Query psy6088
Match_columns 289
No_of_seqs 201 out of 365
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 17:17:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6088.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6088hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3802|consensus 100.0 1.2E-66 2.6E-71 500.5 13.1 139 146-289 198-339 (398)
2 KOG1168|consensus 100.0 3.3E-44 7.1E-49 335.9 7.7 143 146-289 209-354 (385)
3 PF00157 Pou: Pou domain - N-t 100.0 4.4E-41 9.5E-46 260.5 5.6 75 148-222 1-75 (75)
4 smart00352 POU Found in Pit-Oc 100.0 1.6E-32 3.4E-37 212.8 6.9 75 148-222 1-75 (75)
5 TIGR01565 homeo_ZF_HD homeobox 99.0 5.2E-10 1.1E-14 83.3 4.7 46 244-289 1-50 (58)
6 PF00046 Homeobox: Homeobox do 98.8 5.1E-09 1.1E-13 74.6 3.2 44 245-288 1-44 (57)
7 smart00389 HOX Homeodomain. DN 98.7 2.2E-08 4.8E-13 70.4 3.9 45 245-289 1-45 (56)
8 cd00086 homeodomain Homeodomai 98.6 3.3E-08 7.2E-13 69.7 3.7 45 245-289 1-45 (59)
9 KOG0488|consensus 98.6 4.3E-08 9.3E-13 93.5 3.7 46 243-288 171-216 (309)
10 KOG0843|consensus 98.4 3E-07 6.5E-12 82.6 3.7 47 243-289 101-147 (197)
11 KOG2251|consensus 98.3 4.9E-07 1.1E-11 83.2 4.3 48 242-289 35-82 (228)
12 KOG0842|consensus 98.3 6.7E-07 1.4E-11 85.6 4.0 47 242-288 151-197 (307)
13 KOG0489|consensus 98.2 7.4E-07 1.6E-11 82.8 2.3 47 242-288 157-203 (261)
14 KOG0485|consensus 98.1 1.1E-06 2.4E-11 81.2 2.5 47 242-288 102-148 (268)
15 KOG0484|consensus 98.1 1.1E-06 2.4E-11 73.4 1.2 47 242-288 15-61 (125)
16 KOG0487|consensus 97.9 7.1E-06 1.5E-10 78.7 3.1 47 242-288 233-279 (308)
17 KOG0850|consensus 97.8 1.5E-05 3.2E-10 74.1 3.4 46 243-288 121-166 (245)
18 KOG0492|consensus 97.7 2.2E-05 4.7E-10 72.4 3.6 45 244-288 144-188 (246)
19 KOG0494|consensus 97.6 5.7E-05 1.2E-09 71.7 3.6 46 244-289 140-186 (332)
20 KOG2252|consensus 97.6 0.0002 4.3E-09 73.3 7.5 47 242-288 418-464 (558)
21 KOG0486|consensus 97.5 5E-05 1.1E-09 73.4 2.7 49 241-289 109-157 (351)
22 KOG0491|consensus 97.5 1.8E-05 4E-10 70.7 -0.5 48 241-288 97-144 (194)
23 KOG0493|consensus 97.3 0.00018 3.8E-09 68.5 3.2 44 245-288 247-290 (342)
24 COG5576 Homeodomain-containing 97.2 0.00047 1E-08 60.4 4.5 89 193-289 8-96 (156)
25 KOG0490|consensus 97.1 0.00028 6E-09 61.8 2.6 48 242-289 58-105 (235)
26 KOG0849|consensus 96.9 0.0006 1.3E-08 66.3 3.0 46 243-288 175-220 (354)
27 KOG0844|consensus 96.9 0.00047 1E-08 66.9 1.7 46 243-288 180-225 (408)
28 KOG0848|consensus 96.7 0.00056 1.2E-08 65.2 1.2 46 243-288 198-243 (317)
29 PF13560 HTH_31: Helix-turn-he 96.7 0.0012 2.5E-08 48.2 2.6 39 158-202 1-39 (64)
30 KOG4577|consensus 96.7 0.0014 3.1E-08 63.2 3.7 47 243-289 166-212 (383)
31 KOG0775|consensus 95.9 0.064 1.4E-06 51.5 9.9 130 147-288 73-220 (304)
32 TIGR03070 couple_hipB transcri 95.9 0.013 2.8E-07 40.4 4.0 47 158-210 2-50 (58)
33 KOG0774|consensus 95.3 0.014 3E-07 55.9 3.3 46 243-288 187-235 (334)
34 KOG0483|consensus 95.0 0.021 4.6E-07 52.1 3.3 39 250-288 56-94 (198)
35 KOG0847|consensus 95.0 0.012 2.5E-07 55.3 1.6 47 242-288 165-211 (288)
36 PHA01976 helix-turn-helix prot 94.4 0.071 1.5E-06 38.7 4.3 51 158-214 2-54 (67)
37 PF05920 Homeobox_KN: Homeobox 94.3 0.017 3.6E-07 40.1 0.6 24 265-288 7-30 (40)
38 TIGR00270 conserved hypothetic 94.1 0.082 1.8E-06 46.2 4.7 56 154-215 65-122 (154)
39 PRK06424 transcription factor; 93.5 0.12 2.6E-06 44.9 4.6 53 153-211 79-133 (144)
40 PRK10856 cytoskeletal protein 93.1 0.23 5.1E-06 48.1 6.4 66 150-221 6-82 (331)
41 TIGR03830 CxxCG_CxxCG_HTH puta 92.6 0.13 2.8E-06 41.5 3.4 36 161-202 68-103 (127)
42 PF01381 HTH_3: Helix-turn-hel 92.0 0.24 5.2E-06 34.4 3.7 46 163-214 1-48 (55)
43 PRK09726 antitoxin HipB; Provi 91.9 0.28 6E-06 38.2 4.4 48 157-210 11-60 (88)
44 KOG0490|consensus 91.2 0.16 3.5E-06 44.5 2.6 48 242-289 151-198 (235)
45 PRK09943 DNA-binding transcrip 90.6 0.38 8.3E-06 41.8 4.4 52 157-214 6-59 (185)
46 PF12844 HTH_19: Helix-turn-he 89.5 0.51 1.1E-05 33.8 3.6 45 161-211 2-48 (64)
47 PRK09706 transcriptional repre 89.4 0.61 1.3E-05 38.8 4.5 58 157-220 4-66 (135)
48 COG3620 Predicted transcriptio 88.8 0.64 1.4E-05 42.1 4.4 55 161-223 8-62 (187)
49 PRK08359 transcription factor; 88.8 0.69 1.5E-05 41.6 4.7 62 153-220 80-143 (176)
50 PRK10072 putative transcriptio 88.4 0.36 7.8E-06 39.3 2.4 36 161-202 36-71 (96)
51 PHA00542 putative Cro-like pro 86.7 1.1 2.3E-05 34.9 4.0 44 166-215 26-72 (82)
52 PF13744 HTH_37: Helix-turn-he 86.2 0.72 1.6E-05 35.4 2.8 42 153-200 13-54 (80)
53 TIGR02612 mob_myst_A mobile my 85.8 0.71 1.5E-05 40.3 3.0 48 162-215 29-80 (150)
54 PRK08154 anaerobic benzoate ca 85.3 1.6 3.5E-05 41.3 5.3 57 154-216 24-82 (309)
55 PRK13355 bifunctional HTH-doma 84.4 0.8 1.7E-05 45.8 3.0 64 157-221 2-70 (517)
56 cd00093 HTH_XRE Helix-turn-hel 82.6 1.8 4E-05 27.7 3.2 48 161-214 2-51 (58)
57 PRK13890 conjugal transfer pro 82.2 2.1 4.6E-05 35.6 4.2 53 158-216 5-59 (120)
58 TIGR02607 antidote_HigA addict 81.6 2.5 5.4E-05 31.2 4.0 48 161-214 7-57 (78)
59 TIGR01321 TrpR trp operon repr 76.6 5.6 0.00012 32.7 4.9 56 152-220 34-92 (94)
60 PRK04140 hypothetical protein; 76.6 3.1 6.7E-05 40.5 4.0 51 160-216 128-180 (317)
61 PF04218 CENP-B_N: CENP-B N-te 75.7 3.2 6.9E-05 30.0 2.9 39 245-288 1-39 (53)
62 PF01316 Arg_repressor: Argini 72.3 3.9 8.5E-05 31.6 2.8 34 159-196 10-43 (70)
63 smart00530 HTH_XRE Helix-turn- 65.6 11 0.00023 23.8 3.5 45 163-213 2-48 (56)
64 KOG1146|consensus 63.9 5.8 0.00012 45.4 3.1 46 243-288 902-947 (1406)
65 PF11569 Homez: Homeodomain le 61.2 2.8 6.1E-05 31.5 0.1 33 257-289 11-43 (56)
66 COG1476 Predicted transcriptio 58.7 6.1 0.00013 30.7 1.5 23 162-184 5-27 (68)
67 TIGR01529 argR_whole arginine 57.1 6.8 0.00015 33.8 1.7 31 172-203 17-48 (146)
68 PF10691 DUF2497: Protein of u 52.4 8.9 0.00019 30.1 1.6 11 210-220 43-53 (73)
69 TIGR03764 ICE_PFGI_1_parB inte 48.2 12 0.00025 35.8 2.0 53 147-200 107-164 (258)
70 COG1396 HipB Predicted transcr 40.6 43 0.00094 22.6 3.4 38 159-202 2-39 (120)
71 PF04545 Sigma70_r4: Sigma-70, 40.2 14 0.00031 25.4 0.9 35 250-289 4-38 (50)
72 KOG3623|consensus 39.9 23 0.00049 38.9 2.7 33 256-288 568-600 (1007)
73 PF13551 HTH_29: Winged helix- 39.3 1.7E+02 0.0037 22.3 7.1 39 245-283 52-97 (112)
74 PF00872 Transposase_mut: Tran 37.6 14 0.00029 36.3 0.6 27 171-197 114-141 (381)
75 PF04967 HTH_10: HTH DNA bindi 37.5 35 0.00077 25.0 2.7 36 251-286 1-38 (53)
76 PHA03256 BDLF3; Provisional 37.3 67 0.0015 25.6 4.3 38 242-282 8-45 (77)
77 PF13565 HTH_32: Homeodomain-l 37.1 51 0.0011 24.1 3.5 42 153-197 32-76 (77)
78 PRK10458 DNA cytosine methylas 33.8 28 0.00062 35.6 2.2 41 162-202 20-60 (467)
79 PF11774 Lsr2: Lsr2 ; InterPr 33.1 34 0.00073 28.5 2.2 26 199-224 32-57 (110)
80 TIGR02684 dnstrm_HI1420 probab 33.0 55 0.0012 26.2 3.3 37 158-202 32-68 (89)
81 COG1426 Predicted transcriptio 32.7 32 0.0007 32.8 2.3 49 158-206 3-67 (284)
82 COG1400 SEC65 Signal recogniti 32.2 39 0.00084 27.8 2.4 22 267-288 30-51 (93)
83 PRK04280 arginine repressor; P 30.4 27 0.00059 30.3 1.3 30 173-203 20-50 (148)
84 KOG0773|consensus 30.0 50 0.0011 31.5 3.1 45 244-288 239-286 (342)
85 PF01371 Trp_repressor: Trp re 29.7 73 0.0016 25.7 3.5 56 152-220 28-86 (87)
86 PF10157 DUF2365: Uncharacteri 28.0 1.2E+02 0.0026 26.8 4.8 19 192-210 113-131 (149)
87 PRK03975 tfx putative transcri 26.4 67 0.0015 28.0 3.0 41 169-217 19-59 (141)
88 PRK05066 arginine repressor; P 26.2 37 0.0008 29.9 1.4 30 173-203 25-56 (156)
89 PHA02591 hypothetical protein; 25.8 56 0.0012 26.5 2.2 34 154-197 46-79 (83)
90 PF13936 HTH_38: Helix-turn-he 25.4 40 0.00087 23.2 1.2 35 249-288 3-37 (44)
91 COG3827 Uncharacterized protei 24.3 41 0.00089 31.8 1.4 11 210-220 198-208 (231)
92 cd00569 HTH_Hin_like Helix-tur 23.4 1E+02 0.0022 17.3 2.6 32 251-287 6-37 (42)
93 PF07499 RuvA_C: RuvA, C-termi 22.7 54 0.0012 22.9 1.4 22 168-189 11-33 (47)
94 PRK03341 arginine repressor; P 21.9 51 0.0011 29.4 1.4 31 172-203 30-61 (168)
95 PF13613 HTH_Tnp_4: Helix-turn 20.9 48 0.001 23.5 0.9 25 167-197 15-39 (53)
96 KOG0100|consensus 20.8 1.4E+02 0.0031 31.3 4.5 76 147-224 261-359 (663)
97 PF01527 HTH_Tnp_1: Transposas 20.2 37 0.0008 24.8 0.2 38 246-287 2-39 (76)
No 1
>KOG3802|consensus
Probab=100.00 E-value=1.2e-66 Score=500.46 Aligned_cols=139 Identities=66% Similarity=0.984 Sum_probs=127.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcccchHHHHhhhHHHHHHHHHhhcCC
Q psy6088 146 DPDETTDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKWLSDADSTT 225 (289)
Q Consensus 146 ~~ee~~dl~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLSfKNmcKLkPLLekWLeEAE~~~ 225 (289)
.+||.+|+||||+|||.||+|||||||||+|||+|||++||++||||||||||+|||||||||||||||+|||+|||.+.
