Query 029742
Match_columns 188
No_of_seqs 169 out of 233
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 02:57:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029742.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029742hhsearch_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 1.6E-73 3.4E-78 461.1 10.8 146 1-159 1-148 (150)
2 PTZ00034 40S ribosomal protein 100.0 1.3E-62 2.9E-67 389.2 12.1 100 1-100 2-101 (124)
3 PF03501 S10_plectin: Plectin/ 100.0 7.2E-62 1.6E-66 370.5 7.4 94 3-96 1-94 (95)
4 COG5045 Ribosomal protein S10E 100.0 2.8E-48 6.1E-53 298.1 7.3 102 1-102 1-102 (105)
5 cd00090 HTH_ARSR Arsenical Res 93.5 0.091 2E-06 33.9 3.0 69 4-78 5-75 (78)
6 PF03551 PadR: Transcriptional 93.0 0.16 3.5E-06 35.5 3.8 44 35-78 27-75 (75)
7 PTZ00326 phenylalanyl-tRNA syn 92.6 0.085 1.8E-06 50.6 2.6 53 35-90 31-83 (494)
8 PLN02853 Probable phenylalanyl 92.5 0.086 1.9E-06 50.6 2.6 53 36-91 29-81 (492)
9 PF14947 HTH_45: Winged helix- 92.5 0.11 2.4E-06 37.2 2.5 40 36-79 30-69 (77)
10 PRK04172 pheS phenylalanyl-tRN 92.2 0.14 3.1E-06 47.9 3.5 67 6-78 6-72 (489)
11 PF13463 HTH_27: Winged helix 91.5 0.14 3E-06 34.2 1.9 37 36-72 29-68 (68)
12 PRK10141 DNA-binding transcrip 91.3 0.15 3.3E-06 40.1 2.3 71 3-79 13-84 (117)
13 PF13601 HTH_34: Winged helix 90.5 0.27 5.9E-06 35.8 2.9 69 8-81 2-74 (80)
14 PRK03902 manganese transport t 90.2 0.22 4.7E-06 38.7 2.3 71 8-87 10-94 (142)
15 smart00347 HTH_MARR helix_turn 89.5 0.4 8.7E-06 33.1 2.9 69 6-79 10-81 (101)
16 COG3432 Predicted transcriptio 87.8 0.45 9.7E-06 36.9 2.4 39 42-80 48-86 (95)
17 PRK05638 threonine synthase; V 87.7 0.45 9.7E-06 43.7 2.8 66 7-78 372-440 (442)
18 PF14338 Mrr_N: Mrr N-terminal 87.4 0.32 6.9E-06 35.6 1.4 36 41-79 56-91 (92)
19 TIGR02647 DNA conserved hypoth 86.6 0.39 8.5E-06 36.3 1.5 33 38-75 32-64 (77)
20 PF13814 Replic_Relax: Replica 86.5 1 2.2E-05 35.6 3.9 43 41-84 28-78 (191)
21 PF01978 TrmB: Sugar-specific 85.4 0.44 9.6E-06 32.6 1.2 58 6-68 8-65 (68)
22 smart00418 HTH_ARSR helix_turn 85.1 1.3 2.8E-05 27.8 3.2 43 36-78 21-64 (66)
23 TIGR02337 HpaR homoprotocatech 84.8 1.2 2.5E-05 33.3 3.3 43 37-79 54-99 (118)
24 PRK14165 winged helix-turn-hel 84.6 0.95 2.1E-05 39.1 3.1 47 35-81 31-77 (217)
25 PRK09416 lstR lineage-specific 84.0 0.77 1.7E-05 37.5 2.2 46 37-84 75-123 (135)
26 TIGR02702 SufR_cyano iron-sulf 83.9 0.45 9.7E-06 39.2 0.8 65 7-76 2-71 (203)
27 PF09639 YjcQ: YjcQ protein; 83.5 0.84 1.8E-05 33.8 2.0 44 35-78 20-69 (88)
28 PHA00738 putative HTH transcri 83.3 0.81 1.7E-05 36.4 2.0 66 5-75 11-76 (108)
29 PF02002 TFIIE_alpha: TFIIE al 81.6 1.2 2.6E-05 33.1 2.2 65 8-77 15-86 (105)
30 TIGR02719 repress_PhaQ poly-be 77.7 2.7 5.9E-05 34.1 3.3 51 37-87 55-110 (138)
31 PRK06266 transcription initiat 77.7 1.2 2.5E-05 37.2 1.2 70 7-81 23-99 (178)
32 COG1695 Predicted transcriptio 77.6 2.8 6E-05 32.2 3.2 49 37-85 42-95 (138)
33 smart00550 Zalpha Z-DNA-bindin 75.4 0.9 2E-05 31.9 -0.0 64 1-70 1-66 (68)
34 PF10007 DUF2250: Uncharacteri 75.3 2.5 5.4E-05 32.4 2.4 43 36-78 32-91 (92)
35 TIGR03433 padR_acidobact trans 72.0 4.9 0.00011 29.8 3.2 45 36-80 36-85 (100)
36 smart00529 HTH_DTXR Helix-turn 70.2 4.7 0.0001 28.6 2.7 43 35-80 9-51 (96)
37 PF03374 ANT: Phage antirepres 69.9 15 0.00032 27.2 5.4 60 7-81 37-106 (111)
38 TIGR01889 Staph_reg_Sar staphy 69.6 5.5 0.00012 29.7 3.0 43 36-78 54-99 (109)
39 COG1846 MarR Transcriptional r 69.5 5.1 0.00011 28.2 2.7 46 36-81 47-95 (126)
40 PF09382 RQC: RQC domain; Int 66.9 5.3 0.00011 29.1 2.4 45 36-80 53-98 (106)
41 COG1497 Predicted transcriptio 66.1 5.6 0.00012 35.9 2.9 43 35-80 35-77 (260)
42 TIGR02277 PaaX_trns_reg phenyl 65.5 6.4 0.00014 34.7 3.1 43 36-78 31-73 (280)
43 COG1321 TroR Mn-dependent tran 64.8 3.8 8.2E-05 33.4 1.5 74 7-88 11-98 (154)
44 TIGR00373 conserved hypothetic 62.5 7.1 0.00015 31.8 2.6 68 9-81 17-91 (158)
45 PRK11512 DNA-binding transcrip 62.3 8.7 0.00019 29.6 3.0 43 36-78 65-110 (144)
46 PF07381 DUF1495: Winged helix 62.2 5.2 0.00011 30.6 1.7 30 46-75 56-86 (90)
47 PHA02943 hypothetical protein; 61.1 5.6 0.00012 33.8 1.8 60 6-71 11-70 (165)
48 PF01638 HxlR: HxlR-like helix 60.3 11 0.00025 27.2 3.1 41 37-77 31-74 (90)
49 PF07848 PaaX: PaaX-like prote 59.5 7.7 0.00017 28.0 2.1 38 35-72 33-70 (70)
50 TIGR01884 cas_HTH CRISPR locus 58.6 6 0.00013 32.5 1.6 61 6-72 143-203 (203)
51 PRK03573 transcriptional regul 58.2 12 0.00026 28.6 3.1 45 36-80 57-104 (144)
52 KOG2784 Phenylalanyl-tRNA synt 58.0 11 0.00024 36.3 3.4 40 38-78 30-69 (483)
53 PF14531 Kinase-like: Kinase-l 55.3 2.2 4.9E-05 38.2 -1.5 41 40-82 152-192 (288)
54 PRK10870 transcriptional repre 53.5 14 0.0003 30.1 2.9 44 36-79 82-128 (176)
55 TIGR02010 IscR iron-sulfur clu 53.4 6.2 0.00013 30.6 0.8 65 1-70 1-69 (135)
56 PRK10857 DNA-binding transcrip 53.1 5.7 0.00012 32.5 0.6 54 1-58 1-58 (164)
57 COG1378 Predicted transcriptio 51.1 13 0.00029 32.4 2.6 63 6-73 16-78 (247)
58 PRK11014 transcriptional repre 49.4 9.1 0.0002 29.8 1.2 63 1-67 1-67 (141)
59 PRK13777 transcriptional regul 48.8 18 0.00038 30.4 2.9 44 37-80 71-117 (185)
60 COG0640 ArsR Predicted transcr 47.5 18 0.00039 23.9 2.3 68 5-78 24-92 (110)
61 smart00346 HTH_ICLR helix_turn 45.9 18 0.00039 25.2 2.2 44 35-80 30-73 (91)
62 COG2345 Predicted transcriptio 43.6 14 0.00031 32.2 1.6 66 4-74 9-79 (218)
63 COG5124 Protein predicted to b 43.1 20 0.00042 31.5 2.4 73 4-81 7-85 (209)
64 smart00531 TFIIE Transcription 39.4 31 0.00067 27.5 2.8 48 35-82 25-82 (147)
65 PF01043 SecA_PP_bind: SecA pr 39.3 27 0.00059 27.3 2.4 21 67-87 34-54 (113)
66 KOG4412 26S proteasome regulat 35.8 24 0.00051 31.4 1.7 48 5-52 115-164 (226)
67 cd01223 PH_Vav Vav pleckstrin 35.3 20 0.00044 28.7 1.2 58 12-72 24-86 (116)
68 PRK04172 pheS phenylalanyl-tRN 35.2 36 0.00077 32.2 2.9 38 44-82 156-193 (489)
69 PF10662 PduV-EutP: Ethanolami 32.1 22 0.00048 29.0 0.9 38 39-81 105-142 (143)
70 PRK11920 rirA iron-responsive 31.0 20 0.00043 28.8 0.5 61 1-66 1-65 (153)
71 PF13412 HTH_24: Winged helix- 30.3 7.5 0.00016 24.8 -1.7 46 6-56 3-48 (48)
72 PF13309 HTH_22: HTH domain 27.6 42 0.0009 23.5 1.6 26 2-27 20-45 (64)
73 TIGR00738 rrf2_super rrf2 fami 26.9 27 0.00058 26.2 0.5 65 1-71 1-70 (132)
74 COG1542 Uncharacterized conser 26.9 42 0.0009 33.4 2.0 45 37-83 321-366 (593)
75 KOG3233 RNA polymerase III, su 26.2 20 0.00043 33.0 -0.3 25 36-60 111-135 (297)
76 PF02082 Rrf2: Transcriptional 26.1 12 0.00026 26.7 -1.4 54 1-58 1-58 (83)
77 cd00092 HTH_CRP helix_turn_hel 24.0 41 0.0009 21.9 1.0 32 36-70 36-67 (67)
78 PF06969 HemN_C: HemN C-termin 23.1 44 0.00095 22.3 1.0 27 43-73 39-65 (66)
79 PF03962 Mnd1: Mnd1 family; I 23.1 61 0.0013 27.2 2.1 45 36-80 26-71 (188)
80 cd03071 PDI_b'_NRX PDIb' famil 23.0 80 0.0017 25.7 2.6 30 57-86 52-81 (116)
81 PRK06474 hypothetical protein; 22.7 33 0.00072 28.3 0.4 67 3-74 8-81 (178)
82 PF01050 MannoseP_isomer: Mann 22.5 71 0.0015 26.0 2.3 45 17-72 12-62 (151)
83 TIGR01689 EcbF-BcbF capsule bi 22.3 31 0.00066 27.4 0.1 48 36-91 23-70 (126)
84 PRK11050 manganese transport r 20.5 82 0.0018 25.1 2.2 40 35-77 61-100 (152)
85 KOG3433 Protein involved in me 20.5 55 0.0012 28.8 1.3 73 4-81 6-84 (203)
86 PRK09249 coproporphyrinogen II 20.1 84 0.0018 29.1 2.5 33 42-78 401-433 (453)
No 1
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-73 Score=461.11 Aligned_cols=146 Identities=62% Similarity=1.069 Sum_probs=130.4
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhh
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yL 80 (188)
|||||+||++|||+||||||||||||+++++||||+||||||||+||||+|||||||||||||||||||||||+||||||
T Consensus 1 Mlipk~nr~~I~e~Lfkegv~vakkD~~~~kH~el~vpNL~vikaMQSl~SrgYvkeqfaWrH~Yw~LTneGi~yLR~YL 80 (150)
T KOG3344|consen 1 MLIPKANRKAIYEYLFKEGVLVAKKDFNLPKHPELEVPNLHVIKAMQSLKSRGYVKEQFAWRHFYWYLTNEGIEYLREYL 80 (150)
T ss_pred CCcchHHHHHHHHHHHHhcceeeccccCCccCcccCCccHHHHHHHHHHhhhhhHHhhhhhheeeeeechhHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccccccCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCcCccCCCCCCCCCCCCCCCCCCCCCcccc-ccC
Q 029742 81 NLPSEIVPATLKKSAKPAGRPMG-GPGGDRPRGPPRFDGDRPRFGDREGYRGGPRGGDFGGEKGGAPADFQPSFRV-ILL 158 (188)
Q Consensus 81 hLP~eIVPaTlkk~~~~~~rp~~-g~~g~rp~~~~r~~g~r~~~~dR~~YRr~~~~~~~~~kk~Ga~~~~~p~frg-gf~ 158 (188)
|||+|||||||+++++++.||++ |.++++| + ++.+ +||++||++++++ ++|||++++|+||| ||.
