Query psy11709
Match_columns 474
No_of_seqs 307 out of 789
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 16:53:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11709.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11709hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2753|consensus 100.0 6.4E-71 1.4E-75 540.4 33.0 327 5-348 3-329 (378)
2 KOG2908|consensus 100.0 1.5E-32 3.3E-37 271.6 23.6 279 43-347 35-328 (380)
3 KOG2753|consensus 100.0 5.9E-29 1.3E-33 245.0 16.7 173 301-474 127-317 (378)
4 KOG2908|consensus 99.8 4.1E-21 8.8E-26 190.7 7.8 127 345-473 181-316 (380)
5 KOG3250|consensus 99.5 1.5E-14 3.3E-19 135.6 4.7 104 363-474 26-133 (258)
6 KOG3250|consensus 99.3 3.1E-12 6.8E-17 120.2 8.3 116 225-348 26-145 (258)
7 PF01399 PCI: PCI domain; Int 98.9 1.2E-09 2.6E-14 92.2 3.9 90 257-347 2-94 (105)
8 PF01399 PCI: PCI domain; Int 98.5 1.3E-07 2.7E-12 79.8 5.5 80 394-474 1-83 (105)
9 smart00088 PINT motif in prote 97.9 7.1E-06 1.5E-10 67.6 2.2 56 292-347 3-58 (88)
10 smart00753 PAM PCI/PINT associ 97.9 7.1E-06 1.5E-10 67.6 2.2 56 292-347 3-58 (88)
11 KOG2581|consensus 97.8 0.0011 2.4E-08 68.7 17.7 139 196-347 260-412 (493)
12 smart00753 PAM PCI/PINT associ 96.8 0.0011 2.5E-08 54.4 3.6 45 430-474 3-47 (88)
13 smart00088 PINT motif in prote 96.8 0.0011 2.5E-08 54.4 3.6 45 430-474 3-47 (88)
14 KOG1464|consensus 94.5 0.5 1.1E-05 47.4 11.8 141 196-347 244-398 (440)
15 COG5600 Transcription-associat 92.4 16 0.00035 38.3 20.6 213 105-347 146-392 (413)
16 KOG0687|consensus 91.7 18 0.00039 37.4 20.9 211 109-342 124-346 (393)
17 KOG2688|consensus 89.7 2.5 5.4E-05 44.5 10.2 212 107-347 134-373 (394)
18 COG5187 RPN7 26S proteasome re 87.8 19 0.00042 36.7 14.5 184 124-331 149-349 (412)
19 KOG1497|consensus 86.9 41 0.00089 34.8 24.1 115 219-342 222-346 (399)
20 KOG2582|consensus 85.1 46 0.00099 35.0 15.9 257 65-342 74-347 (422)
21 KOG1464|consensus 84.5 1.5 3.3E-05 44.0 4.9 75 395-473 306-386 (440)
22 KOG2758|consensus 81.3 14 0.00029 38.2 10.2 91 257-347 290-383 (432)
23 KOG0686|consensus 79.3 32 0.0007 36.6 12.4 90 257-347 307-399 (466)
24 PF03399 SAC3_GANP: SAC3/GANP/ 76.5 50 0.0011 30.9 12.3 163 141-324 29-203 (204)
25 PF10075 PCI_Csn8: COP9 signal 73.2 4.8 0.0001 36.1 4.1 74 395-472 43-118 (143)
26 KOG2581|consensus 72.9 9.4 0.0002 40.5 6.6 73 395-472 320-399 (493)
27 PF10602 RPN7: 26S proteasome 72.4 63 0.0014 30.1 11.7 94 124-235 70-168 (177)
28 PF08281 Sigma70_r4_2: Sigma-7 69.9 5.3 0.00012 29.3 3.1 29 311-339 24-52 (54)
