Query 032763
Match_columns 134
No_of_seqs 139 out of 241
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 05:38:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032763.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032763hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3344 40s ribosomal protein 100.0 8.4E-47 1.8E-51 292.2 5.5 103 1-120 46-149 (150)
2 PTZ00034 40S ribosomal protein 100.0 5.1E-36 1.1E-40 227.0 6.4 53 1-53 47-99 (124)
3 PF03501 S10_plectin: Plectin/ 100.0 2.6E-36 5.6E-41 219.8 1.9 51 1-51 44-94 (95)
4 COG5045 Ribosomal protein S10E 99.9 8.6E-25 1.9E-29 161.2 3.6 57 1-57 46-102 (105)
5 PF03551 PadR: Transcriptional 90.1 0.16 3.5E-06 33.7 1.3 32 2-33 39-75 (75)
6 PF14947 HTH_45: Winged helix- 90.0 0.093 2E-06 35.7 0.0 29 2-34 41-69 (77)
7 PTZ00326 phenylalanyl-tRNA syn 88.2 0.18 3.8E-06 46.1 0.5 43 1-46 42-84 (494)
8 COG3432 Predicted transcriptio 87.7 0.39 8.5E-06 35.3 2.0 35 2-36 53-87 (95)
9 PF13814 Replic_Relax: Replica 87.6 0.42 9.2E-06 35.8 2.2 37 1-38 33-77 (191)
10 PLN02853 Probable phenylalanyl 87.6 0.2 4.3E-06 45.8 0.5 43 1-46 39-81 (492)
11 PF13601 HTH_34: Winged helix 87.6 0.32 6.9E-06 33.6 1.4 36 2-37 36-75 (80)
12 PRK04172 pheS phenylalanyl-tRN 86.6 0.35 7.6E-06 42.9 1.4 31 2-33 42-72 (489)
13 PF14338 Mrr_N: Mrr N-terminal 82.9 0.39 8.3E-06 33.3 0.0 29 2-33 62-90 (92)
14 PRK09416 lstR lineage-specific 81.6 0.58 1.3E-05 36.3 0.6 37 2-40 85-124 (135)
15 PRK03902 manganese transport t 81.3 0.5 1.1E-05 34.8 0.1 37 2-42 44-94 (142)
16 PF13463 HTH_27: Winged helix 81.3 0.41 9E-06 30.2 -0.3 27 1-27 39-68 (68)
17 smart00347 HTH_MARR helix_turn 80.5 0.91 2E-05 29.6 1.2 34 2-35 46-82 (101)
18 TIGR02337 HpaR homoprotocatech 78.7 1 2.2E-05 31.8 1.0 34 2-35 64-100 (118)
19 COG1695 Predicted transcriptio 75.0 1.8 3.9E-05 31.4 1.5 42 2-43 52-98 (138)
20 cd00090 HTH_ARSR Arsenical Res 73.6 2.6 5.7E-05 25.4 1.8 32 2-33 42-75 (78)
21 PF09639 YjcQ: YjcQ protein; 73.5 0.94 2E-05 31.8 -0.3 32 2-33 32-69 (88)
22 TIGR02719 repress_PhaQ poly-be 72.8 2.2 4.7E-05 32.9 1.5 41 2-42 65-110 (138)
23 PRK14165 winged helix-turn-hel 72.8 2.1 4.5E-05 35.1 1.5 42 1-42 42-83 (217)
24 PF07381 DUF1495: Winged helix 72.2 2.6 5.7E-05 30.5 1.8 30 2-31 57-87 (90)
25 TIGR02647 DNA conserved hypoth 68.6 1.3 2.8E-05 31.9 -0.5 25 1-30 40-64 (77)
26 smart00418 HTH_ARSR helix_turn 68.5 3.3 7.1E-05 24.5 1.3 32 2-33 32-64 (66)
27 TIGR03433 padR_acidobact trans 62.5 4.9 0.00011 28.3 1.5 35 2-36 47-86 (100)
28 PF02002 TFIIE_alpha: TFIIE al 60.3 5.5 0.00012 28.0 1.4 21 13-33 66-87 (105)
29 PRK10141 DNA-binding transcrip 58.8 6.9 0.00015 29.2 1.8 34 2-35 52-85 (117)
30 PF01043 SecA_PP_bind: SecA pr 57.6 11 0.00023 28.0 2.6 22 21-42 33-54 (113)
31 PF01638 HxlR: HxlR-like helix 54.8 6.2 0.00014 27.1 0.9 30 3-32 42-74 (90)
32 COG1497 Predicted transcriptio 54.4 6.3 0.00014 33.9 1.1 32 1-35 46-77 (260)
33 TIGR02277 PaaX_trns_reg phenyl 51.1 11 0.00023 31.5 1.9 31 3-33 43-73 (280)
34 PF10007 DUF2250: Uncharacteri 50.4 9.9 0.00022 27.6 1.4 17 17-33 75-91 (92)
35 PF07848 PaaX: PaaX-like prote 49.0 10 0.00022 25.9 1.3 24 4-27 47-70 (70)
36 COG1846 MarR Transcriptional r 48.0 9.6 0.00021 25.3 1.0 35 2-36 58-95 (126)
37 PRK06266 transcription initiat 47.8 8.6 0.00019 30.4 0.8 25 13-37 75-100 (178)
38 PF03374 ANT: Phage antirepres 47.2 24 0.00051 24.7 2.9 18 19-36 89-106 (111)
39 TIGR02702 SufR_cyano iron-sulf 46.8 6.8 0.00015 30.5 0.1 31 1-31 36-71 (203)
40 TIGR01889 Staph_reg_Sar staphy 45.6 11 0.00024 26.6 1.0 33 2-34 65-100 (109)
41 PF09382 RQC: RQC domain; Int 45.4 6.8 0.00015 27.0 -0.1 34 2-35 64-98 (106)
42 COG5124 Protein predicted to b 44.9 9.4 0.0002 31.8 0.7 36 1-36 49-85 (209)
43 TIGR00373 conserved hypothetic 44.4 10 0.00023 29.2 0.8 35 3-37 51-92 (158)
44 cd03071 PDI_b'_NRX PDIb' famil 43.1 23 0.00051 27.2 2.5 28 14-41 54-81 (116)
45 smart00531 TFIIE Transcription 43.0 21 0.00046 26.9 2.3 23 15-37 59-82 (147)
46 PRK11512 DNA-binding transcrip 40.7 14 0.00031 26.9 1.0 32 2-33 76-110 (144)
47 smart00529 HTH_DTXR Helix-turn 39.5 12 0.00027 25.0 0.5 31 2-35 21-51 (96)
48 PRK03573 transcriptional regul 36.8 18 0.0004 26.1 1.1 35 2-36 68-105 (144)
49 KOG4082 Uncharacterized conser 35.0 7.8 0.00017 32.9 -1.3 29 14-42 132-162 (268)
50 PF14756 Pdase_C33_assoc: Pept 34.4 26 0.00057 27.7 1.6 24 26-49 14-37 (147)
51 PRK04172 pheS phenylalanyl-tRN 33.1 23 0.00049 31.6 1.2 37 2-39 159-195 (489)
52 PRK10870 transcriptional repre 32.7 21 0.00046 27.4 0.9 34 2-35 93-129 (176)
53 COG1321 TroR Mn-dependent tran 31.9 15 0.00032 28.4 -0.1 38 2-42 46-97 (154)