T Consensus 81 hLP~EiVpaTl~~~rP~~~rpr~~g~e~~~p---~--~~~r---~dR~~yR~~~~~~-----~~gA~s~~~~~frg~g~g 147 (150)
T KOG3344|consen 81 HLPPEIVPATLKRSRPETGRPRPPGLEGRGP---A--DGTR---GDRDGYRRGPVPP-----EGGAGSGTEPQFRGRGFG 147 (150)
T ss_pred cCCcccccchhhccCCCCCCCCCCCCCCCCc---c--cccc---cchhhhccCCCCC-----CCCCCccccccccccCCC
Confidence 99999999999997777788765 3333333 1 2222 7999999987743 67999999999999 775
Q ss_pred C
Q 029742 159 P 159 (188)
Q Consensus 159 ~ 159 (188)
-
T Consensus 148 ~ 148 (150)
T KOG3344|consen 148 R 148 (150)
T ss_pred C
Confidence 3
No 2
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=100.00 E-value=1.3e-62 Score=389.23 Aligned_cols=100 Identities=55% Similarity=0.964 Sum_probs=96.7
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhh
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yL 80 (188)
|||||+||++|||+||||||||||||+++|+|||++||||||||+||||+||||||||||||||||+||||||||||+||
T Consensus 2 m~ipK~~r~~Iye~LfkeGVlvakKd~~~~~h~el~vpNL~Vik~mqSL~Srg~Vke~f~WrhyYw~LT~eGieyLR~yL 81 (124)
T PTZ00034 2 VYVPKANRKAIYRYLFKEGVIVCKKDPKGPWHPELNVPNLHVMMLMRSLKSRGLVKEQFAWQHYYYYLTDEGIEYLRTYL 81 (124)
T ss_pred CccchHHHHHHHHHHhhCceEEEecCCCCCCCCccCCccHHHHHHHHccccCCceEEEEeeEEEEEEEchHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccccccCCCCCC
Q 029742 81 NLPSEIVPATLKKSAKPAGR 100 (188)
Q Consensus 81 hLP~eIVPaTlkk~~~~~~r 100 (188)
|||+||||+||+++.++.++
T Consensus 82 ~LP~eivP~T~k~~~~~~~~ 101 (124)
T PTZ00034 82 HLPPDVFPATHKKKSVNFER 101 (124)
T ss_pred CCCcccCchhhcccccCccC
Confidence 99999999999998666433
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=7.2e-62 Score=370.47 Aligned_cols=94 Identities=70% Similarity=1.220 Sum_probs=82.6
Q ss_pred cchhhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhhCC
Q 029742 3 IPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNL 82 (188)
Q Consensus 3 ipKknr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yLhL 82 (188)
|||+||++|||+||||||||||||+++|+|||++||||||||+||||+||||||||||||||||+||||||||||+||||
T Consensus 1 ipk~~r~~Iye~LFkeGVlvakKD~~~~~H~el~vpNL~V~k~mqSL~SrgyVke~faWrh~Yw~LT~eGIeyLR~yL~L 80 (95)
T PF03501_consen 1 IPKKNRIAIYEYLFKEGVLVAKKDFHMPKHPELNVPNLHVIKAMQSLKSRGYVKEQFAWRHYYWYLTNEGIEYLREYLHL 80 (95)
T ss_dssp --HHHHHHHHHHHHHHSEEEEES-TTSCS-TTTSSBHHHHHHHHHHHHHCTSEEEEECTTEEEEEE-HHHHHHHHHHC-S
T ss_pred CCchHHHHHHHHHhhcceEEEEccCCCCCCCccCCCcHHHHHHHhcccchhhhcCeecceEEEEEEcchhHHHHHHHhCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccccccCC
Q 029742 83 PSEIVPATLKKSAK 96 (188)
Q Consensus 83 P~eIVPaTlkk~~~ 96 (188)
|+|||||||+++.+
T Consensus 81 P~eivPaTlk~~~~ 94 (95)
T PF03501_consen 81 PAEIVPATLKKSRR 94 (95)
T ss_dssp STT--TCCCS-S--
T ss_pred ChhhCcHHhccccC
Confidence 99999999998754
No 4
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.8e-48 Score=298.12 Aligned_cols=102 Identities=50% Similarity=0.859 Sum_probs=98.9
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhh
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yL 80 (188)
|||||+||.+|.++||++||.||||||++++|+|++||||||||+||||.|+||||.+|+|||+||+||+||++||||||
T Consensus 1 MLvPk~nr~kIhq~Lf~~gv~vakkDfnl~kH~el~ipNL~vika~qsl~S~GYvkt~~~W~~~YytLT~eGveyLREyL 80 (105)
T COG5045 1 MLVPKENRYKIHQRLFQKGVAVAKKDFNLGKHRELEIPNLHVIKAMQSLISYGYVKTIHVWRHSYYTLTPEGVEYLREYL 80 (105)
T ss_pred CCcchHHHHHHHHHHHHhhhhHhhhhccccCCcccCCCchHHHHHHHHHhhcceeEEEeeeeeeEEEecHHHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCccccccccCCCCCCCC
Q 029742 81 NLPSEIVPATLKKSAKPAGRPM 102 (188)
Q Consensus 81 hLP~eIVPaTlkk~~~~~~rp~ 102 (188)
+||+|+||+|.+.+..++.||+
T Consensus 81 ~lp~e~Vp~t~~~~v~pt~rp~ 102 (105)
T COG5045 81 VLPDEGVPSTEAPAVSPTQRPQ 102 (105)
T ss_pred cCccccCccccccccCcccCCC
Confidence 9999999999998877777764
No 5
>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=93.48 E-value=0.091 Score=33.87 Aligned_cols=69 Identities=13% Similarity=0.234 Sum_probs=49.2
Q ss_pred chhhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeec--hhhHHHHHH
Q 029742 4 PEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLT--NDGIEFLRT 78 (188)
Q Consensus 4 pKknr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LT--nEGIeYLR~ 78 (188)
...++..|+++|.+.+ +..+|.. ..++++.=.|-++|..|++.|++...-.=+..||.+| .+.++.+++
T Consensus 5 ~~~~~~~il~~l~~~~--~~~~ei~----~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~g~~~~~~~~~ 75 (78)
T cd00090 5 SDPTRLRILRLLLEGP--LTVSELA----ERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTDAERLLALLES 75 (78)
T ss_pred cChHHHHHHHHHHHCC--cCHHHHH----HHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCCchHHHHHHHH
Confidence 3567889999998876 3333432 1345777778899999999999885433388999999 566666554
No 6
>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=92.96 E-value=0.16 Score=35.50 Aligned_cols=44 Identities=14% Similarity=0.242 Sum_probs=37.4
Q ss_pred cccCCHHHHHHhhccccccccceeeec-----eeeEEeechhhHHHHHH
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAW-----MHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaW-----rhyYw~LTnEGIeYLR~ 78 (188)
.+|..=.|..+++.|...|+|.....= .--||.||++|.++|+|
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 346667888999999999999987776 46689999999999986
No 7
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=92.55 E-value=0.085 Score=50.62 Aligned_cols=53 Identities=19% Similarity=0.422 Sum_probs=41.3
Q ss_pred cccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhhCCCCCCcccc
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPAT 90 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yLhLP~eIVPaT 90 (188)
+++.--.|+.++.||.|+|+|+-.-- ..-.|.||+||.+||+ -+||++.+=+.
T Consensus 31 ~~~~~~~v~~~~~~L~~kg~v~~~~~-~~~~~~LT~eG~~~~~--~G~PE~rl~~~ 83 (494)
T PTZ00326 31 LNIDHQKVVGAIKSLESANYITTEMK-KSNTWTLTEEGEDYLK--NGSPEYRLWQK 83 (494)
T ss_pred cCCCHHHHHHHHHHHHhCCCEEEEEE-EEEEEEECHHHHHHHH--cCCHHHHHHHH
Confidence 34667899999999999998875443 5678899999999999 46776655333
No 8
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=92.54 E-value=0.086 Score=50.65 Aligned_cols=53 Identities=19% Similarity=0.306 Sum_probs=42.2
Q ss_pred ccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhhCCCCCCccccc
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATL 91 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yLhLP~eIVPaTl 91 (188)
+++--.|+.++.||.++|+|+-.- =..-.|.||+||.+||+ -+||++.|=+.+
T Consensus 29 g~~~~~v~~~~~~L~~kg~v~~~~-~~~~~~~LT~eG~~~l~--~G~PE~rl~~~l 81 (492)
T PLN02853 29 GLDHNEVVGVIKSLHGFRYVDAQD-IKRETWVLTEEGKKYAA--EGSPEVQLFAAV 81 (492)
T ss_pred CCCHHHHHHHHHHHHhCCCEEEEE-EEEEEEEECHHHHHHHH--cCCHHHHHHHHH
Confidence 467789999999999999987654 35678899999999999 467776654444
No 9
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=92.48 E-value=0.11 Score=37.24 Aligned_cols=40 Identities=18% Similarity=0.350 Sum_probs=31.1
Q ss_pred ccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHh
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTY 79 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~y 79 (188)
+++--.+.+.+..|.++|+|++ ..--|.||++|-++|..+
T Consensus 30 ~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 30 NLNYSTLKKYLKELEEKGLIKK----KDGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp T--HHHHHHHHHHHHHTTSEEE----ETTEEEE-HHHHHHHHHH
T ss_pred CcCHHHHHHHHHHHHHCcCeeC----CCCEEEECccHHHHHHHH
Confidence 4566678999999999999944 556679999999999875
No 10
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=92.16 E-value=0.14 Score=47.87 Aligned_cols=67 Identities=15% Similarity=0.248 Sum_probs=46.9
Q ss_pred hhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHH
Q 029742 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 6 knr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~ 78 (188)
.+...|.+.|-.+|-+ .-++. -..+++..=.|+.++++|.++|+|...-. +..+|.||+||.+|+.+
T Consensus 6 ~~e~~vL~~L~~~~~~-s~~eL----A~~l~l~~~tVt~~i~~Le~kGlV~~~~~-~~~~i~LTeeG~~~~~~ 72 (489)
T PRK04172 6 PNEKKVLKALKELKEA-TLEEL----AEKLGLPPEAVMRAAEWLEEKGLVKVEER-VEEVYVLTEEGKKYAEE 72 (489)
T ss_pred HHHHHHHHHHHhCCCC-CHHHH----HHHhCcCHHHHHHHHHHHHhCCCEEEEee-eEEEEEECHHHHHHHHh
Confidence 3445677777544421 11111 11335788899999999999999997644 57899999999999985
No 11
>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=91.47 E-value=0.14 Score=34.24 Aligned_cols=37 Identities=14% Similarity=0.256 Sum_probs=28.7
Q ss_pred ccCCHHHHHHhhcccccccccee---eeceeeEEeechhh
Q 029742 36 DVPNLQVIKLMQSFKSREYVRET---FAWMHYYWYLTNDG 72 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEq---FaWrhyYw~LTnEG 72 (188)
+++-=+|.+++++|..+|||..+ ..=|-.++.||++|
T Consensus 29 ~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 29 GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 46666888999999999999666 34577999999998
No 12
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=91.33 E-value=0.15 Score=40.06 Aligned_cols=71 Identities=11% Similarity=0.190 Sum_probs=55.4
Q ss_pred cchhhHHHHHHHhhhcc-eEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHh
Q 029742 3 IPEKNRKEICKYLFQEG-VCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTY 79 (188)
Q Consensus 3 ipKknr~aIYe~LFkEG-VmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~y 79 (188)
+...+|.+|.+.|.++| +.|. |. ...++++.=.|-+.|+-|+.-|+|...--.|+.||.|+++..+++...
