Query gi|254780125|ref|YP_003064538.1| prophage antirepressor [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 262
No_of_seqs 191 out of 1100
Neff 7.2
Searched_HMMs 39220
Date Sun May 29 15:22:24 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780125.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3617 Prophage antirepressor 100.0 8.2E-33 2.1E-37 244.7 13.7 126 1-127 6-133 (176)
2 pfam02498 Bro-N BRO family, N- 99.8 2.3E-19 6E-24 152.4 9.0 86 13-99 1-91 (91)
3 pfam03374 ANT Phage antirepres 99.4 6.7E-13 1.7E-17 108.1 7.5 98 155-255 3-104 (112)
4 COG3645 Uncharacterized phage- 98.9 1.3E-08 3.4E-13 78.6 10.0 96 149-247 20-117 (135)
5 pfam10547 P22_AR_N P22_AR N-te 97.6 0.00074 1.9E-08 46.1 9.0 75 4-79 3-81 (120)
6 PRK11050 manganese transport r 93.4 0.67 1.7E-05 25.8 9.5 57 170-226 48-105 (155)
7 PRK03902 manganese transport t 92.9 0.48 1.2E-05 26.8 6.5 56 171-226 17-73 (142)
8 smart00529 HTH_DTXR Helix-turn 92.1 0.52 1.3E-05 26.6 5.9 48 179-226 2-50 (96)
9 pfam04512 Baculo_PEP_N Baculov 89.4 1.7 4.4E-05 23.0 7.5 91 10-102 1-94 (100)
10 PRK11525 dinD DNA-damage-induc 88.2 0.92 2.4E-05 24.9 4.5 77 18-94 14-110 (279)
11 COG1321 TroR Mn-dependent tran 88.1 1.6 4E-05 23.3 5.6 56 171-226 19-75 (154)
12 pfam09669 Phage_pRha Phage reg 87.6 1.5 3.9E-05 23.3 5.3 67 27-93 3-75 (86)
13 smart00346 HTH_ICLR helix_turn 84.8 3.1 7.9E-05 21.3 6.4 60 168-227 12-73 (91)
14 PRK10870 transcriptional repre 82.1 3.9 1E-04 20.6 9.1 84 142-226 38-128 (176)
15 PRK10163 DNA-binding transcrip 81.7 4 0.0001 20.5 6.0 50 25-80 40-91 (271)
16 smart00347 HTH_MARR helix_turn 76.3 5.8 0.00015 19.4 5.7 56 171-226 19-81 (101)
17 COG1339 Transcriptional regula 76.1 5.9 0.00015 19.4 5.1 16 24-39 18-33 (214)
18 TIGR02431 pcaR_pcaU beta-ketoa 75.7 6.1 0.00015 19.3 4.8 57 170-227 18-75 (252)
19 pfam00851 Peptidase_C6 Helper 74.8 3.6 9.2E-05 20.8 3.3 36 66-101 331-371 (453)
20 PRK11569 transcriptional repre 74.4 6.5 0.00017 19.1 6.3 29 23-51 41-71 (274)
21 PRK04172 pheS phenylalanyl-tRN 73.9 6.7 0.00017 19.0 5.0 17 26-43 21-37 (501)
22 COG1414 IclR Transcriptional r 73.1 7 0.00018 18.8 6.5 13 26-38 20-32 (246)
23 PRK09834 DNA-binding transcrip 72.7 7.1 0.00018 18.8 6.2 31 23-53 24-56 (264)
24 COG2188 PhnF Transcriptional r 69.2 6.9 0.00017 18.9 3.7 40 179-218 34-74 (236)
25 PRK11512 DNA-binding transcrip 68.7 8.7 0.00022 18.2 6.5 71 153-226 34-111 (144)
26 TIGR01764 excise DNA binding d 68.0 8.9 0.00023 18.1 4.1 41 176-218 1-41 (49)
27 pfam02295 z-alpha Adenosine de 67.2 9.3 0.00024 18.0 4.4 46 172-218 14-65 (66)
28 pfam10341 Est3 Telomerase holo 65.0 4.8 0.00012 20.0 2.2 27 89-115 7-33 (160)
29 PRK10141 DNA-binding transcrip 64.1 11 0.00027 17.6 4.0 47 171-217 23-70 (106)
30 COG3943 Virulence protein [Gen 61.5 7.3 0.00019 18.7 2.6 107 4-113 3-125 (329)
31 COG3355 Predicted transcriptio 60.4 12 0.00031 17.2 4.1 51 156-209 24-76 (126)
32 pfam08624 CRC_subunit Chromati 60.2 12 0.00031 17.2 5.3 65 13-77 34-112 (139)
33 pfam01498 Transposase_5 Transp 59.1 13 0.00033 17.0 5.3 47 176-222 13-62 (72)
34 smart00550 Zalpha Z-DNA-bindin 57.7 14 0.00035 16.9 4.4 40 176-218 22-67 (68)
35 pfam09339 HTH_IclR IclR helix- 57.6 14 0.00035 16.9 3.5 40 168-207 10-50 (52)
36 COG1497 Predicted transcriptio 57.0 14 0.00035 16.8 5.6 76 22-103 22-102 (260)
37 pfam09328 Phytochelatin_C Doma 56.5 14 0.00036 16.7 3.8 29 67-95 36-64 (264)
38 TIGR02702 SufR_cyano iron-sulf 55.3 4.8 0.00012 20.0 0.8 53 20-76 12-71 (215)
39 pfam01325 Fe_dep_repress Iron 52.0 17 0.00042 16.3 4.3 36 171-206 15-51 (58)
40 pfam00756 Esterase Putative es 52.0 13 0.00034 16.9 2.6 25 83-107 83-107 (243)
41 TIGR02607 antidote_HigA addict 51.0 15 0.00038 16.6 2.8 33 168-203 13-45 (81)
42 PTZ00326 phenylalanyl-tRNA syn 50.6 17 0.00045 16.1 4.6 14 26-39 21-34 (505)
43 smart00420 HTH_DEOR helix_turn 49.9 18 0.00046 16.0 3.6 38 170-207 8-46 (53)
44 COG2345 Predicted transcriptio 49.5 18 0.00046 16.0 4.9 71 26-107 26-102 (218)
45 COG3432 Predicted transcriptio 48.5 18 0.00046 16.0 2.9 56 172-227 27-86 (95)
46 smart00345 HTH_GNTR helix_turn 46.9 20 0.00051 15.7 3.7 35 177-211 21-56 (60)
47 PRK10079 putative transcriptio 46.3 20 0.00052 15.7 3.7 33 21-53 31-65 (241)
48 COG1510 Predicted transcriptio 46.2 13 0.00034 16.9 1.9 56 20-78 37-94 (177)
49 TIGR00738 rrf2_super rrf2 fami 45.9 21 0.00052 15.6 4.8 51 172-222 21-74 (133)
50 pfam03484 B5 tRNA synthetase B 45.9 21 0.00052 15.6 5.1 42 175-216 4-45 (69)
51 cd00090 HTH_ARSR Arsenical Res 45.7 21 0.00053 15.6 3.9 41 177-217 21-62 (78)
52 KOG2959 consensus 45.1 11 0.00028 17.5 1.3 17 244-260 161-177 (238)
53 PRK12541 RNA polymerase sigma 44.8 21 0.00054 15.5 8.2 108 74-202 40-152 (161)
54 TIGR03337 phnR transcriptional 41.9 24 0.0006 15.2 3.7 34 21-54 21-56 (231)
55 pfam00392 GntR Bacterial regul 41.4 24 0.00061 15.2 4.0 37 175-211 22-60 (64)
56 pfam00126 HTH_1 Bacterial regu 41.3 24 0.00061 15.2 3.8 44 177-220 14-60 (60)
57 PRK09764 DNA-binding transcrip 41.2 24 0.00062 15.2 3.8 33 21-53 25-59 (239)
58 PRK11402 DNA-binding transcrip 40.5 25 0.00063 15.1 4.1 34 21-54 31-66 (243)
59 pfam08220 HTH_DeoR DeoR-like h 40.3 25 0.00063 15.1 3.6 41 170-211 8-49 (57)
60 pfam07833 Cu_amine_oxidN1 Copp 39.8 23 0.0006 15.3 2.3 19 20-38 1-19 (93)
61 TIGR02989 Sig-70_gvs1 RNA poly 38.8 26 0.00067 14.9 7.8 100 85-201 48-154 (163)
62 pfam07592 Transposase_36 Rhodo 38.3 27 0.00068 14.9 3.3 21 28-48 27-50 (311)
63 KOG2947 consensus 35.4 29 0.00075 14.6 4.7 22 177-199 190-211 (308)
64 KOG2145 consensus 34.7 14 0.00036 16.8 0.5 23 20-42 240-263 (397)
65 TIGR02018 his_ut_repres histid 34.5 30 0.00078 14.5 3.5 54 63-116 20-75 (234)
66 COG4615 PvdE ABC-type sideroph 33.9 31 0.00079 14.4 2.7 20 195-217 460-479 (546)
67 cd07377 WHTH_GntR Winged helix 33.7 31 0.0008 14.4 3.6 37 175-211 23-61 (66)
68 COG1725 Predicted transcriptio 33.4 32 0.00081 14.3 4.0 48 173-220 32-80 (125)
69 TIGR02681 phage_pRha phage reg 33.0 23 0.00059 15.3 1.4 75 18-92 6-96 (112)
70 PRK10434 srlR DNA-bindng trans 31.6 34 0.00086 14.1 3.5 26 25-50 19-46 (256)
71 smart00418 HTH_ARSR helix_turn 31.3 34 0.00087 14.1 4.1 43 174-216 8-51 (66)
72 pfam07037 DUF1323 Putative tra 30.9 35 0.00089 14.1 3.5 45 27-73 2-48 (122)
73 PRK10906 DNA-binding transcrip 30.2 36 0.00091 14.0 3.4 25 25-49 19-45 (252)
74 COG4189 Predicted transcriptio 29.2 37 0.00094 13.9 3.3 62 26-88 38-102 (308)
75 pfam01047 MarR MarR family. Th 29.2 37 0.00094 13.9 5.0 40 170-209 11-51 (59)
76 PRK10411 DNA-binding transcrip 29.0 37 0.00095 13.9 3.3 24 26-49 19-44 (240)
77 TIGR02715 amido_AtzE amidohydr 28.7 38 0.00096 13.8 2.1 19 85-103 345-363 (454)
78 TIGR02337 HpaR homoprotocatech 28.3 38 0.00098 13.8 4.1 70 153-227 22-100 (130)
79 TIGR02441 fa_ox_alpha_mit fatt 27.8 39 0.001 13.7 2.8 43 179-221 576-620 (740)
80 TIGR02529 EutJ ethanolamine ut 27.3 40 0.001 13.7 2.2 36 14-49 10-51 (240)
81 TIGR01345 malate_syn_G malate 27.3 25 0.00064 15.0 0.8 26 79-107 4-29 (726)
82 TIGR01194 cyc_pep_trnsptr cycl 27.0 14 0.00035 16.9 -0.6 42 62-104 50-91 (555)
83 pfam10543 ORF6N ORF6N domain. 26.5 41 0.0011 13.6 5.3 60 19-78 6-85 (87)
84 PRK10632 putative DNA-binding 26.2 42 0.0011 13.5 4.8 43 28-74 19-63 (309)
85 PRK10837 putative DNA-binding 25.9 42 0.0011 13.5 4.5 45 28-76 20-66 (291)
86 COG1597 LCB5 Sphingosine kinas 25.7 43 0.0011 13.5 3.1 55 27-83 93-151 (301)
87 PRK12530 RNA polymerase sigma 25.4 43 0.0011 13.4 7.9 46 157-205 134-179 (191)
88 PRK10086 DNA-binding transcrip 25.3 43 0.0011 13.4 4.8 43 28-74 31-75 (311)
89 pfam01638 HxlR HxlR-like helix 24.8 44 0.0011 13.4 5.5 54 174-228 16-78 (90)
90 smart00874 B5 tRNA synthetase 24.8 44 0.0011 13.4 5.1 42 175-216 4-47 (71)
91 KOG1057 consensus 24.7 24 0.00061 15.2 0.3 32 82-114 393-425 (1018)
92 PRK13777 transcriptional regul 24.5 45 0.0011 13.3 4.2 61 177-239 61-129 (190)
93 PRK09801 transcriptional activ 24.3 45 0.0012 13.3 4.6 42 29-74 24-67 (310)
94 pfam04760 IF2_N Translation in 22.6 48 0.0012 13.1 3.8 29 175-205 2-30 (52)
95 PRK12545 RNA polymerase sigma 22.5 49 0.0012 13.1 8.3 47 156-205 136-182 (201)
96 pfam06970 RepA_N Replication i 22.4 49 0.0012 13.1 2.2 23 177-201 53-75 (76)
97 pfam01978 TrmB Sugar-specific 22.3 49 0.0013 13.0 3.9 38 172-209 18-56 (68)
98 pfam11210 DUF2996 Protein of u 22.2 44 0.0011 13.4 1.2 14 243-256 82-95 (118)
99 pfam06904 Extensin-like_C Exte 22.0 50 0.0013 13.0 3.0 25 82-106 49-73 (178)
100 KOG3198 consensus 21.5 18 0.00047 16.0 -0.8 43 10-52 31-73 (152)
101 PRK13509 transcriptional repre 21.4 51 0.0013 12.9 4.0 25 26-50 20-46 (251)
102 pfam08279 HTH_11 HTH domain. T 21.2 52 0.0013 12.9 4.2 39 170-210 9-50 (55)
103 pfam07750 GcrA GcrA cell cycle 20.9 52 0.0013 12.9 1.6 11 26-36 19-29 (162)
104 pfam04684 BAF1_ABF1 BAF1 / ABF 20.5 53 0.0014 12.8 3.7 81 26-111 190-282 (508)
105 TIGR02787 codY_Gpos GTP-sensin 20.4 54 0.0014 12.8 4.9 73 134-207 160-234 (255)
No 1
>COG3617 Prophage antirepressor [Transcription]
Probab=100.00 E-value=8.2e-33 Score=244.67 Aligned_cols=126 Identities=43% Similarity=0.756 Sum_probs=110.0
Q ss_pred CCCCEEEEECCEEEEEEEEECCEEEEEHHHHHHHHCCCCHHHHHHHHCCCCCEEEEE-CCCCCCCEEEEECHHHHHHHHH
Q ss_conf 986257852996799999438908667999998828968899999845674328872-2799831068971877999998
Q gi|254780125|r 1 MSTITPFEFESNKIRTIVDKDQNIWFVAKDVATALGYENSNEAINAHCKGVAKRYPL-KTEGGIQKVRIISEPDVYRLLV 79 (262)
Q Consensus 1 Mn~l~~f~fe~~~ir~v~~~dge~wF~a~dva~~LGy~~~~~ai~~~~~~~~~~~~~-~~~g~~~~~~~i~E~gly~Li~ 79 (262)
|+.+++|+|+++.||++. .||||||+|+|||++|||+|+++++.+||++......+ ++.|+.|++.+|||+|+|+|||
T Consensus 6 ~~~~~~f~F~~~~vRvv~-~d~epwFva~Dva~~Lg~~n~~k~l~~~~d~~~~~~~l~~~~g~~q~~~iiSE~glY~li~ 84 (176)
T COG3617 6 MTMLQPFTFEDHAVRVVL-DDGEPWFVAADVARALGYTNPSKALQRHCDEVTERMSLTDSLGREQEVRIISESGLYKLIM 84 (176)
T ss_pred CCCCCCEEECCCEEEEEE-ECCCEEEEHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCHHHHHH
T ss_conf 144652740683478997-5896557699999997777888999997555531124466678878417985414899999
Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCHHHHHHHHH
Q ss_conf 57996579999988897899999607-7577533222234257999987
Q gi|254780125|r 80 KSTLPSAQKFERWVFEEVLPTLRKTG-SYSVEAPKLRATSASTVLRVHK 127 (262)
Q Consensus 80 ~s~~p~A~~F~~Wv~~eVLPsIRktG-~Y~~~~~~~~~~~~~~~~~~~~ 127 (262)
+|++|+|++|++||++||||+||||| +|.++.+.......++.+..+.
T Consensus 85 ~sr~~~A~~Fr~WV~~eVLPsIRktG~~~~~~~~~~~~~~~~~~l~~~~ 133 (176)
T COG3617 85 RSRKPEAEKFRRWVTDEVLPSIRKTGSAMRTETKLEEAETVLDFLDGIG 133 (176)
T ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCHHHHHHHH
T ss_conf 7277047999999997650877607870432677765022579898888
No 2
>pfam02498 Bro-N BRO family, N-terminal domain. This family includes the N-terminus of baculovirus BRO and ALI motif proteins. The function of BRO proteins is unknown. It has been suggested that BRO-A and BRO-C are DNA binding proteins that influence host DNA replication and/or transcription. This Pfam domain does not include the characteristic invariant alanine, leucine, isoleucine motif of the ALI proteins.