T Consensus 198 ~~ed~~~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~ 277 (398)
T KOG3802|consen 198 SDEDTPDLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRE 277 (398)
T ss_pred CcccccCHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhccc
Confidence 37899999999999999999999999999999999999999999999999999999999999999999999999999863
Q ss_pred CCCCCCCCCCCChhhh---cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 226 ANPSCLSNPLTTPEAI---GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 226 ~n~~~l~~~l~~~e~~---~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
..+ . .+.+|.+ +|||||||||+..+|.+||++|++|||||++||++||++|+|||||||
T Consensus 278 ~~~-~----~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVR 339 (398)
T KOG3802|consen 278 STG-S----PNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVR 339 (398)
T ss_pred ccC-C----CCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEE
Confidence 322 1 1223433 499999999999999999999999999999999999999999999998
No 2
>KOG1168|consensus
Probab=100.00 E-value=3.3e-44 Score=335.94 Aligned_cols=143 Identities=42% Similarity=0.657 Sum_probs=122.9
Q ss_pred CCCCCCCHHHHHHHHHHHhhhhhhcccchhHHhhhhhhc--cC-CCCcchhhhhhhhcccchHHHHhhhHHHHHHHHHhh
Q psy6088 146 DPDETTDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKL--YG-NDFSQTTISRFEALNLSFKNMCKLKPLLQKWLSDAD 222 (289)
Q Consensus 146 ~~ee~~dl~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~l--yG-~~fSQTTIcRFEaLqLSfKNmcKLkPLLekWLeEAE 222 (289)
..+-..|.+|||.||+.|||||||||+||+|||.||+.| -| ..+||+||||||+|.||++||..|||+|+.||||||
T Consensus 209 ~sD~dtDPReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPILqaWLEeAE 288 (385)
T KOG1168|consen 209 TSDMDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPILQAWLEEAE 288 (385)
T ss_pred CcccCCCHHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHHHHHHHHHH
Confidence 356788999999999999999999999999999999966 46 469999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCChhhhcccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 223 STTANPSCLSNPLTTPEAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 223 ~~~~n~~~l~~~l~~~e~~~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
...++....- .+...-.-+.||||||+|...+|+.||.||..+|+||++.|..||++|+|.|+|||
T Consensus 289 ~a~keK~~~p-d~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVR 354 (385)
T KOG1168|consen 289 AAMKEKDTKP-DINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 354 (385)
T ss_pred HHHHhhccCC-chhhccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEE
Confidence 7644321110 00000112577889999999999999999999999999999999999999999997
No 3
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=100.00 E-value=4.4e-41 Score=260.51 Aligned_cols=75 Identities=76% Similarity=1.250 Sum_probs=70.0
Q ss_pred CCCCCHHHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcccchHHHHhhhHHHHHHHHHhh
Q psy6088 148 DETTDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKWLSDAD 222 (289)
Q Consensus 148 ee~~dl~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLSfKNmcKLkPLLekWLeEAE 222 (289)
|+.++++|||+||++||+|||+|||||+|||.+||.+||++||||||||||+|||||||||||||+|+|||+|||
T Consensus 1 ~~~~~~~ele~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~LS~kn~~klkP~L~kWL~eaE 75 (75)
T PF00157_consen 1 EDTPDLKELEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75 (75)
T ss_dssp --CHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTSCHHHHHHHHHHHHHHHHHHH
T ss_pred CCccCHHHHHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhcccCHHHHHHHHHHHHHHHHhcC
Confidence 567889999999999999999999999999999999999999999999999999999999999999999999997
No 4
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=99.97 E-value=1.6e-32 Score=212.84 Aligned_cols=75 Identities=81% Similarity=1.248 Sum_probs=73.5
Q ss_pred CCCCCHHHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcccchHHHHhhhHHHHHHHHHhh
Q psy6088 148 DETTDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKWLSDAD 222 (289)
Q Consensus 148 ee~~dl~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLSfKNmcKLkPLLekWLeEAE 222 (289)
+|.+|++|||.|++.||.+|+++||||+|||.++|.+||+.+||+||||||++||||||||||||+|++||+|||
T Consensus 1 ~~~~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~l~~wl~~~e 75 (75)
T smart00352 1 DEDTDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAE 75 (75)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHHHHHHHHhcC
Confidence 578999999999999999999999999999999999999999999999999999999999999999999999987
No 5
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.99 E-value=5.2e-10 Score=83.33 Aligned_cols=46 Identities=9% Similarity=0.169 Sum_probs=43.9
Q ss_pred cCCCCccccHHHHHHHHHHHhhCCC----CCHHHHHHHHhhcCCCccccC
Q psy6088 244 RRKKRTSIETSVRVALEKAFLQNPK----PTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 244 kRRkRTsfs~~Qk~~LEk~F~qnpk----PS~~Ei~~LA~~L~LekeVVR 289 (289)
+||.||.|+..|+..||++|..++| |+..+|.+||.+|||+++||+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvK 50 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFK 50 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHee
Confidence 4789999999999999999999999 999999999999999999974
No 6
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=98.77 E-value=5.1e-09 Score=74.56 Aligned_cols=44 Identities=32% Similarity=0.421 Sum_probs=42.2
Q ss_pred CCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 245 RKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 245 RRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
||+|+.|+..++..||.+|..++||+..++..||..|||++++|
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V 44 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQV 44 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccc
Confidence 57899999999999999999999999999999999999998876
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.67 E-value=2.2e-08 Score=70.41 Aligned_cols=45 Identities=38% Similarity=0.474 Sum_probs=42.1
Q ss_pred CCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 245 RKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 245 RRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
+|.|+.|+..++..||.+|..|+||+..++..||..+||++.+|+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVK 45 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 467899999999999999999999999999999999999988774
No 8
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=98.62 E-value=3.3e-08 Score=69.73 Aligned_cols=45 Identities=36% Similarity=0.451 Sum_probs=42.1
Q ss_pred CCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 245 RKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 245 RRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
+|+|+.|+..++..||++|..|+||+..++..||..+||++++|+
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 467899999999999999999999999999999999999988774
No 9
>KOG0488|consensus
Probab=98.56 E-value=4.3e-08 Score=93.49 Aligned_cols=46 Identities=26% Similarity=0.276 Sum_probs=44.4
Q ss_pred ccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
|+||.||+||..|+..||+.|++++|.|..||.+||.+|||+..+|
T Consensus 171 K~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQV 216 (309)
T KOG0488|consen 171 KRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQV 216 (309)
T ss_pred ccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhH
Confidence 6788999999999999999999999999999999999999999887
No 10
>KOG0843|consensus
Probab=98.36 E-value=3e-07 Score=82.63 Aligned_cols=47 Identities=26% Similarity=0.302 Sum_probs=45.1
Q ss_pred ccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
|.||.||+|+++|+..||.+|..|.|-...||+.||+.|+|++.+|+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVk 147 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVK 147 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhh
Confidence 67889999999999999999999999999999999999999999884
No 11
>KOG2251|consensus
Probab=98.32 E-value=4.9e-07 Score=83.16 Aligned_cols=48 Identities=23% Similarity=0.212 Sum_probs=45.4
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
-|.||.||+|+..|+++||+.|.+..||+...|++||.+|||.+.+|+
T Consensus 35 RkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVq 82 (228)
T KOG2251|consen 35 RKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQ 82 (228)
T ss_pred hhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhh
Confidence 477899999999999999999999999999999999999999998874
No 12
>KOG0842|consensus
Probab=98.26 E-value=6.7e-07 Score=85.64 Aligned_cols=47 Identities=23% Similarity=0.282 Sum_probs=45.4
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
.+|||+|..|+..|.-+||+.|.+++|.|..||++||..|+|+.++|
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQV 197 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQV 197 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhe
Confidence 38899999999999999999999999999999999999999999988
No 13
>KOG0489|consensus
Probab=98.18 E-value=7.4e-07 Score=82.77 Aligned_cols=47 Identities=23% Similarity=0.264 Sum_probs=44.6
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
+..||.||.|+..|+.+||+.|..|.|.|...|.+||..|+|+|++|
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQI 203 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQI 203 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHH
Confidence 45688999999999999999999999999999999999999999886
No 14
>KOG0485|consensus
Probab=98.14 E-value=1.1e-06 Score=81.23 Aligned_cols=47 Identities=26% Similarity=0.260 Sum_probs=45.7
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
+||||.||+|+..|...||..|....|.|..||..||.+|.|++.+|
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQV 148 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQV 148 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhh
Confidence 49999999999999999999999999999999999999999999987
No 15
>KOG0484|consensus
Probab=98.08 E-value=1.1e-06 Score=73.43 Aligned_cols=47 Identities=17% Similarity=0.218 Sum_probs=44.0
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
.+.||-||.|+..|+.+||+.|....||+...|++||-+++|++..|
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARV 61 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARV 61 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHH
Confidence 36788999999999999999999999999999999999999998765
No 16
>KOG0487|consensus
Probab=97.89 E-value=7.1e-06 Score=78.71 Aligned_cols=47 Identities=32% Similarity=0.291 Sum_probs=45.2
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
.|-||||.-++..|+.+||+.|..|.|.+.+.|-+||+.|||++++|
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQV 279 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQV 279 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhe
Confidence 47799999999999999999999999999999999999999999988
No 17
>KOG0850|consensus
Probab=97.80 E-value=1.5e-05 Score=74.09 Aligned_cols=46 Identities=26% Similarity=0.213 Sum_probs=44.0
Q ss_pred ccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
|.||.||.++.-|+.+|.+.|.++.|.-..||.+||.+|||+-++|
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQV 166 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQV 166 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHh
Confidence 4588999999999999999999999999999999999999999887
No 18
>KOG0492|consensus
Probab=97.75 E-value=2.2e-05 Score=72.37 Aligned_cols=45 Identities=24% Similarity=0.283 Sum_probs=43.3
Q ss_pred cCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 244 RRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 244 kRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
.||.||-|++.|+-+||+.|....|.|..||.+++..|.|++.+|
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqV 188 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQV 188 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhhe
Confidence 378999999999999999999999999999999999999999987
No 19
>KOG0494|consensus
Probab=97.57 E-value=5.7e-05 Score=71.69 Aligned_cols=46 Identities=26% Similarity=0.268 Sum_probs=42.2
Q ss_pred cCCC-CccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 244 RRKK-RTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 244 kRRk-RTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
|||. ||.|+..|+..||+.|....||+..-|+.||.++.|.+|.|+
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIq 186 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQ 186 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhh
Confidence 4444 999999999999999999999999999999999999998763
No 20
>KOG2252|consensus
Probab=97.55 E-value=0.0002 Score=73.25 Aligned_cols=47 Identities=19% Similarity=0.316 Sum_probs=43.8
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
.+.||.|++|+..||+.|-..|..++||+.+....|+.+|||+...|
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV 464 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTV 464 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHH
Confidence 36688999999999999999999999999999999999999997655
No 21
>KOG0486|consensus
Probab=97.53 E-value=5e-05 Score=73.35 Aligned_cols=49 Identities=20% Similarity=0.241 Sum_probs=46.2
Q ss_pred hcccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 241 IGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 241 ~~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
+.|+||.||.|+..|+.+||..|..|.||+-..|++||--.+|++-.||
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr 157 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 157 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence 4588999999999999999999999999999999999999999988876
No 22
>KOG0491|consensus
Probab=97.50 E-value=1.8e-05 Score=70.68 Aligned_cols=48 Identities=29% Similarity=0.299 Sum_probs=45.4
Q ss_pred hcccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 241 IGRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 241 ~~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
..|+||.||+|+..++.-||+.|+.+.|.|..||.+||..|+|++.+|
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QV 144 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQV 144 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHH
Confidence 458899999999999999999999999999999999999999998776
No 23
>KOG0493|consensus
Probab=97.29 E-value=0.00018 Score=68.52 Aligned_cols=44 Identities=25% Similarity=0.261 Sum_probs=41.9
Q ss_pred CCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 245 RKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 245 RRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
||.||.|+.+|+..|...|..|.|.+-+.|.+||.+|+|++.+|
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQI 290 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQI 290 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHh
Confidence 56899999999999999999999999999999999999998775
No 24
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=97.17 E-value=0.00047 Score=60.41 Aligned_cols=89 Identities=19% Similarity=0.178 Sum_probs=56.5
Q ss_pred hhhhhhhcccchHHHHhhhHHHHHHHHHhhcCCCCCCCCCCCCCChhhhcccCCCCccccHHHHHHHHHHHhhCCCCCHH
Q psy6088 193 TISRFEALNLSFKNMCKLKPLLQKWLSDADSTTANPSCLSNPLTTPEAIGRRRKKRTSIETSVRVALEKAFLQNPKPTSE 272 (289)
Q Consensus 193 TIcRFEaLqLSfKNmcKLkPLLekWLeEAE~~~~n~~~l~~~l~~~e~~~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~ 272 (289)
-++++|+++-.-.-|.+ -.+|..+.|....+. .+... .+.....+++|+--+..|+..||++|..||||+..
T Consensus 8 ~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~-~~~~~---~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~ 79 (156)
T COG5576 8 PLSALESQRMPQIRTIK----TTKNKREVEAADSEM-KLERK---QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSI 79 (156)
T ss_pred cchHHHHhhccchhhcc----chhHHHHHHHHhhhh-hhhhc---ccCCCcCcccceechHHHHHHHHHHhccCCCCCHH
Confidence 35667777544333222 245666665443321 11100 11112334455556789999999999999999999
Q ss_pred HHHHHHhhcCCCccccC
Q psy6088 273 EISVLADNLCMNISLTE 289 (289)
Q Consensus 273 Ei~~LA~~L~LekeVVR 289 (289)
++..|+..|||.++-|+
T Consensus 80 ~r~~L~~~lnm~~ksVq 96 (156)
T COG5576 80 TRIKLSLLLNMPPKSVQ 96 (156)
T ss_pred HHHHHHHhcCCChhhhh
Confidence 99999999999876653
No 25
>KOG0490|consensus
Probab=97.13 E-value=0.00028 Score=61.83 Aligned_cols=48 Identities=23% Similarity=0.049 Sum_probs=44.7
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
.++||.||.|+..++..||+.|.+++||+..-++.+|..+++++..|+
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVq 105 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQ 105 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeee
Confidence 467889999999999999999999999999999999999999987763
No 26
>KOG0849|consensus
Probab=96.91 E-value=0.0006 Score=66.29 Aligned_cols=46 Identities=28% Similarity=0.298 Sum_probs=41.9
Q ss_pred ccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
+.||.||+|+..+..+||+.|..++||+..-|++||.++++.+..|
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~ri 220 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRV 220 (354)
T ss_pred cccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHH
Confidence 4566799999999999999999999999999999999999987544
No 27
>KOG0844|consensus
Probab=96.86 E-value=0.00047 Score=66.86 Aligned_cols=46 Identities=22% Similarity=0.213 Sum_probs=42.8
Q ss_pred ccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
.-||-||.|+.+|+..|||.|-+..|-|...|-+||..|||.+..|
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTI 225 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTI 225 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCccee
Confidence 4478899999999999999999999999999999999999998764
No 28
>KOG0848|consensus
Probab=96.73 E-value=0.00056 Score=65.21 Aligned_cols=46 Identities=26% Similarity=0.217 Sum_probs=43.6
Q ss_pred ccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
-|-|-|.++++.|+-+|||.|..++|.|+..-.+||.-|+|+|++|
T Consensus 198 TkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQV 243 (317)
T KOG0848|consen 198 TKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQV 243 (317)
T ss_pred cccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhh
Confidence 3567899999999999999999999999999999999999999987
No 29
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=96.72 E-value=0.0012 Score=48.25 Aligned_cols=39 Identities=28% Similarity=0.456 Sum_probs=33.6
Q ss_pred HHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhccc
Q psy6088 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNL 202 (289)
Q Consensus 158 ~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqL 202 (289)
+|+..+|..|-..|+||.+|+..+| +|.+||||+|+=..