54 KOG2784 Phenylalanyl-tRNA synt 30.6 29 0.00063 32.0 1.5 32 1-33 38-69 (483)
55 COG1905 NuoE NADH:ubiquinone o 28.9 20 0.00044 28.5 0.2 27 10-42 34-60 (160)
56 KOG3433 Protein involved in me 26.7 18 0.00039 30.1 -0.4 36 1-36 48-84 (203)
57 PRK13777 transcriptional regul 26.6 36 0.00078 27.1 1.2 34 2-35 81-117 (185)
58 PHA00422 hypothetical protein 25.0 52 0.0011 23.3 1.7 17 18-34 49-65 (69)
59 KOG2175 Protein predicted to b 24.6 22 0.00047 32.8 -0.4 25 14-38 200-225 (458)
60 PF08986 DUF1889: Domain of un 24.5 39 0.00085 25.9 1.1 16 24-40 49-65 (119)
61 KOG0921 Dosage compensation co 24.4 95 0.0021 31.9 3.9 10 114-123 1253-1262(1282)
62 PF13516 LRR_6: Leucine Rich r 24.3 50 0.0011 17.2 1.2 12 22-33 13-24 (24)
63 COG3057 SeqA Negative regulato 24.0 38 0.00083 27.7 1.0 24 19-42 144-174 (181)
64 PF01978 TrmB: Sugar-specific 23.2 30 0.00065 22.2 0.2 23 1-23 43-65 (68)
65 PHA00738 putative HTH transcri 22.6 36 0.00078 25.7 0.5 30 1-30 47-76 (108)
66 COG1836 Predicted membrane pro 22.5 49 0.0011 28.4 1.4 15 21-35 220-234 (247)
67 smart00346 HTH_ICLR helix_turn 21.7 38 0.00082 22.2 0.4 33 2-36 42-74 (91)
68 PF08109 Antimicrobial14: Lact 20.8 45 0.00097 20.2 0.6 12 26-37 7-19 (31)
No 1
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.4e-47 Score=292.18 Aligned_cols=103 Identities=62% Similarity=1.145 Sum_probs=87.1
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHHhhCCCCCCccccccccCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCC
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATLKKSAKPAGRPMG-GPGGDRPRGPPRFDGDRPRFG 79 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~eivPaTlkk~~~~~~rpr~-~~~g~r~~~~~r~~g~r~~~~ 79 (134)
||||+|+|||||||||||||||||||||+|||+|||||+||||+||+++.+++.+|++ ++++.++++ +.+ +
T Consensus 46 MQSl~SrgYvkeqfaWrH~Yw~LTneGi~yLR~YLhLP~EiVpaTl~~~rP~~~rpr~~g~e~~~p~~-----~~r---~ 117 (150)
T KOG3344|consen 46 MQSLKSRGYVKEQFAWRHFYWYLTNEGIEYLREYLHLPPEIVPATLKRSRPETGRPRPPGLEGRGPAD-----GTR---G 117 (150)
T ss_pred HHHHhhhhhHHhhhhhheeeeeechhHHHHHHHHhcCCcccccchhhccCCCCCCCCCCCCCCCCccc-----ccc---c
Confidence 8999999999999999999999999999999999999999999999997777888887 555555432 232 6
Q ss_pred CCccccCCCCCCCCCCCCCCCCCCCCcccccCCCCCCccCC
Q 032763 80 DREGYRGGPRGGDFGGEKGGAPADFQPSFRGSGGRPGFGRG 120 (134)
Q Consensus 80 DR~~YRr~~~~~g~~dkK~ga~~~~~~eFrg~~~rgGfGRG 120 (134)
||++||++++++ ++||+++++||||| -|||++
T Consensus 118 dR~~yR~~~~~~-----~~gA~s~~~~~frg----~g~g~~ 149 (150)
T KOG3344|consen 118 DRDGYRRGPVPP-----EGGAGSGTEPQFRG----RGFGRP 149 (150)
T ss_pred chhhhccCCCCC-----CCCCCccccccccc----cCCCCC
Confidence 999999987754 56899999999995 366654
No 2
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=100.00 E-value=5.1e-36 Score=226.96 Aligned_cols=53 Identities=58% Similarity=1.076 Sum_probs=50.8
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHHhhCCCCCCccccccccCCCC
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATLKKSAKPA 53 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~eivPaTlkk~~~~~ 53 (134)
||||+|||||||||||||||||||||||+|||+|||||+||||+||+++.++.
T Consensus 47 mqSL~Srg~Vke~f~WrhyYw~LT~eGieyLR~yL~LP~eivP~T~k~~~~~~ 99 (124)
T PTZ00034 47 MRSLKSRGLVKEQFAWQHYYYYLTDEGIEYLRTYLHLPPDVFPATHKKKSVNF 99 (124)
T ss_pred HHccccCCceEEEEeeEEEEEEEchHHHHHHHHHhCCCcccCchhhcccccCc
Confidence 89999999999999999999999999999999999999999999999986664
No 3
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=100.00 E-value=2.6e-36 Score=219.82 Aligned_cols=51 Identities=76% Similarity=1.359 Sum_probs=43.4
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHHhhCCCCCCccccccccCC
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATLKKSAK 51 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~eivPaTlkk~~~ 51 (134)
||||+|||||||||||||||||||||||||||+|||||+||||+||+++.+
T Consensus 44 mqSL~SrgyVke~faWrh~Yw~LT~eGIeyLR~yL~LP~eivPaTlk~~~~ 94 (95)
T PF03501_consen 44 MQSLKSRGYVKEQFAWRHYYWYLTNEGIEYLREYLHLPAEIVPATLKKSRR 94 (95)
T ss_dssp HHHHHHCTSEEEEECTTEEEEEE-HHHHHHHHHHC-SSTT--TCCCS-S--
T ss_pred HhcccchhhhcCeecceEEEEEEcchhHHHHHHHhCCChhhCcHHhccccC
Confidence 799999999999999999999999999999999999999999999999754
No 4
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=8.6e-25 Score=161.17 Aligned_cols=57 Identities=46% Similarity=0.790 Sum_probs=54.3
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHHhhCCCCCCccccccccCCCCCCCC
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATLKKSAKPAGRPM 57 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~eivPaTlkk~~~~~~rpr 57 (134)
||||.|+||||.+|+|||+||+||+||++|||+|||||+|+||+|.+.+..++.||.