Probab=99.80 E-value=2.3e-19 Score=152.38 Aligned_cols=86 Identities=44% Similarity=0.740 Sum_probs=74.8
Q ss_pred EEEEEEEECCEEEEEHHHHHHHHCCCCHHHHHHHHCCCCCEEE-----EECCCCCCCEEEEECHHHHHHHHHHCCCHHHH
Q ss_conf 7999994389086679999988289688999998456743288-----72279983106897187799999857996579
Q gi|254780125|r 13 KIRTIVDKDQNIWFVAKDVATALGYENSNEAINAHCKGVAKRY-----PLKTEGGIQKVRIISEPDVYRLLVKSTLPSAQ 87 (262)
Q Consensus 13 ~ir~v~~~dge~wF~a~dva~~LGy~~~~~ai~~~~~~~~~~~-----~~~~~g~~~~~~~i~E~gly~Li~~s~~p~A~ 87 (262)
.||++. .+|+|||+|+|||++|||+++++++.+++++..+.. ...+.++.+++.||||+|||+||++|++|.|+
T Consensus 1 ~ir~v~-~~~~~wf~a~dia~~Lgy~~~~~ai~~~v~~~~k~~~~~~~~~~~~~~~~~~~~I~e~Gly~Li~~s~~p~a~ 79 (91)
T pfam02498 1 EVRTVV-INGEPWFVAKDVAKALGYKNPKKAILKHVDDDNKKTLEELTNSIPSNGQQKTVFINESGLYELILRSRKPEAK 79 (91)
T ss_pred CEEEEE-ECCEEEEEHHHHHHHHCCCCHHHHHHHHCCHHHCEEEEEECCCCCCCCCCEEEEECHHHHHHHHHHCCCHHHH
T ss_conf 959999-9998868889999995899889999986798772776653345789987458998153899999974987479
Q ss_pred HHHHHHHHHHHH
Q ss_conf 999988897899
Q gi|254780125|r 88 KFERWVFEEVLP 99 (262)
Q Consensus 88 ~F~~Wv~~eVLP 99 (262)
+||+||+++|||
T Consensus 80 ~F~~Wv~~~vlp 91 (91)
T pfam02498 80 EFRKWVTEEVLP 91 (91)
T ss_pred HHHHHHHCCCCC
T ss_conf 999988636689
No 3
>pfam03374 ANT Phage antirepressor protein KilAC domain. This domain was called the KilAC domain by Iyer and colleagues.
Probab=99.41 E-value=6.7e-13 Score=108.10 Aligned_cols=98 Identities=17% Similarity=0.107 Sum_probs=81.0
Q ss_pred HHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHHCC--CCCC
Q ss_conf 30234200134666541558732399999973899888999999997897685379944365789754355304--7534
Q gi|254780125|r 155 TGVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKLLLKRGLQVSKVSGGYRPTPKGEERGGKMCD--VPMQ 232 (262)
Q Consensus 155 ~~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~~g~~~~~--~p~~ 232 (262)
+++++++||+.|+|.+++++++++++++||.|+ +++.+||++|++.||+||+.+++|.||+++.+.|+.-.. ....
T Consensus 3 ~~i~~~~PKv~~~D~~~~~~~~~~i~~~AK~l~--i~~~~L~~~L~~~~~l~r~~~~~~~pyq~~i~~Gyf~~k~~~~~~ 80 (112)
T pfam03374 3 QQLAEAAPKAEYADAIAASDGLVLVGQIAKLLG--IGENRLFKWLRENGILYRRGSGRWLPYQKHIEKGYFEVKTGVITR 80 (112)
T ss_pred HHHHHHCCCHHHHHHHHCCCCCEEHHHHHHHHC--CCHHHHHHHHHHCCEEEECCCCCCCCHHHHHHCCCEEEEEEEEEC
T ss_conf 588771852699999975799587999999929--999999999998892898899975224789859988999999875
Q ss_pred CC--CCCCEEEEECHHHHHHHHHHH
Q ss_conf 68--833116754501776565310
Q gi|254780125|r 233 HV--EGSTQQLKWNSNLLVSFLQNE 255 (262)
Q Consensus 233 ~~--g~~~~q~~w~~~v~~~~~~~~ 255 (262)
++ ++..+|++|+|.+++ ++.+.
T Consensus 81 ~~G~~~~~~~t~vT~KG~~-~i~~~ 104 (112)
T pfam03374 81 SDGTEHIKPTTKVTPKGQL-WIYEL 104 (112)
T ss_pred CCCCEEEEEEEEEECHHHH-HHHHH
T ss_conf 8998788777799550799-99999
No 4
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=98.92 E-value=1.3e-08 Score=78.61 Aligned_cols=96 Identities=13% Similarity=0.027 Sum_probs=75.5
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHHCC
Q ss_conf 99999830234200134666541558732399999973899888999999997897685379944365789754355304
Q gi|254780125|r 149 RGVTKITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKLLLKRGLQVSKVSGGYRPTPKGEERGGKMCD 228 (262)
Q Consensus 149 ~~~~~~~~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~~g~~~~~ 228 (262)
++..+.+++...+||++|+|.++++.+++.++++||.++ +++++|+.+|.+.|++|+..++.-.||+++++.|. ++.
T Consensus 20 e~~~~~~el~~~~PKv~f~D~v~~~~gli~~re~AK~lk--ige~~l~~~L~e~~~l~~~~~~~n~p~q~~me~Gl-F~V 96 (135)
T COG3645 20 ENEVLTVELAIAAPKVEFADAVVEASGLILFRELAKLLK--IGENRLFAWLRENKYLIKRGGDKNLPTQKHMELGL-FKV 96 (135)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCCCCCEEHHHHHHHHC--CCHHHHHHHHHHCCEEEEECCCCCCCCHHHHHCCC-EEE
T ss_conf 987777777774711388998851766251999999976--37789999999878789706777778566752674-588
Q ss_pred CC--CCCCCCCCEEEEECHHH
Q ss_conf 75--34688331167545017
Q gi|254780125|r 229 VP--MQHVEGSTQQLKWNSNL 247 (262)
Q Consensus 229 ~p--~~~~g~~~~q~~w~~~v 247 (262)
+. -.++++...|.+-+|..
T Consensus 97 Ke~~i~~s~g~~t~~~~T~~t 117 (135)
T COG3645 97 KETSIAHSNGAITQTKTTKKT 117 (135)
T ss_pred EEEEEECCCCCEEEEEECCCC
T ss_conf 766553168723688854642
No 5
>pfam10547 P22_AR_N P22_AR N-terminal domain. This domain was identified by Iyer and colleagues.
Probab=97.58 E-value=0.00074 Score=46.11 Aligned_cols=75 Identities=11% Similarity=0.185 Sum_probs=55.5
Q ss_pred CEEEEECCEEEEEEEEECCEEEEEHHHHHHHHCCCCHHHHHHHHCCCC----CEEEEECCCCCCCEEEEECHHHHHHHHH
Q ss_conf 257852996799999438908667999998828968899999845674----3288722799831068971877999998
Q gi|254780125|r 4 ITPFEFESNKIRTIVDKDQNIWFVAKDVATALGYENSNEAINAHCKGV----AKRYPLKTEGGIQKVRIISEPDVYRLLV 79 (262)
Q Consensus 4 l~~f~fe~~~ir~v~~~dge~wF~a~dva~~LGy~~~~~ai~~~~~~~----~~~~~~~~~g~~~~~~~i~E~gly~Li~ 79 (262)
.+...|.|..+-++ ..||+||...+.+|++||..-.++.-+..-+.. .....+.+.|+.|+|.|++..-|.--++
T Consensus 3 t~~V~F~g~~l~~v-~~ng~~yv~mKpI~e~mGLdw~sQ~~KLk~~~~~~~~~~i~~v~~dGk~rem~clpl~~L~gWL~ 81 (120)
T pfam10547 3 TQTVPFHGQELITV-EQNGEPYVAMKPIVEGMGLSWSSQYRKLMRDDVLSSIVAIMIVASDGKNREMLCLPLRKLNGWLF 81 (120)
T ss_pred CEEECCCCCEEEEE-EECCEEEEEHHHHHHHCCCCHHHHHHHHHCCCHHCCEEEEEEECCCCCEEEEEEEEHHHHHHHHE
T ss_conf 17953269888999-67997887507778762887199999986030121149999973788577899988778666770
No 6
>PRK11050 manganese transport regulator MntR; Provisional
Probab=93.41 E-value=0.67 Score=25.84 Aligned_cols=57 Identities=21% Similarity=0.151 Sum_probs=46.3
Q ss_pred HHCCCCCCCHHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHH
Q ss_conf 41558732399999973899-8889999999978976853799443657897543553
Q gi|254780125|r 170 SSDNDEYLTITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSGGYRPTPKGEERGGKM 226 (262)
Q Consensus 170 ~~~~~~~l~~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~~g~~~ 226 (262)
+...+|.....+||..||+. -|.-.+-+.|.+.|+.....-+...||++|...+...
T Consensus 48 L~~~~G~aR~~DIA~~LgVs~pSVt~mlkrL~~~GlV~~~~Y~~I~LT~~G~~~A~~i 105 (155)
T PRK11050 48 LIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQES 105 (155)
T ss_pred HHHCCCCEEHHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHH
T ss_conf 9982695649999989099933199999999878998871898846897799999999
No 7
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=92.87 E-value=0.48 Score=26.80 Aligned_cols=56 Identities=21% Similarity=0.303 Sum_probs=44.2
Q ss_pred HCCCCCCCHHHHHHHHCCCC-CHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHH
Q ss_conf 15587323999999738998-889999999978976853799443657897543553
Q gi|254780125|r 171 SDNDEYLTITQIGERLNPPQ-RARFLNKLLLKRGLQVSKVSGGYRPTPKGEERGGKM 226 (262)
Q Consensus 171 ~~~~~~l~~t~iak~l~~~~-sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~~g~~~ 226 (262)
....+...+++||+.||+.. |...+-+.|.+.|+......+.-.||++|...+...
T Consensus 17 ~~~~~~vr~~dIA~~L~Vs~~SVs~mikkL~~~Glv~~~~y~~i~LT~~G~~~A~~i 73 (142)
T PRK03902 17 IEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL 73 (142)
T ss_pred HHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCEECCCCCEEECHHHHHHHHHH
T ss_conf 825897129999999789953399999999987992455898756898799999999
No 8
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=92.10 E-value=0.52 Score=26.58 Aligned_cols=48 Identities=29% Similarity=0.309 Sum_probs=39.1
Q ss_pred HHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHH
Q ss_conf 99999973899-8889999999978976853799443657897543553
Q gi|254780125|r 179 ITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSGGYRPTPKGEERGGKM 226 (262)
Q Consensus 179 ~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~~g~~~ 226 (262)
+++||+.||+. -|...+-+.|.+.|+......+...||++|...+...
T Consensus 2 ~~diA~~L~vs~~sVs~~l~~L~~~Gli~~~~y~~i~LT~~G~~~A~~i 50 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRL 50 (96)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHH
T ss_conf 7889988499916799999999988898874998978898799999999
No 9
>pfam04512 Baculo_PEP_N Baculovirus polyhedron envelope protein, PEP, N terminus. Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense structure called the polyhedron envelope or polyhedron calyx. The polyhedron envelope (associated) protein PEP is thought to be an integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper formation of the periphery of polyhedra. It is thought that PEP may stabilize polyhedra and protect them from fusion or aggregation.
Probab=89.42 E-value=1.7 Score=23.03 Aligned_cols=91 Identities=13% Similarity=0.134 Sum_probs=58.4
Q ss_pred CCEEEEEEEEECCEEEEEHHHHHHHHCCCCHHHHHHHHCCCCCEEEE-EC--CCCCCCEEEEECHHHHHHHHHHCCCHHH
Q ss_conf 99679999943890866799999882896889999984567432887-22--7998310689718779999985799657
Q gi|254780125|r 10 ESNKIRTIVDKDQNIWFVAKDVATALGYENSNEAINAHCKGVAKRYP-LK--TEGGIQKVRIISEPDVYRLLVKSTLPSA 86 (262)
Q Consensus 10 e~~~ir~v~~~dge~wF~a~dva~~LGy~~~~~ai~~~~~~~~~~~~-~~--~~g~~~~~~~i~E~gly~Li~~s~~p~A 86 (262)
+|..|-++.+.+..+||.|.+|-++|+.. ..++......+++... +. .........||++=|+=-|+.+.....|
T Consensus 1 dg~~V~v~fd~~~vlWvgaDevl~iL~lp--~s~l~~iP~~~kk~w~dl~~~~~~~d~nK~Fit~~G~~~L~~r~~~~~a 78 (100)
T pfam04512 1 DGTDVPVFFDADMVLWVGADEVLQILRLP--PSALQSLPLSEKKLWKDLEPGCCRVDSNKLFVTALGVGLLCSRTQSERA 78 (100)
T ss_pred CCCCEEEEECCCCEEEECHHHHHHHHCCC--HHHHHHCCHHHHHHHHHCCCCCCCCCCCEEEEEHHHHHHHHCCCCHHHH
T ss_conf 99516699758966897199999996799--8999776879899999758986678885575518769999924657999
Q ss_pred HHHHHHHHHHHHHHHH
Q ss_conf 9999988897899999
Q gi|254780125|r 87 QKFERWVFEEVLPTLR 102 (262)
Q Consensus 87 ~~F~~Wv~~eVLPsIR 102 (262)
-.|--=...|+.-+++
T Consensus 79 d~l~t~Fiad~y~e~~ 94 (100)
T pfam04512 79 DALATIFIADTYRDYC 94 (100)
T ss_pred HHHHHHHHHHHHHHHH
T ss_conf 9999999999999999
No 10
>PRK11525 dinD DNA-damage-inducible protein D; Provisional
Probab=88.24 E-value=0.92 Score=24.88 Aligned_cols=77 Identities=12% Similarity=0.185 Sum_probs=48.4
Q ss_pred EEECCEEEEEHHHHHHHHCCCCHHHHHHHHCCC--------C-------CEEEEE-CCCCCCC--EEEEECHHHHHHHHH
Q ss_conf 943890866799999882896889999984567--------4-------328872-2799831--068971877999998
Q gi|254780125|r 18 VDKDQNIWFVAKDVATALGYENSNEAINAHCKG--------V-------AKRYPL-KTEGGIQ--KVRIISEPDVYRLLV 79 (262)
Q Consensus 18 ~~~dge~wF~a~dva~~LGy~~~~~ai~~~~~~--------~-------~~~~~~-~~~g~~~--~~~~i~E~gly~Li~ 79 (262)
.++||..++.|+|++..|||+..++..+...+. . .....+ ..+|..+ .-..+|--.||.+++
T Consensus 14 ~~e~G~EyW~ARdL~~~LgY~~w~~F~~vI~rA~~ac~~~g~~v~dHF~~v~kmv~~gsGa~R~i~D~~LsRyACYLIaq 93 (279)
T PRK11525 14 IGEEGVEFWSARELAPLLGYSEWRNFQKVIARAKTACENSGHAVSDHFVEVTKMVVLGSGAQREVEDIMLSRYACYLIVQ 93 (279)
T ss_pred CCCCCCEEEEHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCHHHEEHHHHHHHHH
T ss_conf 58999873409987886392889989999999999999869986787898777620577777753100024787789986
Q ss_pred HC--CCHHHHHHHHHHH
Q ss_conf 57--9965799999888
Q gi|254780125|r 80 KS--TLPSAQKFERWVF 94 (262)
Q Consensus 80 ~s--~~p~A~~F~~Wv~ 94 (262)
.. ++|+-..=|-+++
T Consensus 94 NgDp~K~~IA~aQtYFA 110 (279)
T PRK11525 94 NGDPRKPVIAAGQTYFA 110 (279)
T ss_pred CCCCCCHHHHHHHHHHH
T ss_conf 27886389998879999
No 11
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=88.15 E-value=1.6 Score=23.27 Aligned_cols=56 Identities=25% Similarity=0.322 Sum_probs=43.7
Q ss_pred HCCCCCCCHHHHHHHHCCCC-CHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHH
Q ss_conf 15587323999999738998-889999999978976853799443657897543553
Q gi|254780125|r 171 SDNDEYLTITQIGERLNPPQ-RARFLNKLLLKRGLQVSKVSGGYRPTPKGEERGGKM 226 (262)
Q Consensus 171 ~~~~~~l~~t~iak~l~~~~-sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~~g~~~ 226 (262)
...++....++||+.|++.. |...+-+-|.+.|+......+.-.||++|...+...
T Consensus 19 ~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~ 75 (154)
T COG1321 19 LEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKEL 75 (154)
T ss_pred HHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEECCCCEEECCCHHHHHHHH
T ss_conf 843687519999998589927899999999878997884588867883548999999
No 12
>pfam09669 Phage_pRha Phage regulatory protein Rha (Phage_pRha). Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that Rha is a phage regulatory protein.
Probab=87.56 E-value=1.5 Score=23.35 Aligned_cols=67 Identities=15% Similarity=0.138 Sum_probs=45.7
Q ss_pred EHHHHHHHHCCC--CHHHHHHHHCCC----CCEEEEECCCCCCCEEEEECHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 799999882896--889999984567----4328872279983106897187799999857996579999988
Q gi|254780125|r 27 VAKDVATALGYE--NSNEAINAHCKG----VAKRYPLKTEGGIQKVRIISEPDVYRLLVKSTLPSAQKFERWV 93 (262)
Q Consensus 27 ~a~dva~~LGy~--~~~~ai~~~~~~----~~~~~~~~~~g~~~~~~~i~E~gly~Li~~s~~p~A~~F~~Wv 93 (262)
...+||+.+|-. |.-+.|+.+... .......+..|..+....++++|++-|++.-..++|.+|+-=+
T Consensus 3 tS~~IAe~~gk~H~~Vlr~Ir~~~~~~~~~f~~~~y~~~~g~~~~~Y~ltkdg~~lLv~g~tg~ka~~fk~~~ 75 (86)
T pfam09669 3 TSLEIAELFGKRHKNVLRDIENLLKDFLNFFIESSYTDSRGRKYPMYLLTKDGFMLLVMGFTGKKAAEFKAAY 75 (86)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEEEECCCCHHHHHHCCCCCHHHHHHHHH
T ss_conf 7899999988266899999999998886256443677899958779986225278877505774178999999
No 13
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=84.76 E-value=3.1 Score=21.29 Aligned_cols=60 Identities=27% Similarity=0.290 Sum_probs=45.5
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCCC-HHHHHHHHHHCCCEEEC-CCCCEEECHHHHHHHHHHC
Q ss_conf 654155873239999997389988-89999999978976853-7994436578975435530
Q gi|254780125|r 168 LPSSDNDEYLTITQIGERLNPPQR-ARFLNKLLLKRGLQVSK-VSGGYRPTPKGEERGGKMC 227 (262)
Q Consensus 168 d~~~~~~~~l~~t~iak~l~~~~s-a~~~N~lL~~~g~q~Rk-~~~~W~lt~kg~~~g~~~~ 227 (262)
+.+.++..-+++++|++.+|++.| ..++=.-|.+.|+..+. ..+.|.|..+-...|....