29 PF10075 PCI_Csn8: COP9 signal 68.5 27 0.00059 31.1 8.0 76 257-337 43-121 (143)
30 PF09012 FeoC: FeoC like trans 66.5 2.7 5.9E-05 32.9 0.9 42 302-343 3-44 (69)
31 PF09012 FeoC: FeoC like trans 61.1 5.3 0.00012 31.3 1.7 32 440-471 3-34 (69)
32 PF04545 Sigma70_r4: Sigma-70, 53.5 20 0.00043 25.9 3.6 30 311-340 18-47 (50)
33 PF12397 U3snoRNP10: U3 small 52.9 1.1E+02 0.0025 26.2 8.9 89 44-134 1-91 (121)
34 PF14938 SNAP: Soluble NSF att 51.2 2.6E+02 0.0056 27.7 18.5 137 128-280 115-260 (282)
35 PF13404 HTH_AsnC-type: AsnC-t 50.7 18 0.0004 25.7 2.9 25 308-332 12-36 (42)
36 PF10668 Phage_terminase: Phag 44.8 23 0.00049 27.5 2.7 23 311-333 20-42 (60)
37 PF13424 TPR_12: Tetratricopep 44.2 1.4E+02 0.0031 22.8 8.0 70 126-210 4-73 (78)
38 PF13404 HTH_AsnC-type: AsnC-t 43.9 27 0.00058 24.8 2.8 25 444-468 10-34 (42)
39 TIGR02010 IscR iron-sulfur clu 43.8 36 0.00079 30.1 4.4 74 299-375 9-87 (135)
40 PF04147 Nop14: Nop14-like fam 43.0 2.9E+02 0.0062 32.5 12.5 162 44-215 444-622 (840)
41 PF08280 HTH_Mga: M protein tr 42.1 27 0.00058 26.5 2.8 31 433-466 4-34 (59)
42 PF04539 Sigma70_r3: Sigma-70 41.9 30 0.00064 27.3 3.2 24 311-334 18-41 (78)
43 PF08281 Sigma70_r4_2: Sigma-7 41.1 17 0.00036 26.6 1.5 24 449-472 24-47 (54)
44 PF04297 UPF0122: Putative hel 40.5 74 0.0016 27.3 5.5 31 311-341 31-61 (101)
45 PF07389 DUF1500: Protein of u 40.0 46 0.001 27.7 4.0 31 309-341 44-75 (100)
46 TIGR03879 near_KaiC_dom probab 39.5 28 0.0006 28.1 2.6 32 311-342 30-61 (73)
47 PF02082 Rrf2: Transcriptional 39.2 26 0.00057 28.2 2.5 43 302-344 12-56 (83)
48 TIGR03879 near_KaiC_dom probab 38.8 49 0.0011 26.7 3.9 24 449-472 30-53 (73)
49 COG1595 RpoE DNA-directed RNA 38.5 36 0.00077 31.4 3.6 31 311-341 141-171 (182)
50 PRK12537 RNA polymerase sigma 37.9 35 0.00076 31.4 3.5 30 311-340 147-176 (182)
51 PF04539 Sigma70_r3: Sigma-70 37.8 28 0.00062 27.4 2.5 23 449-471 18-40 (78)
52 PF07389 DUF1500: Protein of u 37.2 23 0.0005 29.5 1.8 29 444-474 41-70 (100)
53 PF05918 API5: Apoptosis inhib 35.4 6.8E+02 0.015 28.0 15.4 71 43-118 90-160 (556)
54 PF13518 HTH_28: Helix-turn-he 35.1 63 0.0014 23.0 3.8 27 315-341 14-40 (52)
55 PF03979 Sigma70_r1_1: Sigma-7 34.6 65 0.0014 26.1 4.1 42 301-342 9-53 (82)
56 PF03979 Sigma70_r1_1: Sigma-7 34.2 48 0.001 26.9 3.3 32 440-471 10-44 (82)
57 KOG2758|consensus 33.1 65 0.0014 33.4 4.6 80 395-474 290-372 (432)
58 PRK06759 RNA polymerase factor 32.6 50 0.0011 29.1 3.5 29 312-340 121-149 (154)
59 PF08280 HTH_Mga: M protein tr 32.4 43 0.00093 25.3 2.6 32 295-329 4-35 (59)