T Consensus 13 LadptRl~IL~~L~~~~~~~v~--el----a~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~ 84 (117)
T PRK10141 13 LSDETRLGIVLLLRESGELCVC--DL----CTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKI 84 (117)
T ss_pred hCCHHHHHHHHHHHHcCCcCHH--HH----HHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHH
Confidence 34578999999998754 2221 21 124567888899999999999999999999999999999877777753
No 13
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=90.53 E-value=0.27 Score=35.76 Aligned_cols=69 Identities=19% Similarity=0.324 Sum_probs=44.1
Q ss_pred HHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccce--eeece--eeEEeechhhHHHHHHhhC
Q 029742 8 RKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRE--TFAWM--HYYWYLTNDGIEFLRTYLN 81 (188)
Q Consensus 8 r~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkE--qFaWr--hyYw~LTnEGIeYLR~yLh 81 (188)
|.+|-.+|...+-+-.+ +. . ..++++.=.+-+.|+.|...|||+- .|.=+ -.||.||++|.+.+.+|+.
T Consensus 2 Rl~Il~~L~~~~~~~f~-~L--~--~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~ 74 (80)
T PF13601_consen 2 RLAILALLYANEEATFS-EL--K--EELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVA 74 (80)
T ss_dssp HHHHHHHHHHHSEEEHH-HH--H--HHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHH
T ss_pred HHHHHHHHhhcCCCCHH-HH--H--HHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHH
Confidence 56677777663332211 11 1 1235666777899999999999754 34333 6799999999999999875
No 14
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=90.24 E-value=0.22 Score=38.71 Aligned_cols=71 Identities=20% Similarity=0.255 Sum_probs=49.6
Q ss_pred HHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhh--------------H
Q 029742 8 RKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDG--------------I 73 (188)
Q Consensus 8 r~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEG--------------I 73 (188)
..+||..+-..|.+-+ +|.. ..++|..-.|...++.|..+|||.-. ++-.+.||++| -
T Consensus 10 L~~I~~l~~~~~~~~~-~ela----~~l~vs~~svs~~l~~L~~~Gli~~~---~~~~i~LT~~G~~~a~~~~~~h~~~e 81 (142)
T PRK03902 10 IEQIYLLIEEKGYARV-SDIA----EALSVHPSSVTKMVQKLDKDEYLIYE---KYRGLVLTPKGKKIGKRLVYRHELLE 81 (142)
T ss_pred HHHHHHHHhcCCCcCH-HHHH----HHhCCChhHHHHHHHHHHHCCCEEEe---cCceEEECHHHHHHHHHHHHHHHHHH
Confidence 4577777765554421 1111 13468888999999999999999733 45679999999 4
Q ss_pred HHHHHhhCCCCCCc
Q 029742 74 EFLRTYLNLPSEIV 87 (188)
Q Consensus 74 eYLR~yLhLP~eIV 87 (188)
+|| +.|+.+.+.+
T Consensus 82 ~~l-~~l~~~~~~~ 94 (142)
T PRK03902 82 QFL-RIIGVDESKI 94 (142)
T ss_pred HHH-HHhCcCHHHH
Confidence 566 5688877654
No 15
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=89.48 E-value=0.4 Score=33.14 Aligned_cols=69 Identities=16% Similarity=0.269 Sum_probs=48.6
Q ss_pred hhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhcccccccccee---eeceeeEEeechhhHHHHHHh
Q 029742 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRET---FAWMHYYWYLTNDGIEFLRTY 79 (188)
Q Consensus 6 knr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEq---FaWrhyYw~LTnEGIeYLR~y 79 (188)
.+...|...|...|.+- .+|.. . .++++.=.|-++++.|.++|+|... ..=|..|+.||++|.+.+.+.
T Consensus 10 ~~~~~il~~l~~~~~~~-~~~la--~--~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~ 81 (101)
T smart00347 10 PTQFLVLRILYEEGPLS-VSELA--K--RLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEEL 81 (101)
T ss_pred HHHHHHHHHHHHcCCcC-HHHHH--H--HHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHH
Confidence 34567888888776422 22221 1 2356666788999999999999643 335678999999999988764
No 16
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=87.78 E-value=0.45 Score=36.90 Aligned_cols=39 Identities=18% Similarity=0.231 Sum_probs=33.7
Q ss_pred HHHHhhccccccccceeeeceeeEEeechhhHHHHHHhh
Q 029742 42 VIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 42 ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yL 80 (188)
.-+.++-|.++|+++.|=.=+--.|.||++|..+|++|=
T Consensus 48 ~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~ 86 (95)
T COG3432 48 AQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS 86 (95)
T ss_pred HHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence 457788999999888888887778899999999999874
No 17
>PRK05638 threonine synthase; Validated
Probab=87.65 E-value=0.45 Score=43.75 Aligned_cols=66 Identities=20% Similarity=0.316 Sum_probs=44.2
Q ss_pred hHHHHHHHhhhcceEEEeecCCCCCCCccc--cCCHHHHHHhhccccccccceee-eceeeEEeechhhHHHHHH
Q 029742 7 NRKEICKYLFQEGVCYAKKDYNLAKHPEID--VPNLQVIKLMQSFKSREYVRETF-AWMHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 7 nr~aIYe~LFkEGVmVaKKD~~~pkHpel~--VpNL~ViKamqSLkSrGyVkEqF-aWrhyYw~LTnEGIeYLR~ 78 (188)
.|..|...|.++- +-+ .|. .+ .|+ ++.-.|.+.|+.|+..|+|.... -=|.-||.||++|.++|.+
T Consensus 372 ~r~~IL~~L~~~~-~~~-~el--~~--~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~ 440 (442)
T PRK05638 372 TKLEILKILSERE-MYG-YEI--WK--ALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLEN 440 (442)
T ss_pred hHHHHHHHHhhCC-ccH-HHH--HH--HHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHh
Confidence 4677777776432 111 011 11 222 56678999999999999997541 0166799999999999875
No 18
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=87.45 E-value=0.32 Score=35.59 Aligned_cols=36 Identities=14% Similarity=0.137 Sum_probs=28.2
Q ss_pred HHHHHhhccccccccceeeeceeeEEeechhhHHHHHHh
Q 029742 41 QVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTY 79 (188)
Q Consensus 41 ~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~y 79 (188)
.|-=+++.|+.-|+|.. -. | -.|.||++|.++|.+.
T Consensus 56 ri~Wa~~~L~~aGli~~-~~-r-G~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 56 RIRWARSYLKKAGLIER-PK-R-GIWRITEKGRKALAEH 91 (92)
T ss_pred hHHHHHHHHHHCCCccC-CC-C-CceEECHhHHHHHhhC
Confidence 44557899999999955 33 3 3999999999999863
No 19
>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=86.65 E-value=0.39 Score=36.28 Aligned_cols=33 Identities=15% Similarity=0.198 Sum_probs=28.4
Q ss_pred CCHHHHHHhhccccccccceeeeceeeEEeechhhHHH
Q 029742 38 PNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEF 75 (188)
Q Consensus 38 pNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeY 75 (188)
-+-.++.+++.|..||++...-+= |||+||++-
T Consensus 32 A~p~~i~a~~RLheKGLI~~pdGg-----yLT~~G~~~ 64 (77)
T TIGR02647 32 ASPAAVAAAARLHEKGLTTQPDGG-----YLTSLGLEA 64 (77)
T ss_pred CCHHHHHHHHHHHHcCCccCCCCC-----EecHHHHHH
Confidence 456789999999999999887765 999999963
No 20
>PF13814 Replic_Relax: Replication-relaxation
Probab=86.52 E-value=1 Score=35.65 Aligned_cols=43 Identities=19% Similarity=0.361 Sum_probs=35.1
Q ss_pred HHHHHhhccccccccceeeec--------eeeEEeechhhHHHHHHhhCCCC
Q 029742 41 QVIKLMQSFKSREYVRETFAW--------MHYYWYLTNDGIEFLRTYLNLPS 84 (188)
Q Consensus 41 ~ViKamqSLkSrGyVkEqFaW--------rhyYw~LTnEGIeYLR~yLhLP~ 84 (188)
.+-..|+.|...|||+. +.. ..+.|+||.+|.++|.+-...++
T Consensus 28 ~~~rrL~~L~~~glv~~-~~~~~~~~~g~~~~vy~Lt~~G~~~l~~~~~~~~ 78 (191)
T PF13814_consen 28 TARRRLKRLRELGLVDR-FRRRVGARGGSQPYVYYLTPAGARLLADLRGIRP 78 (191)
T ss_pred HHHHHHHHHhhCCcEEe-ecccccccCCCcceEEEECHHHHHHHHhccCCcc
Confidence 78899999999999954 544 45789999999999998776543
No 21
>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=85.39 E-value=0.44 Score=32.59 Aligned_cols=58 Identities=16% Similarity=0.273 Sum_probs=45.3
Q ss_pred hhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEee
Q 029742 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYL 68 (188)
Q Consensus 6 knr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~L 68 (188)
++-.+||.+|.++|-+-+. |.. .++++|-=.|-+++++|.++|+|+..-.-...|...
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~-eIa----~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAE-EIA----EELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHH-HHH----HHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHHHcCCCCHH-HHH----HHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 4557899999988877655 221 245789999999999999999999988877777654
No 22
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=85.15 E-value=1.3 Score=27.79 Aligned_cols=43 Identities=14% Similarity=0.218 Sum_probs=34.7
Q ss_pred ccCCHHHHHHhhccccccccceeeeceeeEEeech-hhHHHHHH
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN-DGIEFLRT 78 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTn-EGIeYLR~ 78 (188)
+++.-.|.++++.|.++|++...-.=+..||.+|+ .|-+.+.+
T Consensus 21 ~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 21 GLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred CCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 46667899999999999999977656788999999 66666553
No 23
>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=84.75 E-value=1.2 Score=33.29 Aligned_cols=43 Identities=12% Similarity=0.140 Sum_probs=36.6
Q ss_pred cCCHHHHHHhhccccccccceee---eceeeEEeechhhHHHHHHh
Q 029742 37 VPNLQVIKLMQSFKSREYVRETF---AWMHYYWYLTNDGIEFLRTY 79 (188)
Q Consensus 37 VpNL~ViKamqSLkSrGyVkEqF---aWrhyYw~LTnEGIeYLR~y 79 (188)
+..=.|.++++.|..+|+|..+- .-|-.+++||++|.+.+.+-
T Consensus 54 ~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~ 99 (118)
T TIGR02337 54 ILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASL 99 (118)
T ss_pred CCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHh
Confidence 55557899999999999998764 56889999999999998763
No 24
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=84.62 E-value=0.95 Score=39.09 Aligned_cols=47 Identities=11% Similarity=0.222 Sum_probs=40.2
Q ss_pred cccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhhC
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLN 81 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yLh 81 (188)
+++..-.|-+.++.|..+|||.-+-.=|-.+|+||++|.+.|.+-..