T Consensus 1 ~lg~~lr~~R~~~gls~~~lA~~~g------~s~s~v~~iE~G~~ 39 (64)
T PF13560_consen 1 QLGRRLRRLRERAGLSQAQLADRLG------VSQSTVSRIERGRR 39 (64)
T ss_dssp HHHHHHHHHHHCHTS-HHHHHHHHT------S-HHHHHHHHTTSS
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHC------cCHHHHHHHHCCCC
Confidence 5899999999999999999999988 78899999998654
No 30
>KOG4577|consensus
Probab=96.71 E-value=0.0014 Score=63.24 Aligned_cols=47 Identities=19% Similarity=0.376 Sum_probs=44.4
Q ss_pred ccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
--||.||.|+..+++.|...|...|||-.--|++|+.+.||+.+||+
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQ 212 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQ 212 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehh
Confidence 44679999999999999999999999999999999999999999985
No 31
>KOG0775|consensus
Probab=95.90 E-value=0.064 Score=51.55 Aligned_cols=130 Identities=25% Similarity=0.332 Sum_probs=73.3
Q ss_pred CCCCCCHHHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcccchHHHHhhhHHHHH-HH----HHh
Q psy6088 147 PDETTDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQK-WL----SDA 221 (289)
Q Consensus 147 ~ee~~dl~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLSfKNmcKLkPLLek-WL----eEA 221 (289)
-++..|+|-|-+|-+.+-..---++--=--++.|+-.-....| -.--.=.|.=..|.+| .|.|+. || .||
T Consensus 73 L~q~Gd~erL~rFlwsLp~~~~~~~nEsvLkArA~vafH~gnf-~eLY~iLE~h~Fs~~~----h~~LQ~lWl~AhY~EA 147 (304)
T KOG0775|consen 73 LQQGGDIERLGRFLWSLPVCEELLKNESVLKARAVVAFHSGNF-RELYHILENHKFSPHN----HPKLQALWLKAHYKEA 147 (304)
T ss_pred HHhccCHHHHHHHHHcCchHHHHhhhHHHHHHHHHHHHhcccH-HHHHHHHHhccCChhh----hHHHHHHHHHHHHHHH
Confidence 3466889999888876653110000000002223222222222 0111234566667777 444554 44 466
Q ss_pred hcCCCCCCCCCCCCCChhhhcccCC----CCcc---------ccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 222 DSTTANPSCLSNPLTTPEAIGRRRK----KRTS---------IETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 222 E~~~~n~~~l~~~l~~~e~~~RkRR----kRTs---------fs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
|.....+ + .-.+.. |-|| +||. |-..-+..|..+|.+||||+.+|-.+||+.+||+-.+|
T Consensus 148 ek~RGR~--L----gaV~KY-RvRrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 148 EKLRGRP--L----GAVDKY-RVRRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred HHhcCCc--C----Cccccc-eeeccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhh
Confidence 6543221 1 111111 2222 4664 55677899999999999999999999999999998776
No 32
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=95.88 E-value=0.013 Score=40.42 Aligned_cols=47 Identities=23% Similarity=0.330 Sum_probs=38.2
Q ss_pred HHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcc--cchHHHHhh
Q psy6088 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMCKL 210 (289)
Q Consensus 158 ~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLq--LSfKNmcKL 210 (289)
.|++.+|..|...|+||.|++..+| .|++||++.|+=. .++.++.++
T Consensus 2 ~~~~~l~~~r~~~gltq~~lA~~~g------vs~~~vs~~e~g~~~~~~~~~~~i 50 (58)
T TIGR03070 2 QIGMLVRARRKALGLTQADLADLAG------VGLRFIRDVENGKPTVRLDKVLRV 50 (58)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHCCCCCCCHHHHHHH
Confidence 4788899999999999999998876 6789999999753 455555554
No 33
>KOG0774|consensus
Probab=95.34 E-value=0.014 Score=55.89 Aligned_cols=46 Identities=26% Similarity=0.395 Sum_probs=40.0
Q ss_pred ccCCCCccccHHHHHHHHHHHhh---CCCCCHHHHHHHHhhcCCCcccc
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQ---NPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~q---npkPS~~Ei~~LA~~L~LekeVV 288 (289)
..||||-.|+....+.|..||.. |||||-++-++||++.|++-.+|
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQv 235 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQV 235 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhh
Confidence 34566779999999999999975 99999999999999999976554
No 34
>KOG0483|consensus
Probab=95.00 E-value=0.021 Score=52.07 Aligned_cols=39 Identities=23% Similarity=0.204 Sum_probs=37.1
Q ss_pred cccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 250 SIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 250 sfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
-|+.+|...||+.|..+.|..+++...||+.|||..++|
T Consensus 56 Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQV 94 (198)
T KOG0483|consen 56 RLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQV 94 (198)
T ss_pred cccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHH
Confidence 389999999999999999999999999999999998876
No 35
>KOG0847|consensus
Probab=94.98 E-value=0.012 Score=55.28 Aligned_cols=47 Identities=26% Similarity=0.314 Sum_probs=44.2
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
|+|+..|-.|+..++..||+.|++..||-.+++.++|..|||.+.+|
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqv 211 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQV 211 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHH
Confidence 67788999999999999999999999999999999999999998765
No 36
>PHA01976 helix-turn-helix protein
Probab=94.41 E-value=0.071 Score=38.67 Aligned_cols=51 Identities=22% Similarity=0.279 Sum_probs=40.2
Q ss_pred HHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc--ccchHHHHhhhHHH
Q psy6088 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMCKLKPLL 214 (289)
Q Consensus 158 ~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL--qLSfKNmcKLkPLL 214 (289)
.|++.+|..|...|+||.+++..+| .|++||+++|+= ..+..++.|+--+|
T Consensus 2 ~~~~rl~~~R~~~glt~~~lA~~~g------vs~~~v~~~e~g~~~p~~~~l~~ia~~l 54 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAG------VRHSLIYDFEADKRLPNLKTLLRLADAL 54 (67)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 3889999999999999999998876 467899999974 34666666654444
No 37
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=94.25 E-value=0.017 Score=40.06 Aligned_cols=24 Identities=29% Similarity=0.371 Sum_probs=19.2
Q ss_pred hCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 265 QNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 265 qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
.+||||.+|..+||...||++.+|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi 30 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQI 30 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHH
Confidence 589999999999999999998765
No 38
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=94.09 E-value=0.082 Score=46.22 Aligned_cols=56 Identities=23% Similarity=0.348 Sum_probs=44.9
Q ss_pred HHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhh--cccchHHHHhhhHHHH
Q psy6088 154 EELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEA--LNLSFKNMCKLKPLLQ 215 (289)
Q Consensus 154 ~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEa--LqLSfKNmcKLkPLLe 215 (289)
+-.+.|++.+|..|...|+||.+++..+| +|+++|+|+|+ ..-+...+.+|-=+|.
T Consensus 65 ~l~~~~g~~Ir~~Re~~glSqeeLA~~lg------vs~s~IsriE~G~~~Ps~~~l~kLa~~Lg 122 (154)
T TIGR00270 65 ELVEDYGIIIRREREKRGWSQEQLAKKIQ------EKESLIKKIENAEIEPEPKVVEKLEKLLK 122 (154)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHCCCCCCCHHHHHHHHHHhC
Confidence 44467999999999999999999999876 67999999997 4466677666654444
No 39
>PRK06424 transcription factor; Provisional
Probab=93.47 E-value=0.12 Score=44.87 Aligned_cols=53 Identities=25% Similarity=0.330 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcc--cchHHHHhhh
Q psy6088 153 LEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMCKLK 211 (289)
Q Consensus 153 l~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLq--LSfKNmcKLk 211 (289)
.+..+.|+..+|..|-..|+||.+++..+| +++++|+++|+=. .+++.+.||-
T Consensus 79 ~~~~~~~g~~Ir~lRe~~GLSQ~eLA~~iG------vs~stIskiE~G~~~Ps~~~l~kLa 133 (144)
T PRK06424 79 LDIVEDYAELVKNARERLSMSQADLAAKIF------ERKNVIASIERGDLLPDIKTARKLE 133 (144)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHCCCCCCCHHHHHHHH
Confidence 345689999999999999999999998877 4789999999854 4666666553
No 40
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=93.05 E-value=0.23 Score=48.09 Aligned_cols=66 Identities=21% Similarity=0.259 Sum_probs=51.2
Q ss_pred CCCHHHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcccc-----------hHHHHhhhHHHHHHH
Q psy6088 150 TTDLEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLS-----------FKNMCKLKPLLQKWL 218 (289)
Q Consensus 150 ~~dl~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLS-----------fKNmcKLkPLLekWL 218 (289)
..+..+...+.+.+|..|-.+|+||.||...|+ ++..+|.+.|+=+.. .+++||+--+=..||
T Consensus 6 ~~~~~~~~~~G~~Lr~aRe~~GlSq~~vA~~l~------l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~~L 79 (331)
T PRK10856 6 TQDQNEALTTGERLRQAREQLGLTQQAVAERLC------LKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEEL 79 (331)
T ss_pred ccchhHHHHHHHHHHHHHHHcCCCHHHHHHHHC------CCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHHHH
Confidence 345555556889999999999999999999887 468899999987642 467787766666777
Q ss_pred HHh
Q psy6088 219 SDA 221 (289)
Q Consensus 219 eEA 221 (289)
...
T Consensus 80 ~~~ 82 (331)
T PRK10856 80 LPG 82 (331)
T ss_pred HHh
Confidence 655
No 41
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=92.61 E-value=0.13 Score=41.54 Aligned_cols=36 Identities=25% Similarity=0.385 Sum_probs=29.5
Q ss_pred HHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhccc
Q psy6088 161 KTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNL 202 (289)
Q Consensus 161 k~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqL 202 (289)
..+|..|.++|+||.+++..+| +|+.||+|+|+=..
T Consensus 68 ~~i~~~r~~~gltq~~lA~~lg------~~~~tis~~e~g~~ 103 (127)
T TIGR03830 68 PEIRRIRKKLGLSQREAAELLG------GGVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHCCCC
Confidence 4667778999999999887765 46789999999665
No 42
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=91.96 E-value=0.24 Score=34.39 Aligned_cols=46 Identities=33% Similarity=0.452 Sum_probs=34.5
Q ss_pred HhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc--ccchHHHHhhhHHH
Q psy6088 163 FKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMCKLKPLL 214 (289)
Q Consensus 163 FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL--qLSfKNmcKLkPLL 214 (289)
.|..|...|+||.|++..+| .|.+||+|+|+= ..+...+.+|--+|
T Consensus 1 ik~~r~~~gls~~~la~~~g------is~~~i~~~~~g~~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLG------ISRSTISRIENGKRNPSLDTLKKIAKAL 48 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHT------S-HHHHHHHHTTSSTSBHHHHHHHHHHH
T ss_pred CHHHHHHcCCCHHHHHHHhC------CCcchhHHHhcCCCCCCHHHHHHHHHHH
Confidence 36778899999999999987 567899999987 46777766665444
No 43
>PRK09726 antitoxin HipB; Provisional
Probab=91.94 E-value=0.28 Score=38.25 Aligned_cols=48 Identities=33% Similarity=0.504 Sum_probs=37.1
Q ss_pred HHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc--ccchHHHHhh
Q psy6088 157 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMCKL 210 (289)
Q Consensus 157 E~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL--qLSfKNmcKL 210 (289)
+.|++.+|..|...|+||.+++..+| .|++||+++|+= ..+..++.++
T Consensus 11 ~~l~~~lk~~R~~~gltq~elA~~~g------vs~~tis~~e~g~~~ps~~~l~~i 60 (88)
T PRK09726 11 TQLANAMKLVRQQNGWTQSELAKKIG------IKQATISNFENNPDNTTLTTFFKI 60 (88)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHC------cCHHHHHHHHCCCCCCCHHHHHHH
Confidence 47889999999999999999998876 468899999983 2344444333
No 44
>KOG0490|consensus
Probab=91.17 E-value=0.16 Score=44.47 Aligned_cols=48 Identities=23% Similarity=0.396 Sum_probs=44.7
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
.+.++.||.+...+...++..|..++||+...+..|+..+|+.+.+|+
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q 198 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQ 198 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhh
Confidence 367889999999999999999999999999999999999999998863
No 45
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=90.57 E-value=0.38 Score=41.78 Aligned_cols=52 Identities=19% Similarity=0.202 Sum_probs=42.2
Q ss_pred HHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc--ccchHHHHhhhHHH
Q psy6088 157 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMCKLKPLL 214 (289)
Q Consensus 157 E~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL--qLSfKNmcKLkPLL 214 (289)
..+++.+|..|...|+||.+++..+|. |++||+++|+- ..+.+++.+|--.|
T Consensus 6 ~~~g~~l~~~R~~~glt~~elA~~~gi------s~~~is~~E~g~~~p~~~~l~~ia~~l 59 (185)
T PRK09943 6 LAPGKRLSEIRQQQGLSQRRAAELSGL------THSAISTIEQDKVSPAISTLQKLLKVY 59 (185)
T ss_pred hHHHHHHHHHHHHcCCCHHHHHHHHCC------CHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 468899999999999999998888763 78999999985 55667777765544
No 46
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=89.49 E-value=0.51 Score=33.84 Aligned_cols=45 Identities=31% Similarity=0.402 Sum_probs=31.0
Q ss_pred HHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc--ccchHHHHhhh
Q psy6088 161 KTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMCKLK 211 (289)
Q Consensus 161 k~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL--qLSfKNmcKLk 211 (289)
+.+|..|...|+||.+|+..+|. +.++|+++|+= +.+...+.+|-
T Consensus 2 ~~lk~~r~~~~lt~~~~a~~~~i------~~~~i~~~e~g~~~~~~~~l~~i~ 48 (64)
T PF12844_consen 2 ERLKELREEKGLTQKDLAEKLGI------SRSTISKIENGKRKPSVSTLKKIA 48 (64)
T ss_dssp HHHHHHHHHCT--HHHHHHHHTS-------HHHHHHHHTTSS--BHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHCc------CHHHHHHHHCCCcCCCHHHHHHHH
Confidence 56899999999999999998765 57899999953 55555554443
No 47
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=89.36 E-value=0.61 Score=38.75 Aligned_cols=58 Identities=26% Similarity=0.344 Sum_probs=43.9
Q ss_pred HHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcc--cchHHHHhhhHHH---HHHHHH
Q psy6088 157 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMCKLKPLL---QKWLSD 220 (289)
Q Consensus 157 E~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLq--LSfKNmcKLkPLL---ekWLeE 220 (289)
..|.+.+|..|...|+||.+++..+| +|++||+++|+=. .+..++.+|--+| -.||.-
T Consensus 4 ~~~g~rlk~~R~~~gltq~~lA~~~g------vs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~~l~~ 66 (135)
T PRK09706 4 LTLGQRIRYRRKQLKLSQRSLAKAVK------VSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLF 66 (135)
T ss_pred hhHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhc
Confidence 45889999999999999999999876 5578999999654 5555565555554 357764
No 48
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=88.84 E-value=0.64 Score=42.14 Aligned_cols=55 Identities=31% Similarity=0.450 Sum_probs=42.0
Q ss_pred HHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcccchHHHHhhhHHHHHHHHHhhc
Q psy6088 161 KTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKWLSDADS 223 (289)
Q Consensus 161 k~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLSfKNmcKLkPLLekWLeEAE~ 223 (289)
+++|.+|-.||+||.|.+.- - ..||..|.|.|+=+.-+ ..-++|-+|+ .|+|+|.