T Consensus 12 ~~l~~~~~~~sl~eia~~~~l~ksT~~RlL~tL~~~G~l~~~~~~~~Y~lG~~~~~lg~~~~ 73 (91)
T smart00346 12 RALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVLELGQSYL 73 (91)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCEEEECHHHHHHHHHHH
T ss_conf 99972899989999999989099999999999998899688499997753099999999988
No 14
>PRK10870 transcriptional repressor MprA; Provisional
Probab=82.09 E-value=3.9 Score=20.57 Aligned_cols=84 Identities=21% Similarity=0.235 Sum_probs=56.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCC-CHHHHHHHHHHCCCEEECCCC------CEE
Q ss_conf 9999999999998302342001346665415587323999999738998-889999999978976853799------443
Q gi|254780125|r 142 QLLLKVNRGVTKITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQ-RARFLNKLLLKRGLQVSKVSG------GYR 214 (262)
Q Consensus 142 ~~~~~~~~~~~~~~~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~-sa~~~N~lL~~~g~q~Rk~~~------~W~ 214 (262)
..+..........+|+.+.+-.+.... .......+++++||+.+++.. +.-++-.-|.+.||..|..+. .-.
T Consensus 38 ~~l~~~~n~~L~~~GLs~~~f~vL~~L-~~~~~~~l~PseLa~~l~~s~a~iTr~vD~LEkkGlV~R~~s~~DRR~~~V~ 116 (176)
T PRK10870 38 SKLLENRNKMLKAQGINETLFMALITL-ESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQ 116 (176)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHH-HCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEE
T ss_conf 999999998998829988899999999-7189998598999999778710199999999988997872371235347889
Q ss_pred ECHHHHHHHHHH
Q ss_conf 657897543553
Q gi|254780125|r 215 PTPKGEERGGKM 226 (262)
Q Consensus 215 lt~kg~~~g~~~ 226 (262)
||++|...-...
T Consensus 117 LT~~G~~ll~~~ 128 (176)
T PRK10870 117 LTEKGHEFLREV 128 (176)
T ss_pred ECHHHHHHHHHH
T ss_conf 898899999998
No 15
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=81.70 E-value=4 Score=20.48 Aligned_cols=50 Identities=10% Similarity=-0.073 Sum_probs=25.9
Q ss_pred EEEHHHHHHHHCCCCH--HHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHHHHHHHH
Q ss_conf 6679999988289688--9999984567432887227998310689718779999985
Q gi|254780125|r 25 WFVAKDVATALGYENS--NEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDVYRLLVK 80 (262)
Q Consensus 25 wF~a~dva~~LGy~~~--~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gly~Li~~ 80 (262)
-..+.|+|+.||...+ ++.+..+.+....... ..++ .|--=..+++|...
T Consensus 40 ~ltl~eia~~lglpksT~~RlL~tL~~~G~v~~d--~~~~----~Y~lG~~~~~lg~~ 91 (271)
T PRK10163 40 SSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD--SQLG----WWHIGLGVFNVGAA 91 (271)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE--CCCC----CEECCHHHHHHHHH
T ss_conf 9799999999791999999999999968988984--8999----17647899876765
No 16
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=76.27 E-value=5.8 Score=19.38 Aligned_cols=56 Identities=20% Similarity=0.150 Sum_probs=37.8
Q ss_pred HCCCCCCCHHHHHHHHCCCCC-HHHHHHHHHHCCCEEECCCC------CEEECHHHHHHHHHH
Q ss_conf 155873239999997389988-89999999978976853799------443657897543553
Q gi|254780125|r 171 SDNDEYLTITQIGERLNPPQR-ARFLNKLLLKRGLQVSKVSG------GYRPTPKGEERGGKM 226 (262)
Q Consensus 171 ~~~~~~l~~t~iak~l~~~~s-a~~~N~lL~~~g~q~Rk~~~------~W~lt~kg~~~g~~~ 226 (262)
+...+-+++++||+.+++..+ .-.+-+-|.+.||..|.... ...||++|...-...
T Consensus 19 l~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~LT~~G~~~~~~~ 81 (101)
T smart00347 19 LYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEEL 81 (101)
T ss_pred HHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEECHHHHHHHHHH
T ss_conf 997699799999999896887999999999458938982189998858989998999999999
No 17
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=76.15 E-value=5.9 Score=19.36 Aligned_cols=16 Identities=19% Similarity=0.374 Sum_probs=7.5
Q ss_pred EEEEHHHHHHHHCCCC
Q ss_conf 8667999998828968
Q gi|254780125|r 24 IWFVAKDVATALGYEN 39 (262)
Q Consensus 24 ~wF~a~dva~~LGy~~ 39 (262)
+.....++|+-||++.
T Consensus 18 ~~~t~~ela~~l~~S~ 33 (214)
T COG1339 18 VKVTSSELAKRLGVSS 33 (214)
T ss_pred CCCCHHHHHHHHCCCC
T ss_conf 6020899998857470
No 18
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=75.67 E-value=6.1 Score=19.27 Aligned_cols=57 Identities=19% Similarity=0.131 Sum_probs=45.5
Q ss_pred HHCCCCCCCHHHHHHHHCCCC-CHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHHHHC
Q ss_conf 415587323999999738998-8899999999789768537994436578975435530
Q gi|254780125|r 170 SSDNDEYLTITQIGERLNPPQ-RARFLNKLLLKRGLQVSKVSGGYRPTPKGEERGGKMC 227 (262)
Q Consensus 170 ~~~~~~~l~~t~iak~l~~~~-sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~~g~~~~ 227 (262)
+-..+..+|++|+|+.-|.+. +||++=-=|.+.||.. .+++.|.||+|==..|..+-
T Consensus 18 F~~~~~~ltl~~vA~~TGL~RAaARR~LLTL~~LGY~~-~Dg~~F~LTPrvL~LG~aYL 75 (252)
T TIGR02431 18 FGEERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVE-SDGRLFWLTPRVLRLGYAYL 75 (252)
T ss_pred HCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCEE-CCCCCEECCHHHHHHHHHHH
T ss_conf 31037898989999875899479888998465623042-17983310246775332220
No 19
>pfam00851 Peptidase_C6 Helper component proteinase. This protein is found in genome polyproteins of potyviruses.
Probab=74.83 E-value=3.6 Score=20.80 Aligned_cols=36 Identities=22% Similarity=0.320 Sum_probs=15.5
Q ss_pred EEEECHHHHHHHHHHC-----CCHHHHHHHHHHHHHHHHHH
Q ss_conf 6897187799999857-----99657999998889789999
Q gi|254780125|r 66 VRIISEPDVYRLLVKS-----TLPSAQKFERWVFEEVLPTL 101 (262)
Q Consensus 66 ~~~i~E~gly~Li~~s-----~~p~A~~F~~Wv~~eVLPsI 101 (262)
|++..|.-+|--||-+ +-..||.|.++|-+.++|.+
T Consensus 331 mYIAkeGYCYiNIFLAMLvNV~E~~AKdFTK~VRD~ivp~L 371 (453)
T pfam00851 331 MYIAKEGYCYINIFLAMLVNVNEDEAKDFTKMVRDVIVPKL 371 (453)
T ss_pred EEECCCCEEHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 78714871099999999817778888999999999998873
No 20
>PRK11569 transcriptional repressor IclR; Provisional
Probab=74.37 E-value=6.5 Score=19.06 Aligned_cols=29 Identities=17% Similarity=0.123 Sum_probs=17.8
Q ss_pred EEEEEHHHHHHHHCCCCH--HHHHHHHCCCC
Q ss_conf 086679999988289688--99999845674
Q gi|254780125|r 23 NIWFVAKDVATALGYENS--NEAINAHCKGV 51 (262)
Q Consensus 23 e~wF~a~dva~~LGy~~~--~~ai~~~~~~~ 51 (262)
.....+.|+|+.+|+..+ ++.++.+.+..
T Consensus 41 ~~~lsl~eia~~lglpksT~~RlL~tL~~~G 71 (274)
T PRK11569 41 NGSVALTELAQQAGLPNSTTHRLLTTMQQQG 71 (274)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 9998999999987919999999999999769
No 21
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=73.90 E-value=6.7 Score=18.98 Aligned_cols=17 Identities=24% Similarity=0.436 Sum_probs=12.6
Q ss_pred EEHHHHHHHHCCCCHHHH
Q ss_conf 679999988289688999
Q gi|254780125|r 26 FVAKDVATALGYENSNEA 43 (262)
Q Consensus 26 F~a~dva~~LGy~~~~~a 43 (262)
....++|+.+|.. ...+
T Consensus 21 ~~~eeLa~~~g~d-~~~V 37 (501)
T PRK04172 21 ATAEELAEKLGLD-EEAV 37 (501)
T ss_pred CCHHHHHHHCCCC-HHHH
T ss_conf 9999999882999-9999
No 22
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=73.08 E-value=7 Score=18.85 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=8.1
Q ss_pred EEHHHHHHHHCCC
Q ss_conf 6799999882896
Q gi|254780125|r 26 FVAKDVATALGYE 38 (262)
Q Consensus 26 F~a~dva~~LGy~ 38 (262)
....++|+.+|+.
T Consensus 20 l~l~ela~~~glp 32 (246)
T COG1414 20 LSLAELAERLGLP 32 (246)
T ss_pred CCHHHHHHHHCCC
T ss_conf 8799999987919
No 23
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=72.73 E-value=7.1 Score=18.79 Aligned_cols=31 Identities=6% Similarity=-0.110 Sum_probs=20.2
Q ss_pred EEEEEHHHHHHHHCCCCH--HHHHHHHCCCCCE
Q ss_conf 086679999988289688--9999984567432
Q gi|254780125|r 23 NIWFVAKDVATALGYENS--NEAINAHCKGVAK 53 (262)
Q Consensus 23 e~wF~a~dva~~LGy~~~--~~ai~~~~~~~~~ 53 (262)
++...+.|+|+.+|...+ ++.+..+++....
T Consensus 24 ~~~lslsela~~lglpksTv~RlL~tL~~~G~l 56 (264)
T PRK09834 24 DGGATVGLLAELTGLHRTTVRRLLETLQEEGYV 56 (264)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
T ss_conf 999799999999790999999999999978998
No 24
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=69.23 E-value=6.9 Score=18.91 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=26.8
Q ss_pred HHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCCCEEECHH
Q ss_conf 99999973899-88899999999789768537994436578
Q gi|254780125|r 179 ITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSGGYRPTPK 218 (262)
Q Consensus 179 ~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~~W~lt~k 218 (262)
=.++|+.+|+. |+.++.-..|.+.|+.+|.+|..|....+
T Consensus 34 E~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~GtfV~~~ 74 (236)
T COG2188 34 ERELAEQFGVSRMTVRKALDELVEEGLIVRRQGKGTFVASP 74 (236)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCEEEECCC
T ss_conf 89999997988999999999999899889951667898877
No 25
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=68.65 E-value=8.7 Score=18.20 Aligned_cols=71 Identities=11% Similarity=-0.006 Sum_probs=46.3
Q ss_pred HHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCC-HHHHHHHHHHCCCEEECCC--CC----EEECHHHHHHHHH
Q ss_conf 983023420013466654155873239999997389988-8999999997897685379--94----4365789754355
Q gi|254780125|r 153 KITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQR-ARFLNKLLLKRGLQVSKVS--GG----YRPTPKGEERGGK 225 (262)
Q Consensus 153 ~~~~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~s-a~~~N~lL~~~g~q~Rk~~--~~----W~lt~kg~~~g~~ 225 (262)
...++...+-.. ...+...+.++.+++|+.+++..+ .-.+-..|.+.|+..|..+ ++ -.||++|......
T Consensus 34 ~~~gLt~~Q~~v---L~~L~~~~~~t~~eLa~~l~id~~tvt~~ldrLe~~GlI~R~~~p~DrR~~~v~LT~~G~~l~~~ 110 (144)
T PRK11512 34 SPLDITAAQFKV---LCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred HHCCCCHHHHHH---HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCCEEEEEECHHHHHHHHH
T ss_conf 545999999999---99999869979999999978888789999999997879663579877624787889779999999
Q ss_pred H
Q ss_conf 3
Q gi|254780125|r 226 M 226 (262)
Q Consensus 226 ~ 226 (262)
.
T Consensus 111 ~ 111 (144)
T PRK11512 111 C 111 (144)
T ss_pred H
T ss_conf 9
No 26
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This entry identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=68.01 E-value=8.9 Score=18.12 Aligned_cols=41 Identities=24% Similarity=0.351 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHHCCCEEECCCCCEEECHH
Q ss_conf 3239999997389988899999999789768537994436578
Q gi|254780125|r 176 YLTITQIGERLNPPQRARFLNKLLLKRGLQVSKVSGGYRPTPK 218 (262)
Q Consensus 176 ~l~~t~iak~l~~~~sa~~~N~lL~~~g~q~Rk~~~~W~lt~k 218 (262)
.+|+.++|+-||+ |-.-+-+|+++.+|-+-+.|++|++...
T Consensus 1 ~lTv~EaA~yLgv--~~~t~~~l~~~g~l~~~~~G~~~ri~~~ 41 (49)
T TIGR01764 1 YLTVEEAAEYLGV--SKSTVYRLIEEGELPAYRVGRHYRIKRE 41 (49)
T ss_pred CCCHHHHHHHCCC--CHHHHHHHHHCCCCCEEECCCCEECCHH
T ss_conf 9877889977199--9057899997189850006860202499
No 27
>pfam02295 z-alpha Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.
Probab=67.18 E-value=9.3 Score=18.01 Aligned_cols=46 Identities=22% Similarity=0.177 Sum_probs=33.0
Q ss_pred CCCCCCCHHHHHHHHCCCCCHHHHHHHH---HHCCCEEECCCC---CEEECHH
Q ss_conf 5587323999999738998889999999---978976853799---4436578
Q gi|254780125|r 172 DNDEYLTITQIGERLNPPQRARFLNKLL---LKRGLQVSKVSG---GYRPTPK 218 (262)
Q Consensus 172 ~~~~~l~~t~iak~l~~~~sa~~~N~lL---~~~g~q~Rk~~~---~W~lt~k 218 (262)
...+.-+++.+|+..+.+...+.+|+.| .+.|-..+ .++ .|.+|.+
T Consensus 14 ~~~g~~ta~~~ak~~gL~~~k~evN~~Ly~L~~~g~v~~-~~~~PP~W~lt~~ 65 (66)
T pfam02295 14 RNSGGKTATAIALARGLSKEKKEINRILYDLERKGELCK-EDGTPPLWFLTDK 65 (66)
T ss_pred HHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEE-CCCCCCCEEECCC
T ss_conf 964750599999985228758899999999997789410-7998998261357
No 28
>pfam10341 Est3 Telomerase holoenzyme, Est3 subunit. EST3 is a component of the telomerase holoenzyme, involved in telomere replication. It has been demonstrated that Est3 dimerizes and binds to DNA and RNA. Furthermore, Est3 stimulates the dissociation of RNA/DNA hetero-duplexes.
Probab=65.04 E-value=4.8 Score=19.96 Aligned_cols=27 Identities=15% Similarity=0.487 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 999888978999996077577533222
Q gi|254780125|r 89 FERWVFEEVLPTLRKTGSYSVEAPKLR 115 (262)
Q Consensus 89 F~~Wv~~eVLPsIRktG~Y~~~~~~~~ 115 (262)
.+.|+-+.|.|+|.++|.|.++...+.
T Consensus 7 l~~Wl~~~V~~~i~~~~~y~i~~lik~ 33 (160)
T pfam10341 7 LQEWLKDAVTESINSNGRYVIPSLIKK 33 (160)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCHH
T ss_conf 588899999977602462613654765
No 29
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=64.14 E-value=11 Score=17.62 Aligned_cols=47 Identities=17% Similarity=0.162 Sum_probs=31.8
Q ss_pred HCCCCCCCHHHHHHHHCCCCCHH-HHHHHHHHCCCEEECCCCCEEECH
Q ss_conf 15587323999999738998889-999999978976853799443657
Q gi|254780125|r 171 SDNDEYLTITQIGERLNPPQRAR-FLNKLLLKRGLQVSKVSGGYRPTP 217 (262)
Q Consensus 171 ~~~~~~l~~t~iak~l~~~~sa~-~~N~lL~~~g~q~Rk~~~~W~lt~ 217 (262)
+...+-+++.+|++.+|++.++. .-=+.|.+.|+..+...|+|.-|.
