aligned_cols=28 Identities=7% Similarity=0.189 Sum_probs=23.6
Q ss_pred cCCCC-cchhhHHHH-----HhhCCccchhhhhh
Q psy16493 37 ASQQP-LASLVNQQQ-----RLLFRHYDIAQHVL 64 (151)
Q Consensus 37 ~nGRP-Lp~~~R~ki-----~~GvRpcdISrqL~ 64 (151)
.||++ ....+|+|| +.|.+|..++|.|+
T Consensus 19 Ln~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~ 52 (327)
T PRK10423 19 INKDRFVSEAITAKVEAAIKELNYAPSALARSLK 52 (327)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHCCCccHHHHHHh
Confidence 35665 899999998 68999999999875
No 44
>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=27.99 E-value=34 Score=22.93 Aligned_cols=28 Identities=11% Similarity=0.017 Sum_probs=21.9
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhhhhcc
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLLGTLR 79 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL~r~r 79 (151)
..|.++.+||+.|-+ +..=|..=..++.
T Consensus 11 ~~G~~~~eIA~~Lg~-~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 11 LQGWSIKEIAEELGV-PRSTVYSWKDRYK 38 (58)
T ss_pred HcCCCHHHHHHHHCC-ChHHHHHHHHhhC
Confidence 579999999999975 7666666666654
No 45
>PRK09526 lacI lac repressor; Reviewed
Probab=27.62 E-value=47 Score=26.95 Aligned_cols=28 Identities=14% Similarity=0.216 Sum_probs=23.3
Q ss_pred CCCC-cchhhHHHH-----HhhCCccchhhhhhh
Q psy16493 38 SQQP-LASLVNQQQ-----RLLFRHYDIAQHVLH 65 (151)
Q Consensus 38 nGRP-Lp~~~R~ki-----~~GvRpcdISrqL~v 65 (151)
||++ .+.++|+|| +.|..|..++|.|+.
T Consensus 27 n~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~ 60 (342)
T PRK09526 27 NQASHVSAKTREKVEAAMAELNYVPNRVAQQLAG 60 (342)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHhhc
Confidence 5554 889999998 689999999998853
No 46
>KOG0400|consensus
Probab=26.48 E-value=23 Score=28.72 Aligned_cols=64 Identities=22% Similarity=0.352 Sum_probs=40.9
Q ss_pred chhhHHHH----HhhCCccchhhhhhhhhhhh--hh-----hhhhhccCCCccCCCCCcccC---------hHHHHHHHH
Q psy16493 43 ASLVNQQQ----RLLFRHYDIAQHVLHQQQGA--VS-----KLLGTLRPPGLIGGSKPKVAT---------PAVVSKIEQ 102 (151)
Q Consensus 43 p~~~R~ki----~~GvRpcdISrqL~vVSHGC--VS-----KIL~r~r~pG~IGGSKPkvat---------p~V~~kI~~ 102 (151)
++++-.+| ..|++|.+|.-.|+- +||- |+ ||+.=+.. -|-.|+..- -++.+.+|.
T Consensus 30 ~ddvkeqI~K~akKGltpsqIGviLRD-shGi~q~r~v~G~kI~Rilk~----~Gl~PeiPeDLy~likkAv~iRkHLer 104 (151)
T KOG0400|consen 30 ADDVKEQIYKLAKKGLTPSQIGVILRD-SHGIGQVRFVTGNKILRILKS----NGLAPEIPEDLYHLIKKAVAIRKHLER 104 (151)
T ss_pred HHHHHHHHHHHHHcCCChhHceeeeec-ccCcchhheechhHHHHHHHH----cCCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 45666666 679999999999997 9985 33 33322321 355666442 245566777
Q ss_pred HhhhCCCcc
Q psy16493 103 YKRENPTIF 111 (151)
Q Consensus 103 yk~enP~iF 111 (151)
+++++-+=|
T Consensus 105 ~RKD~d~K~ 113 (151)
T KOG0400|consen 105 NRKDKDAKF 113 (151)
T ss_pred hccccccce
Confidence 777775544
No 47
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=26.36 E-value=50 Score=28.14 Aligned_cols=29 Identities=14% Similarity=0.253 Sum_probs=24.8
Q ss_pred cCCCC-cchhhHHHH-----HhhCCccchhhhhhh
Q psy16493 37 ASQQP-LASLVNQQQ-----RLLFRHYDIAQHVLH 65 (151)
Q Consensus 37 ~nGRP-Lp~~~R~ki-----~~GvRpcdISrqL~v 65 (151)
.||.| .+.++|+|+ +.|.+|--.+|.|+.