T Consensus 8 edlrk~Rk~LGitQ~dLA~~----a--GVSQ~~IArlE~G~vdP-rlSt~k~Il~-aL~e~e~ 62 (187)
T COG3620 8 EDLRKRRKELGITQKDLARR----A--GVSQPYIARLEAGKVDP-RLSTVKRILE-ALEEAEK 62 (187)
T ss_pred HHHHHHHHHcCCCHHHHHHH----c--CccHHHHHHHhcCCCCc-cHHHHHHHHH-HHHHhhc
Confidence 45789999999999996543 3 47999999999988876 4566777766 4566664
No 49
>PRK08359 transcription factor; Validated
Probab=88.76 E-value=0.69 Score=41.60 Aligned_cols=62 Identities=18% Similarity=0.267 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhh--cccchHHHHhhhHHHHHHHHH
Q psy6088 153 LEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEA--LNLSFKNMCKLKPLLQKWLSD 220 (289)
Q Consensus 153 l~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEa--LqLSfKNmcKLkPLLekWLeE 220 (289)
.+-.+.|++..|.-|-..|+||.+++..+| +|++||.++|. .+-|++++.||-=+|..=|.+
T Consensus 80 ~elv~dy~~rIkeaRe~kglSQeeLA~~lg------vs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e 143 (176)
T PRK08359 80 EDIVEDYAERVYEAIQKSGLSYEELSHEVG------LSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIE 143 (176)
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHCCCcCCCHHHHHHHHHHhCCcccc
Confidence 355679999999999999999999998865 67899999975 566888888886666554444
No 50
>PRK10072 putative transcriptional regulator; Provisional
Probab=88.40 E-value=0.36 Score=39.28 Aligned_cols=36 Identities=22% Similarity=0.381 Sum_probs=30.2
Q ss_pred HHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhccc
Q psy6088 161 KTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNL 202 (289)
Q Consensus 161 k~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqL 202 (289)
.++|.-|-++|+||.+++..+| +|.+||++.|.=.-
T Consensus 36 ~eik~LR~~~glTQ~elA~~lG------vS~~TVs~WE~G~r 71 (96)
T PRK10072 36 TEFEQLRKGTGLKIDDFARVLG------VSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCC
Confidence 4578889999999999999888 47889999997543
No 51
>PHA00542 putative Cro-like protein
Probab=86.66 E-value=1.1 Score=34.92 Aligned_cols=44 Identities=27% Similarity=0.310 Sum_probs=34.6
Q ss_pred hhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcc---cchHHHHhhhHHHH
Q psy6088 166 RRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN---LSFKNMCKLKPLLQ 215 (289)
Q Consensus 166 rRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLq---LSfKNmcKLkPLLe 215 (289)
.+..-|+||.+++..+|. |++||+|.|+-. .++..+++|--++.
T Consensus 26 ~l~~~glTq~elA~~lgI------s~~tIsr~e~g~~~~p~~~~l~ki~~~~~ 72 (82)
T PHA00542 26 ALIRAGWSQEQIADATDV------SQPTICRIYSGRHKDPRYSVVEKLRHLVL 72 (82)
T ss_pred HHHHCCCCHHHHHHHHCc------CHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence 345679999999988775 789999999754 67888888766654
No 52
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=86.21 E-value=0.72 Score=35.44 Aligned_cols=42 Identities=31% Similarity=0.445 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc
Q psy6088 153 LEELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL 200 (289)
Q Consensus 153 l~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL 200 (289)
.+--..++..++..|-..|+||.|++..|| .||++|+|.|+-
T Consensus 13 ~~~k~~l~~~i~~~~~~~~ltQ~e~A~~lg------isq~~vS~l~~g 54 (80)
T PF13744_consen 13 LEAKAQLMAAIRELREERGLTQAELAERLG------ISQPRVSRLENG 54 (80)
T ss_dssp HHHHHHHHHHHHHHHHCCT--HHHHHHHHT------S-HHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHC------CChhHHHHHHcC
Confidence 334456778888889999999999999986 579999999964
No 53
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=85.84 E-value=0.71 Score=40.32 Aligned_cols=48 Identities=15% Similarity=0.268 Sum_probs=37.6
Q ss_pred HHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcc----cchHHHHhhhHHHH
Q psy6088 162 TFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN----LSFKNMCKLKPLLQ 215 (289)
Q Consensus 162 ~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLq----LSfKNmcKLkPLLe 215 (289)
.+|..|..+|+||.+++..+| .|+.||+++|+=. .|++++.++-=.|.
T Consensus 29 ~Ir~~R~~lGmTq~eLAerlG------VS~~tIs~iE~G~~~~~psl~~L~kIA~aLg 80 (150)
T TIGR02612 29 WVRAIRKALGMSGAQLAGRLG------VTPQRVEALEKSELSGTVTLKTLRAAAEALD 80 (150)
T ss_pred HHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCCCHHHHHHHHHHcC
Confidence 467789999999999998877 4789999999964 57777666654443
No 54
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=85.31 E-value=1.6 Score=41.30 Aligned_cols=57 Identities=18% Similarity=0.233 Sum_probs=45.0
Q ss_pred HHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc--ccchHHHHhhhHHHHH
Q psy6088 154 EELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMCKLKPLLQK 216 (289)
Q Consensus 154 ~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL--qLSfKNmcKLkPLLek 216 (289)
+=+..|.+.+|..|...|+||.+++..+| .|++||+++|+= ..|+++..+|-=.|..
T Consensus 24 ~~~~~~g~rl~~~R~~~gltq~~lA~~~g------vs~~~i~~~E~g~~~ps~~~l~~ia~~l~v 82 (309)
T PRK08154 24 PFLAALGERVRTLRARRGMSRKVLAQASG------VSERYLAQLESGQGNVSILLLRRVARALGC 82 (309)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHC------cCHHHHHHHHCCCCCCCHHHHHHHHHHhCC
Confidence 34467889999999999999999988765 567899999875 4777777777665544
No 55
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=84.45 E-value=0.8 Score=45.80 Aligned_cols=64 Identities=23% Similarity=0.294 Sum_probs=48.8
Q ss_pred HHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcc--cchHHHHhhhHHHH---HHHHHh
Q psy6088 157 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMCKLKPLLQ---KWLSDA 221 (289)
Q Consensus 157 E~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLq--LSfKNmcKLkPLLe---kWLeEA 221 (289)
+.|++.+|..|-+.|+||.|++..+++ +|..+++++|++.|+=. .+.++..+|.-.|. .||...
T Consensus 2 ~~~~~rL~~~r~~~g~tq~~la~~~~~-~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~l~~~ 70 (517)
T PRK13355 2 TTFAERLKQAMKARGLKQEDLVHAAEA-RGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLLGG 70 (517)
T ss_pred chHHHHHHHHHHHCCCCHHHHHHHHHh-ccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHccC
Confidence 468899999999999999999999875 68889999999999754 44444444444443 488543
No 56
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=82.63 E-value=1.8 Score=27.69 Aligned_cols=48 Identities=33% Similarity=0.441 Sum_probs=33.2
Q ss_pred HHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcc--cchHHHHhhhHHH
Q psy6088 161 KTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMCKLKPLL 214 (289)
Q Consensus 161 k~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLq--LSfKNmcKLkPLL 214 (289)
+.++..|...|+|+.+++..+| +|..+|+++|+-. .+++..+++..+|
T Consensus 2 ~~l~~~~~~~~~s~~~~a~~~~------~~~~~v~~~~~g~~~~~~~~~~~i~~~~ 51 (58)
T cd00093 2 ERLKELRKEKGLTQEELAEKLG------VSRSTISRIENGKRNPSLETLEKLAKAL 51 (58)
T ss_pred hHHHHHHHHcCCCHHHHHHHHC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 3456667778999999998876 4556778777753 5666655554444
No 57
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=82.24 E-value=2.1 Score=35.61 Aligned_cols=53 Identities=19% Similarity=0.147 Sum_probs=43.3
Q ss_pred HHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhh--cccchHHHHhhhHHHHH
Q psy6088 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEA--LNLSFKNMCKLKPLLQK 216 (289)
Q Consensus 158 ~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEa--LqLSfKNmcKLkPLLek 216 (289)
-|...++..|...|+||.+|+..+| .|++||+|+|. -+.|+.++.+|--.|..
T Consensus 5 i~~~~l~~ll~~~Glsq~eLA~~~G------is~~~is~iE~g~~~ps~~~l~kIa~aL~v 59 (120)
T PRK13890 5 IFFTNVLRLLDERHMTKKELSERSG------VSISFLSDLTTGKANPSLKVMEAIADALET 59 (120)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHC------cCHHHHHHHHcCCCCCCHHHHHHHHHHHCC
Confidence 4778888889999999999988866 45789999996 46788888888666654
No 58
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized 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 uncoded by the upstream member of the gene pair.