T Consensus 23 L~~~gelcV~eL~~~l~~sQs~vS~HL~~L~~aGlV~~rr~G~~vyY~ 70 (106)
T PRK10141 23 LRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYR 70 (106)
T ss_pred HHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCEEEECCEEEEEE
T ss_conf 987499569999988699888999999999988973037414179987
No 30
>COG3943 Virulence protein [General function prediction only]
Probab=61.48 E-value=7.3 Score=18.72 Aligned_cols=107 Identities=17% Similarity=0.301 Sum_probs=64.2
Q ss_pred CEEEEECCEEEEEEE-EECCEEEEEHHHHHHHHCCCCHHHHHHHHCC-----CCCEE-------EEECCCCC---CCEEE
Q ss_conf 257852996799999-4389086679999988289688999998456-----74328-------87227998---31068
Q gi|254780125|r 4 ITPFEFESNKIRTIV-DKDQNIWFVAKDVATALGYENSNEAINAHCK-----GVAKR-------YPLKTEGG---IQKVR 67 (262)
Q Consensus 4 l~~f~fe~~~ir~v~-~~dge~wF~a~dva~~LGy~~~~~ai~~~~~-----~~~~~-------~~~~~~g~---~~~~~ 67 (262)
++.|.-+...+++-. ...|+.|..-.|+|..... ..+.+..|.+ .+-.. ......|+ +++..
T Consensus 3 ~il~~a~dg~~~~~~~~~~~~lwl~qa~~a~lyq~--t~q~is~hik~i~~e~ele~~at~~~~l~vq~e~~rqvnrn~~ 80 (329)
T COG3943 3 IILYTANDGTAQFALQEFGGQLWLTQADMAELYQT--TKQNISKHIKTILAEGELEEKATVNSYLTVQNEGGRQVNRNIA 80 (329)
T ss_pred EEEEECCCCCEEEEHHHHCCEEEECHHHHHHHHHH--HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHCHHHH
T ss_conf 59996378615555786288220047679999975--4788999999872352054301467687776236601111012
Q ss_pred EECHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 9718779999985799657999998889789999960775775332
Q gi|254780125|r 68 IISEPDVYRLLVKSTLPSAQKFERWVFEEVLPTLRKTGSYSVEAPK 113 (262)
Q Consensus 68 ~i~E~gly~Li~~s~~p~A~~F~~Wv~~eVLPsIRktG~Y~~~~~~ 113 (262)
..|.+.+..+-.+-+.+..-+|+.|.|..+-..+-| |-.+-|+.+
T Consensus 81 hyslpvilavgyrvrs~rg~qfrqwatq~lqeyl~k-gfvmdderl 125 (329)
T COG3943 81 HYSLPVILAVGYRVRSARGTQFRQWATQTLQEYLIK-GFVMDDERL 125 (329)
T ss_pred HHHHHHHHEEEEEECCCCCCHHHHHHHHHHHHHHHH-HCCCCHHHC
T ss_conf 110045410200431644028999999999999985-110255640
No 31
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=60.36 E-value=12 Score=17.17 Aligned_cols=51 Identities=25% Similarity=0.334 Sum_probs=32.7
Q ss_pred HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCC--HHHHHHHHHHCCCEEECC
Q ss_conf 023420013466654155873239999997389988--899999999789768537
Q gi|254780125|r 156 GVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQR--ARFLNKLLLKRGLQVSKV 209 (262)
Q Consensus 156 ~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~s--a~~~N~lL~~~g~q~Rk~ 209 (262)
|+....-.+ +..+++..+-+++-+||+.+|.+.| .+++++ |.++|+.+|.+
T Consensus 24 GLs~~Dv~v--~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~-L~~~GlV~Rek 76 (126)
T COG3355 24 GLSELDVEV--YKALLEENGPLTVDELAEILNRSRSTVYRSLQN-LLEAGLVEREK 76 (126)
T ss_pred CCCHHHHHH--HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH-HHHCCCEEEEE
T ss_conf 896889999--999986469957999999978319999999999-99858866664
No 32
>pfam08624 CRC_subunit Chromatin remodelling complex subunit. This family has been identified as a subunit of chromatin remodelling complexes. Saccharomyces cerevisiae RSC7 and its paralogue the SWI/SNF global transcription activator complex subunit SWP82 have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively.
Probab=60.20 E-value=12 Score=17.16 Aligned_cols=65 Identities=17% Similarity=0.295 Sum_probs=43.9
Q ss_pred EEEEEE--EECCEEEEEHHHHHHHHCCCCHHHHHHHHCCCCC------------EEEEECCCCCCCEEEEECHHHHHHH
Q ss_conf 799999--4389086679999988289688999998456743------------2887227998310689718779999
Q gi|254780125|r 13 KIRTIV--DKDQNIWFVAKDVATALGYENSNEAINAHCKGVA------------KRYPLKTEGGIQKVRIISEPDVYRL 77 (262)
Q Consensus 13 ~ir~v~--~~dge~wF~a~dva~~LGy~~~~~ai~~~~~~~~------------~~~~~~~~g~~~~~~~i~E~gly~L 77 (262)
.++|.. ......+..+.|+|++|||.+..-..+.|..-.. ....++.+-..+.+.+|+-.-+|+.
T Consensus 34 ~~~TFtl~~rg~~lymL~te~aR~lg~rDSy~ff~~~~~L~ki~~~~~Ek~~Li~~~lip~sy~~R~i~~VtARS~F~~ 112 (139)
T pfam08624 34 RVRTFTLPGRGERLYMLSTEPARLLGFRDSYLFFQKHPSLYKIITTQDEKEDLIDRGIIPYSYKGRSITIVTARSVFRE 112 (139)
T ss_pred EEEEEEECCCCCEEEEEEHHHHHHHCCCHHHHHHHHCHHHHEEECCHHHHHHHHHCCCCCCCCCCCEEEEEEHHHHHHH
T ss_conf 8888884688865899867778883643289999858075335279899999997596776446660699977999998
No 33
>pfam01498 Transposase_5 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements.
Probab=59.10 E-value=13 Score=17.03 Aligned_cols=47 Identities=17% Similarity=0.215 Sum_probs=38.0
Q ss_pred CCCHHHHHHHH---CCCCCHHHHHHHHHHCCCEEECCCCCEEECHHHHHH
Q ss_conf 32399999973---899888999999997897685379944365789754
Q gi|254780125|r 176 YLTITQIGERL---NPPQRARFLNKLLLKRGLQVSKVSGGYRPTPKGEER 222 (262)
Q Consensus 176 ~l~~t~iak~l---~~~~sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~~ 222 (262)
..+.++|+..+ |...|..-+.+.|.+.|+-.++......|+.+-...
T Consensus 13 ~~T~~~i~~~l~~~g~~vS~~Tvrr~L~~~g~~~r~~~kkP~Ls~~~~~~ 62 (72)
T pfam01498 13 RITLRDLANELQEIGKSVSRSTIRRRLHKAGLKARKPRKKPLLSAKNKKA 62 (72)
T ss_pred CCCHHHHHHHHHHCCCCCCHHHHHHHHHHCCCCEECCCCCCCCCHHHHHH
T ss_conf 24699999999985997279999999998798435577899999999999
No 34
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=57.73 E-value=14 Score=16.88 Aligned_cols=40 Identities=28% Similarity=0.314 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHH---HHCCCEEECCCC---CEEECHH
Q ss_conf 323999999738998889999999---978976853799---4436578
Q gi|254780125|r 176 YLTITQIGERLNPPQRARFLNKLL---LKRGLQVSKVSG---GYRPTPK 218 (262)
Q Consensus 176 ~l~~t~iak~l~~~~sa~~~N~lL---~~~g~q~Rk~~~---~W~lt~k 218 (262)
..++-+|||.+|+ +-+.+|+.| .+.|-.+ ++++ .|.+|.+
T Consensus 22 ~~tA~~lak~lg~--~Kk~vN~~LY~L~k~g~v~-~~~~~PP~W~l~~~ 67 (68)
T smart00550 22 TSTALQLAKNLGL--PKKEVNRVLYSLEKKGKVC-KQGGTPPLWKLTDK 67 (68)
T ss_pred CCHHHHHHHHHCC--CHHHHHHHHHHHHHCCCEE-CCCCCCCCEEECCC
T ss_conf 4039999999499--8999999999999748831-06998998061456
No 35
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=57.58 E-value=14 Score=16.86 Aligned_cols=40 Identities=23% Similarity=0.255 Sum_probs=29.5
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCCC-HHHHHHHHHHCCCEEE
Q ss_conf 654155873239999997389988-8999999997897685
Q gi|254780125|r 168 LPSSDNDEYLTITQIGERLNPPQR-ARFLNKLLLKRGLQVS 207 (262)
Q Consensus 168 d~~~~~~~~l~~t~iak~l~~~~s-a~~~N~lL~~~g~q~R 207 (262)
+.+......+++++||+.+|++.| ..++=.-|.+.||..+
T Consensus 10 ~~~~~~~~~~~l~eia~~~gl~kstv~RlL~tL~~~G~v~~ 50 (52)
T pfam09339 10 EALAEAPGGLSLTEIARRTGLPKSTAHRLLQTLVELGYVEQ 50 (52)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 99862899989999999989199999999999998819116
No 36
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=57.00 E-value=14 Score=16.80 Aligned_cols=76 Identities=24% Similarity=0.303 Sum_probs=43.2
Q ss_pred CEEEEEHHHHHHHHCCCCHHHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHHHHHHHHCCCHHHHHHHHHH-----HHH
Q ss_conf 908667999998828968899999845674328872279983106897187799999857996579999988-----897
Q gi|254780125|r 22 QNIWFVAKDVATALGYENSNEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDVYRLLVKSTLPSAQKFERWV-----FEE 96 (262)
Q Consensus 22 ge~wF~a~dva~~LGy~~~~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gly~Li~~s~~p~A~~F~~Wv-----~~e 96 (262)
.+|...-+|+|+-||.+ -+++..|.++-...-.+...|+ .-+.|+..|+=.|.-. ...-++|-..+ +..
T Consensus 22 ~qp~v~q~eIA~~lgiT--~QaVsehiK~Lv~eG~i~~~gR--~~Y~iTkkG~e~l~~~--~~dlr~f~~ev~~~l~~~~ 95 (260)
T COG1497 22 RQPRVKQKEIAKKLGIT--LQAVSEHIKELVKEGLIEKEGR--GEYEITKKGAEWLLEQ--LSDLRRFSEEVELVLDYVM 95 (260)
T ss_pred HCCCCCHHHHHHHCCCC--HHHHHHHHHHHHHCCCEEECCC--EEEEEEHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH
T ss_conf 58877888999870987--9999999999986646661487--2589726689999999--9999999999998876677
Q ss_pred HHHHHHH
Q ss_conf 8999996
Q gi|254780125|r 97 VLPTLRK 103 (262)
Q Consensus 97 VLPsIRk 103 (262)
|.|.|-+
T Consensus 96 vw~AIA~ 102 (260)
T COG1497 96 VWTAIAK 102 (260)
T ss_pred HHHHHHH
T ss_conf 8888657
No 37
>pfam09328 Phytochelatin_C Domain of unknown function (DUF1984). Members of this family of functionally uncharacterized domains are found at the C-terminus of plant phytochelatin synthases.
Probab=56.53 E-value=14 Score=16.75 Aligned_cols=29 Identities=24% Similarity=0.413 Sum_probs=24.3
Q ss_pred EEECHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 89718779999985799657999998889
Q gi|254780125|r 67 RIISEPDVYRLLVKSTLPSAQKFERWVFE 95 (262)
Q Consensus 67 ~~i~E~gly~Li~~s~~p~A~~F~~Wv~~ 95 (262)
.+-+-.-+...+|.|--+.+..|-+||.+
T Consensus 36 ~v~~v~~vLs~vf~SLPsn~~~FIKWVaE 64 (264)
T pfam09328 36 NLKDVQEVLSVVFKSLPANFGEFIKWVAE 64 (264)
T ss_pred CCCCHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 43659999999980386508999988871
No 38
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to 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=55.32 E-value=4.8 Score=19.95 Aligned_cols=53 Identities=21% Similarity=0.151 Sum_probs=37.8
Q ss_pred ECCEEEEEHHHHHHHHCCCCHHHHHHHHCCCCCE-------EEEECCCCCCCEEEEECHHHHHH
Q ss_conf 3890866799999882896889999984567432-------88722799831068971877999
Q gi|254780125|r 20 KDQNIWFVAKDVATALGYENSNEAINAHCKGVAK-------RYPLKTEGGIQKVRIISEPDVYR 76 (262)
Q Consensus 20 ~dge~wF~a~dva~~LGy~~~~~ai~~~~~~~~~-------~~~~~~~g~~~~~~~i~E~gly~ 76 (262)
.+|+ -.|.++|..|+.+ -+|||+|-||--. ...-.+-|+.|...=||+.|==+
T Consensus 12 ~~Gq--~sA~~lA~~L~iS--pQAvRrHLKDLe~e~Lv~~~~~~~g~~GRPQy~Y~LS~qGRe~ 71 (215)
T TIGR02702 12 KEGQ--ASALALAEELAIS--PQAVRRHLKDLETEGLVEYKAVLQGTMGRPQYLYQLSRQGREQ 71 (215)
T ss_pred HHHH--HHHHHHHHHHCCC--HHHHHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf 6004--8899999972788--6788765433210103567777650478822542121776776
No 39
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=52.04 E-value=17 Score=16.27 Aligned_cols=36 Identities=28% Similarity=0.318 Sum_probs=28.9
Q ss_pred HCCCCCCCHHHHHHHHCCC-CCHHHHHHHHHHCCCEE
Q ss_conf 1558732399999973899-88899999999789768
Q gi|254780125|r 171 SDNDEYLTITQIGERLNPP-QRARFLNKLLLKRGLQV 206 (262)
Q Consensus 171 ~~~~~~l~~t~iak~l~~~-~sa~~~N~lL~~~g~q~ 206 (262)
....+...+++||+.||+. -|.-.+-+.|.+.|+..
T Consensus 15 ~~~~~~v~~~~iA~~L~Vs~~SVt~mlkkL~~~GlV~ 51 (58)
T pfam01325 15 SEEKGVVKTKDLAERLNVSPSTVSEMLKKLEKDGYVV 51 (58)
T ss_pred HCCCCCEEHHHHHHHHCCCCHHHHHHHHHHHHCCCEE
T ss_conf 8269961299999995999252999999999889978
No 40
>pfam00756 Esterase Putative esterase. This family contains Esterase D. However it is not clear if all members of the family have the same function. This family is related to the pfam00135 family.
Probab=52.01 E-value=13 Score=16.91 Aligned_cols=25 Identities=24% Similarity=0.319 Sum_probs=21.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9657999998889789999960775
Q gi|254780125|r 83 LPSAQKFERWVFEEVLPTLRKTGSY 107 (262)
Q Consensus 83 ~p~A~~F~~Wv~~eVLPsIRktG~Y 107 (262)
.+.+..|.+|+++||+|.|+++-..
T Consensus 83 ~~~~~~~~~~l~~el~p~i~~~y~~ 107 (243)
T pfam00756 83 GPGAYAYETFLTQELPPLLDANFPT 107 (243)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 7536789999999999999985785
No 41
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=50.99 E-value=15 Score=16.57 Aligned_cols=33 Identities=12% Similarity=0.107 Sum_probs=23.4
Q ss_pred HHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCC
Q ss_conf 654155873239999997389988899999999789
Q gi|254780125|r 168 LPSSDNDEYLTITQIGERLNPPQRARFLNKLLLKRG 203 (262)
Q Consensus 168 d~~~~~~~~l~~t~iak~l~~~~sa~~~N~lL~~~g 203 (262)
..++.. .-++++++||.|| .|...+|+++++..
T Consensus 13 eEfL~P-Lg~s~~~LA~~Lg--Vsr~~~sriv~~~~ 45 (81)
T TIGR02607 13 EEFLEP-LGLSVRALAKALG--VSRSTLSRIVNGRR 45 (81)
T ss_pred HHHHHC-CCHHHHHHHHHCC--CCHHHHHHHHHCCC
T ss_conf 775210-4706899998709--99788888874489
No 42
>PTZ00326 phenylalanyl-tRNA synthetase; Provisional
Probab=50.60 E-value=17 Score=16.12 Aligned_cols=14 Identities=21% Similarity=0.283 Sum_probs=10.9
Q ss_pred EEHHHHHHHHCCCC
Q ss_conf 67999998828968
Q gi|254780125|r 26 FVAKDVATALGYEN 39 (262)
Q Consensus 26 F~a~dva~~LGy~~ 39 (262)
.....+|+.+|+..