T Consensus 21 ln~~~~Vs~eTr~kV~~a~~elgY~pN~~Ar~L~~ 55 (333)
T COG1609 21 LNGSPYVSEETREKVLAAIKELGYRPNAVARSLRT 55 (333)
T ss_pred HcCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHh
Confidence 56665 999999998 689999999999964
No 48
>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=26.12 E-value=53 Score=26.49 Aligned_cols=29 Identities=17% Similarity=0.328 Sum_probs=23.9
Q ss_pred cCCCC-cchhhHHHH-----HhhCCccchhhhhhh
Q psy16493 37 ASQQP-LASLVNQQQ-----RLLFRHYDIAQHVLH 65 (151)
Q Consensus 37 ~nGRP-Lp~~~R~ki-----~~GvRpcdISrqL~v 65 (151)
.||++ .+.++|+|| +.|.+|...+|.|+.
T Consensus 22 Ln~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~ 56 (329)
T TIGR01481 22 VNGNPNVKPATRKKVLEVIKRLDYRPNAVARGLAS 56 (329)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHhh
Confidence 35655 889999998 689999999998863
No 49
>PRK04140 hypothetical protein; Provisional
Probab=26.04 E-value=75 Score=28.12 Aligned_cols=41 Identities=10% Similarity=0.088 Sum_probs=30.2
Q ss_pred cccccCCCCcchhhHHHH-HhhCCccchhhhhhhhhhhhhhhhhh
Q psy16493 33 YALAASQQPLASLVNQQQ-RLLFRHYDIAQHVLHQQQGAVSKLLG 76 (151)
Q Consensus 33 Gg~f~nGRPLp~~~R~ki-~~GvRpcdISrqL~vVSHGCVSKIL~ 76 (151)
||.||+=. ...+|+.. ..|+.--++|+.+.+ |.+-|||+..
T Consensus 120 Gg~~v~i~--GerLk~lRe~~GlSq~eLA~~lGV-Sr~tIskyE~ 161 (317)
T PRK04140 120 GGFYVKID--GDVLREAREELGLSLGELASELGV-SRRTISKYEN 161 (317)
T ss_pred CCeeehhh--HHHHHHHHHHcCCCHHHHHHHhCC-CHHHHHHHHc
Confidence 67776422 23444433 789999999999985 9999999985
No 50
>PHA01976 helix-turn-helix protein
Probab=25.86 E-value=47 Score=21.26 Aligned_cols=25 Identities=0% Similarity=0.018 Sum_probs=22.5
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhhh
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLLG 76 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL~ 76 (151)
+.|+...++|+.+-+ |..-|||+..
T Consensus 13 ~~glt~~~lA~~~gv-s~~~v~~~e~ 37 (67)
T PHA01976 13 ARAWSAPELSRRAGV-RHSLIYDFEA 37 (67)
T ss_pred HcCCCHHHHHHHhCC-CHHHHHHHHc
Confidence 789999999999985 9999999875
No 51
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=25.11 E-value=27 Score=23.79 Aligned_cols=48 Identities=19% Similarity=0.189 Sum_probs=30.3
Q ss_pred CccchhhhhhhhhhhhhhhhhhhccCCCccCCC--CCcccChHHHHHHHHH
Q psy16493 55 RHYDIAQHVLHQQQGAVSKLLGTLRPPGLIGGS--KPKVATPAVVSKIEQY 103 (151)
Q Consensus 55 RpcdISrqL~vVSHGCVSKIL~r~r~pG~IGGS--KPkvatp~V~~kI~~y 103 (151)
|+-+||+.+.+ +.+=||++|.++..-|.|==. +--..|+.-.+.++.+
T Consensus 1 ~~~ela~~l~i-s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~ 50 (96)
T smart00529 1 RTSEIAERLNV-SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRL 50 (96)
T ss_pred CHHHHHHHhCC-ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHH
Confidence 56689999985 999999999887644443111 1224466554444443
No 52
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=24.90 E-value=63 Score=26.23 Aligned_cols=27 Identities=4% Similarity=-0.010 Sum_probs=23.0
Q ss_pred CCCC-cchhhHHHH-----HhhCCccchhhhhh
Q psy16493 38 SQQP-LASLVNQQQ-----RLLFRHYDIAQHVL 64 (151)
Q Consensus 38 nGRP-Lp~~~R~ki-----~~GvRpcdISrqL~ 64 (151)
||++ ...++|+|+ +.|.+|...+|.|+
T Consensus 27 n~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~ 59 (331)
T PRK14987 27 RNPEQVSVALRGKIAAALDELGYIPNRAPDILS 59 (331)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCccHHHHHHh
Confidence 5655 889999997 68999999999885
No 53
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=24.79 E-value=58 Score=26.47 Aligned_cols=27 Identities=11% Similarity=0.300 Sum_probs=22.1
Q ss_pred cCCCC---cchhhHHHH-----HhhCCccchhhhhh
Q psy16493 37 ASQQP---LASLVNQQQ-----RLLFRHYDIAQHVL 64 (151)
Q Consensus 37 ~nGRP---Lp~~~R~ki-----~~GvRpcdISrqL~ 64 (151)
+||+| .++++|+|| +.|.+|.- +++++
T Consensus 22 ln~~~~~~vs~~tr~rV~~~a~~lgY~pn~-~~~~~ 56 (327)
T PRK10339 22 LNDDPTLNVKEETKHRILEIAEKLEYKTSS-ARKLQ 56 (327)
T ss_pred hcCCCCCCcCHHHHHHHHHHHHHhCCCCch-hhhhh
Confidence 58887 889999998 68999997 66664
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=24.60 E-value=47 Score=19.00 Aligned_cols=28 Identities=14% Similarity=-0.037 Sum_probs=22.6
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhhhhcc
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLLGTLR 79 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL~r~r 79 (151)
..|...-+||..+.+ +.+-|.+.+.+.+
T Consensus 24 ~~~~~~~~ia~~~~~-s~~~i~~~~~~~~ 51 (55)
T cd06171 24 GEGLSYEEIAEILGI-SRSTVRQRLHRAL 51 (55)
T ss_pred hcCCCHHHHHHHHCc-CHHHHHHHHHHHH
Confidence 378888999999975 9999988886653
No 55
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=24.41 E-value=57 Score=26.75 Aligned_cols=28 Identities=14% Similarity=0.135 Sum_probs=23.0
Q ss_pred CCCC-cchhhHHHH-----HhhCCccchhhhhhh
Q psy16493 38 SQQP-LASLVNQQQ-----RLLFRHYDIAQHVLH 65 (151)
Q Consensus 38 nGRP-Lp~~~R~ki-----~~GvRpcdISrqL~v 65 (151)
||++ ...++|+|| +.|.+|.-++|.|+.
T Consensus 23 n~~~~Vs~~tr~kV~~~a~elgY~pn~~a~~l~~ 56 (346)
T PRK10401 23 NNSALVSADTREAVMKAVSELGYRPNANAQALAT 56 (346)
T ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHhhc
Confidence 4444 889999998 679999999998863
No 56
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=24.10 E-value=32 Score=24.19 Aligned_cols=27 Identities=22% Similarity=0.231 Sum_probs=19.8
Q ss_pred hhCCccchhhhhhhhhhhhhhhhhhhcc
Q psy16493 52 LLFRHYDIAQHVLHQQQGAVSKLLGTLR 79 (151)
Q Consensus 52 ~GvRpcdISrqL~vVSHGCVSKIL~r~r 79 (151)
.|+.+.+|++.|-. |..-||+.|.=+.
T Consensus 2 ~G~tq~eIA~~lGk-s~s~Vs~~l~Ll~ 28 (93)
T PF08535_consen 2 FGWTQEEIAKRLGK-SRSWVSNHLALLD 28 (93)
T ss_dssp TT--HHHHHHHTT---HHHHHHHHGGGS
T ss_pred CCCCHHHHHHHHCC-CHHHHHHHHHHHc
Confidence 68899999999986 9999999996443
No 57
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=24.08 E-value=32 Score=25.19 Aligned_cols=30 Identities=27% Similarity=0.400 Sum_probs=23.5
Q ss_pred CCccchhhhhhhhhhhhhhhhhhhccCCCcc
Q psy16493 54 FRHYDIAQHVLHQQQGAVSKLLGTLRPPGLI 84 (151)
Q Consensus 54 vRpcdISrqL~vVSHGCVSKIL~r~r~pG~I 84 (151)
+.-.|||.++.+ |...|.|+|..++.-|.|
T Consensus 26 ~s~~eia~~l~i-s~~~v~~~l~~L~~~Gli 55 (130)
T TIGR02944 26 YSAAEIAEQTGL-NAPTVSKILKQLSLAGIV 55 (130)
T ss_pred ccHHHHHHHHCc-CHHHHHHHHHHHHHCCcE
Confidence 566799999985 999999999887644443
No 58
>PF15311 HYLS1_C: Hydrolethalus syndrome protein 1 C-terminus
Probab=23.91 E-value=58 Score=24.27 Aligned_cols=27 Identities=37% Similarity=0.848 Sum_probs=18.6
Q ss_pred HHHHHHHhhh-----CC-----CcchHHHHhhhhhcC
Q psy16493 97 VSKIEQYKRE-----NP-----TIFAWEIRERLISED 123 (151)
Q Consensus 97 ~~kI~~yk~e-----nP-----~iFaWEIRdrLi~~g 123 (151)
|++-..|++| -| .-+=|+||++|+...