T Consensus 46 ~qsl~S~GYvkt~~~W~~~YytLT~eGveyLREyL~lp~e~Vp~t~~~~v~pt~rp~ 102 (105)
T COG5045 46 MQSLISYGYVKTIHVWRHSYYTLTPEGVEYLREYLVLPDEGVPSTEAPAVSPTQRPQ 102 (105)
T ss_pred HHHHhhcceeEEEeeeeeeEEEecHHHHHHHHHHhcCccccCccccccccCcccCCC
Confidence 799999999999999999999999999999999999999999999999877777775
No 5
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=90.14 E-value=0.16 Score=33.67 Aligned_cols=32 Identities=19% Similarity=0.340 Sum_probs=25.7
Q ss_pred CCcccccccceeeec-----ceeEEEechhhHHHHHH
Q 032763 2 QSFKSREYVRETFAW-----MHYYWYLTNDGIEFLRT 33 (134)
Q Consensus 2 qSLkSrg~Vke~FaW-----rh~Yw~LTneGI~yLR~ 33 (134)
+.|..+|+|+....= .--||.||++|.++|++
T Consensus 39 ~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 39 KRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp HHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred HHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 457788888877665 45689999999999985
No 6
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=90.00 E-value=0.093 Score=35.67 Aligned_cols=29 Identities=21% Similarity=0.421 Sum_probs=22.4
Q ss_pred CCcccccccceeeecceeEEEechhhHHHHHHh
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGIEFLRTY 34 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~y 34 (134)
..|.++|+|+. ..-.|.||++|.+||..+
T Consensus 41 ~~L~~~gLI~~----~~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 41 KELEEKGLIKK----KDGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp HHHHHTTSEEE----ETTEEEE-HHHHHHHHHH
T ss_pred HHHHHCcCeeC----CCCEEEECccHHHHHHHH
Confidence 45888999944 555679999999999875
No 7
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=88.16 E-value=0.18 Score=46.08 Aligned_cols=43 Identities=23% Similarity=0.452 Sum_probs=31.9
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHHhhCCCCCCccccc
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATL 46 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~eivPaTl 46 (134)
+.||.++|+|+-.-- ..-+|.||+||.+||. -+||+..|=+.|
T Consensus 42 ~~~L~~kg~v~~~~~-~~~~~~LT~eG~~~~~--~G~PE~rl~~~l 84 (494)
T PTZ00326 42 IKSLESANYITTEMK-KSNTWTLTEEGEDYLK--NGSPEYRLWQKL 84 (494)
T ss_pred HHHHHhCCCEEEEEE-EEEEEEECHHHHHHHH--cCCHHHHHHHHh
Confidence 358999998765443 5678899999999999 467766554333
No 8
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=87.75 E-value=0.39 Score=35.35 Aligned_cols=35 Identities=17% Similarity=0.228 Sum_probs=28.6
Q ss_pred CCcccccccceeeecceeEEEechhhHHHHHHhhC
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLN 36 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLh 36 (134)
+-|.++|+++.+=.=+--.|.||++|..+|++|=-
T Consensus 53 ~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~~ 87 (95)
T COG3432 53 EMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYSE 87 (95)
T ss_pred HHHHhCCCEEeccCCccceEEEChhHHHHHHHHHH
Confidence 34778898877777777788999999999998743
No 9
>PF13814 Replic_Relax: Replication-relaxation
Probab=87.63 E-value=0.42 Score=35.76 Aligned_cols=37 Identities=22% Similarity=0.432 Sum_probs=28.0
Q ss_pred CCCcccccccceeeec--------ceeEEEechhhHHHHHHhhCCC
Q 032763 1 MQSFKSREYVRETFAW--------MHYYWYLTNDGIEFLRTYLNLP 38 (134)
Q Consensus 1 mqSLkSrg~Vke~FaW--------rh~Yw~LTneGI~yLR~yLhLP 38 (134)
|+.|...|||+. |.. ..+.|+||.+|+++|.+-..++
T Consensus 33 L~~L~~~glv~~-~~~~~~~~~g~~~~vy~Lt~~G~~~l~~~~~~~ 77 (191)
T PF13814_consen 33 LKRLRELGLVDR-FRRRVGARGGSQPYVYYLTPAGARLLADLRGIR 77 (191)
T ss_pred HHHHhhCCcEEe-ecccccccCCCcceEEEECHHHHHHHHhccCCc
Confidence 456788888854 444 4578999999999998876654
No 10
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=87.62 E-value=0.2 Score=45.81 Aligned_cols=43 Identities=21% Similarity=0.312 Sum_probs=32.6
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHHhhCCCCCCccccc
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATL 46 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~eivPaTl 46 (134)
+.||.++|+|+-.- =..-+|.||+||.+||. -+||+..|=+.|
T Consensus 39 ~~~L~~kg~v~~~~-~~~~~~~LT~eG~~~l~--~G~PE~rl~~~l 81 (492)
T PLN02853 39 IKSLHGFRYVDAQD-IKRETWVLTEEGKKYAA--EGSPEVQLFAAV 81 (492)
T ss_pred HHHHHhCCCEEEEE-EEEEEEEECHHHHHHHH--cCCHHHHHHHHH
Confidence 35899999887553 35678899999999999 567776654444
No 11
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=87.59 E-value=0.32 Score=33.56 Aligned_cols=36 Identities=22% Similarity=0.413 Sum_probs=25.4
Q ss_pred CCcccccccce--eeecc--eeEEEechhhHHHHHHhhCC
Q 032763 2 QSFKSREYVRE--TFAWM--HYYWYLTNDGIEFLRTYLNL 37 (134)
Q Consensus 2 qSLkSrg~Vke--~FaWr--h~Yw~LTneGI~yLR~yLhL 37 (134)
+.|...|||+- .|.=+ -.||.||++|.+.+.+|+..
T Consensus 36 ~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~ 75 (80)
T PF13601_consen 36 KKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAA 75 (80)
T ss_dssp HHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHH
T ss_pred HHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHH
Confidence 45777888753 33333 67999999999999998753
No 12
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=86.59 E-value=0.35 Score=42.93 Aligned_cols=31 Identities=13% Similarity=0.265 Sum_probs=26.2
Q ss_pred CCcccccccceeeecceeEEEechhhHHHHHH
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 33 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~ 33 (134)
.+|.++|||...-. +..+|.||+||.+|+.+
T Consensus 42 ~~Le~kGlV~~~~~-~~~~i~LTeeG~~~~~~ 72 (489)
T PRK04172 42 EWLEEKGLVKVEER-VEEVYVLTEEGKKYAEE 72 (489)
T ss_pred HHHHhCCCEEEEee-eEEEEEECHHHHHHHHh
Confidence 57999999987644 57899999999999984
No 13
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=82.91 E-value=0.39 Score=33.33 Aligned_cols=29 Identities=17% Similarity=0.269 Sum_probs=21.8
Q ss_pred CCcccccccceeeecceeEEEechhhHHHHHH
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 33 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~ 33 (134)
+.|+.-|+|.. -. .-+|.||++|.++|.+
T Consensus 62 ~~L~~aGli~~-~~--rG~~~iT~~G~~~l~~ 90 (92)
T PF14338_consen 62 SYLKKAGLIER-PK--RGIWRITEKGRKALAE 90 (92)
T ss_pred HHHHHCCCccC-CC--CCceEECHhHHHHHhh
Confidence 35677788844 33 3489999999999986
No 14
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=81.59 E-value=0.58 Score=36.32 Aligned_cols=37 Identities=19% Similarity=0.495 Sum_probs=29.1
Q ss_pred CCcccccccceeeec---ceeEEEechhhHHHHHHhhCCCCC
Q 032763 2 QSFKSREYVRETFAW---MHYYWYLTNDGIEFLRTYLNLPSE 40 (134)
Q Consensus 2 qSLkSrg~Vke~FaW---rh~Yw~LTneGI~yLR~yLhLP~e 40 (134)
+.|...|||... | +-=||.||++|.++|.+.+.-|.+
T Consensus 85 ~RLE~~GlI~s~--~~~~~RK~Y~ITe~Gre~L~e~~~~~~~ 124 (135)
T PRK09416 85 HRLEQNRFIQSS--WDHEGAKYYQLTDKGNKMLRKAEKNATK 124 (135)
T ss_pred HHHHHCCCeEEe--ecCCCceEEEECHHHHHHHHHHHhCHHH
Confidence 457788999753 4 347899999999999999886543
No 15
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=81.33 E-value=0.5 Score=34.78 Aligned_cols=37 Identities=22% Similarity=0.272 Sum_probs=26.8
Q ss_pred CCcccccccceeeecceeEEEechhhH--------------HHHHHhhCCCCCCc
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGI--------------EFLRTYLNLPSEIV 42 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI--------------~yLR~yLhLP~eiv 42 (134)
+.|..+|||.-. ++..|.||++|. .|| +.|+++.+.|
T Consensus 44 ~~L~~~Gli~~~---~~~~i~LT~~G~~~a~~~~~~h~~~e~~l-~~l~~~~~~~ 94 (142)
T PRK03902 44 QKLDKDEYLIYE---KYRGLVLTPKGKKIGKRLVYRHELLEQFL-RIIGVDESKI 94 (142)
T ss_pred HHHHHCCCEEEe---cCceEEECHHHHHHHHHHHHHHHHHHHHH-HHhCcCHHHH
Confidence 457888999733 456799999994 466 5677776654
No 16
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=81.29 E-value=0.41 Score=30.19 Aligned_cols=27 Identities=15% Similarity=0.234 Sum_probs=20.3
Q ss_pred CCCccccccccee---eecceeEEEechhh
Q 032763 1 MQSFKSREYVRET---FAWMHYYWYLTNDG 27 (134)
Q Consensus 1 mqSLkSrg~Vke~---FaWrh~Yw~LTneG 27 (134)
|++|..+|||..+ ..=|..|+.||++|
T Consensus 39 i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 39 IKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 3578889999666 34577999999998
No 17
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=80.48 E-value=0.91 Score=29.64 Aligned_cols=34 Identities=18% Similarity=0.261 Sum_probs=25.5
Q ss_pred CCccccccccee---eecceeEEEechhhHHHHHHhh
Q 032763 2 QSFKSREYVRET---FAWMHYYWYLTNDGIEFLRTYL 35 (134)
Q Consensus 2 qSLkSrg~Vke~---FaWrh~Yw~LTneGI~yLR~yL 35 (134)
+.|.++|+|... ..=+..|+.||++|.+++....