T Consensus 21 ~~s~ela~~~g~~~ 34 (505)
T PTZ00326 21 VTSLAVAEDLSIDH 34 (505)
T ss_pred CCHHHHHHHHCCCH
T ss_conf 99999999859699
No 43
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=49.91 E-value=18 Score=16.05 Aligned_cols=38 Identities=16% Similarity=0.123 Sum_probs=30.9
Q ss_pred HHCCCCCCCHHHHHHHHCCC-CCHHHHHHHHHHCCCEEE
Q ss_conf 41558732399999973899-888999999997897685
Q gi|254780125|r 170 SSDNDEYLTITQIGERLNPP-QRARFLNKLLLKRGLQVS 207 (262)
Q Consensus 170 ~~~~~~~l~~t~iak~l~~~-~sa~~~N~lL~~~g~q~R 207 (262)
.+..++.+++.++++.+|+. ++.++=-..|.+.|...|
T Consensus 8 ~l~~~~~~~i~~La~~~~VS~~TiRRDl~~L~~~g~i~r 46 (53)
T smart00420 8 LLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred HHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf 999869797999999989799999996999998899899
No 44
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=49.48 E-value=18 Score=16.00 Aligned_cols=71 Identities=18% Similarity=0.191 Sum_probs=39.1
Q ss_pred EEHHHHHHHHCCCCHHHHHHHHCC----CCCEEEEECC--CCCCCEEEEECHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf 679999988289688999998456----7432887227--9983106897187799999857996579999988897899
Q gi|254780125|r 26 FVAKDVATALGYENSNEAINAHCK----GVAKRYPLKT--EGGIQKVRIISEPDVYRLLVKSTLPSAQKFERWVFEEVLP 99 (262)
Q Consensus 26 F~a~dva~~LGy~~~~~ai~~~~~----~~~~~~~~~~--~g~~~~~~~i~E~gly~Li~~s~~p~A~~F~~Wv~~eVLP 99 (262)
..+.|+|+.||.+ ..++++|-+ +......... .|+.+..+-+++.|-- .-.++.= =++..++-
T Consensus 26 ~sa~elA~~Lgis--~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~--------~f~~~y~-~l~~~~l~ 94 (218)
T COG2345 26 VSADELAEELGIS--PMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE--------QFPKRYG-ELALALLD 94 (218)
T ss_pred CCHHHHHHHHCCC--HHHHHHHHHHHHHCCCEEEEECCCCCCCCCEEEEECCCCHH--------HCCHHHH-HHHHHHHH
T ss_conf 2499999885999--89999999999868666876425789997333220026265--------4453248-99999999
Q ss_pred HHHHHCCC
Q ss_conf 99960775
Q gi|254780125|r 100 TLRKTGSY 107 (262)
Q Consensus 100 sIRktG~Y 107 (262)
+++++|+=
T Consensus 95 ~l~~~~G~ 102 (218)
T COG2345 95 ALEETGGE 102 (218)
T ss_pred HHHHHCCH
T ss_conf 99985459
No 45
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=48.49 E-value=18 Score=16.04 Aligned_cols=56 Identities=27% Similarity=0.277 Sum_probs=39.1
Q ss_pred CCCCCCCHHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCC---CEEECHHHHHHHHHHC
Q ss_conf 558732399999973899-8889999999978976853799---4436578975435530
Q gi|254780125|r 172 DNDEYLTITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSG---GYRPTPKGEERGGKMC 227 (262)
Q Consensus 172 ~~~~~l~~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~---~W~lt~kg~~~g~~~~ 227 (262)
.+.+...+|.|.-..|.. ..++..-..|.+.|+..+++++ ..++|+||..+-..+.
T Consensus 27 ~~~~~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~ 86 (95)
T COG3432 27 ISEGGIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS 86 (95)
T ss_pred HCCCCCCCEEEEEECCCCHHHHHHHHHHHHHCCCEEECCCCCCCEEEECHHHHHHHHHHH
T ss_conf 417999862466432767799999999998678778614886445898856899999999
No 46
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=46.92 E-value=20 Score=15.74 Aligned_cols=35 Identities=14% Similarity=0.102 Sum_probs=28.0
Q ss_pred CCHHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCC
Q ss_conf 2399999973899-8889999999978976853799
Q gi|254780125|r 177 LTITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSG 211 (262)
Q Consensus 177 l~~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~ 211 (262)
-+..++|+.++++ .+.++.-+.|.+.|+.+++.+.
T Consensus 21 Ps~~~la~~~~vSr~tvr~A~~~L~~~G~i~~~~g~ 56 (60)
T smart00345 21 PSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 109999999894999999999999988978996685
No 47
>PRK10079 putative transcriptional regulator; Provisional
Probab=46.35 E-value=20 Score=15.68 Aligned_cols=33 Identities=9% Similarity=-0.023 Sum_probs=23.8
Q ss_pred CCEEEEEHHHHHHHHCCCC--HHHHHHHHCCCCCE
Q ss_conf 8908667999998828968--89999984567432
Q gi|254780125|r 21 DQNIWFVAKDVATALGYEN--SNEAINAHCKGVAK 53 (262)
Q Consensus 21 dge~wF~a~dva~~LGy~~--~~~ai~~~~~~~~~ 53 (262)
-|+..=.=.++|+.+|-+. .++|+..+.++...
T Consensus 31 ~G~~LPsE~eLa~~y~VSR~TVR~Al~~L~~eGli 65 (241)
T PRK10079 31 CGDYLPAEQQLAARFEVNRHTLRRAIDQLVERGWV 65 (241)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
T ss_conf 98919699999999798899999999999977987
No 48
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=46.24 E-value=13 Score=16.92 Aligned_cols=56 Identities=16% Similarity=0.154 Sum_probs=36.9
Q ss_pred ECCEEEEEHHHHHHHHCCCCH--HHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHHHHHH
Q ss_conf 389086679999988289688--99999845674328872279983106897187799999
Q gi|254780125|r 20 KDQNIWFVAKDVATALGYENS--NEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDVYRLL 78 (262)
Q Consensus 20 ~dge~wF~a~dva~~LGy~~~--~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gly~Li 78 (262)
-..+| .++.+++++||++.+ +.+++.+.+..-... ... .|.+.-.|+.++++|..-
T Consensus 37 ls~~P-mtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~-~~~-~G~Rk~~F~a~~df~~~f 94 (177)
T COG1510 37 LSRKP-LTLDEIAEALGMSKSNVSMGLKKLQDWNLVKK-VFE-KGDRKDYFEAEKDFSQIF 94 (177)
T ss_pred ECCCC-CCHHHHHHHHCCCCCHHHHHHHHHHHCCHHHH-HHC-CCCCHHHHCCCCHHHHHH
T ss_conf 06999-66999999977780128899999985456885-304-675301000064099999
No 49
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator); InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio 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 strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators..
Probab=45.93 E-value=21 Score=15.64 Aligned_cols=51 Identities=25% Similarity=0.330 Sum_probs=35.0
Q ss_pred CCCCCCCHHHHHHHHCCCCC-HHHHHHHHHHCCCEE--ECCCCCEEECHHHHHH
Q ss_conf 55873239999997389988-899999999789768--5379944365789754
Q gi|254780125|r 172 DNDEYLTITQIGERLNPPQR-ARFLNKLLLKRGLQV--SKVSGGYRPTPKGEER 222 (262)
Q Consensus 172 ~~~~~l~~t~iak~l~~~~s-a~~~N~lL~~~g~q~--Rk~~~~W~lt~kg~~~ 222 (262)
...+.+++.+||+..+++.+ ...+-.-|...|+.. |..+|-..|.....++
T Consensus 21 ~~~~~v~~~~ia~~~~Is~~yL~K~l~~L~~~GlV~S~rG~~GGY~L~~~~~~I 74 (133)
T TIGR00738 21 ADEGPVSVKEIAERQGISRSYLEKVLRTLRKAGLVESVRGPGGGYRLARPPEEI 74 (133)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCHHHC
T ss_conf 688760789999884899879999999887707642115898563107753430
No 50
>pfam03484 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=45.85 E-value=21 Score=15.63 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHHCCCEEECCCCCEEEC
Q ss_conf 732399999973899888999999997897685379944365
Q gi|254780125|r 175 EYLTITQIGERLNPPQRARFLNKLLLKRGLQVSKVSGGYRPT 216 (262)
Q Consensus 175 ~~l~~t~iak~l~~~~sa~~~N~lL~~~g~q~Rk~~~~W~lt 216 (262)
-.++...+-+.+|...+....-..|...|+.....++.|..+
T Consensus 4 i~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~~~~~~v~ 45 (69)
T pfam03484 4 ITLDLEKINRLLGIELSPEEIKKILKRLGFKVEEDEDTLKVT 45 (69)
T ss_pred EEECHHHHHHHHCCCCCHHHHHHHHHHCCCEEEECCCEEEEE
T ss_conf 998799999971888799999999998699899479869998
No 51
>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=45.70 E-value=21 Score=15.62 Aligned_cols=41 Identities=29% Similarity=0.263 Sum_probs=26.4
Q ss_pred CCHHHHHHHHCCCCCH-HHHHHHHHHCCCEEECCCCCEEECH
Q ss_conf 2399999973899888-9999999978976853799443657
Q gi|254780125|r 177 LTITQIGERLNPPQRA-RFLNKLLLKRGLQVSKVSGGYRPTP 217 (262)
Q Consensus 177 l~~t~iak~l~~~~sa-~~~N~lL~~~g~q~Rk~~~~W~lt~ 217 (262)
+++++|++.++++.++ ..--+.|.+.|+..+...++|..|.
T Consensus 21 ~~~~eia~~l~is~~~vs~hL~~L~~~Gli~~~~~~~~~~y~ 62 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYS 62 (78)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCEEEEE
T ss_conf 069999877784878999999999988986899988999999
No 52
>KOG2959 consensus
Probab=45.05 E-value=11 Score=17.49 Aligned_cols=17 Identities=18% Similarity=0.257 Sum_probs=6.0
Q ss_pred CHHHHHHHHHHHCCCCC
Q ss_conf 50177656531023567
Q gi|254780125|r 244 NSNLLVSFLQNELINTP 260 (262)
Q Consensus 244 ~~~v~~~~~~~~~~~~~ 260 (262)
+|++.|.|+.=|+|++|
T Consensus 161 NPsiydkLi~FcdI~E~ 177 (238)
T KOG2959 161 NPSIYDKLIDFCDIKEP 177 (238)
T ss_pred CCHHHHHHHHHHCCCCC
T ss_conf 80899999988631664
No 53
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=44.83 E-value=21 Score=15.53 Aligned_cols=108 Identities=12% Similarity=0.076 Sum_probs=49.4
Q ss_pred HHHHHHHCCCHHHHHHHHHHHH----HHHHHHHHHCCCCCCCCCCCCC-CHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9999985799657999998889----7899999607757753322223-4257999987899998864036689999999
Q gi|254780125|r 74 VYRLLVKSTLPSAQKFERWVFE----EVLPTLRKTGSYSVEAPKLRAT-SASTVLRVHKHLEELAKQAGLKDNQLLLKVN 148 (262)
Q Consensus 74 ly~Li~~s~~p~A~~F~~Wv~~----eVLPsIRktG~Y~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 148 (262)
+.++.-+...-....|+-|++. ..+-.+||...+......+... ..+.......... +.
T Consensus 40 Flk~~~~~~~~~~~~~~~WL~~Ia~N~~~d~~Rk~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~ 103 (161)
T PRK12541 40 FYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTTTVEEFHLPNVPSTEHEYFVKH----------------EI 103 (161)
T ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHCCCCCCCCHHHHHHHH----------------HH
T ss_conf 99999836131667568999999999999999986044655255540468999627789999----------------99
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf 999998302342001346665415587323999999738998889999999978
Q gi|254780125|r 149 RGVTKITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKLLLKR 202 (262)
Q Consensus 149 ~~~~~~~~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~sa~~~N~lL~~~ 202 (262)
.. ....+..+.+..-.. ..+..-.-++..+||..+|+ |...+-..|+..
T Consensus 104 ~~--~~~~l~~Lp~~~R~v-~~L~~~~g~s~~EIA~~lgi--s~~tVk~~l~RA 152 (161)
T PRK12541 104 AS--WLDSLSSLPLERRNV-LLLRDYYGFSYKEIAEMTGL--SLAKVKIELHRG 152 (161)
T ss_pred HH--HHHHHHCCCHHHHHH-HHHHHHCCCCHHHHHHHHCC--CHHHHHHHHHHH
T ss_conf 99--999998199999999-99899749999999999893--999999999999
No 54
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=41.89 E-value=24 Score=15.23 Aligned_cols=34 Identities=9% Similarity=-0.037 Sum_probs=23.9
Q ss_pred CCEEEEEHHHHHHHHCCCC--HHHHHHHHCCCCCEE
Q ss_conf 8908667999998828968--899999845674328
Q gi|254780125|r 21 DQNIWFVAKDVATALGYEN--SNEAINAHCKGVAKR 54 (262)
Q Consensus 21 dge~wF~a~dva~~LGy~~--~~~ai~~~~~~~~~~ 54 (262)
.|+..=.=.++|+.+|.+. .++|+..+.++....
T Consensus 21 ~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~ 56 (231)
T TIGR03337 21 PGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIY 56 (231)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf 959785899999997979999999999999879969
No 55
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=41.44 E-value=24 Score=15.18 Aligned_cols=37 Identities=14% Similarity=0.138 Sum_probs=28.5
Q ss_pred CCC-CHHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCC
Q ss_conf 732-399999973899-8889999999978976853799
Q gi|254780125|r 175 EYL-TITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSG 211 (262)
Q Consensus 175 ~~l-~~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~ 211 (262)
..+ +..++|+.++++ .+.++.-+.|.+.|+.++..+.
T Consensus 22 ~~LPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~ 60 (64)
T pfam00392 22 DKLPSERELAAEFGVSRTTVREALRRLEAEGLVERRPGR 60 (64)
T ss_pred CCCHHHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 998479999999796999999999999988938997795
No 56
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=41.25 E-value=24 Score=15.16 Aligned_cols=44 Identities=32% Similarity=0.457 Sum_probs=27.2
Q ss_pred CCHHHHHHHHCCCCC--HHHHHHHHHHCCCE-EECCCCCEEECHHHH
Q ss_conf 239999997389988--89999999978976-853799443657897
Q gi|254780125|r 177 LTITQIGERLNPPQR--ARFLNKLLLKRGLQ-VSKVSGGYRPTPKGE 220 (262)
Q Consensus 177 l~~t~iak~l~~~~s--a~~~N~lL~~~g~q-~Rk~~~~W~lt~kg~ 220 (262)
-+++..|+.|+++.+ .+.+.+|=...|.. +.+.++.+.||+.|+
T Consensus 14 gs~~~AA~~l~isqs~vs~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~ 60 (60)
T pfam00126 14 GSFTAAAERLGLSQPAVSRQIKRLEEELGVPLFERTTRGLRLTPAGE 60 (60)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCEEEEECCCCEEECCCCC
T ss_conf 99999999979898899999999999959970788899742893749
No 57
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=41.15 E-value=24 Score=15.15 Aligned_cols=33 Identities=9% Similarity=0.076 Sum_probs=23.1
Q ss_pred CCEEEEEHHHHHHHHCCCC--HHHHHHHHCCCCCE
Q ss_conf 8908667999998828968--89999984567432
Q gi|254780125|r 21 DQNIWFVAKDVATALGYEN--SNEAINAHCKGVAK 53 (262)
Q Consensus 21 dge~wF~a~dva~~LGy~~--~~~ai~~~~~~~~~ 53 (262)
.|+..=.=.++|+-+|.+. .++|+..+.++...
T Consensus 25 ~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli 59 (239)
T PRK09764 25 PGDALPTESALQTEFGVSRVTVRQALRQLVEQQIL 59 (239)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
T ss_conf 95999299999999797999999999999978999
No 58
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=40.50 E-value=25 Score=15.09 Aligned_cols=34 Identities=9% Similarity=-0.031 Sum_probs=23.6
Q ss_pred CCEEEEEHHHHHHHHCCCC--HHHHHHHHCCCCCEE
Q ss_conf 8908667999998828968--899999845674328
Q gi|254780125|r 21 DQNIWFVAKDVATALGYEN--SNEAINAHCKGVAKR 54 (262)
Q Consensus 21 dge~wF~a~dva~~LGy~~--~~~ai~~~~~~~~~~ 54 (262)
.|+..=.=.++|+.+|.+. .++|++.+..+....
T Consensus 31 ~G~~LPsE~eLa~~y~VSR~TVR~Al~~L~~eGli~ 66 (243)
T PRK11402 31 AGQQIPTENELCTQYNVSRITIRKAISDLVADGVLI 66 (243)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
T ss_conf 979893999999997979999999999999789999
No 59
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=40.34 E-value=25 Score=15.07 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=32.1
Q ss_pred HHCCCCCCCHHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCC
Q ss_conf 41558732399999973899-8889999999978976853799
Q gi|254780125|r 170 SSDNDEYLTITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSG 211 (262)
Q Consensus 170 ~~~~~~~l~~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~ 211 (262)
.+...+.+++.++++.+++. ++.++=-..|.+.|...| ..|
T Consensus 8 ~l~~~~~v~i~~La~~f~VS~~TiRRDl~~L~~~g~i~R-~~G 49 (57)
T pfam08220 8 LLKQQGTLSVEELAELLGVSEMTIRRDLNELEEQGLLTR-THG 49 (57)
T ss_pred HHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-EEC
T ss_conf 999869797999999989599999996999998899899-749
No 60
>pfam07833 Cu_amine_oxidN1 Copper amine oxidase N-terminal domain. Copper amine oxidases catalyse the oxidative deamination of primary amines to the corresponding aldehydes, while reducing molecular oxygen to hydrogen peroxide. These enzymes are dimers of identical subunits, each comprising four domains. The N-terminal domain, which is absent in some amine oxidases, consists of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the 'stalk' of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other.