T Consensus 31 L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~ 77 (217)
T PRK14165 31 TGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYA 77 (217)
T ss_pred HCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHH
Confidence 46889999999999999999987666688999999999998765443
No 25
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=84.01 E-value=0.77 Score=37.54 Aligned_cols=46 Identities=17% Similarity=0.394 Sum_probs=37.5
Q ss_pred cCCHHHHHHhhccccccccceeeec---eeeEEeechhhHHHHHHhhCCCC
Q 029742 37 VPNLQVIKLMQSFKSREYVRETFAW---MHYYWYLTNDGIEFLRTYLNLPS 84 (188)
Q Consensus 37 VpNL~ViKamqSLkSrGyVkEqFaW---rhyYw~LTnEGIeYLR~yLhLP~ 84 (188)
+..=.|.-+++.|...|+|... | +-=||.||++|.++|.+++.-|.
T Consensus 75 ~s~GtIYp~L~RLE~~GlI~s~--~~~~~RK~Y~ITe~Gre~L~e~~~~~~ 123 (135)
T PRK09416 75 GNEGSLYTLLHRLEQNRFIQSS--WDHEGAKYYQLTDKGNKMLRKAEKNAT 123 (135)
T ss_pred CCCccHHHHHHHHHHCCCeEEe--ecCCCceEEEECHHHHHHHHHHHhCHH
Confidence 4455778899999999999764 5 34689999999999999988654
No 26
>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=83.95 E-value=0.45 Score=39.18 Aligned_cols=65 Identities=15% Similarity=0.327 Sum_probs=47.1
Q ss_pred hHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceee-----eceeeEEeechhhHHHH
Q 029742 7 NRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETF-----AWMHYYWYLTNDGIEFL 76 (188)
Q Consensus 7 nr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqF-----aWrhyYw~LTnEGIeYL 76 (188)
+|.+|...|.+.|-+-+ .|.- ..++|..-.|-+.++.|.+.|+|...- .=+.++|.||++|.+.+
T Consensus 2 tr~~IL~~L~~~~~~t~-~eLA----~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~ 71 (203)
T TIGR02702 2 TKEDILSYLLKQGQATA-AALA----EALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF 71 (203)
T ss_pred HHHHHHHHHHHcCCCCH-HHHH----HHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence 57889999987664321 2211 134577888999999999999997652 23678899999998654
No 27
>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=83.53 E-value=0.84 Score=33.81 Aligned_cols=44 Identities=16% Similarity=0.213 Sum_probs=30.2
Q ss_pred cccCCHHHHHHhhccccccccceeeece------eeEEeechhhHHHHHH
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAWM------HYYWYLTNDGIEFLRT 78 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaWr------hyYw~LTnEGIeYLR~ 78 (188)
.++.+-+...+|+.|...||++-..-++ .--=.+|-+||+||.|
T Consensus 20 ~~~~~~~~~~il~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~E 69 (88)
T PF09639_consen 20 PDITDSYWSDILRMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEE 69 (88)
T ss_dssp HTS-HHHHHHHHHHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHH
Confidence 3466689999999999999998433322 2233478999999998
No 28
>PHA00738 putative HTH transcription regulator
Probab=83.28 E-value=0.81 Score=36.36 Aligned_cols=66 Identities=11% Similarity=0.124 Sum_probs=51.2
Q ss_pred hhhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHH
Q 029742 5 EKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEF 75 (188)
Q Consensus 5 Kknr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeY 75 (188)
..+|++|.+.|.+.+-++|- |.. ..+++.--.|.+.|+-|+.-|+|...--=|+-||.|+++=-+|
T Consensus 11 dptRr~IL~lL~~~e~~~V~-eLa----e~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~~~~~ 76 (108)
T PHA00738 11 KILRRKILELIAENYILSAS-LIS----HTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIRENSKEI 76 (108)
T ss_pred CHHHHHHHHHHHHcCCccHH-HHH----HhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCCccHH
Confidence 46899999999986533332 332 1235677789999999999999999999999999999876544
No 29
>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=81.55 E-value=1.2 Score=33.07 Aligned_cols=65 Identities=22% Similarity=0.475 Sum_probs=37.4
Q ss_pred HHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccce------eeeceeeEEeechhhH-HHHH
Q 029742 8 RKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRE------TFAWMHYYWYLTNDGI-EFLR 77 (188)
Q Consensus 8 r~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkE------qFaWrhyYw~LTnEGI-eYLR 77 (188)
-..|.+.|..+|+|- .+|.. ..++++.=+|-++|..|...|+|+. +-+|..|||+++.+.| +.|+
T Consensus 15 ~~~Il~~L~~~~~l~-de~la----~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~~~~ik 86 (105)
T PF02002_consen 15 AVRILDALLRKGELT-DEDLA----KKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQIIDVIK 86 (105)
T ss_dssp THHHHHHHHHH--B--HHHHH----HTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH-----
T ss_pred HHHHHHHHHHcCCcC-HHHHH----HHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHHHHHHH
Confidence 356788888888753 33322 1345788899999999999999954 4589999999999887 3443
No 30
>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=77.70 E-value=2.7 Score=34.13 Aligned_cols=51 Identities=14% Similarity=0.200 Sum_probs=37.4
Q ss_pred cCCHHHHHHhhccccccccceee----e-ceeeEEeechhhHHHHHHhhCCCCCCc
Q 029742 37 VPNLQVIKLMQSFKSREYVRETF----A-WMHYYWYLTNDGIEFLRTYLNLPSEIV 87 (188)
Q Consensus 37 VpNL~ViKamqSLkSrGyVkEqF----a-WrhyYw~LTnEGIeYLR~yLhLP~eIV 87 (188)
|..=.|.-+|+.|...|+|.... + =+--||.||++|.++|.+.+.--.++.
T Consensus 55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~~~~ 110 (138)
T TIGR02719 55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFEHYQ 110 (138)
T ss_pred CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHH
Confidence 45556788999999999998521 1 114789999999999998876544443
No 31
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.69 E-value=1.2 Score=37.21 Aligned_cols=70 Identities=17% Similarity=0.294 Sum_probs=49.8
Q ss_pred hHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccc-----e-eeeceeeEEeechhhH-HHHHHh
Q 029742 7 NRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVR-----E-TFAWMHYYWYLTNDGI-EFLRTY 79 (188)
Q Consensus 7 nr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVk-----E-qFaWrhyYw~LTnEGI-eYLR~y 79 (188)
....|...|.+.|.+- |-.+. ..+++..=.|-|+|+.|...|+|. + .-+|=.|||.||.+-| +-|+..
T Consensus 23 ~~~~Vl~~L~~~g~~t---deeLA--~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~ 97 (178)
T PRK06266 23 EGFEVLKALIKKGEVT---DEEIA--EQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKK 97 (178)
T ss_pred cHhHHHHHHHHcCCcC---HHHHH--HHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHH
Confidence 4566777777767543 21111 134688889999999999999987 1 4689999999998776 666665
Q ss_pred hC
Q 029742 80 LN 81 (188)
Q Consensus 80 Lh 81 (188)
+|
T Consensus 98 ~~ 99 (178)
T PRK06266 98 KM 99 (178)
T ss_pred HH
Confidence 54
No 32
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=77.58 E-value=2.8 Score=32.17 Aligned_cols=49 Identities=14% Similarity=0.157 Sum_probs=37.3
Q ss_pred cCCHHHHHHhhccccccccceeeece-----eeEEeechhhHHHHHHhhCCCCC
Q 029742 37 VPNLQVIKLMQSFKSREYVRETFAWM-----HYYWYLTNDGIEFLRTYLNLPSE 85 (188)
Q Consensus 37 VpNL~ViKamqSLkSrGyVkEqFaWr-----hyYw~LTnEGIeYLR~yLhLP~e 85 (188)
+.-=.+..+++.|.+.|||.....=+ ==||.||++|-++|.+.+....+
T Consensus 42 ~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~~~ 95 (138)
T COG1695 42 PSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEWGA 95 (138)
T ss_pred CCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHHHH
Confidence 33446778899999999998765444 26899999999999998844433
No 33
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=75.40 E-value=0.9 Score=31.92 Aligned_cols=64 Identities=17% Similarity=0.280 Sum_probs=44.8
Q ss_pred CccchhhHHHHHHHhhhcce--EEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeech
Q 029742 1 MIIPEKNRKEICKYLFQEGV--CYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN 70 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGV--mVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTn 70 (188)
|+.+..++.+|+++|-+.|= +-++ |. -.+++|+.=.|-++|.+|++.|+|.-.=. .--+|.|+.
T Consensus 1 ~~~~~~~~~~IL~~L~~~g~~~~ta~-eL----a~~lgl~~~~v~r~L~~L~~~G~V~~~~~-~~~~W~i~~ 66 (68)
T smart00550 1 SLTQDSLEEKILEFLENSGDETSTAL-QL----AKNLGLPKKEVNRVLYSLEKKGKVCKQGG-TPPLWKLTD 66 (68)
T ss_pred CCCchHHHHHHHHHHHHCCCCCcCHH-HH----HHHHCCCHHHHHHHHHHHHHCCCEEecCC-CCCceEeec
Confidence 46678889999999987653 2221 21 12456888899999999999999965433 224677764
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=75.33 E-value=2.5 Score=32.39 Aligned_cols=43 Identities=21% Similarity=0.338 Sum_probs=34.1
Q ss_pred ccCCHHHHHHhhccccccccceeeec-----------------eeeEEeechhhHHHHHH
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFAW-----------------MHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFaW-----------------rhyYw~LTnEGIeYLR~ 78 (188)
.+|==.|..+++.|...|+|.+.-+= -|-||-||.+|-.+||+
T Consensus 32 ~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~k~K~~~e~~~hHtYY~LTr~G~~llR~ 91 (92)
T PF10007_consen 32 KIPLEEVREALEKLEEMGLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTREGELLLRE 91 (92)
T ss_pred CCCHHHHHHHHHHHHHCCCeEEecCcccchhhhhcccchhhhcCCceeeecHhHHHHHhc
Confidence 46666788888888888888665432 48999999999999996
No 35
>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=72.00 E-value=4.9 Score=29.82 Aligned_cols=45 Identities=13% Similarity=0.231 Sum_probs=34.9
Q ss_pred ccCCHHHHHHhhccccccccceeee-----ceeeEEeechhhHHHHHHhh
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFA-----WMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFa-----WrhyYw~LTnEGIeYLR~yL 80 (188)
++..=.|..+++.|..+|+|..... =+=-||.||++|.++|.+..
T Consensus 36 ~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~ 85 (100)
T TIGR03433 36 QVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAET 85 (100)
T ss_pred ccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHH
Confidence 4556678889999999999987421 12379999999999998754
No 36
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=70.22 E-value=4.7 Score=28.59 Aligned_cols=43 Identities=19% Similarity=0.208 Sum_probs=34.2
Q ss_pred cccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhh
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yL 80 (188)
++|+--.|.++++.|.++|+|...=+ -.++||++|.+.+....