60 PF13518 HTH_28: Helix-turn-he 31.9 57 0.0012 23.2 3.1 28 443-472 6-33 (52)
61 PF01603 B56: Protein phosphat 31.8 1.9E+02 0.0041 30.7 8.2 118 60-178 101-226 (409)
62 smart00421 HTH_LUXR helix_turn 31.7 70 0.0015 22.6 3.6 26 313-338 18-43 (58)
63 PF10668 Phage_terminase: Phag 31.4 39 0.00084 26.2 2.1 23 449-471 20-42 (60)
64 KOG2688|consensus 30.9 1.5E+02 0.0033 31.5 7.0 74 395-471 273-359 (394)
65 cd06170 LuxR_C_like C-terminal 30.5 76 0.0016 22.5 3.6 27 312-338 14-40 (57)
66 TIGR02983 SigE-fam_strep RNA p 29.8 57 0.0012 29.1 3.4 29 312-340 125-153 (162)
67 TIGR02999 Sig-70_X6 RNA polyme 29.7 58 0.0013 29.7 3.5 29 312-340 149-177 (183)
68 PRK09642 RNA polymerase sigma 29.3 61 0.0013 28.9 3.5 30 311-340 120-149 (160)
69 PRK09047 RNA polymerase factor 29.0 63 0.0014 28.7 3.5 30 312-341 121-150 (161)
70 TIGR00738 rrf2_super rrf2 fami 28.8 64 0.0014 28.0 3.4 73 301-375 11-87 (132)
71 PRK09651 RNA polymerase sigma 28.7 84 0.0018 28.6 4.4 32 311-342 133-164 (172)
72 KOG2582|consensus 28.6 1.2E+02 0.0026 32.1 5.7 80 394-473 259-340 (422)
73 PF08784 RPA_C: Replication pr 28.6 46 0.001 27.8 2.4 44 298-341 49-93 (102)
74 PRK12523 RNA polymerase sigma 28.5 61 0.0013 29.4 3.4 30 312-341 134-163 (172)
75 cd06445 ATase The DNA repair p 28.2 53 0.0011 26.4 2.6 27 438-464 4-30 (79)
76 PRK12514 RNA polymerase sigma 28.2 63 0.0014 29.5 3.4 29 312-340 144-172 (179)
77 PF12569 NARP1: NMDA receptor- 28.0 8.5E+02 0.018 26.9 14.4 146 137-309 201-363 (517)
78 smart00346 HTH_ICLR helix_turn 27.6 77 0.0017 25.4 3.5 45 300-344 6-51 (91)
79 TIGR03643 conserved hypothetic 27.4 96 0.0021 24.9 3.7 37 304-341 5-41 (72)
80 TIGR02947 SigH_actino RNA poly 27.3 67 0.0014 29.8 3.5 30 312-341 146-175 (193)
81 PRK12529 RNA polymerase sigma 27.0 67 0.0014 29.5 3.4 29 312-340 142-170 (178)
82 PRK12520 RNA polymerase sigma 26.5 71 0.0015 29.5 3.5 30 312-341 146-175 (191)
83 PRK10857 DNA-binding transcrip 26.3 91 0.002 28.9 4.1 79 298-378 8-90 (164)
84 PRK12547 RNA polymerase sigma 26.3 75 0.0016 28.6 3.5 30 312-341 127-156 (164)
85 PRK12527 RNA polymerase sigma 26.3 76 0.0016 28.3 3.5 31 311-341 119-149 (159)
86 PRK12522 RNA polymerase sigma 25.9 75 0.0016 28.8 3.5 31 311-341 133-163 (173)
87 PRK08301 sporulation sigma fac 25.8 75 0.0016 30.5 3.6 31 311-341 196-226 (234)
88 PF05920 Homeobox_KN: Homeobox 25.6 75 0.0016 22.4 2.6 22 317-338 17-38 (40)
89 PRK12530 RNA polymerase sigma 25.4 77 0.0017 29.4 3.5 30 312-341 149-178 (189)
90 PF03635 Vps35: Vacuolar prote 24.9 5.4E+02 0.012 29.9 10.8 158 62-239 450-649 (762)