T Consensus 19 VarY~~Yk~~W~~~k~PGE~~r~~lRw~IRe~ml~~~ 55 (89)
T PF15311_consen 19 VARYHEYKQEWDRFKAPGEKNRKDLRWNIREQMLYQD 55 (89)
T ss_pred chhHHHHHHHHHhcCCCCcccHHHHHHHHHHHHHhCC
Confidence 4455666663 23 236799999999988
No 59
>cd07498 Peptidases_S8_15 Peptidase S8 family domain, uncharacterized subfamily 15. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=23.57 E-value=93 Score=24.46 Aligned_cols=31 Identities=23% Similarity=0.296 Sum_probs=27.3
Q ss_pred ccChHHHHHHHHHhhhCCCcchHHHHhhhhh
Q psy16493 91 VATPAVVSKIEQYKRENPTIFAWEIRERLIS 121 (151)
Q Consensus 91 vatp~V~~kI~~yk~enP~iFaWEIRdrLi~ 121 (151)
.|||-|---+.-++..+|.+-..|||+.|..
T Consensus 211 ~Aap~vaG~~All~~~~p~l~~~~i~~~L~~ 241 (242)
T cd07498 211 FASPVAAGVAALILSANPNLTPAEVEDILTS 241 (242)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Confidence 4788888888899999999999999999874
No 60
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=23.09 E-value=99 Score=20.08 Aligned_cols=35 Identities=26% Similarity=0.248 Sum_probs=27.8
Q ss_pred HHHHhhhhhcCCCCCCCCCCCChhhHHHhhhhcccccC
Q psy16493 113 WEIRERLISEDVGVNGLALQTPPRNAIEEIKYSTLRKG 150 (151)
Q Consensus 113 WEIRdrLi~~gvC~~~~vPSVSSInRilR~k~~~~~~g 150 (151)
=|+|++|.+-|+ ...|-++|=-++...|......|
T Consensus 9 ~eL~~~L~~~G~---~~gPIt~sTR~vy~kkL~~~~~~ 43 (44)
T smart00540 9 AELRAELKQYGL---PPGPITDTTRKLYEKKLRKLRRG 43 (44)
T ss_pred HHHHHHHHHcCC---CCCCcCcchHHHHHHHHHHHHcC
Confidence 489999999999 66788888777877777666554
No 61
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=22.89 E-value=30 Score=22.86 Aligned_cols=31 Identities=23% Similarity=0.357 Sum_probs=23.6
Q ss_pred hCCccchhhhhhhhhhhhhhhhhhhccCCCcc
Q psy16493 53 LFRHYDIAQHVLHQQQGAVSKLLGTLRPPGLI 84 (151)
Q Consensus 53 GvRpcdISrqL~vVSHGCVSKIL~r~r~pG~I 84 (151)
++..-+|++.+.+ +++.||+.|.++..-|.+
T Consensus 24 ~~~~~~la~~~~~-s~~~i~~~l~~L~~~g~v 54 (101)
T smart00347 24 PLSVSELAKRLGV-SPSTVTRVLDRLEKKGLI 54 (101)
T ss_pred CcCHHHHHHHHCC-CchhHHHHHHHHHHCCCe
Confidence 4677789998875 999999999886544443
No 62
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=22.82 E-value=1.9e+02 Score=25.61 Aligned_cols=105 Identities=13% Similarity=0.184 Sum_probs=62.4
Q ss_pred eecccCcchhHHHHhhhhhhccccchhhhhcccccCCCCcchhhHHHHHhhCCccchhhhhhhhhhhhhhhhhhhccCCC
Q psy16493 3 FVFVDFPEEQYWILRHLTLFNKLIGSLRELYALAASQQPLASLVNQQQRLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPG 82 (151)
Q Consensus 3 ~~~~~~~~~~~~i~~~~~~~~~~~~~vNqLGg~f~nGRPLp~~~R~ki~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG 82 (151)
||-.|+++-...|++|+.. =-.|=..|.+|+.+=..+=.+ -.|+.+.+++...|- .-|.+. .|
T Consensus 153 lv~aDysqiElRilA~ls~-------D~~l~~~~~~g~Dih~~~A~~-~~g~~~~~v~~~~R~-----~aK~~~----~g 215 (377)
T cd08637 153 LLSADYSQIELRILAHLSG-------DEALIEAFKNGEDIHTRTAAE-VFGVPPEEVTPEMRR-----IAKAVN----FG 215 (377)
T ss_pred EEEechhHhHHHHHHHHhC-------CHHHHHHHhcCCCHHHHHHHH-HhCCChhhCCHHHHh-----hhhHhh----cc
Confidence 5778999999999998752 122445577776553222122 246666566544442 123321 22
Q ss_pred ccCCCCC-------cccChHHHHHHHHHhhhCCCcchHH--HHhhhhhcCC