Probab=81.58 E-value=2.5 Score=31.24 Aligned_cols=48 Identities=21% Similarity=0.280 Sum_probs=35.5
Q ss_pred HHHh-hhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc--ccchHHHHhhhHHH
Q psy6088 161 KTFK-QRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMCKLKPLL 214 (289)
Q Consensus 161 k~FK-qrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL--qLSfKNmcKLkPLL 214 (289)
+.++ ..|-..|+||.|++..+| .|++||++.|+= .++..++.+|--.|
T Consensus 7 ~~i~~~~~~~~~~t~~~lA~~~g------is~~tis~~~~g~~~~~~~~~~~l~~~l 57 (78)
T TIGR02607 7 EILREEFLEPLGLSIRALAKALG------VSRSTLSRIVNGRRGITADMALRLAKAL 57 (78)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHc
Confidence 4466 567889999999999887 468899999974 34666666665444
No 59
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=76.60 E-value=5.6 Score=32.66 Aligned_cols=56 Identities=20% Similarity=0.318 Sum_probs=42.8
Q ss_pred CHHHHHHHHHHHhhhh--hhcccchhHHhhhhhhccCCCCcchhhhhhhhcccchHHHHh-hhHHHHHHHHH
Q psy6088 152 DLEELEQFAKTFKQRR--IKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCK-LKPLLQKWLSD 220 (289)
Q Consensus 152 dl~ELE~FAk~FKqrR--IkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLSfKNmcK-LkPLLekWLeE 220 (289)
+.+|++.++..++--+ +.-|.||.+|...+| .|.+||+|-|+ +.| +-|-...||+.
T Consensus 34 Tp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lG------iS~atIsR~sn-------~lk~~~~~~~~~l~~ 92 (94)
T TIGR01321 34 TRSEREDLGDRIRIVNELLNGNMSQREIASKLG------VSIATITRGSN-------NLKTMDPNFKQFLRK 92 (94)
T ss_pred CHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhC------CChhhhhHHHh-------hcccCCHHHHHHHHh
Confidence 4678888888887766 345899999998876 47899999874 333 56888889874
No 60
>PRK04140 hypothetical protein; Provisional
Probab=76.59 E-value=3.1 Score=40.49 Aligned_cols=51 Identities=29% Similarity=0.541 Sum_probs=42.6
Q ss_pred HHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhh--cccchHHHHhhhHHHHH
Q psy6088 160 AKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEA--LNLSFKNMCKLKPLLQK 216 (289)
Q Consensus 160 Ak~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEa--LqLSfKNmcKLkPLLek 216 (289)
++.+|..|-..|+||.+++..+|. |+.||+++|. -+.+..++.+|--+|..
T Consensus 128 GerLk~lRe~~GlSq~eLA~~lGV------Sr~tIskyE~G~~~Ps~e~~~kLa~~Lgv 180 (317)
T PRK04140 128 GDVLREAREELGLSLGELASELGV------SRRTISKYENGGMNASIEVAIKLEEILDV 180 (317)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 578889999999999999999864 6889999998 67788888887666554
No 61
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=75.73 E-value=3.2 Score=29.96 Aligned_cols=39 Identities=15% Similarity=0.216 Sum_probs=29.1
Q ss_pred CCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 245 RKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 245 RRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
||+|.+++-.++..+=+.+...+ -..+||+++|+.+..|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv 39 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTV 39 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHH
Confidence 57899999999999999998877 4778999999987665
No 62
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=72.28 E-value=3.9 Score=31.59 Aligned_cols=34 Identities=24% Similarity=0.337 Sum_probs=22.6
Q ss_pred HHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhh
Q psy6088 159 FAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISR 196 (289)
Q Consensus 159 FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcR 196 (289)
+.+.++.+.|. ||.|+-..|... |...+|+||||
T Consensus 10 I~~li~~~~i~---sQ~eL~~~L~~~-Gi~vTQaTiSR 43 (70)
T PF01316_consen 10 IKELISEHEIS---SQEELVELLEEE-GIEVTQATISR 43 (70)
T ss_dssp HHHHHHHS------SHHHHHHHHHHT-T-T--HHHHHH
T ss_pred HHHHHHHCCcC---CHHHHHHHHHHc-CCCcchhHHHH
Confidence 33444555554 999999999885 99999999998
No 63
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=65.56 E-value=11 Score=23.81 Aligned_cols=45 Identities=31% Similarity=0.422 Sum_probs=29.9
Q ss_pred HhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhcc--cchHHHHhhhHH
Q psy6088 163 FKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMCKLKPL 213 (289)
Q Consensus 163 FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLq--LSfKNmcKLkPL 213 (289)
++..|-..|+|+.|++..+| .+..+|+++|.-. .+.+.+.++..+
T Consensus 2 i~~~~~~~~~s~~~la~~~~------i~~~~i~~~~~~~~~~~~~~~~~i~~~ 48 (56)
T smart00530 2 LKELREEKGLTQEELAEKLG------VSRSTLSRIENGKRKPSLETLKKLAKA 48 (56)
T ss_pred HHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHCCCCCCCHHHHHHHHHH
Confidence 34556677999999998876 4567888888754 245555444433
No 64
>KOG1146|consensus
Probab=63.88 E-value=5.8 Score=45.36 Aligned_cols=46 Identities=20% Similarity=0.237 Sum_probs=43.1
Q ss_pred ccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 243 RRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 243 RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
-+|++||-++..+++.+...|....||.-++++.+-+.++++++||
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i 947 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVI 947 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchh
Confidence 3456899999999999999999999999999999999999999986
No 65
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=61.25 E-value=2.8 Score=31.50 Aligned_cols=33 Identities=21% Similarity=0.327 Sum_probs=24.4
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 257 VALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 257 ~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
.-|++||.....+.-.++..|.++.+|+-+.||
T Consensus 11 ~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr 43 (56)
T PF11569_consen 11 QPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVR 43 (56)
T ss_dssp HHHHHHHHHT----TTHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHH
Confidence 459999999999999999999999999988775
No 66
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=58.74 E-value=6.1 Score=30.73 Aligned_cols=23 Identities=30% Similarity=0.479 Sum_probs=20.0
Q ss_pred HHhhhhhhcccchhHHhhhhhhc
Q psy6088 162 TFKQRRIKLGFTQGDVGLAMGKL 184 (289)
Q Consensus 162 ~FKqrRIkLG~TQaDVG~ALg~l 184 (289)
.+|.-|..+|+||++.+..+|..
T Consensus 5 k~k~~R~~~~ltQ~elA~~vgVs 27 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVGVS 27 (68)
T ss_pred HHHHHHHHhCcCHHHHHHHcCcC
Confidence 67888999999999999988753
No 67
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=57.06 E-value=6.8 Score=33.81 Aligned_cols=31 Identities=26% Similarity=0.296 Sum_probs=25.5
Q ss_pred cchhHHhhhhhhccCCCCcchhhhh-hhhcccc
Q psy6088 172 FTQGDVGLAMGKLYGNDFSQTTISR-FEALNLS 203 (289)
Q Consensus 172 ~TQaDVG~ALg~lyG~~fSQTTIcR-FEaLqLS 203 (289)
.||.|+-..|.+. |...||+||+| |+.|.+.
T Consensus 17 ~tqeeL~~~L~~~-G~~vsqaTIsRdL~elglv 48 (146)
T TIGR01529 17 STQEELVALLKAE-GIEVTQATVSRDLRELGAV 48 (146)
T ss_pred CCHHHHHHHHHHh-CCCcCHHHHHHHHHHcCCE
Confidence 5999999999554 88899999999 6777764
No 68
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=52.43 E-value=8.9 Score=30.05 Aligned_cols=11 Identities=45% Similarity=1.368 Sum_probs=10.0
Q ss_pred hhHHHHHHHHH
Q psy6088 210 LKPLLQKWLSD 220 (289)
Q Consensus 210 LkPLLekWLeE 220 (289)
|||.|+.||++
T Consensus 43 LRPmLkeWLD~ 53 (73)
T PF10691_consen 43 LRPMLKEWLDE 53 (73)
T ss_pred HHHHHHHHHHh
Confidence 69999999985
No 69
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=48.18 E-value=12 Score=35.81 Aligned_cols=53 Identities=21% Similarity=0.249 Sum_probs=34.0
Q ss_pred CCCCCCHHHHHH--HHHHHhh---hhhhcccchhHHhhhhhhccCCCCcchhhhhhhhc
Q psy6088 147 PDETTDLEELEQ--FAKTFKQ---RRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL 200 (289)
Q Consensus 147 ~ee~~dl~ELE~--FAk~FKq---rRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaL 200 (289)
.+...|+.-+|+ +.+.++. +-...|+||.++...||+- |-..|+++|+|+..+
T Consensus 107 N~qR~dLsfIE~A~~~~~l~~l~e~~~g~~ltq~ela~~lgk~-g~~isrs~Isn~lrl 164 (258)
T TIGR03764 107 NDLRGDLTFIEKALGVQKARALYEKELGESLSQRELARRLSAD-GYPISQSHISRMGDT 164 (258)
T ss_pred HHhhcCCCHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHhccc-CCCCCHHHHHHHHHH
Confidence 445566655553 2222221 2223789999999999873 345788999988765
No 70
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=40.56 E-value=43 Score=22.61 Aligned_cols=38 Identities=32% Similarity=0.427 Sum_probs=29.5
Q ss_pred HHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhccc
Q psy6088 159 FAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNL 202 (289)
Q Consensus 159 FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqL 202 (289)
|.+.++..|-..|+||.+|+..+|. +-.+|..+|.-.-
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~------~~~~~~~~e~~~~ 39 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGV------SRSTISRIERGRS 39 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCC
Confidence 5677888899999999888888776 5567777776655
No 71
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=40.21 E-value=14 Score=25.38 Aligned_cols=35 Identities=11% Similarity=0.228 Sum_probs=25.3
Q ss_pred cccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccccC
Q psy6088 250 SIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLTE 289 (289)
Q Consensus 250 sfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVVR 289 (289)
.+++.++..+..+|.. .....+||+.+|++.+.|+
T Consensus 4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~ 38 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVR 38 (50)