T Consensus 9 l~is~stvs~~l~~L~~~glI~r~~~---~~~~lT~~g~~~~~~~~ 51 (96)
T smart00529 9 LNVSPPTVTQMLKKLEKDGLVEYEPY---RGITLTEKGRRLARRLL 51 (96)
T ss_pred hCCChHHHHHHHHHHHHCCCEEEcCC---CceEechhHHHHHHHHH
Confidence 35777789999999999999887543 36899999998776544
No 37
>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=69.95 E-value=15 Score=27.20 Aligned_cols=60 Identities=22% Similarity=0.385 Sum_probs=39.6
Q ss_pred hHHHHHHHhhhcceEEE-eecCCCCCCCccccCCHHHHHHhhcccccccccee-eecee--------eEEeechhhHHHH
Q 029742 7 NRKEICKYLFQEGVCYA-KKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRET-FAWMH--------YYWYLTNDGIEFL 76 (188)
Q Consensus 7 nr~aIYe~LFkEGVmVa-KKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEq-FaWrh--------yYw~LTnEGIeYL 76 (188)
.+...++.|-++|++.- .++.+.|.. ...++||.... ..|.| ..=+.|.+|++||
T Consensus 37 ~~~~l~~~Lr~~g~l~~~~~~~~~p~q---------------~~~~~G~~~~k~~~~~~~~g~~~~~~~~~iT~kG~~~i 101 (111)
T PF03374_consen 37 GRNKLFQWLREKGWLYRRGKGRNLPYQ---------------KYIDAGYFEVKETTYTHSDGEGKTSSQTRITPKGLEWI 101 (111)
T ss_pred CHHHHHHHHHhCCceEECCCCCcccCh---------------hhhccceEEEeeeEeecCCCCcEEEEEEEEehhHHHHH
Confidence 46788999999999986 344555543 33455664333 22222 4567899999999
Q ss_pred HHhhC
Q 029742 77 RTYLN 81 (188)
Q Consensus 77 R~yLh 81 (188)
.+.|+
T Consensus 102 ~~~l~ 106 (111)
T PF03374_consen 102 AKRLA 106 (111)
T ss_pred HHHHH
Confidence 98764
No 38
>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=69.56 E-value=5.5 Score=29.70 Aligned_cols=43 Identities=5% Similarity=0.145 Sum_probs=37.8
Q ss_pred ccCCHHHHHHhhccccccccceeeec---eeeEEeechhhHHHHHH
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFAW---MHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFaW---rhyYw~LTnEGIeYLR~ 78 (188)
++..=.|-+++..|..+|||+..=+. |-.|-+||++|.+-+.+
T Consensus 54 ~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~ 99 (109)
T TIGR01889 54 LIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIES 99 (109)
T ss_pred CCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHH
Confidence 47888899999999999999987777 78999999999987754
No 39
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=69.49 E-value=5.1 Score=28.19 Aligned_cols=46 Identities=17% Similarity=0.243 Sum_probs=39.4
Q ss_pred ccCCHHHHHHhhccccccccceeee---ceeeEEeechhhHHHHHHhhC
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTYLN 81 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFa---WrhyYw~LTnEGIeYLR~yLh 81 (188)
.|..=.|..++++|..+|||+..-+ =|-.+..||++|-+.+.+..-
T Consensus 47 ~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~ 95 (126)
T COG1846 47 GLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95 (126)
T ss_pred CCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence 4777788999999999999988777 688999999999999886443
No 40
>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=66.89 E-value=5.3 Score=29.09 Aligned_cols=45 Identities=22% Similarity=0.269 Sum_probs=37.9
Q ss_pred ccCCHHHHHHhhccccccccceeee-ceeeEEeechhhHHHHHHhh
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFA-WMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFa-WrhyYw~LTnEGIeYLR~yL 80 (188)
+++.-.+...++.|...||+.+... |.+-|-.||++|-++|+.-.
T Consensus 53 ~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~l~g~~ 98 (106)
T PF09382_consen 53 DMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKLTPKGKELLNGKQ 98 (106)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE-GGGHHHHCTTS
T ss_pred cCCHHHHHHHHHHHHHcCCceecCCcccccEEEECHHHHHHHCCCc
Confidence 3788889999999999999988775 89999999999999998643
No 41
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=66.11 E-value=5.6 Score=35.95 Aligned_cols=43 Identities=14% Similarity=0.207 Sum_probs=35.5
Q ss_pred cccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhh
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yL 80 (188)
|+|.=.-|.-.+++|.+-|||++ - .--+|-+|.||.++|-+.|
T Consensus 35 lgiT~QaVsehiK~Lv~eG~i~~--~-gR~~Y~iTkkG~e~l~~~~ 77 (260)
T COG1497 35 LGITLQAVSEHIKELVKEGLIEK--E-GRGEYEITKKGAEWLLEQL 77 (260)
T ss_pred cCCCHHHHHHHHHHHHhccceee--c-CCeeEEEehhHHHHHHHHH
Confidence 45888889999999999999999 2 2346799999999986654
No 42
>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=65.53 E-value=6.4 Score=34.73 Aligned_cols=43 Identities=9% Similarity=0.155 Sum_probs=33.7
Q ss_pred ccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHH
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~ 78 (188)
+|..=.|..++.-|+++|++...=.=|--||.||++|.+.|.+
T Consensus 31 gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~ 73 (280)
T TIGR02277 31 GINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAA 73 (280)
T ss_pred CCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHH
Confidence 4677778899999999999977411123566999999999986
No 43
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=64.83 E-value=3.8 Score=33.42 Aligned_cols=74 Identities=22% Similarity=0.177 Sum_probs=55.6
Q ss_pred hHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhH-------------
Q 029742 7 NRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGI------------- 73 (188)
Q Consensus 7 nr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGI------------- 73 (188)
...+||+.+-+.|.+- -+|... .|+|.-=.|.+.++-|.+.|||+-. ++....||++|-
T Consensus 11 YL~~Iy~l~~~~~~~~-~~diA~----~L~Vsp~sVt~ml~rL~~~GlV~~~---~y~gi~LT~~G~~~a~~~~r~hrll 82 (154)
T COG1321 11 YLETIYELLEEKGFAR-TKDIAE----RLKVSPPSVTEMLKRLERLGLVEYE---PYGGVTLTEKGREKAKELLRKHRLL 82 (154)
T ss_pred HHHHHHHHHhccCccc-HHHHHH----HhCCCcHHHHHHHHHHHHCCCeEEe---cCCCeEEChhhHHHHHHHHHHHHHH
Confidence 4568888776555443 345431 4678888999999999999999753 345779999997
Q ss_pred -HHHHHhhCCCCCCcc
Q 029742 74 -EFLRTYLNLPSEIVP 88 (188)
Q Consensus 74 -eYLR~yLhLP~eIVP 88 (188)
.||.+.|+++.+.+=
T Consensus 83 e~fL~~~lg~~~~~~~ 98 (154)
T COG1321 83 ERFLVDVLGLDWEEAH 98 (154)
T ss_pred HHHHHHHhCCCHHHHH
Confidence 578889999987764
No 44
>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=62.50 E-value=7.1 Score=31.79 Aligned_cols=68 Identities=16% Similarity=0.281 Sum_probs=45.8
Q ss_pred HHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhcccccccc---c---eeeeceeeEEeechhhH-HHHHHhhC
Q 029742 9 KEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYV---R---ETFAWMHYYWYLTNDGI-EFLRTYLN 81 (188)
Q Consensus 9 ~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyV---k---EqFaWrhyYw~LTnEGI-eYLR~yLh 81 (188)
+.|...|+..|+|- ..|.. ..+++..=.|-|++..|...|+| + +.=+|.-|||+++.+-| +-|+..+|
T Consensus 17 v~Vl~aL~~~~~~t-dEeLa----~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~ 91 (158)
T TIGR00373 17 GLVLFSLGIKGEFT-DEEIS----LELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRKLE 91 (158)
T ss_pred HHHHHHHhccCCCC-HHHHH----HHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHHHH
Confidence 34555566555431 11111 13457888899999999999999 3 34499999999877655 67776555
No 45
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=62.33 E-value=8.7 Score=29.62 Aligned_cols=43 Identities=12% Similarity=0.094 Sum_probs=37.1
Q ss_pred ccCCHHHHHHhhccccccccceee---eceeeEEeechhhHHHHHH
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETF---AWMHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqF---aWrhyYw~LTnEGIeYLR~ 78 (188)
.+..=.|.++++.|..+|||...- .=|-.+.+||++|.+-+.+
T Consensus 65 ~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 65 SVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred CCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 478888999999999999998764 4788999999999987765
No 46
>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=62.17 E-value=5.2 Score=30.60 Aligned_cols=30 Identities=23% Similarity=0.180 Sum_probs=22.1
Q ss_pred hhcccccccc-ceeeeceeeEEeechhhHHH
Q 029742 46 MQSFKSREYV-RETFAWMHYYWYLTNDGIEF 75 (188)
Q Consensus 46 mqSLkSrGyV-kEqFaWrhyYw~LTnEGIeY 75 (188)
-.||.+-|+| .|.-.=.--||.||++|.++
T Consensus 56 e~SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~ 86 (90)
T PF07381_consen 56 EDSLVGLGLVEEEEEKGGFKYYRLTEKGKRI 86 (90)
T ss_pred chhHHHcCCeeEeeecCCeeEEEeChhhhhH
Confidence 3589999999 33332344599999999875
No 47
>PHA02943 hypothetical protein; Provisional
Probab=61.08 E-value=5.6 Score=33.84 Aligned_cols=60 Identities=13% Similarity=0.171 Sum_probs=44.1
Q ss_pred hhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechh
Q 029742 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTND 71 (188)
Q Consensus 6 knr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnE 71 (188)
.....|.|+| ++|+.-.. . +.+ .+.++-=+|-=+++-|.+-|+|++.==-+--||+|.+.
T Consensus 11 ~R~~eILE~L-k~G~~Tts-e--IAk--aLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~d 70 (165)
T PHA02943 11 TRMIKTLRLL-ADGCKTTS-R--IAN--KLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDED 70 (165)
T ss_pred HHHHHHHHHH-hcCCccHH-H--HHH--HHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEEChH
Confidence 4567899999 99976321 0 111 23567778888899999999999966556789999983
No 48
>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=60.28 E-value=11 Score=27.23 Aligned_cols=41 Identities=15% Similarity=0.160 Sum_probs=30.3
Q ss_pred cCCHHHHHHhhccccccccceeee---ceeeEEeechhhHHHHH
Q 029742 37 VPNLQVIKLMQSFKSREYVRETFA---WMHYYWYLTNDGIEFLR 77 (188)
Q Consensus 37 VpNL~ViKamqSLkSrGyVkEqFa---WrhyYw~LTnEGIeYLR 77 (188)
|++--+.+.++.|...|+|..+.. =.+..|.||+.|.+.+.
T Consensus 31 is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~ 74 (90)
T PF01638_consen 31 ISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP 74 (90)
T ss_dssp S-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred hHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence 566678899999999999966532 13578999999998764
No 49
>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=59.49 E-value=7.7 Score=27.99 Aligned_cols=38 Identities=18% Similarity=0.261 Sum_probs=30.7
Q ss_pred cccCCHHHHHHhhccccccccceeeeceeeEEeechhh
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDG 72 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEG 72 (188)
++|..=-|--+|--|+++|.+...=.=|.-||.||++|
T Consensus 33 ~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 33 FGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp TT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred cCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCCC
Confidence 34666677788999999999999988999999999987
No 50
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=58.62 E-value=6 Score=32.55 Aligned_cols=61 Identities=13% Similarity=0.142 Sum_probs=42.9
Q ss_pred hhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhh
Q 029742 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDG 72 (188)
Q Consensus 6 knr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEG 72 (188)
.....|.++|-+.|-+- -+|.. ..++++-=.|-+.++.|+..|+|+..-. |.-+|.||++|
T Consensus 143 ~~~~~IL~~l~~~g~~s-~~eia----~~l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~~lT~~G 203 (203)
T TIGR01884 143 REELKVLEVLKAEGEKS-VKNIA----KKLGKSLSTISRHLRELEKKGLVEQKGR-KGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHHHHHcCCcC-HHHHH----HHHCcCHHHHHHHHHHHHHCCCEEEEcC-CccEEEeCCCC
Confidence 44567888887654211 11211 1234666678899999999999998866 88899999987
No 51
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=58.19 E-value=12 Score=28.59 Aligned_cols=45 Identities=4% Similarity=0.093 Sum_probs=37.6
Q ss_pred ccCCHHHHHHhhccccccccceeee---ceeeEEeechhhHHHHHHhh
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFa---WrhyYw~LTnEGIeYLR~yL 80 (188)
.+..=.|.+++..|..+|||...=+ =|..+-+||++|.+.+.+..