91 PF02082 Rrf2: Transcriptional 24.9 65 0.0014 25.9 2.5 33 439-471 11-45 (83)
92 TIGR02944 suf_reg_Xantho FeS a 24.5 83 0.0018 27.4 3.4 43 302-344 13-56 (130)
93 PF10985 DUF2805: Protein of u 24.5 1.2E+02 0.0025 24.5 3.7 37 304-341 4-40 (73)
94 PRK07037 extracytoplasmic-func 24.4 81 0.0018 28.1 3.4 28 312-339 124-151 (163)
95 PRK09646 RNA polymerase sigma 24.3 85 0.0018 29.2 3.6 29 312-340 157-185 (194)
96 KOG1060|consensus 24.1 8.9E+02 0.019 28.4 11.7 119 49-180 414-534 (968)
97 TIGR03001 Sig-70_gmx1 RNA poly 24.0 81 0.0018 31.0 3.5 30 312-341 176-205 (244)
98 PRK09645 RNA polymerase sigma 24.0 86 0.0019 28.3 3.5 30 312-341 133-162 (173)
99 PRK12525 RNA polymerase sigma 23.7 5.3E+02 0.012 23.0 12.4 30 311-340 132-161 (168)
100 PF13542 HTH_Tnp_ISL3: Helix-t 23.7 1.2E+02 0.0026 21.7 3.6 24 314-337 28-51 (52)
101 PF13384 HTH_23: Homeodomain-l 23.6 72 0.0016 22.7 2.3 29 313-341 17-45 (50)
102 cd00280 TRFH Telomeric Repeat 23.6 1.7E+02 0.0036 28.1 5.2 51 397-448 18-68 (200)
103 PRK07452 DNA polymerase III su 23.6 7.2E+02 0.016 24.9 10.6 129 326-464 131-270 (326)
104 PRK12528 RNA polymerase sigma 23.3 95 0.0021 27.7 3.6 29 311-339 127-155 (161)
105 PF13730 HTH_36: Helix-turn-he 23.3 1.5E+02 0.0033 21.5 4.1 45 297-341 7-53 (55)
106 PRK11179 DNA-binding transcrip 22.8 87 0.0019 28.3 3.2 97 309-415 19-124 (153)
107 PF09339 HTH_IclR: IclR helix- 22.8 1.2E+02 0.0026 22.0 3.5 37 300-336 4-41 (52)
108 KOG0212|consensus 22.7 1.1E+03 0.024 26.5 13.8 110 9-122 298-408 (675)
109 cd06171 Sigma70_r4 Sigma70, re 22.7 1.2E+02 0.0026 20.7 3.4 27 312-338 25-51 (55)
110 PRK12511 RNA polymerase sigma 22.6 94 0.002 28.8 3.5 30 312-341 126-155 (182)
111 PRK12513 RNA polymerase sigma 22.6 90 0.002 28.8 3.4 31 311-341 153-183 (194)
112 TIGR01128 holA DNA polymerase 22.5 7.1E+02 0.015 24.3 10.1 128 324-467 110-252 (302)
113 smart00344 HTH_ASNC helix_turn 22.4 91 0.002 26.0 3.1 34 311-344 15-48 (108)
114 PRK12519 RNA polymerase sigma 22.1 98 0.0021 28.6 3.5 30 312-341 156-185 (194)
115 COG1017 Hmp Hemoglobin-like fl 22.1 4.6E+02 0.0099 24.0 7.5 66 114-179 41-111 (150)
116 TIGR02960 SigX5 RNA polymerase 22.0 1.5E+02 0.0032 29.9 5.1 30 312-341 157-186 (324)
117 PRK12516 RNA polymerase sigma 21.7 1E+02 0.0022 28.7 3.5 30 312-341 131-160 (187)
118 PRK12517 RNA polymerase sigma 21.6 1E+02 0.0022 28.7 3.5 30 312-341 143-172 (188)
119 PRK12512 RNA polymerase sigma 21.5 1E+02 0.0022 28.1 3.5 30 312-341 146-175 (184)
120 PF12840 HTH_20: Helix-turn-he 21.5 94 0.002 23.3 2.7 35 309-343 20-54 (61)