Q psy16493 83 LIGGSKP-------KVATPAVVSKIEQYKRENPTIFAWE--IRERLISEDV 124 (151)
Q Consensus 83 ~IGGSKP-------kvatp~V~~kI~~yk~enP~iFaWE--IRdrLi~~gv 124 (151)
.+-|.-+ .++..++.+.++.|....|++.+|- +.+.....|.
T Consensus 216 ~~YG~g~~~la~~lg~s~~eA~~~~~~f~~~~p~v~~~~~~~~~~a~~~g~ 266 (377)
T cd08637 216 IIYGISAFGLSQQLGISRKEAKEYIDRYFARYPGVKEYMEETVEEAREKGY 266 (377)
T ss_pred hhcCcchhHHHHHcCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHcCc
Confidence 2222111 2445678888999999999999995 4555555553
No 63
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=22.63 E-value=43 Score=25.94 Aligned_cols=47 Identities=26% Similarity=0.150 Sum_probs=32.2
Q ss_pred CCccchhhhhhhhhhhhhhhhhhhccC-------CCccCCC---C-CcccC-hHHHHHHH
Q psy16493 54 FRHYDIAQHVLHQQQGAVSKLLGTLRP-------PGLIGGS---K-PKVAT-PAVVSKIE 101 (151)
Q Consensus 54 vRpcdISrqL~vVSHGCVSKIL~r~r~-------pG~IGGS---K-Pkvat-p~V~~kI~ 101 (151)
+.-.+||.++.+ |...+.|||..++. .|.-||. | |+-.| -+|++.++
T Consensus 25 ~s~~eIA~~~~i-s~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~eItl~dIi~ave 83 (153)
T PRK11920 25 SRIPEIARAYGV-SELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVVRVTE 83 (153)
T ss_pred CcHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHHHCcHHHHHHHHc
Confidence 445689999985 99999999977652 4666885 2 33222 35666664
No 64
>PRK02919 oxaloacetate decarboxylase subunit gamma; Provisional
Probab=22.54 E-value=1.7e+02 Score=21.17 Aligned_cols=42 Identities=19% Similarity=0.318 Sum_probs=24.1
Q ss_pred hhhhhhhhhhhhhccCCCccCC--CCCcc---------cChHHHHHHHHHhhhC
Q psy16493 65 HQQQGAVSKLLGTLRPPGLIGG--SKPKV---------ATPAVVSKIEQYKREN 107 (151)
Q Consensus 65 vVSHGCVSKIL~r~r~pG~IGG--SKPkv---------atp~V~~kI~~yk~en 107 (151)
+.--..+||++++|-+ ...-- .+|+. .+|.+...|.+||+.+
T Consensus 29 I~~i~~ms~l~~~~~p-e~~~~~~~~~~~~~~~~d~~~l~avIsAAI~~hR~~~ 81 (82)
T PRK02919 29 IFAIRGMSALINRFFP-EPVAAPAPRPVPVAPVDDFTRLKPVIAAAIHHHRRLN 81 (82)
T ss_pred HHHHHHHHHHHHhhCC-CccCCCCCCCcCCCCCCCcchhHHHHHHHHHHHHhcC
Confidence 3345689999999862 11111 12211 1245666799998865
No 65
>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=22.47 E-value=1.7e+02 Score=17.75 Aligned_cols=26 Identities=8% Similarity=0.133 Sum_probs=21.2
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhhhh
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLLGT 77 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL~r 77 (151)
..|+...|+|+.+.+ |..-||+++.-
T Consensus 7 ~~gls~~~la~~~gi-s~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGI-SRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS--HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCC-CcchhHHHhcC
Confidence 789999999999985 99999999864
No 66
>PRK06474 hypothetical protein; Provisional
Probab=22.34 E-value=46 Score=26.49 Aligned_cols=38 Identities=16% Similarity=0.156 Sum_probs=28.8
Q ss_pred cchhhHHHH-----Hhh--CCccchhhhhhhhhhhhhhhhhhhcc
Q psy16493 42 LASLVNQQQ-----RLL--FRHYDIAQHVLHQQQGAVSKLLGTLR 79 (151)
Q Consensus 42 Lp~~~R~ki-----~~G--vRpcdISrqL~vVSHGCVSKIL~r~r 79 (151)
|.+..|.+| ..+ ..+++|+.+|.-++...|+..|..+.