T Consensus 46 ~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~ 82 (101)
T smart00347 46 DRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELL 82 (101)
T ss_pred HHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHH
Confidence 467888998643 3346789999999998887643
No 18
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=78.66 E-value=1 Score=31.78 Aligned_cols=34 Identities=15% Similarity=0.110 Sum_probs=27.4
Q ss_pred CCcccccccceee---ecceeEEEechhhHHHHHHhh
Q 032763 2 QSFKSREYVRETF---AWMHYYWYLTNDGIEFLRTYL 35 (134)
Q Consensus 2 qSLkSrg~Vke~F---aWrh~Yw~LTneGI~yLR~yL 35 (134)
+.|..+|||..+- .-|-.+++||++|.+.+.+..
T Consensus 64 ~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~ 100 (118)
T TIGR02337 64 ARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLS 100 (118)
T ss_pred HHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhh
Confidence 4678889988764 468899999999999987643
No 19
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=74.95 E-value=1.8 Score=31.42 Aligned_cols=42 Identities=14% Similarity=0.207 Sum_probs=30.3
Q ss_pred CCcccccccceeeecc-----eeEEEechhhHHHHHHhhCCCCCCcc
Q 032763 2 QSFKSREYVRETFAWM-----HYYWYLTNDGIEFLRTYLNLPSEIVP 43 (134)
Q Consensus 2 qSLkSrg~Vke~FaWr-----h~Yw~LTneGI~yLR~yLhLP~eivP 43 (134)
+.|.+.|||.....=+ =-||.||++|.++|.+.+.....++.
T Consensus 52 ~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~~~~~~ 98 (138)
T COG1695 52 KRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEWGALLS 98 (138)
T ss_pred HHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHHHHHHH
Confidence 4677888888654433 26899999999999988855444433
No 20
>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=73.62 E-value=2.6 Score=25.43 Aligned_cols=32 Identities=16% Similarity=0.225 Sum_probs=21.7
Q ss_pred CCcccccccceeeecceeEEEec--hhhHHHHHH
Q 032763 2 QSFKSREYVRETFAWMHYYWYLT--NDGIEFLRT 33 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LT--neGI~yLR~ 33 (134)
..|++.|+|...-.=+..||.|| .+.++.|++
T Consensus 42 ~~L~~~g~i~~~~~~~~~~~~~~~g~~~~~~~~~ 75 (78)
T cd00090 42 KKLEEAGLVESRREGRRVYYSLTDAERLLALLES 75 (78)
T ss_pred HHHHHCCCeEEEEeccEEEEEeCCchHHHHHHHH
Confidence 45777888775332288999999 566666554
No 21
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=73.46 E-value=0.94 Score=31.81 Aligned_cols=32 Identities=19% Similarity=0.236 Sum_probs=18.7
Q ss_pred CCcccccccceeeecc------eeEEEechhhHHHHHH
Q 032763 2 QSFKSREYVRETFAWM------HYYWYLTNDGIEFLRT 33 (134)
Q Consensus 2 qSLkSrg~Vke~FaWr------h~Yw~LTneGI~yLR~ 33 (134)
+.|+..|||+-..-++ .--=.+|-+||+||.+
T Consensus 32 ~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~E 69 (88)
T PF09639_consen 32 RMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEE 69 (88)
T ss_dssp HHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHH
T ss_pred HHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHH
Confidence 4577788886332222 2223478899999998
No 22
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=72.84 E-value=2.2 Score=32.89 Aligned_cols=41 Identities=12% Similarity=0.195 Sum_probs=28.4
Q ss_pred CCcccccccceee----e-cceeEEEechhhHHHHHHhhCCCCCCc
Q 032763 2 QSFKSREYVRETF----A-WMHYYWYLTNDGIEFLRTYLNLPSEIV 42 (134)
Q Consensus 2 qSLkSrg~Vke~F----a-Wrh~Yw~LTneGI~yLR~yLhLP~eiv 42 (134)
+.|...|+|.... + =+--||.||++|.++|.+.+.--.++.
T Consensus 65 ~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~~~~ 110 (138)
T TIGR02719 65 RKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFEHYQ 110 (138)
T ss_pred HHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHH
Confidence 4577888887521 1 114789999999999988776544443
No 23
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=72.83 E-value=2.1 Score=35.12 Aligned_cols=42 Identities=17% Similarity=0.218 Sum_probs=31.0
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHHhhCCCCCCc
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIV 42 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~eiv 42 (134)
++.|..+|||+-+-.=+-.+|+||++|.+.|.+-+.--.+|+
T Consensus 42 Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~~~if 83 (217)
T PRK14165 42 LKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYADYSRIF 83 (217)
T ss_pred HHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHHHHHHh
Confidence 356888999977665688999999999998766544333343
No 24
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=72.21 E-value=2.6 Score=30.53 Aligned_cols=30 Identities=23% Similarity=0.188 Sum_probs=21.9
Q ss_pred CCccccccc-ceeeecceeEEEechhhHHHH
Q 032763 2 QSFKSREYV-RETFAWMHYYWYLTNDGIEFL 31 (134)
Q Consensus 2 qSLkSrg~V-ke~FaWrh~Yw~LTneGI~yL 31 (134)
.||.+-|+| .|.-.=..-||.||++|+++.
T Consensus 57 ~SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~ 87 (90)
T PF07381_consen 57 DSLVGLGLVEEEEEKGGFKYYRLTEKGKRIA 87 (90)
T ss_pred hhHHHcCCeeEeeecCCeeEEEeChhhhhHH
Confidence 489999999 333322444999999999763
No 25
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=68.59 E-value=1.3 Score=31.89 Aligned_cols=25 Identities=20% Similarity=0.256 Sum_probs=19.6
Q ss_pred CCCcccccccceeeecceeEEEechhhHHH
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEF 30 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~y 30 (134)
++.|..||++...-+= |||+||++-
T Consensus 40 ~~RLheKGLI~~pdGg-----yLT~~G~~~ 64 (77)
T TIGR02647 40 AARLHEKGLTTQPDGG-----YLTSLGLEA 64 (77)
T ss_pred HHHHHHcCCccCCCCC-----EecHHHHHH
Confidence 3567889998877664 999999953
No 26
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=68.48 E-value=3.3 Score=24.47 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=23.3
Q ss_pred CCcccccccceeeecceeEEEech-hhHHHHHH
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTN-DGIEFLRT 33 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTn-eGI~yLR~ 33 (134)
+.|.++|+|...-.=+..||.||+ .+.+.+.+
T Consensus 32 ~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 32 KKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred HHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 457788998866656788999999 55565543
No 27
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=62.53 E-value=4.9 Score=28.27 Aligned_cols=35 Identities=14% Similarity=0.273 Sum_probs=25.1
Q ss_pred CCcccccccceee-----ecceeEEEechhhHHHHHHhhC
Q 032763 2 QSFKSREYVRETF-----AWMHYYWYLTNDGIEFLRTYLN 36 (134)
Q Consensus 2 qSLkSrg~Vke~F-----aWrh~Yw~LTneGI~yLR~yLh 36 (134)
..|..+|+|.... .=+--||.||++|.++|.+.+.
T Consensus 47 ~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~ 86 (100)
T TIGR03433 47 HRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETE 86 (100)
T ss_pred HHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHH
Confidence 4577888887642 1123799999999999987543
No 28
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=60.27 E-value=5.5 Score=27.95 Aligned_cols=21 Identities=33% Similarity=1.023 Sum_probs=9.3
Q ss_pred eeecceeEEEechhhH-HHHHH
Q 032763 13 TFAWMHYYWYLTNDGI-EFLRT 33 (134)
Q Consensus 13 ~FaWrh~Yw~LTneGI-~yLR~ 33 (134)
+-+|-.|||+++.+.| +.|+.