Probab=39.82 E-value=23 Score=15.25 Aligned_cols=19 Identities=26% Similarity=0.358 Sum_probs=15.8
Q ss_pred ECCEEEEEHHHHHHHHCCC
Q ss_conf 3890866799999882896
Q gi|254780125|r 20 KDQNIWFVAKDVATALGYE 38 (262)
Q Consensus 20 ~dge~wF~a~dva~~LGy~ 38 (262)
.||..+..++.+|++||++
T Consensus 1 ~~g~~~vPlr~i~e~lG~~ 19 (93)
T pfam07833 1 KNGRTLVPLRAIAEALGAK 19 (93)
T ss_pred CCCEEEEEHHHHHHHCCCE
T ss_conf 9988999979989873999
No 61
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=38.84 E-value=26 Score=14.92 Aligned_cols=100 Identities=21% Similarity=0.211 Sum_probs=55.9
Q ss_pred HHHHHHHHHHH----HHHHHHHHHCCCCCCCCCCCCC-CHHHHHHHHHHHHHHHHHH--CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 57999998889----7899999607757753322223-4257999987899998864--036689999999999998302
Q gi|254780125|r 85 SAQKFERWVFE----EVLPTLRKTGSYSVEAPKLRAT-SASTVLRVHKHLEELAKQA--GLKDNQLLLKVNRGVTKITGV 157 (262)
Q Consensus 85 ~A~~F~~Wv~~----eVLPsIRktG~Y~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~i 157 (262)
....|-.|++. +|+-..||.|-=- .... -+++....++......... ....-.++. .|+..
T Consensus 48 ~~~~F~aWa~~iArn~vl~~~r~~~R~~-----~~l~~f~D~l~e~lA~~~~~~~~~~~~~~~~~AL~---~C~~~---- 115 (163)
T TIGR02989 48 PGTDFGAWARGIARNKVLNHRRKLGRDR-----ERLVVFDDELLEALAAELEEAEEADRSEDELQALE---GCLEK---- 115 (163)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCCC-----HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHH---HHHHH----
T ss_conf 8989767899999999999987302441-----27776259999999998755522788178999999---87863----
Q ss_pred HHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 34200134666541558732399999973899888999999997
Q gi|254780125|r 158 DQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKLLLK 201 (262)
Q Consensus 158 ~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~sa~~~N~lL~~ 201 (262)
+ |...-....+.+..-.++++||+..| +|..++.+.|+-
T Consensus 116 --L-~~~~R~Ll~~rY~~G~~~~~~A~~~g--~~~~A~~~~L~R 154 (163)
T TIGR02989 116 --L-PERQRELLQLRYQRGVSLEALAEQLG--RTVNAVYKALSR 154 (163)
T ss_pred --C-CHHHHHHHHHHHCCCCCHHHHHHHHC--CHHHHHHHHHHH
T ss_conf --5-97889999998227978789998847--138999999999
No 62
>pfam07592 Transposase_36 Rhodopirellula transposase. These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces.
Probab=38.27 E-value=27 Score=14.86 Aligned_cols=21 Identities=29% Similarity=0.501 Sum_probs=8.4
Q ss_pred HHHHHHHH---CCCCHHHHHHHHC
Q ss_conf 99999882---8968899999845
Q gi|254780125|r 28 AKDVATAL---GYENSNEAINAHC 48 (262)
Q Consensus 28 a~dva~~L---Gy~~~~~ai~~~~ 48 (262)
++.+|+.| ||+-.+..+.++.
T Consensus 27 ~r~la~eL~~~G~~vs~~tV~~lL 50 (311)
T pfam07592 27 TRKLAEELNQRGYKVSRETVGRLL 50 (311)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 999999999759874288999999
No 63
>KOG2947 consensus
Probab=35.44 E-value=29 Score=14.56 Aligned_cols=22 Identities=14% Similarity=0.114 Sum_probs=14.9
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 23999999738998889999999
Q gi|254780125|r 177 LTITQIGERLNPPQRARFLNKLL 199 (262)
Q Consensus 177 l~~t~iak~l~~~~sa~~~N~lL 199 (262)
.--.++|+.+|. +|+++.-.-|
T Consensus 190 fvsK~~a~~~gf-ks~rea~~~l 211 (308)
T KOG2947 190 FVSKDVAKHLGF-KSPREACEGL 211 (308)
T ss_pred EEEHHHHHHHCC-CCHHHHHHHH
T ss_conf 987898765454-8889999999
No 64
>KOG2145 consensus
Probab=34.65 E-value=14 Score=16.78 Aligned_cols=23 Identities=39% Similarity=0.628 Sum_probs=11.1
Q ss_pred ECCEEEEE-HHHHHHHHCCCCHHH
Q ss_conf 38908667-999998828968899
Q gi|254780125|r 20 KDQNIWFV-AKDVATALGYENSNE 42 (262)
Q Consensus 20 ~dge~wF~-a~dva~~LGy~~~~~ 42 (262)
+|.+|||- .+|||..|||+.|.-
T Consensus 240 iDQDPyFRmtRDvA~rlg~~Kpal 263 (397)
T KOG2145 240 IDQDPYFRMTRDVAPRLGYPKPAL 263 (397)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCCE
T ss_conf 167727776553445418998421
No 65
>TIGR02018 his_ut_repres histidine utilization repressor; InterPro: IPR010248 This entry represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0006547 histidine metabolic process, 0045892 negative regulation of transcription DNA-dependent.
Probab=34.53 E-value=30 Score=14.47 Aligned_cols=54 Identities=15% Similarity=0.130 Sum_probs=38.4
Q ss_pred CCEEEEECHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC
Q ss_conf 310689718779999985799657999998889789999960775775--332222
Q gi|254780125|r 63 IQKVRIISEPDVYRLLVKSTLPSAQKFERWVFEEVLPTLRKTGSYSVE--APKLRA 116 (262)
Q Consensus 63 ~~~~~~i~E~gly~Li~~s~~p~A~~F~~Wv~~eVLPsIRktG~Y~~~--~~~~~~ 116 (262)
...-.+=+|.-|-.----||.-.-|..+.-+.+-+|-=.|..|.+..+ .+...+
T Consensus 20 ~~g~R~PsE~EL~~~~G~SRMTvnrALreLt~~G~l~R~qg~GTFVA~ae~k~~s~ 75 (234)
T TIGR02018 20 PPGHRIPSENELVAQFGVSRMTVNRALRELTDAGLLERRQGVGTFVARAEPKAQSA 75 (234)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEECCCCCCCCCH
T ss_conf 87675687799997748723357899998875681881278500441777653101
No 66
>COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]
Probab=33.88 E-value=31 Score=14.40 Aligned_cols=20 Identities=25% Similarity=0.288 Sum_probs=10.0
Q ss_pred HHHHHHHCCCEEECCCCCEEECH
Q ss_conf 99999978976853799443657
Q gi|254780125|r 195 LNKLLLKRGLQVSKVSGGYRPTP 217 (262)
Q Consensus 195 ~N~lL~~~g~q~Rk~~~~W~lt~ 217 (262)
+++||.|..|.. =++|-.-+
T Consensus 460 l~AllEeR~Ilv---~DEWAADQ 479 (546)
T COG4615 460 LLALLEERDILV---LDEWAADQ 479 (546)
T ss_pred HHHHHHHCCEEE---EEHHHCCC
T ss_conf 999973098688---60121246
No 67
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=33.74 E-value=31 Score=14.38 Aligned_cols=37 Identities=19% Similarity=0.186 Sum_probs=28.3
Q ss_pred CCC-CHHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCC
Q ss_conf 732-399999973899-8889999999978976853799
Q gi|254780125|r 175 EYL-TITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSG 211 (262)
Q Consensus 175 ~~l-~~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~ 211 (262)
..+ +..++|+.+|++ .+.++.-..|.+.|+.++..+.
T Consensus 23 ~~LPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~ 61 (66)
T cd07377 23 DRLPSERELAEELGVSRTTVREALRELEAEGLVERRPGR 61 (66)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 999279999999798889999999999988958997382
No 68
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=33.42 E-value=32 Score=14.35 Aligned_cols=48 Identities=15% Similarity=0.191 Sum_probs=31.4
Q ss_pred CCCCCCHHHHHHHHCCC-CCHHHHHHHHHHCCCEEECCCCCEEECHHHH
Q ss_conf 58732399999973899-8889999999978976853799443657897
Q gi|254780125|r 173 NDEYLTITQIGERLNPP-QRARFLNKLLLKRGLQVSKVSGGYRPTPKGE 220 (262)
Q Consensus 173 ~~~~l~~t~iak~l~~~-~sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~ 220 (262)
...+-+++++|+.+++. -+..+..+.|.+.|+.+.+.+..-..++.+.
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~ 80 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGKGTFVTEDAK 80 (125)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCEEEEECCCCH
T ss_conf 8889759999998198988999999999978877986670579747714
No 69
>TIGR02681 phage_pRha phage regulatory protein, Rha family; InterPro: IPR014054 Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that Rha is a phage regulatory protein..
Probab=32.95 E-value=23 Score=15.26 Aligned_cols=75 Identities=13% Similarity=0.112 Sum_probs=52.3
Q ss_pred EEECCEEEEEHHHHHHHHCCCC--HHHHHHH----HCCC---C------CEEEEECCCCCCC-EEEEECHHHHHHHHHHC
Q ss_conf 9438908667999998828968--8999998----4567---4------3288722799831-06897187799999857
Q gi|254780125|r 18 VDKDQNIWFVAKDVATALGYEN--SNEAINA----HCKG---V------AKRYPLKTEGGIQ-KVRIISEPDVYRLLVKS 81 (262)
Q Consensus 18 ~~~dge~wF~a~dva~~LGy~~--~~~ai~~----~~~~---~------~~~~~~~~~g~~~-~~~~i~E~gly~Li~~s 81 (262)
-+..+.+.-..--+|...|-+. .=+-|+. .++. | .....++-.|..| .+..++++|.--|+|+=
T Consensus 6 ~~~~~~~vt~Sl~~A~~FGK~H~NvirdI~~qle~~~e~~~~EF~~LNFe~~~Y~~e~n~~~yPmy~lT~dgF~lv~MgY 85 (112)
T TIGR02681 6 FTKENVVVTDSLKLAEVFGKRHDNVIRDIKSQLELLIEADETEFALLNFEETEYLDEQNKKQYPMYNLTKDGFTLVVMGY 85 (112)
T ss_pred CCCCCEEEECHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCCCCCEECCHHHHCCCCEEEEECCC
T ss_conf 24276234223578864196032157876766540114676201102654545321577731764220301002432265
Q ss_pred CCHHHHHHHHH
Q ss_conf 99657999998
Q gi|254780125|r 82 TLPSAQKFERW 92 (262)
Q Consensus 82 ~~p~A~~F~~W 92 (262)
+.|+|=+|+--
T Consensus 86 ~t~kAMk~K~~ 96 (112)
T TIGR02681 86 TTPKAMKMKEK 96 (112)
T ss_pred CCHHHHHHHHH
T ss_conf 78567998999
No 70
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=31.59 E-value=34 Score=14.15 Aligned_cols=26 Identities=4% Similarity=-0.041 Sum_probs=15.9
Q ss_pred EEEHHHHHHHHCCCC--HHHHHHHHCCC
Q ss_conf 667999998828968--89999984567
Q gi|254780125|r 25 WFVAKDVATALGYEN--SNEAINAHCKG 50 (262)
Q Consensus 25 wF~a~dva~~LGy~~--~~~ai~~~~~~ 50 (262)
.....|+|+.||.+. .++-+..+.+.
T Consensus 19 ~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 19 KCSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred CEEHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 7999999998796998999849999878
No 71
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=31.34 E-value=34 Score=14.12 Aligned_cols=43 Identities=23% Similarity=0.176 Sum_probs=25.8
Q ss_pred CCCCCHHHHHHHHCCCCCH-HHHHHHHHHCCCEEECCCCCEEEC
Q ss_conf 8732399999973899888-999999997897685379944365
Q gi|254780125|r 174 DEYLTITQIGERLNPPQRA-RFLNKLLLKRGLQVSKVSGGYRPT 216 (262)
Q Consensus 174 ~~~l~~t~iak~l~~~~sa-~~~N~lL~~~g~q~Rk~~~~W~lt 216 (262)
.+.+++++|++.++++.+. ..--+.|.+.|+......|++..|
T Consensus 8 ~~~~~~~ela~~l~is~~tvs~HL~~L~~~Glv~~~~~G~~~~Y 51 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYY 51 (66)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCEEEE
T ss_conf 39966999999988298888799999998892689998689999
No 72
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=30.88 E-value=35 Score=14.07 Aligned_cols=45 Identities=20% Similarity=0.306 Sum_probs=28.8
Q ss_pred EHHHHHHHHCCCCHHHHHHHHCCCCCEEEE-E-CCCCCCCEEEEECHHH
Q ss_conf 799999882896889999984567432887-2-2799831068971877
Q gi|254780125|r 27 VAKDVATALGYENSNEAINAHCKGVAKRYP-L-KTEGGIQKVRIISEPD 73 (262)
Q Consensus 27 ~a~dva~~LGy~~~~~ai~~~~~~~~~~~~-~-~~~g~~~~~~~i~E~g 73 (262)
...++|..+||+ ++.|++-++.+..... . -..||.-....|++.-
T Consensus 2 T~eELa~~~G~s--rQtINkwaRkeGW~t~~~~GVQGGkArlihId~~V 48 (122)
T pfam07037 2 TPEELAELTGYS--RQTINRWVRKEGWKTSPKPGVKGGKARLIHIDEQV 48 (122)
T ss_pred CHHHHHHHHCCH--HHHHHHHHHHCCCCCCCCCCCCCCEEEEEEECHHH
T ss_conf 878998874712--99999999973870488788657612455414889
No 73
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=30.18 E-value=36 Score=13.99 Aligned_cols=25 Identities=4% Similarity=0.193 Sum_probs=14.4
Q ss_pred EEEHHHHHHHHCCCC--HHHHHHHHCC
Q ss_conf 667999998828968--8999998456
Q gi|254780125|r 25 WFVAKDVATALGYEN--SNEAINAHCK 49 (262)
Q Consensus 25 wF~a~dva~~LGy~~--~~~ai~~~~~ 49 (262)
.....|+|+.||.+. .++-+..+.+
T Consensus 19 ~v~v~eLa~~~~VS~~TIRRDL~~Le~ 45 (252)
T PRK10906 19 YVSTEELVEHFSVSPQTIRRDLNELAE 45 (252)
T ss_pred CEEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 899999999879699899882999987
No 74
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=29.23 E-value=37 Score=13.88 Aligned_cols=62 Identities=24% Similarity=0.255 Sum_probs=33.1
Q ss_pred EEHHHHHHHHCCCCHHHH--HHHHCCCC-CEEEEECCCCCCCEEEEECHHHHHHHHHHCCCHHHHH
Q ss_conf 679999988289688999--99845674-3288722799831068971877999998579965799
Q gi|254780125|r 26 FVAKDVATALGYENSNEA--INAHCKGV-AKRYPLKTEGGIQKVRIISEPDVYRLLVKSTLPSAQK 88 (262)
Q Consensus 26 F~a~dva~~LGy~~~~~a--i~~~~~~~-~~~~~~~~~g~~~~~~~i~E~gly~Li~~s~~p~A~~ 88 (262)
.+.+++|+.||....-.+ ++.+.+.. -.++......|.|++ |++--+-..+-|.-+++.+.-
T Consensus 38 lNvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~karkG~QKi-C~s~~~ei~i~F~~r~~~~~~ 102 (308)
T COG4189 38 LNVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVKARKGSQKI-CISTTDEIEINFPDRTESLDL 102 (308)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCCCEEE-EEEECCEEEEECCCCCCHHHH
T ss_conf 87899998858865666655788886472463100133675067-675325599965999842441
No 75
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=29.21 E-value=37 Score=13.88 Aligned_cols=40 Identities=20% Similarity=0.184 Sum_probs=28.0
Q ss_pred HHCCCCCCCHHHHHHHHCCCCC-HHHHHHHHHHCCCEEECC
Q ss_conf 4155873239999997389988-899999999789768537
Q gi|254780125|r 170 SSDNDEYLTITQIGERLNPPQR-ARFLNKLLLKRGLQVSKV 209 (262)
Q Consensus 170 ~~~~~~~l~~t~iak~l~~~~s-a~~~N~lL~~~g~q~Rk~ 209 (262)
.+...+-++.++||+.+++..+ .-.+-+-|.+.||..|..
T Consensus 11 ~l~~~~~~s~~~la~~~~~~~~~vs~~i~~Le~~glv~R~~ 51 (59)
T pfam01047 11 ILYEHGPLTVSELAEKLGVDRSTVTRVLDRLEKKGLIERSR 51 (59)
T ss_pred HHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
T ss_conf 99946992999999998858654999999998897988627
No 76
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=28.98 E-value=37 Score=13.85 Aligned_cols=24 Identities=13% Similarity=0.178 Sum_probs=13.5
Q ss_pred EEHHHHHHHHCCCC--HHHHHHHHCC
Q ss_conf 67999998828968--8999998456
Q gi|254780125|r 26 FVAKDVATALGYEN--SNEAINAHCK 49 (262)
Q Consensus 26 F~a~dva~~LGy~~--~~~ai~~~~~ 49 (262)
....|+|+.||.+. .++-+..+.+
T Consensus 19 v~v~eLa~~~~VS~~TIRRDL~~Le~ 44 (240)
T PRK10411 19 LTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred EEHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 99999999889599899982998977
No 77
>TIGR02715 amido_AtzE amidohydrolase, AtzE family; InterPro: IPR014087 Members of this protein family are aminohydrolases related to, but distinct from, glutamyl-tRNA(Gln) amidotransferase subunit A. The best-characterised member is from Pseudomonas sp., which hydrolyses ammonia from the three-nitrogen compound biuret to yield allophanate. Allophanate is also an intermediate in urea degradation by the urea carboxylase/allophanate hydrolase pathway, an alternative to urease..