T ss_dssp TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHH
T ss_pred hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHH
Confidence 4678899999999922 2347788999999987653
No 72
>KOG3623|consensus
Probab=39.89 E-value=23 Score=38.91 Aligned_cols=33 Identities=21% Similarity=0.353 Sum_probs=31.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 256 RVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 256 k~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
...|..||..|.-|+.+|...||++.|+..+||
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vv 600 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVV 600 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHH
Confidence 678899999999999999999999999999987
No 73
>PF13551 HTH_29: Winged helix-turn helix
Probab=39.27 E-value=1.7e+02 Score=22.28 Aligned_cols=39 Identities=23% Similarity=0.373 Sum_probs=28.2
Q ss_pred CCCCccccHHHHHHHHHHHhhCC-----CCCHHHHHH-H-HhhcCC
Q psy6088 245 RKKRTSIETSVRVALEKAFLQNP-----KPTSEEISV-L-ADNLCM 283 (289)
Q Consensus 245 RRkRTsfs~~Qk~~LEk~F~qnp-----kPS~~Ei~~-L-A~~L~L 283 (289)
.+.++.+++++...|.+.+..+| ..+..++.+ | .+..++
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~ 97 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGI 97 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCc
Confidence 33444499999999999999988 466777776 5 444444
No 74
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=37.56 E-value=14 Score=36.29 Aligned_cols=27 Identities=37% Similarity=0.639 Sum_probs=25.7
Q ss_pred ccchhHHhhhhhhccC-CCCcchhhhhh
Q psy6088 171 GFTQGDVGLAMGKLYG-NDFSQTTISRF 197 (289)
Q Consensus 171 G~TQaDVG~ALg~lyG-~~fSQTTIcRF 197 (289)
|+|-.||+.+|..+|| ..+|-+||+|+
T Consensus 114 G~Str~i~~~l~~l~g~~~~S~s~vSri 141 (381)
T PF00872_consen 114 GVSTRDIEEALEELYGEVAVSKSTVSRI 141 (381)
T ss_pred ccccccccchhhhhhcccccCchhhhhh
Confidence 9999999999999999 78999999985
No 75
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=37.52 E-value=35 Score=25.05 Aligned_cols=36 Identities=22% Similarity=0.278 Sum_probs=28.2
Q ss_pred ccHHHHHHHHHHHhhC--CCCCHHHHHHHHhhcCCCcc
Q psy6088 251 IETSVRVALEKAFLQN--PKPTSEEISVLADNLCMNIS 286 (289)
Q Consensus 251 fs~~Qk~~LEk~F~qn--pkPS~~Ei~~LA~~L~Leke 286 (289)
+++.|+..|...|..- -+|-.....+||+.||+++.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~s 38 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKS 38 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHH
Confidence 4678899999888774 34666778899999999864
No 76
>PHA03256 BDLF3; Provisional
Probab=37.27 E-value=67 Score=25.65 Aligned_cols=38 Identities=18% Similarity=0.082 Sum_probs=32.6
Q ss_pred cccCCCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcC
Q psy6088 242 GRRRKKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLC 282 (289)
Q Consensus 242 ~RkRRkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~ 282 (289)
.++-|||..|+......+-.+| ++|=+.-+.+++..++
T Consensus 8 ~~~sK~~~~IsE~df~~~~~ff---~rpLp~lVaevska~~ 45 (77)
T PHA03256 8 ERQDKKRGTIGEREFGELLSWD---PTDLPRTVARVYVAVG 45 (77)
T ss_pred ccccccCCccCHHHHHHHHHHc---CCcHHHHHHHHHHHhc
Confidence 3667889999999999999999 6788888999888875
No 77
>PF13565 HTH_32: Homeodomain-like domain
Probab=37.08 E-value=51 Score=24.14 Aligned_cols=42 Identities=14% Similarity=0.227 Sum_probs=30.4
Q ss_pred HHHHHHHHHHH-hhhhhhcccchhHHhhhhhhccCCCC--cchhhhhh
Q psy6088 153 LEELEQFAKTF-KQRRIKLGFTQGDVGLAMGKLYGNDF--SQTTISRF 197 (289)
Q Consensus 153 l~ELE~FAk~F-KqrRIkLG~TQaDVG~ALg~lyG~~f--SQTTIcRF 197 (289)
.+|++++...+ +... ..|=..|...|...||..+ |-+||.|+
T Consensus 32 ~~e~~~~i~~~~~~~p---~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHP---RWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCC---CCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 34454444444 3333 7788899999999999888 99999986
No 78
>PRK10458 DNA cytosine methylase; Provisional
Probab=33.80 E-value=28 Score=35.57 Aligned_cols=41 Identities=10% Similarity=0.080 Sum_probs=35.9
Q ss_pred HHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhccc
Q psy6088 162 TFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNL 202 (289)
Q Consensus 162 ~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqL 202 (289)
.++.+|...+|||.++...|+..-.+..|..||.|+|+=..
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (467)
T PRK10458 20 QALLEKLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKS 60 (467)
T ss_pred HHHHHHHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCC
Confidence 46778899999999999999988888899999999998643
No 79
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=33.09 E-value=34 Score=28.53 Aligned_cols=26 Identities=27% Similarity=0.443 Sum_probs=22.2
Q ss_pred hcccchHHHHhhhHHHHHHHHHhhcC
Q psy6088 199 ALNLSFKNMCKLKPLLQKWLSDADST 224 (289)
Q Consensus 199 aLqLSfKNmcKLkPLLekWLeEAE~~ 224 (289)
-+|||-+|+-||+-.|..|++.+-+.
T Consensus 32 eIDLs~~na~~lr~~l~~yi~~arr~ 57 (110)
T PF11774_consen 32 EIDLSAENAAKLRDALAPYIAAARRV 57 (110)
T ss_dssp EEEE-HHHHHHHHHHHHHHHHHSEEE
T ss_pred EEECCHHHHHHHHHHHHHHHHHheEc
Confidence 47999999999999999999988654
No 80
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=33.00 E-value=55 Score=26.17 Aligned_cols=37 Identities=16% Similarity=0.135 Sum_probs=28.1
Q ss_pred HHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhhhhccc
Q psy6088 158 QFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNL 202 (289)
Q Consensus 158 ~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqL 202 (289)
.|...+|.-|-..|+|| |+..-| .|++||+|+|+=.-
T Consensus 32 ~~~~~l~~~r~~~glSq------LAe~~G--Is~stLs~iE~g~~ 68 (89)
T TIGR02684 32 YIAHALGYIARARGMTQ------LARKTG--LSRESLYKALSGKG 68 (89)
T ss_pred HHHHHHHHHHHHCChHH------HHHHHC--CCHHHHHHHHcCCC
Confidence 46677888888889995 555554 48899999998653
No 81
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=32.74 E-value=32 Score=32.84 Aligned_cols=49 Identities=22% Similarity=0.325 Sum_probs=36.7
Q ss_pred HHHHHHhhhhhhcccchhHHhhhhh---------------hccCCCCcchhhhhhhh-cccchHH
Q psy6088 158 QFAKTFKQRRIKLGFTQGDVGLAMG---------------KLYGNDFSQTTISRFEA-LNLSFKN 206 (289)
Q Consensus 158 ~FAk~FKqrRIkLG~TQaDVG~ALg---------------~lyG~~fSQTTIcRFEa-LqLSfKN 206 (289)
.+.+.||+.|..+|+|..||...++ ++-|..|.+-.|.++-. |+|-...
T Consensus 3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~ 67 (284)
T COG1426 3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDE 67 (284)
T ss_pred cHHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHhcCccccccchHHHHHHHHHHHHHhCCCHHH
Confidence 4678999999999999999988764 33466788877776533 6666544
No 82
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=32.24 E-value=39 Score=27.82 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHHhhcCCCcccc
Q psy6088 267 PKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 267 pkPS~~Ei~~LA~~L~LekeVV 288 (289)
.+|+.+||.+.+++||++-.|+
T Consensus 30 ~~P~~~ei~~a~~~LGl~~~v~ 51 (93)
T COG1400 30 ENPSLEEIAEALRELGLKPKVE 51 (93)
T ss_pred cCCCHHHHHHHHHHcCCCeeec
Confidence 4899999999999999987554
No 83
>PRK04280 arginine repressor; Provisional
Probab=30.45 E-value=27 Score=30.34 Aligned_cols=30 Identities=30% Similarity=0.397 Sum_probs=21.3
Q ss_pred chhHHhhhhhhccCCCCcchhhhh-hhhcccc
Q psy6088 173 TQGDVGLAMGKLYGNDFSQTTISR-FEALNLS 203 (289)
Q Consensus 173 TQaDVG~ALg~lyG~~fSQTTIcR-FEaLqLS 203 (289)
||.|.-..|... |...+|.|||| ...|.|-
T Consensus 20 tQeeL~~~L~~~-Gi~vTQATiSRDikeL~lv 50 (148)
T PRK04280 20 TQDELVDRLREE-GFNVTQATVSRDIKELHLV 50 (148)
T ss_pred CHHHHHHHHHHc-CCCeehHHHHHHHHHcCCE
Confidence 777777777766 77788888887 4545543
No 84
>KOG0773|consensus
Probab=30.02 E-value=50 Score=31.52 Aligned_cols=45 Identities=13% Similarity=0.256 Sum_probs=36.2
Q ss_pred cCCCCccccHHHHHHHHHHHhh---CCCCCHHHHHHHHhhcCCCcccc
Q psy6088 244 RRKKRTSIETSVRVALEKAFLQ---NPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 244 kRRkRTsfs~~Qk~~LEk~F~q---npkPS~~Ei~~LA~~L~LekeVV 288 (289)
+.|++..+.......|+.+... .|||+-.+-..||.+.||+..+|
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv 286 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQV 286 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccC
Confidence 3445668888888888866555 69999999999999999998765
No 85
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=29.75 E-value=73 Score=25.67 Aligned_cols=56 Identities=23% Similarity=0.296 Sum_probs=39.8
Q ss_pred CHHHHHHHHHHHhhhh--hhcccchhHHhhhhhhccCCCCcchhhhhhhhcccchHHHHhh-hHHHHHHHHH
Q psy6088 152 DLEELEQFAKTFKQRR--IKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKL-KPLLQKWLSD 220 (289)
Q Consensus 152 dl~ELE~FAk~FKqrR--IkLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLSfKNmcKL-kPLLekWLeE 220 (289)
.++|++.++..|+--+ +.=|.||.+|...+|. |-.||+|- +|++|= -+-..+||+.
T Consensus 28 T~~E~~~l~~R~~va~~lL~~g~syreIa~~tgv------S~aTItRv-------sr~Lk~~~~~y~~~l~r 86 (87)
T PF01371_consen 28 TPDELEALAQRWQVAKELLDEGKSYREIAEETGV------SIATITRV-------SRCLKYGDDGYRKVLER 86 (87)
T ss_dssp SHHHHHHHHHHHHHHHHHHHTTSSHHHHHHHHTS------THHHHHHH-------HHHHHHSHCHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHhCC------CHHHHHHH-------HHHHHcCCHHHHHHHhh
Confidence 4689999999998766 5569999999888764 45799995 333333 2355666653
No 86
>PF10157 DUF2365: Uncharacterized conserved protein (DUF2365); InterPro: IPR019314 This entry is found in a highly conserved family of proteins which have no known function.