T Consensus 57 ~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~ 104 (144)
T PRK03573 57 GIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVE 104 (144)
T ss_pred CCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHH
Confidence 3677788999999999999987644 47889999999999887643
No 52
>KOG2784 consensus Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=57.95 E-value=11 Score=36.32 Aligned_cols=40 Identities=20% Similarity=0.241 Sum_probs=31.1
Q ss_pred CCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHH
Q 029742 38 PNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 38 pNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~ 78 (188)
-.-+|.-+++||.++|++.-+ -=-+.=|-||+||.++.++
T Consensus 30 ~h~~~v~al~SL~a~~~i~~~-~~~~~~~~LT~EG~~i~~e 69 (483)
T KOG2784|consen 30 DHQQVVGALKSLQAGGVIEVK-DVETKTYELTAEGEEIARE 69 (483)
T ss_pred hhHHHHHHHHHHhhcCceEEE-eeeeEEEeeChhHHHHHhc
Confidence 344567799999998876533 3357789999999999996
No 53
>PF14531 Kinase-like: Kinase-like; PDB: 3DZO_A 2W1Z_A 3BYV_A 3Q5Z_A 3Q60_A.
Probab=55.25 E-value=2.2 Score=38.16 Aligned_cols=41 Identities=27% Similarity=0.423 Sum_probs=31.7
Q ss_pred HHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhhCC
Q 029742 40 LQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNL 82 (188)
Q Consensus 40 L~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yLhL 82 (188)
+|+|++.++|.+.|.|.-++.|..++ +.++|.-||.++-++
T Consensus 152 ~Q~I~lvA~Lh~~GlVHgdi~~~nfl--l~~~G~v~Lg~F~~~ 192 (288)
T PF14531_consen 152 VQMIRLVANLHSYGLVHGDIKPENFL--LDQDGGVFLGDFSSL 192 (288)
T ss_dssp HHHHHHHHHHHHTTEEEST-SGGGEE--E-TTS-EEE--GGGE
T ss_pred HHHHHHHHHHhhcceEecccceeeEE--EcCCCCEEEcChHHH
Confidence 56699999999999999999999997 788999999987544
No 54
>PRK10870 transcriptional repressor MprA; Provisional
Probab=53.52 E-value=14 Score=30.14 Aligned_cols=44 Identities=18% Similarity=0.290 Sum_probs=37.2
Q ss_pred ccCCHHHHHHhhccccccccceeee---ceeeEEeechhhHHHHHHh
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFA---WMHYYWYLTNDGIEFLRTY 79 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFa---WrhyYw~LTnEGIeYLR~y 79 (188)
.++.=.|..+++.|..+|||..+=+ =|-.+-+||++|.+.+.+.
T Consensus 82 ~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i 128 (176)
T PRK10870 82 GSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREV 128 (176)
T ss_pred CCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence 4788889999999999999986543 4668899999999998864
No 55
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=53.38 E-value=6.2 Score=30.58 Aligned_cols=65 Identities=12% Similarity=0.083 Sum_probs=44.1
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCCCCCCCcc----ccCCHHHHHHhhccccccccceeeeceeeEEeech
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI----DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN 70 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~~pkHpel----~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTn 70 (188)
|.+.++.+.+|.-.++ |....+-....-.+| ++|-=+|-|+|+.|+..|+|..+=+ ..--|.|+.
T Consensus 1 M~ls~~~~YAl~~l~~----La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G-~~Ggy~l~~ 69 (135)
T TIGR02010 1 MRLTTKGRYAVTAMLD----LALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRG-PGGGYQLGR 69 (135)
T ss_pred CcCCcHHHHHHHHHHH----HHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeC-CCCCEeccC
Confidence 8889999988887776 443322222223344 5999999999999999999987433 333445543
No 56
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=53.11 E-value=5.7 Score=32.54 Aligned_cols=54 Identities=13% Similarity=0.151 Sum_probs=36.7
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCCCCCCCcc----ccCCHHHHHHhhcccccccccee
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI----DVPNLQVIKLMQSFKSREYVRET 58 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~~pkHpel----~VpNL~ViKamqSLkSrGyVkEq 58 (188)
|.|.++.+.++.-.++ |....+-....-.+| ++|.=+|-|+|+.|+..|+|..+
T Consensus 1 M~ls~~~~yAl~~l~~----lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 1 MRLTSKGRYAVTAMLD----VALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CcCCcHHHHHHHHHHH----HHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 7888888888877664 222222111222333 58999999999999999999874
No 57
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=51.07 E-value=13 Score=32.37 Aligned_cols=63 Identities=16% Similarity=0.177 Sum_probs=49.4
Q ss_pred hhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhH
Q 029742 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGI 73 (188)
Q Consensus 6 knr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGI 73 (188)
++=.++|-.|..-|.+-|+.=.. -.+||-=.|...|+||.+||+|..+-+=--.|-..-.+=+
T Consensus 16 ~yEa~vY~aLl~~g~~tA~eis~-----~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~p~~~ 78 (247)
T COG1378 16 EYEAKVYLALLCLGEATAKEISE-----ASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVPPEEL 78 (247)
T ss_pred HHHHHHHHHHHHhCCccHHHHHH-----HcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeCCHHHH
Confidence 44568999999999999873222 2359999999999999999999999776667777665543
No 58
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=49.35 E-value=9.1 Score=29.80 Aligned_cols=63 Identities=10% Similarity=0.111 Sum_probs=42.6
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCCCCCCCc----cccCCHHHHHHhhccccccccceeeeceeeEEe
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPE----IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWY 67 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~~pkHpe----l~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~ 67 (188)
|-++++...+|...++-- ...+-....-.+ ++||--.|-|+|+.|+..|+|+..=+=.-.|..
T Consensus 1 M~ls~~~~YAl~~~i~la----~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l 67 (141)
T PRK11014 1 MQLTSFTDYGLRALIYMA----SLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRL 67 (141)
T ss_pred CcCchHHhHHHHHHHHHh----cCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeee
Confidence 788899988888877621 111111222223 369999999999999999999887654334443
No 59
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=48.78 E-value=18 Score=30.45 Aligned_cols=44 Identities=18% Similarity=0.217 Sum_probs=36.1
Q ss_pred cCCHHHHHHhhccccccccceee---eceeeEEeechhhHHHHHHhh
Q 029742 37 VPNLQVIKLMQSFKSREYVRETF---AWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 37 VpNL~ViKamqSLkSrGyVkEqF---aWrhyYw~LTnEGIeYLR~yL 80 (188)
+..=.|..+++.|..+|||.-+- -=|-.+=+||++|.+.+.+..
T Consensus 71 l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~ 117 (185)
T PRK13777 71 MHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETM 117 (185)
T ss_pred CCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 44455889999999999998654 458999999999999987643
No 60
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=47.54 E-value=18 Score=23.87 Aligned_cols=68 Identities=12% Similarity=0.103 Sum_probs=47.3
Q ss_pred hhhHHHHHHHhhhc-ceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHH
Q 029742 5 EKNRKEICKYLFQE-GVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 5 Kknr~aIYe~LFkE-GVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~ 78 (188)
..+|.+|...|.+. .+.+..=.. .+++.--.|...+..|...|+|....-=++.||.|+++.|..+.+
T Consensus 24 ~~~r~~il~~l~~~~~~~~~~l~~------~~~~~~~~v~~hL~~L~~~glv~~~~~~~~~~~~l~~~~~~~~~~ 92 (110)
T COG0640 24 DPTRLEILSLLAEGGELTVGELAE------ALGLSQSTVSHHLKVLREAGLVELRREGRLRLYRLADEKVAELLE 92 (110)
T ss_pred CHHHHHHHHHHHhcCCccHHHHHH------HHCCChhHHHHHHHHHHHCCCeEEEecccEEEEecCcHHHHHHHH
Confidence 34688899998875 232211111 114566678888999999999999888788888999887655443
No 61
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=45.93 E-value=18 Score=25.15 Aligned_cols=44 Identities=16% Similarity=0.290 Sum_probs=35.8
Q ss_pred cccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhh
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yL 80 (188)
++++-=.|-+.++.|.+.|++... +..-.|.|+++.+++-..++
T Consensus 30 l~i~~~tv~r~l~~L~~~g~l~~~--~~~~~y~l~~~~~~~~~~~~ 73 (91)
T smart00346 30 LGLSKSTAHRLLNTLQELGYVEQD--GQNGRYRLGPKVLELGQSYL 73 (91)
T ss_pred hCCCHHHHHHHHHHHHHCCCeeec--CCCCceeecHHHHHHHHHHH
Confidence 468888999999999999999764 34456899999988877665
No 62
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=43.59 E-value=14 Score=32.25 Aligned_cols=66 Identities=18% Similarity=0.248 Sum_probs=50.3
Q ss_pred chhhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccceeeece-----eeEEeechhhHH
Q 029742 4 PEKNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVRETFAWM-----HYYWYLTNDGIE 74 (188)
Q Consensus 4 pKknr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVkEqFaWr-----hyYw~LTnEGIe 74 (188)
+-.+|..|-+.|-+.|=+-|. |. =.+|+|++-.|-+.|+.|.-+|+|.-++.=. .+-|.||..|++
T Consensus 9 ~~~tr~~il~lL~~~g~~sa~-el----A~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 9 SGSTRERILELLKKSGPVSAD-EL----AEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred CccHHHHHHHHHhccCCccHH-HH----HHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 345778888888877665544 22 1256799999999999999999998884322 468899999996
No 63
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=43.12 E-value=20 Score=31.51 Aligned_cols=73 Identities=18% Similarity=0.297 Sum_probs=50.8
Q ss_pred chhhHHHHHHHhhhcceEEEeecCCCCCCCc-cc----cCCHHHHHHhhccccccccc-eeeeceeeEEeechhhHHHHH
Q 029742 4 PEKNRKEICKYLFQEGVCYAKKDYNLAKHPE-ID----VPNLQVIKLMQSFKSREYVR-ETFAWMHYYWYLTNDGIEFLR 77 (188)
Q Consensus 4 pKknr~aIYe~LFkEGVmVaKKD~~~pkHpe-l~----VpNL~ViKamqSLkSrGyVk-EqFaWrhyYw~LTnEGIeYLR 77 (188)
+-+..+.+.+.+|.+ .|||..-+.-| |. |-=..|--++|||..-|.|+ |..+=..+||..-++|++-+-
T Consensus 7 s~~eKrr~L~aI~~~-----SKdFFqLkEvEkLGSKK~IVl~tVKd~lQqlVDDgvV~~EK~GtsN~YWsF~s~~~qk~~ 81 (209)
T COG5124 7 SLAEKRRRLEAIFHD-----SKDFFQLKEVEKLGSKKQIVLMTVKDLLQQLVDDGVVSVEKCGTSNIYWSFKSQTLQKLY 81 (209)
T ss_pred cHHHHHHHHHHHHhc-----cHHHHHHHHHHHhccccccHHHHHHHHHHHHhhcCceeeeeeccceeEEecchHHHHHHH
Confidence 345677888888865 46765322111 11 22234566899999999986 788999999999999998766
Q ss_pred HhhC
Q 029742 78 TYLN 81 (188)
Q Consensus 78 ~yLh 81 (188)
+-+.
T Consensus 82 ~~~~ 85 (209)
T COG5124 82 DSSE 85 (209)
T ss_pred HHHH
Confidence 5444
No 64
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=39.43 E-value=31 Score=27.48 Aligned_cols=48 Identities=23% Similarity=0.610 Sum_probs=33.8
Q ss_pred cccCCHHHHHHhhcccccccc-----c----eeeeceeeEEeec-hhhHHHHHHhhCC
Q 029742 35 IDVPNLQVIKLMQSFKSREYV-----R----ETFAWMHYYWYLT-NDGIEFLRTYLNL 82 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyV-----k----EqFaWrhyYw~LT-nEGIeYLR~yLhL 82 (188)
+.++.=+|-|++..|..-+++ + ++=+|-.|||+++ +.-|+-|+..++.