Probab=28.70 E-value=38 Score=13.82 Aligned_cols=19 Identities=32% Similarity=0.714 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q ss_conf 5799999888978999996
Q gi|254780125|r 85 SAQKFERWVFEEVLPTLRK 103 (262)
Q Consensus 85 ~A~~F~~Wv~~eVLPsIRk 103 (262)
.|++||+|.-++|.+-=++
T Consensus 345 ~AQrFR~~fR~~~~~lF~~ 363 (454)
T TIGR02715 345 QAQRFRRWFRDKVRELFQR 363 (454)
T ss_pred HHHHHHHHHHHHHHHHHHC
T ss_conf 8768899999998778622
No 78
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR; InterPro: IPR012712 This Helix-Turn-Helix transcriptional regulator is a member of the MarR family and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0010124 phenylacetate catabolic process, 0016481 negative regulation of transcription.
Probab=28.32 E-value=38 Score=13.78 Aligned_cols=70 Identities=20% Similarity=0.190 Sum_probs=48.2
Q ss_pred HHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHH---CCCCCHHHHHHHHHHCCCEEECCC--CC----EEECHHHHHHH
Q ss_conf 9830234200134666541558732399999973---899888999999997897685379--94----43657897543
Q gi|254780125|r 153 KITGVDQLEAMDIKHLPSSDNDEYLTITQIGERL---NPPQRARFLNKLLLKRGLQVSKVS--GG----YRPTPKGEERG 223 (262)
Q Consensus 153 ~~~~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l---~~~~sa~~~N~lL~~~g~q~Rk~~--~~----W~lt~kg~~~g 223 (262)
.++++.+.|=+ -..+++.+|.+-.+++|+.. .+.+ -+.=+-|-..|+..|++. ++ -.+|++|...-
T Consensus 22 ~~h~lTEQQWR---ilR~L~~~G~~e~~~LA~~A~iL~PSL--TgiL~rLE~~glv~R~k~~~DQRR~~~~lT~~G~~L~ 96 (130)
T TIGR02337 22 REHGLTEQQWR---ILRVLAEKGSMEFTELADRACILRPSL--TGILARLEKRGLVVRLKASNDQRRVYISLTKKGQALY 96 (130)
T ss_pred HHCCCCHHHHH---HHHHHHCCCCCCHHHHHHHHCCCCCCH--HHHHHHHHHCCCEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 53779647899---999883389948687886641479965--7899999745870225888774412422237899999
Q ss_pred HHHC
Q ss_conf 5530
Q gi|254780125|r 224 GKMC 227 (262)
Q Consensus 224 ~~~~ 227 (262)
....
T Consensus 97 ~~~~ 100 (130)
T TIGR02337 97 ESVS 100 (130)
T ss_pred HHHH
T ss_conf 9851
No 79
>TIGR02441 fa_ox_alpha_mit fatty acid oxidation complex, alpha subunit, mitochondrial; InterPro: IPR012803 Members of this family represent the alpha subunit of the mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (4.2.1.17 from EC) and 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC). Some characterization of these proteins has been done in human (P40939 from SWISSPROT), pig (Q29554 from SWISSPROT) and rat (Q64428 from SWISSPROT). The beta subunit has acetyl-CoA C-acyltransferase (2.3.1.16 from EC) activity.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0004300 enoyl-CoA hydratase activity, 0006635 fatty acid beta-oxidation, 0005739 mitochondrion, 0016507 fatty acid beta-oxidation multienzyme complex.
Probab=27.83 E-value=39 Score=13.72 Aligned_cols=43 Identities=19% Similarity=0.156 Sum_probs=33.7
Q ss_pred HHHHHHHHC--CCCCHHHHHHHHHHCCCEEECCCCCEEECHHHHH
Q ss_conf 999999738--9988899999999789768537994436578975
Q gi|254780125|r 179 ITQIGERLN--PPQRARFLNKLLLKRGLQVSKVSGGYRPTPKGEE 221 (262)
Q Consensus 179 ~t~iak~l~--~~~sa~~~N~lL~~~g~q~Rk~~~~W~lt~kg~~ 221 (262)
+.++||.+| .|.....+-..|-..|+.=||-++-..+|+.++.
T Consensus 576 A~dLgKafGeRfgGG~~~ll~~lV~~GflGRK~GKGif~Y~~g~k 620 (740)
T TIGR02441 576 AEDLGKAFGERFGGGSLELLSELVKAGFLGRKSGKGIFIYQEGKK 620 (740)
T ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCEEEEECCCEE
T ss_conf 987787705566888789999998624772302540688468351
No 80
>TIGR02529 EutJ ethanolamine utilization protein EutJ family protein; InterPro: IPR013366 Salmonella typhimurium is capable of growth on ethanolamine as a sole source of carbon nitrogen and energy . During growth on this compound the cells form a multimolecular structure known as a metabolosome, which is similar to the carboxysome used by some photosynthetic bacteria to fix CO2, and is thought to contain the enzymes needed to metabolise this compound to acetyl-CoA. The metabolosome is not directly involved in the biochemistry of ethanolamine utilization - instead its role is thought to be to concentrate the enzymes involved in this process, while also protecting the cell from the build-up of toxic intermediates . The genes involved in growth on ethanolamine are encoded in a 17-gene operon known as the ethanolamine utilization (eut) operon. EutJ shows similarity to chaperonins and may play a role in assembly of the metabolosme , though it is not necessary for growth on this compound..
Probab=27.26 E-value=40 Score=13.65 Aligned_cols=36 Identities=11% Similarity=0.124 Sum_probs=29.1
Q ss_pred EEEEEEECCEEEEEHHHHHHHH------CCCCHHHHHHHHCC
Q ss_conf 9999943890866799999882------89688999998456
Q gi|254780125|r 14 IRTIVDKDQNIWFVAKDVATAL------GYENSNEAINAHCK 49 (262)
Q Consensus 14 ir~v~~~dge~wF~a~dva~~L------Gy~~~~~ai~~~~~ 49 (262)
|-+|+|.||+|.|+.-+.|.+- .|-.+-..+++|-+
T Consensus 10 V~vVLD~d~~PVAg~~~~a~VVRDG~VVDf~~A~~iV~rLK~ 51 (240)
T TIGR02529 10 VIVVLDEDGQPVAGVMQFADVVRDGIVVDFLEAVEIVKRLKD 51 (240)
T ss_pred EEEEEECCCCEEEEEECHHHEEECCEEEECHHHHHHHHHHHH
T ss_conf 999984599638998532323553437820447889999998
No 81
>TIGR01345 malate_syn_G malate synthase G; InterPro: IPR006253 These sequences represent the G isozyme of malate synthase. Malate synthase G (MSG, 723 residues) is an enzyme of the glyoxylate pathway, that catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA , this biochemical bypass is used by microorganisms (bacteria, yeast, and fungi) for biosynthesis under anaerobic conditions . Enzymes of the glyoxylate bypass have been implicated as virulence factors in several pathogens, including Mycobacterium tuberculosis , , . The X-ray structure of the ternary abortive complex of MSG with pyruvate (glyoxylate mimic) and acetyl-CoA has been determined and shown to have the same structure as in the complex with glyoxylate .; GO: 0004474 malate synthase activity, 0006097 glyoxylate cycle.
Probab=27.26 E-value=25 Score=15.05 Aligned_cols=26 Identities=42% Similarity=0.503 Sum_probs=21.2
Q ss_pred HHCCCHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 85799657999998889789999960775
Q gi|254780125|r 79 VKSTLPSAQKFERWVFEEVLPTLRKTGSY 107 (262)
Q Consensus 79 ~~s~~p~A~~F~~Wv~~eVLPsIRktG~Y 107 (262)
-.|++..|+.|.++|.++|||- ||.=
T Consensus 4 ~~g~lqva~~l~~Fv~e~vLPg---tG~d 29 (726)
T TIGR01345 4 DAGRLQVAKKLKDFVEEEVLPG---TGVD 29 (726)
T ss_pred ECCCCHHHHHHHHHHHHHCCCC---CCCC
T ss_conf 0343225678888664313788---8867
No 82
>TIGR01194 cyc_pep_trnsptr cyclic peptide transporter; InterPro: IPR005898 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. This model describes a family of cyclic peptide transporters in bacteria. Syringomycin is an amphipathic, cyclic lipodepsipeptide when inserted into host causes formation of channels, permeable to a variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake.; GO: 0005524 ATP binding, 0015197 peptide transporter activity, 0015833 peptide transport, 0016021 integral to membrane.
Probab=27.01 E-value=14 Score=16.87 Aligned_cols=42 Identities=19% Similarity=0.229 Sum_probs=24.0
Q ss_pred CCCEEEEECHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8310689718779999985799657999998889789999960
Q gi|254780125|r 62 GIQKVRIISEPDVYRLLVKSTLPSAQKFERWVFEEVLPTLRKT 104 (262)
Q Consensus 62 ~~~~~~~i~E~gly~Li~~s~~p~A~~F~~Wv~~eVLPsIRkt 104 (262)
+.++..+++-.||.-+++-++. .|.-|..++-..++..+|+.
T Consensus 50 ~~~QG~Ll~F~GL~~~AL~~~~-~~~~~~~Y~~~~I~~~~R~~ 91 (555)
T TIGR01194 50 FLRQGVLLSFVGLSLLALLFRI-VADLFTAYVSQRIIARLRKE 91 (555)
T ss_pred CCCCCHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHH
T ss_conf 4565123357889999999986-53334567888999999999
No 83
>pfam10543 ORF6N ORF6N domain. This domain was identified by Iyer and colleagues.
Probab=26.48 E-value=41 Score=13.56 Aligned_cols=60 Identities=18% Similarity=0.190 Sum_probs=34.7
Q ss_pred EECCEEEEEHHHHHHHHCCC--CHHHHHHHHCCCCC---EEE---------------EECCCCCCCEEEEECHHHHHHHH
Q ss_conf 43890866799999882896--88999998456743---288---------------72279983106897187799999
Q gi|254780125|r 19 DKDQNIWFVAKDVATALGYE--NSNEAINAHCKGVA---KRY---------------PLKTEGGIQKVRIISEPDVYRLL 78 (262)
Q Consensus 19 ~~dge~wF~a~dva~~LGy~--~~~~ai~~~~~~~~---~~~---------------~~~~~g~~~~~~~i~E~gly~Li 78 (262)
...|+.-....|+|+..|.. +.++++++..+... ... ....++.....++++|.|.++++
T Consensus 6 e~rgqrV~t~~~LA~lyg~~t~~i~~~~~rN~~RF~eg~~~F~L~~~E~~~l~~~~~~~~~~~~~~~~~l~TE~G~~mla 85 (87)
T pfam10543 6 EYRGQRVMTDEDLAELYGVETGTINQAFKRNRDRFPEGKFYFELTGEELKELRSQFVTSKISGRARKPYLFTERGAAMLS 85 (87)
T ss_pred EECCEEEEEHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCEEEEECHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHC
T ss_conf 98896897789999995968579999999857647787479996389999999861302457887786887898699875
No 84
>PRK10632 putative DNA-binding transcriptional regulator; Provisional
Probab=26.22 E-value=42 Score=13.53 Aligned_cols=43 Identities=9% Similarity=0.054 Sum_probs=20.9
Q ss_pred HHHHHHHHCCCCH--HHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHH
Q ss_conf 9999988289688--9999984567432887227998310689718779
Q gi|254780125|r 28 AKDVATALGYENS--NEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDV 74 (262)
Q Consensus 28 a~dva~~LGy~~~--~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gl 74 (262)
-...|+.||.+.+ ++.|+.+-+.-......-+. ....+|+.|-
T Consensus 19 fs~AA~~L~~s~saVSr~I~~LE~~LG~~Lf~Rtt----R~l~LT~~G~ 63 (309)
T PRK10632 19 FTAAARQLQMSVSSISQTVSKLEDELQVKLLNRST----RSIGLTEAGR 63 (309)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECC----CCCEECHHHH
T ss_conf 99999997959889999999999997995689789----9712898999
No 85
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=25.86 E-value=42 Score=13.49 Aligned_cols=45 Identities=9% Similarity=0.050 Sum_probs=23.1
Q ss_pred HHHHHHHHCCCCH--HHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHHHH
Q ss_conf 9999988289688--999998456743288722799831068971877999
Q gi|254780125|r 28 AKDVATALGYENS--NEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDVYR 76 (262)
Q Consensus 28 a~dva~~LGy~~~--~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gly~ 76 (262)
-.-.|+.|+.+.| ++.|+.+-+........-+..+ .-.++.|-.-
T Consensus 20 ft~AA~~L~isQpavS~~I~~LE~~Lg~~Lf~R~~r~----v~lT~~G~~l 66 (291)
T PRK10837 20 TTQASVMLALSQSAVSAALTDLEGQLGVQLFDRVGKR----LVVNEHGRLL 66 (291)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECCCC----CCCCHHHHHH
T ss_conf 9999999888878999999999999699228985996----5246859999
No 86
>COG1597 LCB5 Sphingosine kinase and enzymes related to eukaryotic diacylglycerol kinase [Lipid metabolism / General function prediction only]
Probab=25.65 E-value=43 Score=13.46 Aligned_cols=55 Identities=22% Similarity=0.241 Sum_probs=33.7
Q ss_pred EHHHHHHHHCCCC--HHHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHH--HHHHHHCCC
Q ss_conf 7999998828968--89999984567432887227998310689718779--999985799
Q gi|254780125|r 27 VAKDVATALGYEN--SNEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDV--YRLLVKSTL 83 (262)
Q Consensus 27 ~a~dva~~LGy~~--~~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gl--y~Li~~s~~ 83 (262)
.++|+|++||+.+ +..++....+.+.....+-..++.. .|+|-.|+ ..-+.....
T Consensus 93 T~NdfAr~Lgip~~~~~~Al~~i~~g~~~~vDlg~~~~~~--~fin~a~~G~~a~~~~~~~ 151 (301)
T COG1597 93 TANDFARALGIPLDDIEAALELIKSGETRKVDLGQVNGRR--YFINNAGIGFDAEVVAAVE 151 (301)
T ss_pred CHHHHHHHCCCCCHHHHHHHHHHHCCCEEEEEHHHCCCCC--EEEEEECCCCCHHHHHHCC
T ss_conf 5778899859994549999999863986997534338954--6988740450238887514
No 87
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.39 E-value=43 Score=13.43 Aligned_cols=46 Identities=22% Similarity=0.190 Sum_probs=26.0
Q ss_pred HHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCE
Q ss_conf 2342001346665415587323999999738998889999999978976
Q gi|254780125|r 157 VDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKLLLKRGLQ 205 (262)
Q Consensus 157 i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~sa~~~N~lL~~~g~q 205 (262)
++.+.++.-....+.... -++..+||+.+|+ |...+-..|+.+..+
T Consensus 134 l~~LP~~~R~v~~Lr~~~-~ls~~EIA~~l~i--s~~tVksrL~RAR~~ 179 (191)
T PRK12530 134 LNKLPAQQARVFMMREFL-ELSSEQICQECHI--TTSNLHVLLYRARLQ 179 (191)
T ss_pred HHHCCHHHHHHHHHHHHC-CCCHHHHHHHHCC--CHHHHHHHHHHHHHH
T ss_conf 986999999999999992-9999999999896--999999999999999
No 88
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=25.29 E-value=43 Score=13.42 Aligned_cols=43 Identities=14% Similarity=0.101 Sum_probs=22.2
Q ss_pred HHHHHHHHCCCCH--HHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHH
Q ss_conf 9999988289688--9999984567432887227998310689718779
Q gi|254780125|r 28 AKDVATALGYENS--NEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDV 74 (262)
Q Consensus 28 a~dva~~LGy~~~--~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gl 74 (262)
-.-.|+.||.+.+ ++.|+.+-+.-......-+. ....+|+.|-
T Consensus 31 ft~AA~~L~vsqsaVS~~I~~LE~~LG~~Lf~R~~----R~l~LT~aG~ 75 (311)
T PRK10086 31 FALAADELSLTPSAVSHRINQLEEELGIKLFVRSH----RKVELTEEGK 75 (311)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECC----CCEEEHHHHH
T ss_conf 99999997869899999999999985984389759----9168909999
No 89
>pfam01638 HxlR HxlR-like helix-turn-helix. HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.
Probab=24.81 E-value=44 Score=13.36 Aligned_cols=54 Identities=19% Similarity=0.191 Sum_probs=38.6
Q ss_pred CCCCCHHHHHHHHCCCCCHHHHHHH---HHHCCCEEECC------CCCEEECHHHHHHHHHHCC
Q ss_conf 8732399999973899888999999---99789768537------9944365789754355304
Q gi|254780125|r 174 DEYLTITQIGERLNPPQRARFLNKL---LLKRGLQVSKV------SGGYRPTPKGEERGGKMCD 228 (262)
Q Consensus 174 ~~~l~~t~iak~l~~~~sa~~~N~l---L~~~g~q~Rk~------~~~W~lt~kg~~~g~~~~~ 228 (262)
.|.....++.+.+. |+|.+-+... |.+.|+..|+. +-.+.||++|.+.-+.+..