121 PRK12543 RNA polymerase sigma 21.4 98 0.0021 28.3 3.4 30 312-341 132-161 (179)
122 PRK12536 RNA polymerase sigma 21.3 1E+02 0.0022 28.3 3.4 29 312-340 144-172 (181)
123 PRK12533 RNA polymerase sigma 21.2 1E+02 0.0022 29.6 3.5 29 312-340 149-177 (216)
124 TIGR02952 Sig70_famx2 RNA poly 21.2 1E+02 0.0022 27.5 3.4 29 312-340 137-165 (170)
125 smart00550 Zalpha Z-DNA-bindin 21.2 91 0.002 24.3 2.6 32 313-344 22-53 (68)
126 PRK09649 RNA polymerase sigma 21.0 1.1E+02 0.0023 28.3 3.5 28 312-339 145-172 (185)
127 PRK11920 rirA iron-responsive 20.9 98 0.0021 28.2 3.2 72 301-377 11-88 (153)
128 TIGR02939 RpoE_Sigma70 RNA pol 20.7 1.1E+02 0.0024 27.9 3.5 29 312-340 153-181 (190)
129 TIGR02943 Sig70_famx1 RNA poly 20.5 1.1E+02 0.0024 28.4 3.5 29 312-340 146-174 (188)
130 PF08784 RPA_C: Replication pr 20.5 89 0.0019 26.1 2.6 37 435-471 48-85 (102)
131 PRK12540 RNA polymerase sigma 20.4 1.1E+02 0.0024 28.2 3.5 30 312-341 126-155 (182)
132 TIGR02950 SigM_subfam RNA poly 20.3 1.1E+02 0.0024 26.8 3.4 29 312-340 120-148 (154)
133 TIGR02954 Sig70_famx3 RNA poly 20.1 1.1E+02 0.0024 27.5 3.4 29 312-340 134-162 (169)
134 PF11242 DUF2774: Protein of u 20.0 1.5E+02 0.0032 23.2 3.4 30 312-341 12-41 (63)
No 1
>KOG2753|consensus
Probab=100.00 E-value=6.4e-71 Score=540.38 Aligned_cols=327 Identities=43% Similarity=0.675 Sum_probs=317.4
Q ss_pred CCCCceeecCChHHHHHHHHHHHHhhccccccccccCCchHHHHHHHHhhhhhhcCCChhhHHHHHHHHHHHHhccChHH
Q psy11709 5 VQPPPVFIDLLLEDQALELRVYLKNLGAEISDEKSTKGIEDDLHKIIGVCDACFQDANEADIESVLNSIVSMLVLINPER 84 (474)
Q Consensus 5 ~~~~~~~vd~~~~d~~~El~~yl~~~~~~~~~~~~~~~~~~~l~ki~~~~~~~~~~~~eke~e~~~nlli~ll~~~~~~~ 84 (474)
|++.|+|+|.++++|++|+|+|++.++++++.+.++++.++++..++++|+.|++ .|||++|+++|++++++...++|+
T Consensus 3 ~~e~P~f~dis~~~Ql~elr~yl~~~eaeis~e~~~kgl~~~l~~ii~~c~v~~k-~~ekdle~vlnsi~sLi~~~~~e~ 81 (378)
T KOG2753|consen 3 SEEVPVFADISFEEQLAELRAYLKKLEAEISEEASEKGLEEDLLMIIEACDVLAK-IPEKDLECVLNSIVSLIKNAPPEK 81 (378)
T ss_pred CccCceEEEecHHHHHHHHHHHHhhcCcccchhhhccCHHHHHHHHHHHhHHhhc-CCcchHHHHHHHHHHHHHhCCHHH
Confidence 4578999999999999999999999999999887778899999999999999986 889999999999999999999999
Q ss_pred HHHHHHHHHHHHhcccCCCChhhHHHHHHHHHhccCCCCcchHHHHHHHHHHHHhcCchhHHHhhHHHHHHhhhcCCCCH
Q psy11709 85 AENLILAFSEKLSKASDAKLGPVTLRVLWLLFQSLEPTSPMRYHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQCPPSN 164 (474)
Q Consensus 85 ~~~~v~~l~~~l~~~~~~~~~~~~l~~L~~lfn~l~~~s~~r~~v~~~il~~a~~~~~~~~l~~~l~~l~~~l~~w~~~~ 164 (474)
..+.+..+|+++++++.+..|.+||++|++|||.++...|.||+||++++++|.+++.++.+.+.++.+++|+++|+++.