Probab=28.00 E-value=1.2e+02 Score=26.78 Aligned_cols=19 Identities=47% Similarity=0.548 Sum_probs=11.6
Q ss_pred hhhhhhhhcccchHHHHhh
Q psy6088 192 TTISRFEALNLSFKNMCKL 210 (289)
Q Consensus 192 TTIcRFEaLqLSfKNmcKL 210 (289)
+.|.++|.||=+.+.+.+|
T Consensus 113 ~liakceELn~~M~~v~~L 131 (149)
T PF10157_consen 113 TLIAKCEELNESMKPVYKL 131 (149)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4667777777555555444
No 87
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=26.43 E-value=67 Score=27.99 Aligned_cols=41 Identities=24% Similarity=0.283 Sum_probs=31.9
Q ss_pred hcccchhHHhhhhhhccCCCCcchhhhhhhhcccchHHHHhhhHHHHHH
Q psy6088 169 KLGFTQGDVGLAMGKLYGNDFSQTTISRFEALNLSFKNMCKLKPLLQKW 217 (289)
Q Consensus 169 kLG~TQaDVG~ALg~lyG~~fSQTTIcRFEaLqLSfKNmcKLkPLLekW 217 (289)
.-|+||.+|+..|| .|+.||++.|+- -.+++-+.+.-|.=|
T Consensus 19 ~~GlTq~EIAe~LG------iS~~tVs~ie~r--a~kkLr~~~~tl~~~ 59 (141)
T PRK03975 19 ERGLTQQEIADILG------TSRANVSSIEKR--ARENIEKARETLAFA 59 (141)
T ss_pred HcCCCHHHHHHHHC------CCHHHHHHHHHH--HHHHHHHHHHHHHHH
Confidence 57999999999987 577899999985 446667777776434
No 88
>PRK05066 arginine repressor; Provisional
Probab=26.24 E-value=37 Score=29.87 Aligned_cols=30 Identities=27% Similarity=0.467 Sum_probs=23.6
Q ss_pred chhHHhhhhhhccCCC-Ccchhhhh-hhhcccc
Q psy6088 173 TQGDVGLAMGKLYGND-FSQTTISR-FEALNLS 203 (289)
Q Consensus 173 TQaDVG~ALg~lyG~~-fSQTTIcR-FEaLqLS 203 (289)
||.|.-..|... |.. .+|.|||| ...|.+-
T Consensus 25 tQeeL~~~L~~~-Gi~~vTQATiSRDikeL~lv 56 (156)
T PRK05066 25 SQGEIVTALQEQ-GFDNINQSKVSRMLTKFGAV 56 (156)
T ss_pred CHHHHHHHHHHC-CCCeecHHHHHHHHHHcCCE
Confidence 888888888776 888 88999998 5656655
No 89
>PHA02591 hypothetical protein; Provisional
Probab=25.75 E-value=56 Score=26.50 Aligned_cols=34 Identities=21% Similarity=0.469 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhhhhhhcccchhHHhhhhhhccCCCCcchhhhhh
Q psy6088 154 EELEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRF 197 (289)
Q Consensus 154 ~ELE~FAk~FKqrRIkLG~TQaDVG~ALg~lyG~~fSQTTIcRF 197 (289)
+|+-..|+++. ++||||.+|+..|| .||.++.++
T Consensus 46 dd~~~vA~eL~----eqGlSqeqIA~~LG------VsqetVrKY 79 (83)
T PHA02591 46 DDLISVTHELA----RKGFTVEKIASLLG------VSVRKVRRY 79 (83)
T ss_pred chHHHHHHHHH----HcCCCHHHHHHHhC------CCHHHHHHH
Confidence 45567777774 78999999999987 456666654
No 90
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=25.38 E-value=40 Score=23.22 Aligned_cols=35 Identities=17% Similarity=0.131 Sum_probs=15.9
Q ss_pred ccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCcccc
Q psy6088 249 TSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISLT 288 (289)
Q Consensus 249 Tsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeVV 288 (289)
.-++..++..++..+. ...-+.+||+.||.++..|
T Consensus 3 ~~Lt~~eR~~I~~l~~-----~G~s~~~IA~~lg~s~sTV 37 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE-----QGMSIREIAKRLGRSRSTV 37 (44)
T ss_dssp ---------HHHHHHC-----S---HHHHHHHTT--HHHH
T ss_pred cchhhhHHHHHHHHHH-----cCCCHHHHHHHHCcCcHHH
Confidence 4577788888888865 3455677999999887654
No 91
>COG3827 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.27 E-value=41 Score=31.75 Aligned_cols=11 Identities=55% Similarity=1.316 Sum_probs=9.9
Q ss_pred hhHHHHHHHHH
Q psy6088 210 LKPLLQKWLSD 220 (289)
Q Consensus 210 LkPLLekWLeE 220 (289)
|||.|+.||++
T Consensus 198 LRPmLqdWLDk 208 (231)
T COG3827 198 LRPMLQDWLDK 208 (231)
T ss_pred HHHHHHHHHHc
Confidence 79999999974
No 92
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=23.40 E-value=1e+02 Score=17.35 Aligned_cols=32 Identities=9% Similarity=0.094 Sum_probs=20.4
Q ss_pred ccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccc
Q psy6088 251 IETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISL 287 (289)
Q Consensus 251 fs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeV 287 (289)
++.+.+..+...|.. .+ -..++|+.+|+.+..
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~t 37 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRST 37 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHH
Confidence 556666666666653 22 456778888887654
No 93
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=22.71 E-value=54 Score=22.93 Aligned_cols=22 Identities=27% Similarity=0.520 Sum_probs=17.3
Q ss_pred hhcccchhHHhhhhhhcc-CCCC
Q psy6088 168 IKLGFTQGDVGLAMGKLY-GNDF 189 (289)
Q Consensus 168 IkLG~TQaDVG~ALg~ly-G~~f 189 (289)
+.|||+..++-.++..+. +...
T Consensus 11 ~~LGy~~~e~~~av~~~~~~~~~ 33 (47)
T PF07499_consen 11 ISLGYSKAEAQKAVSKLLEKPGM 33 (47)
T ss_dssp HHTTS-HHHHHHHHHHHHHSTTS
T ss_pred HHcCCCHHHHHHHHHHhhcCCCC
Confidence 689999999999998886 4444
No 94
>PRK03341 arginine repressor; Provisional
Probab=21.86 E-value=51 Score=29.41 Aligned_cols=31 Identities=23% Similarity=0.384 Sum_probs=21.7
Q ss_pred cchhHHhhhhhhccCCCCcchhhhh-hhhcccc
Q psy6088 172 FTQGDVGLAMGKLYGNDFSQTTISR-FEALNLS 203 (289)
Q Consensus 172 ~TQaDVG~ALg~lyG~~fSQTTIcR-FEaLqLS 203 (289)
.||.|+-..|... |...||.||+| ...|.+.
T Consensus 30 ~tQ~eL~~~L~~~-Gi~vTQaTiSRDl~eL~~~ 61 (168)
T PRK03341 30 RSQAELAALLADE-GIEVTQATLSRDLDELGAV 61 (168)
T ss_pred ccHHHHHHHHHHc-CCcccHHHHHHHHHHhcCE
Confidence 3788877777665 77788888887 5555544
No 95
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=20.86 E-value=48 Score=23.48 Aligned_cols=25 Identities=36% Similarity=0.619 Sum_probs=19.2
Q ss_pred hhhcccchhHHhhhhhhccCCCCcchhhhhh
Q psy6088 167 RIKLGFTQGDVGLAMGKLYGNDFSQTTISRF 197 (289)
Q Consensus 167 RIkLG~TQaDVG~ALg~lyG~~fSQTTIcRF 197 (289)
+.+.|.|..|+|. +|| .|++|+||.
T Consensus 15 ~LR~~~~~~~La~----~Fg--Is~stvsri 39 (53)
T PF13613_consen 15 YLRLNLTFQDLAY----RFG--ISQSTVSRI 39 (53)
T ss_pred HHHcCCcHhHHhh----hee--ecHHHHHHH
Confidence 4788999988754 455 589999984
No 96
>KOG0100|consensus
Probab=20.76 E-value=1.4e+02 Score=31.27 Aligned_cols=76 Identities=37% Similarity=0.531 Sum_probs=48.6
Q ss_pred CCCCCCHHHHHHHHHHHhhhhhh--------cc-------------cchhHHhhhhhhcc-CCCCcch-hhhhhhhcccc
Q psy6088 147 PDETTDLEELEQFAKTFKQRRIK--------LG-------------FTQGDVGLAMGKLY-GNDFSQT-TISRFEALNLS 203 (289)
Q Consensus 147 ~ee~~dl~ELE~FAk~FKqrRIk--------LG-------------~TQaDVG~ALg~ly-G~~fSQT-TIcRFEaLqLS 203 (289)
..|.-|.+-+|-|++.+|.+-=+ +| -+|-.|-..+-.+| |.+||.| |=.|||.||+-
T Consensus 261 GGEDFD~rvm~~fiklykkK~gkDv~kdnkA~~KLrRe~EkAKRaLSsqhq~riEIeS~fdG~DfSEtLtRAkFEElNmD 340 (663)
T KOG0100|consen 261 GGEDFDQRVMEYFIKLYKKKHGKDVRKDNKAVQKLRREVEKAKRALSSQHQVRIEIESLFDGVDFSETLTRAKFEELNMD 340 (663)
T ss_pred CccchHHHHHHHHHHHHhhhcCCccchhhHHHHHHHHHHHHHHhhhccccceEEeeeeccccccccchhhhhHHHHhhhH
Confidence 44667789999999999865210 11 13444444444555 7889986 45689999865
Q ss_pred hHHHHhhhHHHHHHHHHhhcC
Q psy6088 204 FKNMCKLKPLLQKWLSDADST 224 (289)
Q Consensus 204 fKNmcKLkPLLekWLeEAE~~ 224 (289)
+=. .-|||+ +|-|+|++-.
T Consensus 341 LFr-~TlkPv-~kvl~Ds~lk 359 (663)
T KOG0100|consen 341 LFR-KTLKPV-QKVLEDSDLK 359 (663)
T ss_pred HHH-HhhHHH-HHHHhhcCcc
Confidence 321 346776 6778887743
No 97
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=20.19 E-value=37 Score=24.77 Aligned_cols=38 Identities=16% Similarity=0.266 Sum_probs=23.8
Q ss_pred CCCccccHHHHHHHHHHHhhCCCCCHHHHHHHHhhcCCCccc
Q psy6088 246 KKRTSIETSVRVALEKAFLQNPKPTSEEISVLADNLCMNISL 287 (289)
Q Consensus 246 RkRTsfs~~Qk~~LEk~F~qnpkPS~~Ei~~LA~~L~LekeV 287 (289)
|+|..|+.+++..+=..+ .-+..-+.++|..+|+....
T Consensus 2 ~~r~~ys~e~K~~~v~~~----~~~g~sv~~va~~~gi~~~~ 39 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREY----LESGESVSEVAREYGISPST 39 (76)
T ss_dssp -SS----HHHHHHHHHHH----HHHHCHHHHHHHHHTS-HHH
T ss_pred CCCCCCCHHHHHHHHHHH----HHCCCceEeeeccccccccc
Confidence 567889999888776666 23457788999999987543
Done!