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~ 52 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMV 52 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 667788887 222 78899999985459999998886554
No 67
>PF03734 YkuD: L,D-transpeptidase catalytic domain; InterPro: IPR005490 This family of proteins are found in a range of bacteria. The conserved region contains a conserved histidine and cysteine, suggesting that these proteins have an enzymatic activity. Several members of this family contain peptidoglycan binding domains. So these proteins may use peptidoglycan or a precursor as a substrate. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of this family may play an important role in cell wall biology. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.; GO: 0016740 transferase activity; PDB: 3ZQD_A 1Y7M_B 4A52_A 2HKL_C 1ZAT_A.
Probab=21.94 E-value=23 Score=25.31 Aligned_cols=7 Identities=14% Similarity=0.534 Sum_probs=5.8
Q ss_pred hhhhhhh
Q psy16493 66 QQQGAVS 72 (151)
Q Consensus 66 VSHGCVS 72 (151)
+|||||.
T Consensus 117 ~S~GCIr 123 (144)
T PF03734_consen 117 ASHGCIR 123 (144)
T ss_dssp EESSSEE
T ss_pred CCCCEec
Confidence 4999985
No 68
>cd08638 DNA_pol_A_theta DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation. DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondri
Probab=21.81 E-value=1.7e+02 Score=25.86 Aligned_cols=105 Identities=20% Similarity=0.181 Sum_probs=59.8
Q ss_pred eecccCcchhHHHHhhhhhhccccchhhhhcccccCCCCcchhhHHHHHhhCCccchhhhhhhhhhhhhhhhhhhccCCC
Q psy16493 3 FVFVDFPEEQYWILRHLTLFNKLIGSLRELYALAASQQPLASLVNQQQRLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPG 82 (151)
Q Consensus 3 ~~~~~~~~~~~~i~~~~~~~~~~~~~vNqLGg~f~nGRPLp~~~R~ki~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG 82 (151)
||-+|+++-..-|++|+..= -.|-..|.+|..+=..+=.++ .|+...+++...|. .-|.++ .|
T Consensus 142 lv~~DysqiElRvlA~ls~D-------~~l~~~~~~g~Dih~~~A~~~-~g~~~~~v~~~~R~-----~aK~~~----fg 204 (373)
T cd08638 142 LLSADYSQLELRILAHLSGD-------PALIELLNSGGDVFKMIAAQW-LGKPVEEVTDEERQ-----QAKQLV----YG 204 (373)
T ss_pred EEEechhhhHHHHHHHHhCC-------HHHHHHHhcCCCHHHHHHHHH-hCCChhhCCHHHHH-----HHhHHH----Hh
Confidence 57789999999999987421 133345556665443222222 45555455544442 124331 22
Q ss_pred ccCCCC-------CcccChHHHHHHHHHhhhCCCcchHH--HHhhhhhcCC
Q psy16493 83 LIGGSK-------PKVATPAVVSKIEQYKRENPTIFAWE--IRERLISEDV 124 (151)
Q Consensus 83 ~IGGSK-------Pkvatp~V~~kI~~yk~enP~iFaWE--IRdrLi~~gv 124 (151)
.+-|.- -.++..++.+.|+.|.+..|++.+|- +++...+.|.
T Consensus 205 ~~YG~g~~~La~~l~~s~~eA~~~i~~f~~~~p~v~~~~~~~~~~a~~~g~ 255 (373)
T cd08638 205 ILYGMGAKSLAEQLGVSEEEAKQFIESFKNAYPGVRRFIRETIERARRNGF 255 (373)
T ss_pred hHhCCcHHHHHHHhCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHHcCc
Confidence 222221 12445678889999999999999995 3444444454
No 69
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=21.32 E-value=72 Score=18.71 Aligned_cols=28 Identities=14% Similarity=0.107 Sum_probs=23.5
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhhhhcc
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLLGTLR 79 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL~r~r 79 (151)
..|....+||..+.+ |.+=|.+.+.++.