T Consensus 66 ~~~~~~~yw~i~~~~~~~~ik~ 87 (105)
T PF02002_consen 66 ERGWTRYYWYIDYDQIIDVIKY 87 (105)
T ss_dssp -----EEEEE-THHHH------
T ss_pred CCcEEEEEEEEcHHHHHHHHHH
Confidence 5689999999999887 44443
No 29
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=58.78 E-value=6.9 Score=29.18 Aligned_cols=34 Identities=3% Similarity=-0.047 Sum_probs=28.1
Q ss_pred CCcccccccceeeecceeEEEechhhHHHHHHhh
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 35 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yL 35 (134)
+-|+.-|+|...--.|+.||.|+++..++|...+
T Consensus 52 ~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~ 85 (117)
T PRK10141 52 ALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKII 85 (117)
T ss_pred HHHHHCCceEEEEEcCEEEEEECchHHHHHHHHH
Confidence 4578889999999999999999988777777633
No 30
>PF01043 SecA_PP_bind: SecA preprotein cross-linking domain; InterPro: IPR011130 The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain [].; GO: 0017038 protein import, 0016020 membrane; PDB: 3DIN_B 3JUX_A 3IQY_A 2IBM_A 3DL8_A 3JV2_B 3IQM_A 1TF2_A 1TF5_A 1M74_A ....
Probab=57.56 E-value=11 Score=28.01 Aligned_cols=22 Identities=27% Similarity=0.357 Sum_probs=18.2
Q ss_pred EEechhhHHHHHHhhCCCCCCc
Q 032763 21 WYLTNDGIEFLRTYLNLPSEIV 42 (134)
Q Consensus 21 w~LTneGI~yLR~yLhLP~eiv 42 (134)
..||++||+.+.++|+++.++.
T Consensus 33 v~LT~~G~~~~e~~~~~~~~l~ 54 (113)
T PF01043_consen 33 VELTEKGIEKAEKLLGISDNLY 54 (113)
T ss_dssp EEESHHHHHHHHHHHTSSSSTT
T ss_pred eeEhHHHHHHHHHHhhhccccc
Confidence 3799999999999999854443
No 31
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=54.77 E-value=6.2 Score=27.06 Aligned_cols=30 Identities=20% Similarity=0.188 Sum_probs=19.1
Q ss_pred Ccccccccceeee---cceeEEEechhhHHHHH
Q 032763 3 SFKSREYVRETFA---WMHYYWYLTNDGIEFLR 32 (134)
Q Consensus 3 SLkSrg~Vke~Fa---Wrh~Yw~LTneGI~yLR 32 (134)
.|...|+|..+.. =.+..|.||++|.+.+.
T Consensus 42 ~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~ 74 (90)
T PF01638_consen 42 ELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP 74 (90)
T ss_dssp HHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred HHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence 4556677654321 13678999999998764
No 32
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=54.44 E-value=6.3 Score=33.89 Aligned_cols=32 Identities=16% Similarity=0.254 Sum_probs=23.9
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHHhh
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 35 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yL 35 (134)
|++|.+-|||++. ---||-+|.||.++|-+.|
T Consensus 46 iK~Lv~eG~i~~~---gR~~Y~iTkkG~e~l~~~~ 77 (260)
T COG1497 46 IKELVKEGLIEKE---GRGEYEITKKGAEWLLEQL 77 (260)
T ss_pred HHHHHhccceeec---CCeeEEEehhHHHHHHHHH
Confidence 3567888888882 2357899999999986544
No 33
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=51.06 E-value=11 Score=31.55 Aligned_cols=31 Identities=10% Similarity=0.203 Sum_probs=22.5
Q ss_pred CcccccccceeeecceeEEEechhhHHHHHH
Q 032763 3 SFKSREYVRETFAWMHYYWYLTNDGIEFLRT 33 (134)
Q Consensus 3 SLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~ 33 (134)
-|+++|+|...=.=+--||.||++|.+.|.+
T Consensus 43 RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~ 73 (280)
T TIGR02277 43 RLVAQGWLQSERKGRRSFYSLTDKGRRRFAA 73 (280)
T ss_pred HHHHCCCEEeeecCCCCEEEECHHHHHHHHH
Confidence 4778888876411123677999999999986
No 34
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=50.43 E-value=9.9 Score=27.62 Aligned_cols=17 Identities=41% Similarity=0.669 Sum_probs=15.7
Q ss_pred ceeEEEechhhHHHHHH
Q 032763 17 MHYYWYLTNDGIEFLRT 33 (134)
Q Consensus 17 rh~Yw~LTneGI~yLR~ 33 (134)
-|-||-||.+|=.+||+
T Consensus 75 hHtYY~LTr~G~~llR~ 91 (92)
T PF10007_consen 75 HHTYYRLTREGELLLRE 91 (92)
T ss_pred CCceeeecHhHHHHHhc
Confidence 58999999999999985
No 35
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=49.01 E-value=10 Score=25.93 Aligned_cols=24 Identities=21% Similarity=0.326 Sum_probs=19.5
Q ss_pred cccccccceeeecceeEEEechhh
Q 032763 4 FKSREYVRETFAWMHYYWYLTNDG 27 (134)
Q Consensus 4 LkSrg~Vke~FaWrh~Yw~LTneG 27 (134)
|+++|++...=.=|.-||.||++|
T Consensus 47 l~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 47 LVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp HHHTTSEEEECCCTEEEEEE-HHH
T ss_pred HHHcCceeeeecCccceEeeCCCC
Confidence 677888888877889999999986
No 36
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=47.98 E-value=9.6 Score=25.29 Aligned_cols=35 Identities=17% Similarity=0.208 Sum_probs=28.0
Q ss_pred CCcccccccceeee---cceeEEEechhhHHHHHHhhC
Q 032763 2 QSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTYLN 36 (134)
Q Consensus 2 qSLkSrg~Vke~Fa---Wrh~Yw~LTneGI~yLR~yLh 36 (134)
+.|..+|||+..-. =|-.+..||++|-+.+.+..-
T Consensus 58 ~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~ 95 (126)
T COG1846 58 KRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95 (126)
T ss_pred HHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence 46778888887666 578999999999999886443
No 37
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=47.76 E-value=8.6 Score=30.38 Aligned_cols=25 Identities=16% Similarity=0.389 Sum_probs=19.1
Q ss_pred eeecceeEEEechhhH-HHHHHhhCC
Q 032763 13 TFAWMHYYWYLTNDGI-EFLRTYLNL 37 (134)
Q Consensus 13 ~FaWrh~Yw~LTneGI-~yLR~yLhL 37 (134)
.-.|=.|||+||.+=| +.|+..+|-
T Consensus 75 ~~Gr~~y~w~l~~~~i~d~ik~~~~~ 100 (178)
T PRK06266 75 ETNWYTYTWKPELEKLPEIIKKKKME 100 (178)
T ss_pred CCCcEEEEEEeCHHHHHHHHHHHHHH
Confidence 4689999999998877 666666543
No 38
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=47.15 E-value=24 Score=24.66 Aligned_cols=18 Identities=22% Similarity=0.313 Sum_probs=15.0
Q ss_pred eEEEechhhHHHHHHhhC
Q 032763 19 YYWYLTNDGIEFLRTYLN 36 (134)
Q Consensus 19 ~Yw~LTneGI~yLR~yLh 36 (134)
..=++|.+|++||.+.|+
T Consensus 89 ~~~~iT~kG~~~i~~~l~ 106 (111)
T PF03374_consen 89 SQTRITPKGLEWIAKRLA 106 (111)
T ss_pred EEEEEehhHHHHHHHHHH
Confidence 456789999999998774
No 39
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=46.84 E-value=6.8 Score=30.51 Aligned_cols=31 Identities=13% Similarity=0.293 Sum_probs=22.9
Q ss_pred CCCcccccccceee-----ecceeEEEechhhHHHH
Q 032763 1 MQSFKSREYVRETF-----AWMHYYWYLTNDGIEFL 31 (134)
Q Consensus 1 mqSLkSrg~Vke~F-----aWrh~Yw~LTneGI~yL 31 (134)
|+.|.++|+|...- .=+.++|+||++|.+.+
T Consensus 36 L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~ 71 (203)
T TIGR02702 36 LKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF 71 (203)
T ss_pred HHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence 35688899997652 23678899999998644
No 40
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=45.64 E-value=11 Score=26.59 Aligned_cols=33 Identities=3% Similarity=0.085 Sum_probs=26.4
Q ss_pred CCcccccccceeeec---ceeEEEechhhHHHHHHh
Q 032763 2 QSFKSREYVRETFAW---MHYYWYLTNDGIEFLRTY 34 (134)
Q Consensus 2 qSLkSrg~Vke~FaW---rh~Yw~LTneGI~yLR~y 34 (134)
..|..+|||+..=+. |-.|-+||++|.+.+-+-
T Consensus 65 ~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~ 100 (109)
T TIGR01889 65 KKLSKKGYLSKERSEDDERKVIISINKEQRSKIESL 100 (109)
T ss_pred HHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHH
Confidence 357788998877666 789999999999887653
No 41
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=45.38 E-value=6.8 Score=26.97 Aligned_cols=34 Identities=24% Similarity=0.274 Sum_probs=26.9
Q ss_pred CCcccccccceeee-cceeEEEechhhHHHHHHhh
Q 032763 2 QSFKSREYVRETFA-WMHYYWYLTNDGIEFLRTYL 35 (134)
Q Consensus 2 qSLkSrg~Vke~Fa-Wrh~Yw~LTneGI~yLR~yL 35 (134)
+.|...||+.+.+. |.+-|-.||++|-++|+.-.