T Consensus 82 ~e~~v~a~~ekva~q~n~~~~~l~L~vLsnLfn~~d~~~~aR~~Vy~~lv~la~~~~~~~~i~~~lk~~~~~lkew~~~v 161 (378)
T KOG2753|consen 82 VEEMVKAICEKVAKQPNDKTASLRLQVLSNLFNGVDKPTPARYQVYMSLVTLAASCKLIEYIVPNLKQLDDWLKEWNISV 161 (378)
T ss_pred hHHHHHHHHHHHhcCccCCCcccHHHHHHHHHhccCCCchHHHHHHHHHHHHHhhcceeeeecccHHHHHHHHHhCCCCH
Confidence 99999999999999987777899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHhhhhccccccchHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHcCCCcccchhh
Q psy11709 165 EQMQKLLRLLHQALLASKQYRLLRMQTKSSLCSKTELAAKVMIELLSTYTAENASQAREDAQACILAALADPNTFLLHPL 244 (474)
Q Consensus 165 ~~~~~ly~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ay~~~l~~L~t~~~~~~~e~~~~A~~~i~~aL~~p~~f~f~~L 244 (474)
+++|.+|++++++++. .+..+++.++|..||+||+.+|+++|+++|.+|++.|+.+|++|.||+|
T Consensus 162 edqrel~r~v~~al~~---------------~k~~~~s~kvmt~lLgtyt~dnas~AredA~rcV~~av~dP~~F~fD~L 226 (378)
T KOG2753|consen 162 EDQRELLRAVHKALKD---------------NKSVDESSKVMTELLGTYTEDNASEAREDAMRCVVEAVKDPKIFLFDHL 226 (378)
T ss_pred HHHHHHHHHHHHHHHh---------------cchhhhHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHcCCceeccchh
Confidence 9999999999999999 7778999999999999999999999999999999999999999999999
Q ss_pred cCCchhhhcccccHHHHHHHHhhCChhHHHHHHhhchHhHHhhcCCCHHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhC
Q psy11709 245 LTLKPVKFLEGELIHDLLNIFVAEKVNTYQDFYKQHKEYIVNKLGLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELD 324 (474)
Q Consensus 245 l~~p~v~~L~~~~l~~LL~iF~~g~l~~y~~f~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~ 324 (474)
+.+|+|++|+++.+||||.||.+|.+++|..|++.|++|+ +++|++||++.+||||||||+||..+++|||++|+++|+
T Consensus 227 l~L~pV~qLE~d~i~qLL~IF~s~~L~aYveF~~~N~~Fv-qs~gl~~E~~~~KMRLLTlm~LA~es~eisy~~l~k~Lq 305 (378)
T KOG2753|consen 227 LTLPPVKQLEGDLIHQLLKIFVSGKLDAYVEFVAANSGFV-QSQGLVHEQNMAKMRLLTLMSLAEESNEISYDTLAKELQ 305 (378)
T ss_pred ccCchHHHhccchHHHHHHHHHhcchHHHHHHHHhChHHH-HHhcccHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhc
Confidence 9999999999999999999999999999999999999999 999999999999999999999999999999999999999
Q ss_pred CChhhHHHHHHhhhhHHHHHHHHH
Q psy11709 325 LNPNQIEAFIIDGKIAAKVMIELL 348 (474)
Q Consensus 325 i~~~eVE~~VI~aI~aglv~~klL 348 (474)
|.+||||.|||+||++|+|+||+-
T Consensus 306 I~edeVE~fVIdaI~aklV~~kid 329 (378)
T KOG2753|consen 306 INEDEVELFVIDAIRAKLVEGKID 329 (378)
T ss_pred cCHHHHHHHHHHHHHHHHHHhhHH
Confidence 999999999999999999999983
No 2
>KOG2908|consensus
Probab=100.00 E-value=1.5e-32 Score=271.61 Aligned_cols=279 Identities=18% Similarity=0.215 Sum_probs=221.8
Q ss_pred chHHHHHHHHhhh-hhhcCCChhhHHHHHHHHHHHHhc-cChHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHhccC
Q psy11709 43 IEDDLHKIIGVCD-ACFQDANEADIESVLNSIVSMLVL-INPERAENLILAFSEKLSKASDAKLGPVTLRVLWLLFQSLE 120 (474)
Q Consensus 43 ~~~~l~ki~~~~~-~~~~~~~eke~e~~~nlli~ll~~-~~~~~~~~~v~~l~~~l~~~~~~~~~~~~l~~L~~lfn~l~ 120 (474)
|-..--+++.-.+ .+|..+| ..-..|.-+++-+-. .+| ... ..+|-.++++.+ .+..++++|..+-|.+.