T Consensus 25 l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~ 82 (147)
T smart00531 25 LGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDK 82 (147)
T ss_pred hCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHH
Confidence 357777888888888884442 2 1223999999999 5666777776664
No 65
>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=39.31 E-value=27 Score=27.30 Aligned_cols=21 Identities=29% Similarity=0.415 Sum_probs=17.6
Q ss_pred eechhhHHHHHHhhCCCCCCc
Q 029742 67 YLTNDGIEFLRTYLNLPSEIV 87 (188)
Q Consensus 67 ~LTnEGIeYLR~yLhLP~eIV 87 (188)
.||++|++.+.++|++++++.
T Consensus 34 ~LT~~G~~~~e~~~~~~~~l~ 54 (113)
T PF01043_consen 34 ELTEKGIEKAEKLLGISDNLY 54 (113)
T ss_dssp EESHHHHHHHHHHHTSSSSTT
T ss_pred eEhHHHHHHHHHHhhhccccc
Confidence 799999999999999854443
No 66
>KOG4412 consensus 26S proteasome regulatory complex, subunit PSMD10 [Posttranslational modification, protein turnover, chaperones]
Probab=35.77 E-value=24 Score=31.37 Aligned_cols=48 Identities=29% Similarity=0.344 Sum_probs=41.8
Q ss_pred hhhHHHHHHHhhhcceEEEeecCC--CCCCCccccCCHHHHHHhhccccc
Q 029742 5 EKNRKEICKYLFQEGVCYAKKDYN--LAKHPEIDVPNLQVIKLMQSFKSR 52 (188)
Q Consensus 5 Kknr~aIYe~LFkEGVmVaKKD~~--~pkHpel~VpNL~ViKamqSLkSr 52 (188)
-|+|..|-+.|...|..+-.||-. .|.|---.|-||+||+.+-|+.+-
T Consensus 115 gK~r~eIaqlLle~ga~i~~kD~~~qtplHRAAavGklkvie~Li~~~a~ 164 (226)
T KOG4412|consen 115 GKGRLEIAQLLLEKGALIRIKDKQGQTPLHRAAAVGKLKVIEYLISQGAP 164 (226)
T ss_pred cCChhhHHHHHHhcCCCCcccccccCchhHHHHhccchhhHHHHHhcCCC
Confidence 367999999999999999999965 577877789999999999998864
No 67
>cd01223 PH_Vav Vav pleckstrin homology (PH) domain. Vav pleckstrin homology (PH) domain. Vav acts as a guanosine nucleotide exchange factor(GEF) for Rho/Rac proteins. Mammalian Vav proteins consist of a calponin homology (CH) domain, an acidic region, a rho-GEF (DH)domain, a PH domain, a Zinc finger region and an SH2 domain, flanked by two SH3 domains. In invertebrates such as Drosophila and C.elegans, Vav is missing the N-terminal SH3 domain . PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=35.30 E-value=20 Score=28.67 Aligned_cols=58 Identities=12% Similarity=0.170 Sum_probs=35.5
Q ss_pred HHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhh-----ccccccccceeeeceeeEEeechhh
Q 029742 12 CKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQ-----SFKSREYVRETFAWMHYYWYLTNDG 72 (188)
Q Consensus 12 Ye~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamq-----SLkSrGyVkEqFaWrhyYw~LTnEG 72 (188)
|-+||...|||||.....+-+|+....+-++|...+ |.-+.|..+ -|+|++|....+|
T Consensus 24 yiFLFDk~lI~CK~~~~~~~~~~Y~~Ke~~~l~~~~I~~~~~~d~~~~~~---~~~~~f~L~~~~~ 86 (116)
T cd01223 24 YIFLFDKAVIVCKALGDNTGDMQYTYKDIHDLADYKIENNPSRDTEGRDT---RWKYGFYLAHKQG 86 (116)
T ss_pred EEEEecceEEEEEecCCCCCCccEEhHHhhhhheeeeEecCccCcccCCc---ceEEEEEEEecCC
Confidence 456999999999977664446666555555544422 111223222 4999888777655
No 68
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=35.15 E-value=36 Score=32.16 Aligned_cols=38 Identities=29% Similarity=0.420 Sum_probs=31.6
Q ss_pred HHhhccccccccceeeeceeeEEeechhhHHHHHHhhCC
Q 029742 44 KLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNL 82 (188)
Q Consensus 44 KamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yLhL 82 (188)
+.++.|+.|++|++ -.+..++..||++|.+++.+.+.+
T Consensus 156 ~~l~~LkkRkL~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 193 (489)
T PRK04172 156 KVLKELKKRKLVEE-KERTERSVELTDAGLELLKEGIEL 193 (489)
T ss_pred HHHHHHHhcCCeEE-EEEEEEEEEEccchhhhhhccccc
Confidence 46889999998877 678999999999999999765443
No 69
>PF10662 PduV-EutP: Ethanolamine utilisation - propanediol utilisation; InterPro: IPR012381 Members of this family function in ethanolamine [] and propanediol [] degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively. The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems. Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose [, ]. More than 1% of the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect [, ]. The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella [, , ]. Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 cellular biogenic amine metabolic process
Probab=32.07 E-value=22 Score=29.02 Aligned_cols=38 Identities=26% Similarity=0.402 Sum_probs=27.9
Q ss_pred CHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhhC
Q 029742 39 NLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLN 81 (188)
Q Consensus 39 NL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yLh 81 (188)
+-.+-++-+-|+..|. ++.|-= =..|+|||+-|++||+
T Consensus 105 ~~~i~~a~~~L~~aG~-~~if~v----S~~~~eGi~eL~~~L~ 142 (143)
T PF10662_consen 105 DANIERAKKWLKNAGV-KEIFEV----SAVTGEGIEELKDYLE 142 (143)
T ss_pred hhhHHHHHHHHHHcCC-CCeEEE----ECCCCcCHHHHHHHHh
Confidence 5566677788888776 445421 2579999999999996
No 70
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=31.01 E-value=20 Score=28.82 Aligned_cols=61 Identities=20% Similarity=0.249 Sum_probs=42.5
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCCCCCCCcc----ccCCHHHHHHhhccccccccceeeeceeeEE
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPEI----DVPNLQVIKLMQSFKSREYVRETFAWMHYYW 66 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~~pkHpel----~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw 66 (188)
|.+.++...+|.-.++ |....+-.+ .=.+| +||--++-|+|+.|+..|+|+.+=+=+--|+
T Consensus 1 M~ls~~~~YAlr~L~~----LA~~~~~~~-s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~ 65 (153)
T PRK11920 1 MRLTKQTNYAIRMLMY----CAANDGKLS-RIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVR 65 (153)
T ss_pred CcCchHHhHHHHHHHH----HHhCCCCcC-cHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCee
Confidence 7888999988877765 332222111 11234 5999999999999999999998776433443
No 71
>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=30.26 E-value=7.5 Score=24.76 Aligned_cols=46 Identities=11% Similarity=0.320 Sum_probs=30.6
Q ss_pred hhHHHHHHHhhhcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccc
Q 029742 6 KNRKEICKYLFQEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVR 56 (188)
Q Consensus 6 knr~aIYe~LFkEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVk 56 (188)
.+..+|..+|.+++-+- .+|.. ..++++-=.|-+.++.|+..|+|+
T Consensus 3 ~~~~~Il~~l~~~~~~t-~~ela----~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 3 ETQRKILNYLRENPRIT-QKELA----EKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHHCTTS--HHHHH----HHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHHcCCCC-HHHHH----HHhCCCHHHHHHHHHHHHHCcCcC
Confidence 46778999998765432 11211 123567778899999999999985
No 72
>PF13309 HTH_22: HTH domain
Probab=27.58 E-value=42 Score=23.48 Aligned_cols=26 Identities=23% Similarity=0.501 Sum_probs=22.2
Q ss_pred ccchhhHHHHHHHhhhcceEEEeecC
Q 029742 2 IIPEKNRKEICKYLFQEGVCYAKKDY 27 (188)
Q Consensus 2 lipKknr~aIYe~LFkEGVmVaKKD~ 27 (188)
.|++++|++|-+.|.++|+.-.|.-.
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav 45 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAV 45 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHH
Confidence 47889999999999999999877543
No 73
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=26.87 E-value=27 Score=26.22 Aligned_cols=65 Identities=12% Similarity=0.060 Sum_probs=41.4
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCC-CCCCCcc----ccCCHHHHHHhhccccccccceeeeceeeEEeechh
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYN-LAKHPEI----DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTND 71 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~-~pkHpel----~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnE 71 (188)
|.+.++.+.+|.-.++ +. +.+-. ...-.+| ++|--.|-++|+.|++.|+|...=+..- -|.|+..
T Consensus 1 M~ls~~~~~al~~l~~----la-~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~g-gy~l~~~ 70 (132)
T TIGR00738 1 MKLTKKTEYALRALLD----LA-LNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGG-GYRLARP 70 (132)
T ss_pred CcCccHHHHHHHHHHH----HH-hCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCC-CccCCCC
Confidence 7788888888777665 22 22111 1222233 5899999999999999999986434332 2445443
No 74
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=26.85 E-value=42 Score=33.40 Aligned_cols=45 Identities=18% Similarity=0.225 Sum_probs=35.7
Q ss_pred cCCHHHHHHhhccccccccceeee-ceeeEEeechhhHHHHHHhhCCC
Q 029742 37 VPNLQVIKLMQSFKSREYVRETFA-WMHYYWYLTNDGIEFLRTYLNLP 83 (188)
Q Consensus 37 VpNL~ViKamqSLkSrGyVkEqFa-WrhyYw~LTnEGIeYLR~yLhLP 83 (188)
+-.| |.-++.+|.|.|++|.... -.-.||.||..|-+-|.+ |.-|
T Consensus 321 ~~Dl-vt~aL~~LEs~glik~ev~k~g~l~yvlTe~Gekvle~-l~k~ 366 (593)
T COG1542 321 IDDL-VTAALYTLESFGLIKREVVKNGDLTYVLTEFGEKVLED-LEKS 366 (593)
T ss_pred ccch-HHHHHHhhhhccchhhhhhhcCceEEEehhhhHHHHhc-ccCc
Confidence 6778 9999999999999986554 334699999999988765 4443
No 75
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=26.18 E-value=20 Score=33.04 Aligned_cols=25 Identities=20% Similarity=0.477 Sum_probs=21.0
Q ss_pred ccCCHHHHHHhhccccccccceeee
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFA 60 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFa 60 (188)
++|-..|-|.++||.|+.++|+.=+
T Consensus 111 nLp~~~v~K~LkSLEsKkLIKsVKs 135 (297)
T KOG3233|consen 111 NLPQTVVNKILKSLESKKLIKSVKS 135 (297)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 3577789999999999999998643
No 76
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=26.11 E-value=12 Score=26.66 Aligned_cols=54 Identities=13% Similarity=0.216 Sum_probs=32.0
Q ss_pred CccchhhHHHHHHHhhhcceEEEeecCCCCCCCc----cccCCHHHHHHhhcccccccccee
Q 029742 1 MIIPEKNRKEICKYLFQEGVCYAKKDYNLAKHPE----IDVPNLQVIKLMQSFKSREYVRET 58 (188)
Q Consensus 1 MlipKknr~aIYe~LFkEGVmVaKKD~~~pkHpe----l~VpNL~ViKamqSLkSrGyVkEq 58 (188)
|-+.++.+.+|.-.++ |....|-....=.| +++|--+|-|+|+.|+..|+|+..