T Consensus 64 ~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~l~g~~ 98 (106)
T PF09382_consen 64 RQLILEGYLSEDNGGFAYPYLKLTPKGKELLNGKQ 98 (106)
T ss_dssp HHHHHTTSEEEEECCCCTEEEEE-GGGHHHHCTTS
T ss_pred HHHHHcCCceecCCcccccEEEECHHHHHHHCCCc
Confidence 45778899977765 89999999999999998643
No 42
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=44.90 E-value=9.4 Score=31.81 Aligned_cols=36 Identities=17% Similarity=0.277 Sum_probs=29.7
Q ss_pred CCCcccccccc-eeeecceeEEEechhhHHHHHHhhC
Q 032763 1 MQSFKSREYVR-ETFAWMHYYWYLTNDGIEFLRTYLN 36 (134)
Q Consensus 1 mqSLkSrg~Vk-e~FaWrh~Yw~LTneGI~yLR~yLh 36 (134)
+|||..-|+|+ |..+=..+||+.-+++|+-+-+-+.
T Consensus 49 lQqlVDDgvV~~EK~GtsN~YWsF~s~~~qk~~~~~~ 85 (209)
T COG5124 49 LQQLVDDGVVSVEKCGTSNIYWSFKSQTLQKLYDSSE 85 (209)
T ss_pred HHHHhhcCceeeeeeccceeEEecchHHHHHHHHHHH
Confidence 57888989986 7888899999999999987655443
No 43
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=44.39 E-value=10 Score=29.18 Aligned_cols=35 Identities=17% Similarity=0.482 Sum_probs=23.7
Q ss_pred Cccccccc---c---eeeecceeEEEechhhH-HHHHHhhCC
Q 032763 3 SFKSREYV---R---ETFAWMHYYWYLTNDGI-EFLRTYLNL 37 (134)
Q Consensus 3 SLkSrg~V---k---e~FaWrh~Yw~LTneGI-~yLR~yLhL 37 (134)
.|...|+| + +.=.|.-|||+++-+=| +-|+..+|-
T Consensus 51 ~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~~ 92 (158)
T TIGR00373 51 ALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRKLEE 92 (158)
T ss_pred HHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHHHHH
Confidence 45556666 2 23489999999987665 777766653
No 44
>cd03071 PDI_b'_NRX PDIb' family, NRX subgroup, redox inactive TRX-like domain b'; composed of vertebrate nucleoredoxins (NRX). NRX is a 400-amino acid nuclear protein with one redox active TRX domain followed by one redox inactive TRX-like domain homologous to the b' domain of PDI. In vitro studies show that NRX has thiol oxidoreductase activity and that it may be involved in the redox regulation of transcription, in a manner different from that of TRX or glutaredoxin. NRX enhances the activation of NF-kB by TNFalpha, as well as PMA-1 induced AP-1 and FK-induced CREB activation. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. The mouse NRX gene is implicated in streptozotocin-induced diabetes. Similar to PDI, the b' domain of NRX is likely involved in substrate recognition.
Probab=43.12 E-value=23 Score=27.24 Aligned_cols=28 Identities=29% Similarity=0.335 Sum_probs=23.1
Q ss_pred eecceeEEEechhhHHHHHHhhCCCCCC
Q 032763 14 FAWMHYYWYLTNDGIEFLRTYLNLPSEI 41 (134)
Q Consensus 14 FaWrh~Yw~LTneGI~yLR~yLhLP~ei 41 (134)
=+=+.|++.+.+|=.+.||+|++||.+.
T Consensus 54 dap~~f~~a~ede~tdsLRDf~nL~d~~ 81 (116)
T cd03071 54 EAPLLFFVAGEDDMTDSLRDYTNLPEAA 81 (116)
T ss_pred CcceeeeeeccchHHHHHHHhcCCCccC
Confidence 3446788889999999999999999653
No 45
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=42.95 E-value=21 Score=26.89 Aligned_cols=23 Identities=26% Similarity=0.928 Sum_probs=17.8
Q ss_pred ecceeEEEec-hhhHHHHHHhhCC
Q 032763 15 AWMHYYWYLT-NDGIEFLRTYLNL 37 (134)
Q Consensus 15 aWrh~Yw~LT-neGI~yLR~yLhL 37 (134)
+|-.|||+|+ +.=|..|+..++.
T Consensus 59 ~~~~~yw~i~y~~~~~vik~r~~~ 82 (147)
T smart00531 59 TWYRYYWYINYDTLLDVVKYKLDK 82 (147)
T ss_pred eEEEEEEEecHHHHHHHHHHHHHH
Confidence 4999999999 5566777776665
No 46
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=40.71 E-value=14 Score=26.88 Aligned_cols=32 Identities=13% Similarity=0.072 Sum_probs=25.4
Q ss_pred CCcccccccceee---ecceeEEEechhhHHHHHH
Q 032763 2 QSFKSREYVRETF---AWMHYYWYLTNDGIEFLRT 33 (134)
Q Consensus 2 qSLkSrg~Vke~F---aWrh~Yw~LTneGI~yLR~ 33 (134)
+.|..+|||...- .=|-.+.+||++|.+.+.+
T Consensus 76 ~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 76 DRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred HHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 4577889988654 4688999999999988765
No 47
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=39.48 E-value=12 Score=24.95 Aligned_cols=31 Identities=19% Similarity=0.121 Sum_probs=23.3
Q ss_pred CCcccccccceeeecceeEEEechhhHHHHHHhh
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 35 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yL 35 (134)
+.|.++|||...=+ -.++||++|.+.+...+
T Consensus 21 ~~L~~~glI~r~~~---~~~~lT~~g~~~~~~~~ 51 (96)
T smart00529 21 KKLEKDGLVEYEPY---RGITLTEKGRRLARRLL 51 (96)
T ss_pred HHHHHCCCEEEcCC---CceEechhHHHHHHHHH
Confidence 46888899877543 37999999998776554
No 48
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=36.82 E-value=18 Score=26.06 Aligned_cols=35 Identities=6% Similarity=0.018 Sum_probs=27.0
Q ss_pred CCcccccccceeee---cceeEEEechhhHHHHHHhhC
Q 032763 2 QSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTYLN 36 (134)
Q Consensus 2 qSLkSrg~Vke~Fa---Wrh~Yw~LTneGI~yLR~yLh 36 (134)
..|..+|||...-+ =|..+-+||++|.+.+.+...