T Consensus 16 ~~g~s~~eia~~l~i-s~~tv~~~~~~~~ 43 (58)
T smart00421 16 AEGLTNKEIAERLGI-SEKTVKTHLSNIM 43 (58)
T ss_pred HcCCCHHHHHHHHCC-CHHHHHHHHHHHH
Confidence 578999999999985 9988888887754
No 70
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=21.12 E-value=2.9e+02 Score=26.84 Aligned_cols=123 Identities=13% Similarity=0.149 Sum_probs=82.3
Q ss_pred eecccCcchhHHHHhhhhhhccccchhhhhcccccCCCCcchhhHHHHHhhCCccchhhhhhhhhhhhhhhhhhhccCCC
Q psy16493 3 FVFVDFPEEQYWILRHLTLFNKLIGSLRELYALAASQQPLASLVNQQQRLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPG 82 (151)
Q Consensus 3 ~~~~~~~~~~~~i~~~~~~~~~~~~~vNqLGg~f~nGRPLp~~~R~ki~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG 82 (151)
+++.|.|+=+-=|++|+.. --.|=-.|.+|.-+-..+=-+ -.|+..-|+....|. .-|..+ .|
T Consensus 366 ~i~aDYSQIELRilAHls~-------D~~Ll~AF~~g~DiH~~TA~~-vFgv~~~~Vt~e~Rr-----~AKaIN----FG 428 (593)
T COG0749 366 LISADYSQIELRILAHLSQ-------DEGLLRAFTEGEDIHTATAAE-VFGVPIEEVTSEQRR-----KAKAIN----FG 428 (593)
T ss_pred EEEechHHHHHHHHHHhcC-------CHHHHHHHhcCccHHHHHHHH-HhCCChhhCCHHHhh-----hhhhhc----cc
Confidence 5678999888888888743 223335677776543222222 257777777776664 123332 66
Q ss_pred ccCCCCCc-------ccChHHHHHHHHHhhhCCCcchHH--HHhhhhhcCCC-----CCCCCCCCChhhHHHhh
Q psy16493 83 LIGGSKPK-------VATPAVVSKIEQYKRENPTIFAWE--IRERLISEDVG-----VNGLALQTPPRNAIEEI 142 (151)
Q Consensus 83 ~IGGSKPk-------vatp~V~~kI~~yk~enP~iFaWE--IRdrLi~~gvC-----~~~~vPSVSSInRilR~ 142 (151)
.|=|-... ...-++-..|+.|-...|++..|+ +++...++|-- -+..+|.+.|-|+.+|.
T Consensus 429 iiYG~safgLa~~L~I~~~eA~~~I~~YF~rypgv~~ym~~~~~~ar~~GyV~Tl~gRRry~p~i~s~n~~~R~ 502 (593)
T COG0749 429 LIYGMSAFGLAQQLGIPRKEAKEYIDRYFERYPGVKEYMERTKEEAREDGYVETLFGRRRYLPDINSSNRVVRA 502 (593)
T ss_pred eeeccchhhHHHHcCCChHHHHHHHHHHHHhChHHHHHHHHHHHHHHHcCceeecccccccCcccccCCHHHHH
Confidence 66554332 344678888999999999999998 56666777643 45668999999999873
No 71
>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=21.01 E-value=71 Score=17.76 Aligned_cols=25 Identities=8% Similarity=0.147 Sum_probs=20.6
Q ss_pred HhhCCccchhhhhhhhhhhhhhhhhh
Q psy16493 51 RLLFRHYDIAQHVLHQQQGAVSKLLG 76 (151)
Q Consensus 51 ~~GvRpcdISrqL~vVSHGCVSKIL~ 76 (151)
+.|+...++|+.+.+ +.+-|++.+.