T Consensus 16 ~g~~rF~el~~~l~-gis~~vLs~rLk~L~~~gli~r~~~~~~p~~~eY~LT~~G~~l~pvl~~ 78 (90)
T pfam01638 16 DGPKRFSELKRALP-GISQKMLTQRLRELEQDGIINREVYPEVPPKVEYSLTEKGRSLEPILQA 78 (90)
T ss_pred CCCCCHHHHHHHCC-CCCHHHHHHHHHHHHHCCCEEEEECCCCCCCEEEEECCCHHHHHHHHHH
T ss_conf 49988999997765-7698999999999998899376456999993687439078789999999
No 90
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=24.78 E-value=44 Score=13.35 Aligned_cols=42 Identities=19% Similarity=0.169 Sum_probs=31.9
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHHCCCEEECCC--CCEEEC
Q ss_conf 732399999973899888999999997897685379--944365
Q gi|254780125|r 175 EYLTITQIGERLNPPQRARFLNKLLLKRGLQVSKVS--GGYRPT 216 (262)
Q Consensus 175 ~~l~~t~iak~l~~~~sa~~~N~lL~~~g~q~Rk~~--~~W~lt 216 (262)
-.++...+.+.+|+..+...+.++|...|+...... +.|..+
T Consensus 4 i~~~~~~i~~~lG~~i~~~~i~~~L~~lg~~~~~~~~~~~~~v~ 47 (71)
T smart00874 4 ITLRRERINRLLGLDLSAEEIEEILKRLGFEVEVSGDDDTLEVT 47 (71)
T ss_pred EEECHHHHHHHHCCCCCHHHHHHHHHHCCCEEEECCCCCEEEEE
T ss_conf 99879999987088879999999999869989965789759997
No 91
>KOG1057 consensus
Probab=24.74 E-value=24 Score=15.16 Aligned_cols=32 Identities=31% Similarity=0.319 Sum_probs=13.6
Q ss_pred CCHHHHHHHHHHHHHHHHHH-HHHCCCCCCCCCC
Q ss_conf 99657999998889789999-9607757753322
Q gi|254780125|r 82 TLPSAQKFERWVFEEVLPTL-RKTGSYSVEAPKL 114 (262)
Q Consensus 82 ~~p~A~~F~~Wv~~eVLPsI-RktG~Y~~~~~~~ 114 (262)
|+|+ .+|+--|+++-+=.+ -|.++|-..+...
T Consensus 393 RTPK-QK~K~~vt~~~f~~L~ek~~G~~~~e~kl 425 (1018)
T KOG1057 393 RTPK-QKMKLSVTSPKFLGLFEKYDGYKKEETKL 425 (1018)
T ss_pred CCCC-CEEEEEECCHHHHHHHHHHCCCCCCCEEE
T ss_conf 7866-32357742478899888607830100120
No 92
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=24.46 E-value=45 Score=13.31 Aligned_cols=61 Identities=26% Similarity=0.169 Sum_probs=37.6
Q ss_pred CCHHHHHHHHCCC--CCHHHHHHHHHHCCCEE-EC----CCCC-EEECHHHHHHHHHHCCCCCCCCCCCCE
Q ss_conf 2399999973899--88899999999789768-53----7994-436578975435530475346883311
Q gi|254780125|r 177 LTITQIGERLNPP--QRARFLNKLLLKRGLQV-SK----VSGG-YRPTPKGEERGGKMCDVPMQHVEGSTQ 239 (262)
Q Consensus 177 l~~t~iak~l~~~--~sa~~~N~lL~~~g~q~-Rk----~~~~-W~lt~kg~~~g~~~~~~p~~~~g~~~~ 239 (262)
-++++|||- |+- -+|+-+-+-|.+.|+.. +| +|.. -.||++|.+.-...- ..|.+...++|
T Consensus 61 AsISdiAkf-GVMHVSTaFNFSKkLEeRG~L~fsKk~~DKRNTYi~LT~~G~e~~l~~~-~~y~p~~~~v~ 129 (190)
T PRK13777 61 ASISEIAKF-GVMHVSTAFNFSKKLEERGYLVFSKKEDDKRNTYIELTDKGEELLLRLM-EEYDPENNSVF 129 (190)
T ss_pred CCHHHHHHH-CCEEEEEHHHHHHHHHHCCCEECCCCCCCCCCCEEEECCCHHHHHHHHH-HHCCCCCCHHH
T ss_conf 839999870-7246300320557777553453340024655535886501689999999-85196634234
No 93
>PRK09801 transcriptional activator TtdR; Provisional
Probab=24.27 E-value=45 Score=13.29 Aligned_cols=42 Identities=14% Similarity=0.151 Sum_probs=20.3
Q ss_pred HHHHHHHCCCCH--HHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHH
Q ss_conf 999988289688--9999984567432887227998310689718779
Q gi|254780125|r 29 KDVATALGYENS--NEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDV 74 (262)
Q Consensus 29 ~dva~~LGy~~~--~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gl 74 (262)
.--|+.||.+.+ ++.|+.+-+........-+. ...-+||.|-
T Consensus 24 s~AA~~L~vs~saVSr~I~~LE~~LG~~Lf~R~t----R~l~LTeaG~ 67 (310)
T PRK09801 24 SAAAATLGQTPAFVTKRIQILENTLATTLLNRSA----RGVALTESGQ 67 (310)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEECC----CCEECCHHHH
T ss_conf 9999997959889999999999986993761489----9840159999
No 94
>pfam04760 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.
Probab=22.63 E-value=48 Score=13.08 Aligned_cols=29 Identities=24% Similarity=0.371 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHHCCCE
Q ss_conf 7323999999738998889999999978976
Q gi|254780125|r 175 EYLTITQIGERLNPPQRARFLNKLLLKRGLQ 205 (262)
Q Consensus 175 ~~l~~t~iak~l~~~~sa~~~N~lL~~~g~q 205 (262)
..+++.++|+.++ +++..+-+.|...|+-
T Consensus 2 ~~itV~elA~~l~--~~~~~vi~~L~~~Gi~ 30 (52)
T pfam04760 2 EKIRVYELAKELG--VSSKELIKKLFKLGIM 30 (52)
T ss_pred CCEEHHHHHHHHC--CCHHHHHHHHHHCCCE
T ss_conf 8173999999988--8899999999987985
No 95
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=22.53 E-value=49 Score=13.07 Aligned_cols=47 Identities=17% Similarity=0.097 Sum_probs=26.5
Q ss_pred HHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHCCCE
Q ss_conf 02342001346665415587323999999738998889999999978976
Q gi|254780125|r 156 GVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKLLLKRGLQ 205 (262)
Q Consensus 156 ~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~sa~~~N~lL~~~g~q 205 (262)
-++.+.++.-....+..- .-++..+||..||+ |...+..+|+...-+
T Consensus 136 aL~~LP~~~R~v~~Lr~~-egls~~EIA~~L~i--s~~tVksrL~RAR~~ 182 (201)
T PRK12545 136 CLDHLPEQIGRVFMMREF-LDFEIDDICTELTL--TANHCSVLLYRARTR 182 (201)
T ss_pred HHHHCCHHHHHHHHHHHH-HCCCHHHHHHHHCC--CHHHHHHHHHHHHHH
T ss_conf 999599999889899999-28989999999896--999999999999999
No 96
>pfam06970 RepA_N Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included.
Probab=22.44 E-value=49 Score=13.06 Aligned_cols=23 Identities=22% Similarity=0.132 Sum_probs=13.8
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 2399999973899888999999997
Q gi|254780125|r 177 LTITQIGERLNPPQRARFLNKLLLK 201 (262)
Q Consensus 177 l~~t~iak~l~~~~sa~~~N~lL~~ 201 (262)
++..++++.|| +|...+-+++.|
T Consensus 53 ft~~el~~~L~--~s~~~v~k~~kE 75 (76)
T pfam06970 53 FTNEELMELLN--CSKQKVIKIKKE 75 (76)
T ss_pred EEHHHHHHHHC--CCHHHHHHHHHC
T ss_conf 64999999978--788899999961
No 97
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=22.31 E-value=49 Score=13.04 Aligned_cols=38 Identities=21% Similarity=0.111 Sum_probs=27.9
Q ss_pred CCCCCCCHHHHHHHHCCCCC-HHHHHHHHHHCCCEEECC
Q ss_conf 55873239999997389988-899999999789768537
Q gi|254780125|r 172 DNDEYLTITQIGERLNPPQR-ARFLNKLLLKRGLQVSKV 209 (262)
Q Consensus 172 ~~~~~l~~t~iak~l~~~~s-a~~~N~lL~~~g~q~Rk~ 209 (262)
-..+..++.+||+.+|+..+ ....-.-|.+.|+..+..
T Consensus 18 l~~g~~t~~eia~~~~i~r~~vY~~L~~L~~kGlv~~~~ 56 (68)
T pfam01978 18 LKLGPATADEIAEESGVPRSKVYEVLRSLEKKGLVEREK 56 (68)
T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf 981998899999995988989999999999889889867
No 98
>pfam11210 DUF2996 Protein of unknown function (DUF2996). This family of proteins has no known function.
Probab=22.18 E-value=44 Score=13.37 Aligned_cols=14 Identities=36% Similarity=0.351 Sum_probs=9.3
Q ss_pred ECHHHHHHHHHHHC
Q ss_conf 45017765653102
Q gi|254780125|r 243 WNSNLLVSFLQNEL 256 (262)
Q Consensus 243 w~~~v~~~~~~~~~ 256 (262)
=.|+.+++|+-||-
T Consensus 82 ~~PS~lEsFLIDEk 95 (118)
T pfam11210 82 SEPSTLESFLIDEK 95 (118)
T ss_pred CCCCHHHHHHCCCC
T ss_conf 99511000110101
No 99
>pfam06904 Extensin-like_C Extensin-like protein C-terminus. This family represents the C-terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress. Note that many family members of this family are hypothetical.
Probab=22.02 E-value=50 Score=13.00 Aligned_cols=25 Identities=32% Similarity=0.517 Sum_probs=21.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9965799999888978999996077
Q gi|254780125|r 82 TLPSAQKFERWVFEEVLPTLRKTGS 106 (262)
Q Consensus 82 ~~p~A~~F~~Wv~~eVLPsIRktG~ 106 (262)
+=|.|..|..|+.+.|.|.-+...+
T Consensus 49 ~C~~A~al~~W~~~~v~PaA~~~~g 73 (178)
T pfam06904 49 SCPLALALARWVRQGVQPAARRIFG 73 (178)
T ss_pred ECHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 0788999999999626799998738
No 100
>KOG3198 consensus
Probab=21.49 E-value=18 Score=15.98 Aligned_cols=43 Identities=21% Similarity=0.159 Sum_probs=25.5
Q ss_pred CCEEEEEEEEECCEEEEEHHHHHHHHCCCCHHHHHHHHCCCCC
Q ss_conf 9967999994389086679999988289688999998456743
Q gi|254780125|r 10 ESNKIRTIVDKDQNIWFVAKDVATALGYENSNEAINAHCKGVA 52 (262)
Q Consensus 10 e~~~ir~v~~~dge~wF~a~dva~~LGy~~~~~ai~~~~~~~~ 52 (262)
||..|..-...++..+-...|||+.|||.-.-.-.+.|.+|..
T Consensus 31 EGRripke~aVeNP~a~eI~Dvl~~lgl~~~~E~~K~hPrD~~ 73 (152)
T KOG3198 31 EGRRIPKEKAVENPLAKEIADVLRALGLNCLLEPNKKHPRDFV 73 (152)
T ss_pred HCCCCCHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCHHCC
T ss_conf 3362478786128442589999998198530253535820207
No 101
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=21.42 E-value=51 Score=12.92 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=14.3
Q ss_pred EEHHHHHHHHCCCC--HHHHHHHHCCC
Q ss_conf 67999998828968--89999984567
Q gi|254780125|r 26 FVAKDVATALGYEN--SNEAINAHCKG 50 (262)
Q Consensus 26 F~a~dva~~LGy~~--~~~ai~~~~~~ 50 (262)
...+|+|+.|+-+. .++-++.+.+.
T Consensus 20 v~v~eLa~~~~VS~~TIRRDL~~Le~~ 46 (251)
T PRK13509 20 VTVEKVIERLGISPATARRDINKLDES 46 (251)
T ss_pred EEHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 989999999896998999839999878
No 102
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=21.19 E-value=52 Score=12.89 Aligned_cols=39 Identities=18% Similarity=0.222 Sum_probs=25.3
Q ss_pred HHCCCCCCCHHHHHHHHCCCCCHHHHH---HHHHHCCCEEECCC
Q ss_conf 415587323999999738998889999---99997897685379
Q gi|254780125|r 170 SSDNDEYLTITQIGERLNPPQRARFLN---KLLLKRGLQVSKVS 210 (262)
Q Consensus 170 ~~~~~~~l~~t~iak~l~~~~sa~~~N---~lL~~~g~q~Rk~~ 210 (262)
+.++++.++..+||+.|++ |-+.+. +.|.+.|+......
T Consensus 9 L~~~~~~vt~~~La~~l~V--Sr~TV~rdi~~L~~~G~~I~s~~ 50 (55)
T pfam08279 9 LLQAREPISGQELAEKLGV--SRRTIRRDIKALEALGVPIESEP 50 (55)
T ss_pred HHHCCCCCCHHHHHHHHCC--CHHHHHHHHHHHHHCCCCEEECC
T ss_conf 9976999189999999698--89999999999998899788468
No 103
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery.
Probab=20.93 E-value=52 Score=12.85 Aligned_cols=11 Identities=36% Similarity=0.634 Sum_probs=5.1
Q ss_pred EEHHHHHHHHC
Q ss_conf 67999998828
Q gi|254780125|r 26 FVAKDVATALG 36 (262)
Q Consensus 26 F~a~dva~~LG 36 (262)
..|.+||+.||
T Consensus 19 lSaSqIA~~LG 29 (162)
T pfam07750 19 LSASQIAAQLG 29 (162)
T ss_pred CCHHHHHHHHC
T ss_conf 65999999976
No 104
>pfam04684 BAF1_ABF1 BAF1 / ABF1 chromatin reorganising factor. ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 S. cerevisiae ). The N-terminal two thirds of the protein are necessary for DNA binding, and the N-terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilize the protein structure.
Probab=20.46 E-value=53 Score=12.79 Aligned_cols=81 Identities=10% Similarity=0.285 Sum_probs=52.1
Q ss_pred EEHHHHHHHHCCC-CHHHHHHHHCCCCCEEEEECCCCCCCEEEEECHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH---
Q ss_conf 6799999882896-889999984567432887227998310689718779999985799657999998889789999---
Q gi|254780125|r 26 FVAKDVATALGYE-NSNEAINAHCKGVAKRYPLKTEGGIQKVRIISEPDVYRLLVKSTLPSAQKFERWVFEEVLPTL--- 101 (262)
Q Consensus 26 F~a~dva~~LGy~-~~~~ai~~~~~~~~~~~~~~~~g~~~~~~~i~E~gly~Li~~s~~p~A~~F~~Wv~~eVLPsI--- 101 (262)
|++.-|-++|.-. +-...+..+|.++..+ -...+-.-||-|+|+..+|..-.-=....|-+-+.+.+-.-|
T Consensus 190 FVLTKIPkILQ~DLkFD~ILEsLcNd~DnT-----VAKFRVsqYVEESGilDIiKqRYGLTd~d~dKKlLSqIARRVTTY 264 (508)
T pfam04684 190 FVLSKIPKILQVDLKFDAILESLCNDDDNT-----VAKFRVAQYVEESGIIDIIKQRYGLTDAEMDKKMLSNIARRVTTD 264 (508)
T ss_pred HHHHCCCHHHHCCCCHHHHHHHHHCCCCCC-----EEEEEHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 887405288763354999999984477885-----001107566524228999999718748888899999999887653
Q ss_pred --------HHHCCCCCCC
Q ss_conf --------9607757753
Q gi|254780125|r 102 --------RKTGSYSVEA 111 (262)
Q Consensus 102 --------RktG~Y~~~~ 111 (262)
.|.|.|..|.
T Consensus 265 KARFVLKkKK~G~Y~~p~ 282 (508)
T pfam04684 265 KARFVLKRKKDGVYALPN 282 (508)
T ss_pred HHEEEEEECCCCCCCCCC
T ss_conf 420365502377314886
No 105
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY; InterPro: IPR014154 This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. All have a C-terminal helix-turn-helix DNA-binding region..
Probab=20.43 E-value=54 Score=12.78 Aligned_cols=73 Identities=18% Similarity=0.210 Sum_probs=43.9
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHH--HHHCCCEEE
Q ss_conf 86403668999999999999830234200134666541558732399999973899888999999--997897685
Q gi|254780125|r 134 KQAGLKDNQLLLKVNRGVTKITGVDQLEAMDIKHLPSSDNDEYLTITQIGERLNPPQRARFLNKL--LLKRGLQVS 207 (262)
Q Consensus 134 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~pk~~~~d~~~~~~~~l~~t~iak~l~~~~sa~~~N~l--L~~~g~q~R 207 (262)
+.-..+.+.+..++-+..-..-.-.|++-=..-.+.+=-.+|.|.+..||-+-|++.| -=+|+| |..+|++.+
T Consensus 160 ~~~e~Eee~R~~a~VqmAi~TLSYSEL~AV~aIf~ELdG~EG~LvAS~IAD~vGITRS-VIVNALRKlESAGvIES 234 (255)
T TIGR02787 160 KAEEIEEEARKKAAVQMAINTLSYSELEAVEAIFEELDGNEGLLVASKIADRVGITRS-VIVNALRKLESAGVIES 234 (255)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCHH-HHHHHHHHHHHCCEEEC
T ss_conf 6555699999999999998720288999999998422899662775302071266033-55454344420764130
Done!