T Consensus 68 ~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~ 105 (144)
T PRK03573 68 DQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVEA 105 (144)
T ss_pred HHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHHH
Confidence 35778899887643 478899999999998876543
No 49
>KOG4082 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.00 E-value=7.8 Score=32.91 Aligned_cols=29 Identities=28% Similarity=0.714 Sum_probs=23.9
Q ss_pred eecceeEEEechhhH--HHHHHhhCCCCCCc
Q 032763 14 FAWMHYYWYLTNDGI--EFLRTYLNLPSEIV 42 (134)
Q Consensus 14 FaWrh~Yw~LTneGI--~yLR~yLhLP~eiv 42 (134)
.+|=--+|+|...|+ .-|-+|+|||..||
T Consensus 132 taWF~afYllsKSGVDViaLLewiHlpdaIi 162 (268)
T KOG4082|consen 132 TAWFGAFYLLSKSGVDVIALLEWIHLPDAII 162 (268)
T ss_pred HHHHHHhheeeccCCcHHHHHHHHcCcHHHH
Confidence 467777888999998 45789999999986
No 50
>PF14756 Pdase_C33_assoc: Peptidase_C33-associated domain
Probab=34.37 E-value=26 Score=27.67 Aligned_cols=24 Identities=29% Similarity=0.562 Sum_probs=20.2
Q ss_pred hhHHHHHHhhCCCCCCcccccccc
Q 032763 26 DGIEFLRTYLNLPSEIVPATLKKS 49 (134)
Q Consensus 26 eGI~yLR~yLhLP~eivPaTlkk~ 49 (134)
.=+.-|-+..|||+.++|+.|..-
T Consensus 14 acldrla~vmhlps~~ipaalaem 37 (147)
T PF14756_consen 14 ACLDRLAEVMHLPSSVIPAALAEM 37 (147)
T ss_pred HHHHHHHHHhcCccchhHHHHHHh
Confidence 346778999999999999999763
No 51
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=33.08 E-value=23 Score=31.65 Aligned_cols=37 Identities=27% Similarity=0.357 Sum_probs=29.5
Q ss_pred CCcccccccceeeecceeEEEechhhHHHHHHhhCCCC
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPS 39 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~ 39 (134)
+.|+.|++|++ -.+..++..||++|.+++.+.+.+-.
T Consensus 159 ~~LkkRkL~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 195 (489)
T PRK04172 159 KELKKRKLVEE-KERTERSVELTDAGLELLKEGIELKE 195 (489)
T ss_pred HHHHhcCCeEE-EEEEEEEEEEccchhhhhhccccccc
Confidence 56889998877 67888999999999999977544433
No 52
>PRK10870 transcriptional repressor MprA; Provisional
Probab=32.75 E-value=21 Score=27.44 Aligned_cols=34 Identities=26% Similarity=0.379 Sum_probs=26.0
Q ss_pred CCcccccccceeee---cceeEEEechhhHHHHHHhh
Q 032763 2 QSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTYL 35 (134)
Q Consensus 2 qSLkSrg~Vke~Fa---Wrh~Yw~LTneGI~yLR~yL 35 (134)
+.|..+|||...-+ =|-.+-+||++|++.+.+..
T Consensus 93 ~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~ 129 (176)
T PRK10870 93 DELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVL 129 (176)
T ss_pred HHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 45788899876533 35688899999999988643
No 53
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=31.89 E-value=15 Score=28.39 Aligned_cols=38 Identities=24% Similarity=0.099 Sum_probs=28.6
Q ss_pred CCcccccccceeeecceeEEEechhhH--------------HHHHHhhCCCCCCc
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGI--------------EFLRTYLNLPSEIV 42 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI--------------~yLR~yLhLP~eiv 42 (134)
+-|.+.|||+-. .+....||++|- .||.+.|.++.+++
T Consensus 46 ~rL~~~GlV~~~---~y~gi~LT~~G~~~a~~~~r~hrlle~fL~~~lg~~~~~~ 97 (154)
T COG1321 46 KRLERLGLVEYE---PYGGVTLTEKGREKAKELLRKHRLLERFLVDVLGLDWEEA 97 (154)
T ss_pred HHHHHCCCeEEe---cCCCeEEChhhHHHHHHHHHHHHHHHHHHHHHhCCCHHHH
Confidence 447788888652 345679999997 57888899997765
No 54
>KOG2784 consensus Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=30.55 E-value=29 Score=32.00 Aligned_cols=32 Identities=19% Similarity=0.205 Sum_probs=24.1
Q ss_pred CCCcccccccceeeecceeEEEechhhHHHHHH
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 33 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~ 33 (134)
++||.+.+++.- --=-+.-|-||+||.+++++
T Consensus 38 l~SL~a~~~i~~-~~~~~~~~~LT~EG~~i~~e 69 (483)
T KOG2784|consen 38 LKSLQAGGVIEV-KDVETKTYELTAEGEEIARE 69 (483)
T ss_pred HHHHhhcCceEE-EeeeeEEEeeChhHHHHHhc
Confidence 368888776543 23357789999999999986
No 55
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=28.88 E-value=20 Score=28.53 Aligned_cols=27 Identities=30% Similarity=0.550 Sum_probs=21.8
Q ss_pred cceeeecceeEEEechhhHHHHHHhhCCCCCCc
Q 032763 10 VRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIV 42 (134)
Q Consensus 10 Vke~FaWrh~Yw~LTneGI~yLR~yLhLP~eiv 42 (134)
+.++|. +|+++.|+|+-++||+|..-|
T Consensus 34 aQ~~~G------~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 34 AQEQFG------WLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred HHHHhC------CCCHHHHHHHHHHhCCCHHHh
Confidence 456666 599999999999999996543
No 56
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=26.74 E-value=18 Score=30.13 Aligned_cols=36 Identities=25% Similarity=0.475 Sum_probs=30.9
Q ss_pred CCCccccccc-ceeeecceeEEEechhhHHHHHHhhC
Q 032763 1 MQSFKSREYV-RETFAWMHYYWYLTNDGIEFLRTYLN 36 (134)
Q Consensus 1 mqSLkSrg~V-ke~FaWrh~Yw~LTneGI~yLR~yLh 36 (134)
||||..-|+| +|...=..|||..-.|+|.-++.+|.
T Consensus 48 LQsLvDD~lV~~eKIgtSnyywsfps~a~~~~ks~~q 84 (203)
T KOG3433|consen 48 LQSLVDDGLVIKEKIGTSNYYWSFPSEAICDRKSVLQ 84 (203)
T ss_pred HHHHhccchHHHHHhcccccccccchHHHHHHHHHHH
Confidence 5889988886 67888889999999999988887764
No 57
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=26.65 E-value=36 Score=27.11 Aligned_cols=34 Identities=24% Similarity=0.293 Sum_probs=27.0
Q ss_pred CCcccccccceee---ecceeEEEechhhHHHHHHhh
Q 032763 2 QSFKSREYVRETF---AWMHYYWYLTNDGIEFLRTYL 35 (134)
Q Consensus 2 qSLkSrg~Vke~F---aWrh~Yw~LTneGI~yLR~yL 35 (134)
+.|..+|||.-.- .=|..+=+||++|.+.+.+..