T Consensus 10 ~~~~s~~~~a~~~~~-~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGV-SRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCC-CHHHHHHHHc
Confidence 678889999999875 8888888764
No 72
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=20.94 E-value=1.1e+02 Score=22.75 Aligned_cols=63 Identities=14% Similarity=0.199 Sum_probs=36.8
Q ss_pred cCcchhHHHHhhhhhhccccchhhhhcccccCCCCcchhhHHHH--HhhCCccchhhhhhhhh--hhhhhhhh
Q psy16493 7 DFPEEQYWILRHLTLFNKLIGSLRELYALAASQQPLASLVNQQQ--RLLFRHYDIAQHVLHQQ--QGAVSKLL 75 (151)
Q Consensus 7 ~~~~~~~~i~~~~~~~~~~~~~vNqLGg~f~nGRPLp~~~R~ki--~~GvRpcdISrqL~vVS--HGCVSKIL 75 (151)
.++|++||++-.++... ...-++.|-.-+|.|.+ |+.+ +.||.+...|+.|.... |.=|.+|+
T Consensus 22 ~vs~e~F~lLl~ls~Ir-S~kiI~AL~dyLV~G~s-----rkeac~~~gV~~syfs~~L~rL~~v~~~V~~l~ 88 (91)
T PF03333_consen 22 KVSEEHFWLLLELSSIR-SEKIIAALRDYLVDGLS-----RKEACERHGVNQSYFSRALNRLNRVSQIVEQLS 88 (91)
T ss_dssp -S-HHHHHHHHHHS-----HHHHHHHHHHHTT--------HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHG
T ss_pred CcCHHHHHHHHHHCCCC-cHHHHHHHHHHHHcCCc-----HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 57899999987664432 34567889999999998 3334 78999999998876433 34444443
No 73
>COG1376 ErfK Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.69 E-value=29 Score=27.92 Aligned_cols=7 Identities=14% Similarity=0.472 Sum_probs=5.7
Q ss_pred hhhhhhh
Q psy16493 66 QQQGAVS 72 (151)
Q Consensus 66 VSHGCVS 72 (151)
+|||||.
T Consensus 201 ~ShGCIR 207 (232)
T COG1376 201 VSHGCIR 207 (232)
T ss_pred cCCceEe
Confidence 5999983
No 74
>smart00482 POLAc DNA polymerase A domain.
Probab=20.37 E-value=1.7e+02 Score=23.49 Aligned_cols=104 Identities=16% Similarity=0.182 Sum_probs=58.6
Q ss_pred eecccCcchhHHHHhhhhhhccccchhhhhcccccCCCCcchhhHHHHHhhCCccchhhhhhhhhhhhhhhhhhhccCCC
Q psy16493 3 FVFVDFPEEQYWILRHLTLFNKLIGSLRELYALAASQQPLASLVNQQQRLLFRHYDIAQHVLHQQQGAVSKLLGTLRPPG 82 (151)
Q Consensus 3 ~~~~~~~~~~~~i~~~~~~~~~~~~~vNqLGg~f~nGRPLp~~~R~ki~~GvRpcdISrqL~vVSHGCVSKIL~r~r~pG 82 (151)
+|-+|+++-...|++|+.. =..|-..|.+|..+=..+=.++ .|.-+.++....|- ..|.++ -|
T Consensus 16 lv~~DysqiElRilA~ls~-------D~~l~~~~~~g~D~h~~~A~~~-~g~~~~~v~~~~R~-----~aK~~~----~g 78 (206)
T smart00482 16 LVSADYSQIELRILAHLSG-------DENLLEAFNNGGDIHSKTAAQV-FGVPEEEVTKELRR-----AAKAIN----FG 78 (206)
T ss_pred EEEeeHHHHHHHHHHHHcC-------CHHHHHHHhcCCCHHHHHHHHH-hCCChhhCCHHHHH-----HHhHHH----HH
Confidence 5778999999999998853 2344455666665433222222 35544454433332 123321 11
Q ss_pred ccCCCCC-------cccChHHHHHHHHHhhhCCCcchHH--HHhhhhhcC
Q psy16493 83 LIGGSKP-------KVATPAVVSKIEQYKRENPTIFAWE--IRERLISED 123 (151)
Q Consensus 83 ~IGGSKP-------kvatp~V~~kI~~yk~enP~iFaWE--IRdrLi~~g 123 (151)
.+-|.-+ .++..++.+.++.|.+..|++-+|- +.++..+.|
T Consensus 79 ~~YG~g~~~la~~lg~s~~ea~~~~~~f~~~~p~v~~~~~~~~~~a~~~g 128 (206)
T smart00482 79 IIYGMGAKGLAEQLGISEAEAKELIKAYFARFPGVKRYIKRTLEEARRKG 128 (206)
T ss_pred hhhccchhHHHHHcCCCHHHHHHHHHHHHHHCccHHHHHHHHHHHHHhCC
Confidence 1111111 1445667888999999999999994 334444444
Done!