T Consensus 1 M~~s~~~~~Al~~l~~----la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 1 MKLSKRTDYALRILLY----LARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp S---HHHHHHHHHHHH----HHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCCCcHHHHHHHHHHH----HHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 6677777777766655 22222211111123 358889999999999999999764
No 77
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=24.01 E-value=41 Score=21.86 Aligned_cols=32 Identities=3% Similarity=0.066 Sum_probs=24.7
Q ss_pred ccCCHHHHHHhhccccccccceeeeceeeEEeech
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTN 70 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTn 70 (188)
+++--.|.++|+.|...|+|...- .-.|.|||
T Consensus 36 g~s~~tv~r~l~~L~~~g~i~~~~---~~~~~l~~ 67 (67)
T cd00092 36 GLTRETVSRTLKELEEEGLISRRG---RGKYRVNP 67 (67)
T ss_pred CCCHHHHHHHHHHHHHCCCEEecC---CCeEEeCC
Confidence 488889999999999999998754 12456654
No 78
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=23.15 E-value=44 Score=22.34 Aligned_cols=27 Identities=15% Similarity=0.060 Sum_probs=19.9
Q ss_pred HHHhhccccccccceeeeceeeEEeechhhH
Q 029742 43 IKLMQSFKSREYVRETFAWMHYYWYLTNDGI 73 (188)
Q Consensus 43 iKamqSLkSrGyVkEqFaWrhyYw~LTnEGI 73 (188)
.+.++.|...|+|+. ..-.+.||++|.
T Consensus 39 ~~~l~~l~~~Gll~~----~~~~l~lT~~G~ 65 (66)
T PF06969_consen 39 QKELEELQEDGLLEI----DGGRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHHTTSEEE-----SSEEEE-TTTG
T ss_pred HHHHHHHHHCCCEEE----eCCEEEECcccC
Confidence 677889999999843 456789999984
No 79
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=23.14 E-value=61 Score=27.20 Aligned_cols=45 Identities=20% Similarity=0.389 Sum_probs=37.5
Q ss_pred ccCCHHHHHHhhccccccccc-eeeeceeeEEeechhhHHHHHHhh
Q 029742 36 DVPNLQVIKLMQSFKSREYVR-ETFAWMHYYWYLTNDGIEFLRTYL 80 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVk-EqFaWrhyYw~LTnEGIeYLR~yL 80 (188)
.|.-..|--.+|||.+-|.|. |..+=..|||..-++-..=+++.+
T Consensus 26 gI~~~~VKdvlq~LvDDglV~~EKiGssn~YWsFps~~~~~~~~~~ 71 (188)
T PF03962_consen 26 GIVSMSVKDVLQSLVDDGLVHVEKIGSSNYYWSFPSQAKQKRQNKL 71 (188)
T ss_pred CCchhhHHHHHHHHhccccchhhhccCeeEEEecChHHHHHHHHHH
Confidence 466789999999999999985 778888999999998877666543
No 80
>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=23.03 E-value=80 Score=25.67 Aligned_cols=30 Identities=30% Similarity=0.351 Sum_probs=24.4
Q ss_pred eeeeceeeEEeechhhHHHHHHhhCCCCCC
Q 029742 57 ETFAWMHYYWYLTNDGIEFLRTYLNLPSEI 86 (188)
Q Consensus 57 EqFaWrhyYw~LTnEGIeYLR~yLhLP~eI 86 (188)
+.=+=+.|.+-..+|=-+.||+|++||.+.
T Consensus 52 ~~dap~~f~~a~ede~tdsLRDf~nL~d~~ 81 (116)
T cd03071 52 EEEAPLLFFVAGEDDMTDSLRDYTNLPEAA 81 (116)
T ss_pred CCCcceeeeeeccchHHHHHHHhcCCCccC
Confidence 334457888899999999999999999653
No 81
>PRK06474 hypothetical protein; Provisional
Probab=22.74 E-value=33 Score=28.26 Aligned_cols=67 Identities=13% Similarity=0.248 Sum_probs=45.7
Q ss_pred cchhhHHHHHHHhhhcce-EEEeecCCCCCCCcc-ccCCHHHHHHhhccccccccceeee-----ceeeEEeechhhHH
Q 029742 3 IPEKNRKEICKYLFQEGV-CYAKKDYNLAKHPEI-DVPNLQVIKLMQSFKSREYVRETFA-----WMHYYWYLTNDGIE 74 (188)
Q Consensus 3 ipKknr~aIYe~LFkEGV-mVaKKD~~~pkHpel-~VpNL~ViKamqSLkSrGyVkEqFa-----WrhyYw~LTnEGIe 74 (188)
+....|.+|.+.|.+.+- +-|+ +.. ..+ +|+---|...|+.|..-|+|+..-- =+.-||.++++++.
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~-el~----~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~ 81 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPL-ELV----KILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAK 81 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHH-HHH----HHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceee
Confidence 345789999999987543 3222 211 112 3666678899999999999986432 23578999998864
No 82
>PF01050 MannoseP_isomer: Mannose-6-phosphate isomerase; InterPro: IPR001538 Mannose-6-phosphate isomerase or phosphomannose isomerase (5.3.1.8 from EC) (PMI) is the enzyme that catalyses the interconversion of mannose-6-phosphate and fructose-6-phosphate. In eukaryotes PMI is involved in the synthesis of GDP-mannose, a constituent of N- and O-linked glycans and GPI anchors and in prokaryotes it participates in a variety of pathways, including capsular polysaccharide biosynthesis and D-mannose metabolism. PMI's belong to the cupin superfamily whose functions range from isomerase and epimerase activities involved in the modification of cell wall carbohydrates in bacteria and plants, to non-enzymatic storage proteins in plant seeds, and transcription factors linked to congenital baldness in mammals []. Three classes of PMI have been defined []. The type II phosphomannose isomerases are bifunctional enzymes 5.3.1.8 from EC. This entry covers the isomerase region of the protein []. The guanosine diphospho-D-mannose pyrophosphorylase region is described in another InterPro entry (see IPR005836 from INTERPRO).; GO: 0016779 nucleotidyltransferase activity, 0005976 polysaccharide metabolic process
Probab=22.54 E-value=71 Score=26.01 Aligned_cols=45 Identities=18% Similarity=0.277 Sum_probs=29.5
Q ss_pred hcceEEEeecCCCCCCCccccCCHHHHHHhhccccccccc------eeeeceeeEEeechhh
Q 029742 17 QEGVCYAKKDYNLAKHPEIDVPNLQVIKLMQSFKSREYVR------ETFAWMHYYWYLTNDG 72 (188)
Q Consensus 17 kEGVmVaKKD~~~pkHpel~VpNL~ViKamqSLkSrGyVk------EqFaWrhyYw~LTnEG 72 (188)
.|++|||.||... .|-+.+..|++++.-. +.-.|-+|.....+++
T Consensus 12 ~DaiLV~~k~~~q-----------~vK~~v~~lk~~~~~E~~~~~~~~rpWG~~~~l~~~~~ 62 (151)
T PF01050_consen 12 PDAILVADKDRSQ-----------DVKEVVEQLKQKGRYEAKEHRRVYRPWGSYEVLDEGEG 62 (151)
T ss_pred CCEEEEECcHHhh-----------hhHHHHHhhhcccccccccceeEecCCcEEEEEEccCC
Confidence 4788888888642 3445566666665433 3468998888776655
No 83
>TIGR01689 EcbF-BcbF capsule biosynthesis phosphatase. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology.
Probab=22.26 E-value=31 Score=27.39 Aligned_cols=48 Identities=19% Similarity=0.211 Sum_probs=39.4
Q ss_pred ccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHHHhhCCCCCCccccc
Q 029742 36 DVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRTYLNLPSEIVPATL 91 (188)
Q Consensus 36 ~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~yLhLP~eIVPaTl 91 (188)
+.+|..++++++.|+++|+.---.+=|.+.+...|=|. +..+.+|.|+
T Consensus 23 ~~~~~~~ie~L~~l~~~G~~IiiaTGR~~~~~~~n~~~--------i~~~~~~~t~ 70 (126)
T TIGR01689 23 VAPILAVIEKLRHYKALGFEIVISSSRNMRTYEGNVGK--------INIHTLPIII 70 (126)
T ss_pred cccCHHHHHHHHHHHHCCCEEEEECCCCchhhhccccc--------cchhhHHHHH
Confidence 56999999999999999998777888999999877666 5566666665
No 84
>PRK11050 manganese transport regulator MntR; Provisional
Probab=20.54 E-value=82 Score=25.05 Aligned_cols=40 Identities=18% Similarity=0.219 Sum_probs=31.3
Q ss_pred cccCCHHHHHHhhccccccccceeeeceeeEEeechhhHHHHH
Q 029742 35 IDVPNLQVIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLR 77 (188)
Q Consensus 35 l~VpNL~ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR 77 (188)
++|..-.|-++++.|.+.|+|...-. --..||++|...++
T Consensus 61 l~is~stVsr~l~~Le~~GlI~r~~~---~~v~LT~~G~~l~~ 100 (152)
T PRK11050 61 LGVSQPTVAKMLKRLARDGLVEMRPY---RGVFLTPEGEKLAQ 100 (152)
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEecC---CceEECchHHHHHH
Confidence 35888899999999999999975432 23689999987644
No 85
>KOG3433 consensus Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=20.49 E-value=55 Score=28.76 Aligned_cols=73 Identities=23% Similarity=0.369 Sum_probs=53.7
Q ss_pred chhhHHHHHHHhhhcceEEEeecCCCCCC-----CccccCCHHHHHHhhcccccccc-ceeeeceeeEEeechhhHHHHH
Q 029742 4 PEKNRKEICKYLFQEGVCYAKKDYNLAKH-----PEIDVPNLQVIKLMQSFKSREYV-RETFAWMHYYWYLTNDGIEFLR 77 (188)
Q Consensus 4 pKknr~aIYe~LFkEGVmVaKKD~~~pkH-----pel~VpNL~ViKamqSLkSrGyV-kEqFaWrhyYw~LTnEGIeYLR 77 (188)
+....+.|...+|.| -|||..-+. |--+|---.|-.++|||..-|.| +|..+=..|||..-.|||.=++
T Consensus 6 s~~ekr~~l~eIf~e-----skDff~LkelEKlG~kKgIv~~tvKdvLQsLvDD~lV~~eKIgtSnyywsfps~a~~~~k 80 (203)
T KOG3433|consen 6 SSDEKRMILLEIFQE-----SKDFFQLKELEKLGSKKGIVWQTVKDVLQSLVDDGLVIKEKIGTSNYYWSFPSEAICDRK 80 (203)
T ss_pred chHHHHHHHHHHHHh-----hHhHHHHHHHHHhCCccceehhHHHHHHHHHhccchHHHHHhcccccccccchHHHHHHH
Confidence 445677888888877 356542221 11124455788899999999996 6788889999999999998888
Q ss_pred HhhC
Q 029742 78 TYLN 81 (188)
Q Consensus 78 ~yLh 81 (188)
.+|.
T Consensus 81 s~~q 84 (203)
T KOG3433|consen 81 SVLQ 84 (203)
T ss_pred HHHH
Confidence 7765
No 86
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=20.08 E-value=84 Score=29.10 Aligned_cols=33 Identities=12% Similarity=0.100 Sum_probs=26.3
Q ss_pred HHHHhhccccccccceeeeceeeEEeechhhHHHHHH
Q 029742 42 VIKLMQSFKSREYVRETFAWMHYYWYLTNDGIEFLRT 78 (188)
Q Consensus 42 ViKamqSLkSrGyVkEqFaWrhyYw~LTnEGIeYLR~ 78 (188)
++++++.|..+|++.. ..-.|.||++|.-++..
T Consensus 401 ~~~~l~~l~~~gll~~----~~~~~~lT~~G~~~~d~ 433 (453)
T PRK09249 401 ELERLAPLEADGLVEL----DENGITVTPKGRLLVRN 433 (453)
T ss_pred HHHHHHHHHHCCCEEE----ECCEEEECccchHHHHH
Confidence 4567889999999874 34579999999988764
Done!