T Consensus 81 ~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~ 117 (185)
T PRK13777 81 KKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETM 117 (185)
T ss_pred HHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 4578899998553 458899999999999887643
No 58
>PHA00422 hypothetical protein
Probab=25.04 E-value=52 Score=23.33 Aligned_cols=17 Identities=29% Similarity=0.659 Sum_probs=14.7
Q ss_pred eeEEEechhhHHHHHHh
Q 032763 18 HYYWYLTNDGIEFLRTY 34 (134)
Q Consensus 18 h~Yw~LTneGI~yLR~y 34 (134)
-.-|-+|-.|+.||+.+
T Consensus 49 ~g~W~vT~~G~~fL~~~ 65 (69)
T PHA00422 49 AGAWEITASGVRFLKQM 65 (69)
T ss_pred cceEEEeccHHHHHHHh
Confidence 35799999999999975
No 59
>KOG2175 consensus Protein predicted to be involved in carbohydrate metabolism [Carbohydrate transport and metabolism]
Probab=24.55 E-value=22 Score=32.78 Aligned_cols=25 Identities=28% Similarity=0.452 Sum_probs=21.5
Q ss_pred eecceeEEEechhhH-HHHHHhhCCC
Q 032763 14 FAWMHYYWYLTNDGI-EFLRTYLNLP 38 (134)
Q Consensus 14 FaWrh~Yw~LTneGI-~yLR~yLhLP 38 (134)
..|.-+||+|+++|| ..|-.+++.|
T Consensus 200 ~~~~~~fkTlv~~~i~~~le~~~~~~ 225 (458)
T KOG2175|consen 200 QSRDAFFKTLVNKGILDALEYVLKMP 225 (458)
T ss_pred chhhHHHHHHHHhhhHHHHHHHhcCC
Confidence 467789999999999 7777788888
No 60
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=24.51 E-value=39 Score=25.91 Aligned_cols=16 Identities=38% Similarity=0.860 Sum_probs=10.1
Q ss_pred chhhH-HHHHHhhCCCCC
Q 032763 24 TNDGI-EFLRTYLNLPSE 40 (134)
Q Consensus 24 TneGI-~yLR~yLhLP~e 40 (134)
|.+|| .||.+ |+.|+.
T Consensus 49 TAKGi~KyL~e-lGvPas 65 (119)
T PF08986_consen 49 TAKGIFKYLKE-LGVPAS 65 (119)
T ss_dssp HHHHHHHHHHH-CT----
T ss_pred HHHHHHHHHHH-cCCCCC
Confidence 67899 89987 887743
No 61
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=24.42 E-value=95 Score=31.92 Aligned_cols=10 Identities=70% Similarity=1.395 Sum_probs=6.6
Q ss_pred CCCccCCCCC
Q 032763 114 RPGFGRGGGG 123 (134)
Q Consensus 114 rgGfGRGr~~ 123 (134)
+||||||+++
T Consensus 1253 sGGfgrgggr 1262 (1282)
T KOG0921|consen 1253 SGGFGRGGGR 1262 (1282)
T ss_pred CCCcCCCCCC
Confidence 6777776553
No 62
>PF13516 LRR_6: Leucine Rich repeat; PDB: 3RGZ_A 3RJ0_A 3RIZ_A 3RGX_A 1DFJ_I 2BNH_A 3VQ1_A 3VQ2_A 2Z64_A 2OMX_A ....
Probab=24.29 E-value=50 Score=17.23 Aligned_cols=12 Identities=25% Similarity=0.448 Sum_probs=9.6
Q ss_pred EechhhHHHHHH
Q 032763 22 YLTNDGIEFLRT 33 (134)
Q Consensus 22 ~LTneGI~yLR~ 33 (134)
-||++|+++|-+
T Consensus 13 ~i~~~g~~~l~~ 24 (24)
T PF13516_consen 13 QITDEGASALAN 24 (24)
T ss_dssp BEHHHHHHHHHH
T ss_pred cCCHHHHHHhCC
Confidence 389999999853
No 63
>COG3057 SeqA Negative regulator of replication initiationR [DNA replication, recombination, and repair]
Probab=23.97 E-value=38 Score=27.68 Aligned_cols=24 Identities=33% Similarity=0.801 Sum_probs=17.3
Q ss_pred eEEEechhh-------HHHHHHhhCCCCCCc
Q 032763 19 YYWYLTNDG-------IEFLRTYLNLPSEIV 42 (134)
Q Consensus 19 ~Yw~LTneG-------I~yLR~yLhLP~eiv 42 (134)
=||.+||-. ||-+-.-.++|+|++
T Consensus 144 PyWVITNtNtgRK~~M~e~~MqsM~fP~~li 174 (181)
T COG3057 144 PYWVITNTNTGRKCSMIEHIMQSMQFPAELI 174 (181)
T ss_pred CeEEEecCCchhHHHHHHHHHHHccCCHHHH
Confidence 499999854 566666788887664
No 64
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=23.17 E-value=30 Score=22.16 Aligned_cols=23 Identities=13% Similarity=0.202 Sum_probs=18.0
Q ss_pred CCCcccccccceeeecceeEEEe
Q 032763 1 MQSFKSREYVRETFAWMHYYWYL 23 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~L 23 (134)
|++|..+|+|+..-.-...|+..
T Consensus 43 L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 43 LKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHCCCEEEEcCceEEEEEe
Confidence 35789999999988877777654
No 65
>PHA00738 putative HTH transcription regulator
Probab=22.58 E-value=36 Score=25.74 Aligned_cols=30 Identities=10% Similarity=0.160 Sum_probs=25.0
Q ss_pred CCCcccccccceeeecceeEEEechhhHHH
Q 032763 1 MQSFKSREYVRETFAWMHYYWYLTNDGIEF 30 (134)
Q Consensus 1 mqSLkSrg~Vke~FaWrh~Yw~LTneGI~y 30 (134)
|+-|+.-|+|...--=||.||.|+++=-+|
T Consensus 47 LKvLreAGLV~srK~Gr~vyY~Ln~~~~~~ 76 (108)
T PHA00738 47 LKILNEQGYIELYKEGRTLYAKIRENSKEI 76 (108)
T ss_pred HHHHHHCCceEEEEECCEEEEEECCCccHH
Confidence 345888999999999999999999876554
No 66
>COG1836 Predicted membrane protein [Function unknown]
Probab=22.52 E-value=49 Score=28.36 Aligned_cols=15 Identities=60% Similarity=1.096 Sum_probs=12.8
Q ss_pred EEechhhHHHHHHhh
Q 032763 21 WYLTNDGIEFLRTYL 35 (134)
Q Consensus 21 w~LTneGI~yLR~yL 35 (134)
|+||||++++|-..+
T Consensus 220 g~LtN~~VNflaT~~ 234 (247)
T COG1836 220 GYLTNEGVNFLATFL 234 (247)
T ss_pred eeecccchhHHHHHH
Confidence 589999999998765
No 67
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=21.70 E-value=38 Score=22.21 Aligned_cols=33 Identities=18% Similarity=0.282 Sum_probs=24.1
Q ss_pred CCcccccccceeeecceeEEEechhhHHHHHHhhC
Q 032763 2 QSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLN 36 (134)
Q Consensus 2 qSLkSrg~Vke~FaWrh~Yw~LTneGI~yLR~yLh 36 (134)
+.|.+.|||... +..-.|.|+++.+++-..++.
T Consensus 42 ~~L~~~g~l~~~--~~~~~y~l~~~~~~~~~~~~~ 74 (91)
T smart00346 42 NTLQELGYVEQD--GQNGRYRLGPKVLELGQSYLS 74 (91)
T ss_pred HHHHHCCCeeec--CCCCceeecHHHHHHHHHHHh
Confidence 467888998764 334568999999888777653
No 68
>PF08109 Antimicrobial14: Lactocin 705 family; InterPro: IPR012517 This family consists of lactocin 705 which is a bacteriocin produced by Lactobacillus casei CRL 705. Lactocin 705 is a class IIb bacteriocin, whose activity depends upon the complementation of two peptides (705-alpha and 705-beta) of 33 amino acid residues each. Lactocin 705 is active against several Gram-positive bacteria, including food-borne pathogens and is a good candidate to be used for biopreservation of fermented meats [].
Probab=20.76 E-value=45 Score=20.17 Aligned_cols=12 Identities=50% Similarity=0.982 Sum_probs=9.7
Q ss_pred hhH-HHHHHhhCC
Q 032763 26 DGI-EFLRTYLNL 37 (134)
Q Consensus 26 eGI-~yLR~yLhL 37 (134)
.|| .||..|||=
T Consensus 7 qgipdflkgylhg 19 (31)
T PF08109_consen 7 QGIPDFLKGYLHG 19 (31)
T ss_pred cccHHHHHHHHhh
Confidence 467 899999985
Done!