T Consensus 35 W~QLt~~l~~fvd~~~f~~~~--~~l~lY~NFvsefe~kINp---lsl-vei~l~~~~~~~--D~~~al~~Le~i~~~~~ 106 (380)
T KOG2908|consen 35 WHQLTLALVDFVDDPPFQAGD--LLLQLYLNFVSEFETKINP---LSL-VEILLVVSEQIS--DKDEALEFLEKIIEKLK 106 (380)
T ss_pred HHHHHHHHHHHHhccccccch--HHHHHHHHHHHHHhhccCh---HHH-HHHHHHHHHHhc--cHHHHHHHHHHHHHHHH
Confidence 3344444444333 5665443 335555555554443 463 344 344555555443 57789999999999998
Q ss_pred CCCcchHHHHHHHHHHHH---hcCchhHHHhhHHHHHHhhhcCC-CCHHHHHHHHHHHHHHHHHhHHHHHHhhhhccccc
Q psy11709 121 PTSPMRYHVYYHLVQIAQ---NADQIKSVFKDVDHLKQQFSQCP-PSNEQMQKLLRLLHQALLASKQYRLLRMQTKSSLC 196 (474)
Q Consensus 121 ~~s~~r~~v~~~il~~a~---~~~~~~~l~~~l~~l~~~l~~w~-~~~~~~~~ly~~i~~~~~~~~~~~~~~~~~~~~~~ 196 (474)
..+.....+|+ ..+.++ ..|++..+++.|+++++.+++.+ +++.+|.+||.+.++||+. .
T Consensus 107 ~~~e~~av~~~-~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~~v~~~Vh~~fY~lssqYyk~---------------~ 170 (380)
T KOG2908|consen 107 EYKEPDAVIYI-LTEIARLKLEINDLKEIKKLLDDLKSMLDSLDGVTSNVHSSFYSLSSQYYKK---------------I 170 (380)
T ss_pred hhccchhHHHH-HHHHHHHHHhcccHHHHHHHHHHHHHHHhcccCCChhhhhhHHHHHHHHHHH---------------H
Confidence 77553344443 444443 45789999999999999999988 5666999999999999999 8
Q ss_pred cchHHHHHHHHHHhcccCCCCh--hhHHHHHHHHHHHHHcCCCcccchhhcCCchhhhcccc---cHHHHHHHHhhCChh
Q psy11709 197 SKTELAAKVMIELLSTYTAENA--SQAREDAQACILAALADPNTFLLHPLLTLKPVKFLEGE---LIHDLLNIFVAEKVN 271 (474)
Q Consensus 197 ~~~~~ay~~~l~~L~t~~~~~~--~e~~~~A~~~i~~aL~~p~~f~f~~Ll~~p~v~~L~~~---~l~~LL~iF~~g~l~ 271 (474)
++.+.+|+++|+||+|.+.++. ++.++.|..++.+||.+.++||||||++||+...|.|| |++++|.+|++||+.
T Consensus 171 ~d~a~yYr~~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~ 250 (380)
T KOG2908|consen 171 GDFASYYRHALLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLK 250 (380)
T ss_pred HhHHHHHHHHHHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHH
Confidence 9999999999999999877665 57779999999999999999999999999999999996 999999999999999
Q ss_pred HHHHHHhhchHhHHhhcCCCHHHHHHHHHHHHHHHhhhc----CCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHHHHH
Q psy11709 272 TYQDFYKQHKEYIVNKLGLDHQENLRKMRLLTFMQLAET----KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVMIEL 347 (474)
Q Consensus 272 ~y~~f~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La~~----~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~~kl 347 (474)
.|++.+..+.++ ..++-++..+.+||||||||+++|. .|.+||++||++++||.+|||.+||+|++.|++.|.+
T Consensus 251 ~f~~l~~~~~~~--p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVMKAlslgLikG~I 328 (380)
T KOG2908|consen 251 RFESLKGVWGKQ--PDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELLVMKALSLGLIKGSI 328 (380)
T ss_pred HHHHHHHHhccC--chHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHHHHHHHHhccceeeee
Confidence 999998776331 1222357899999999999999997 7999999999999999999999999999999999765
No 3
>KOG2753|consensus
Probab=99.96 E-value=5.9e-29 Score=244.98 Aligned_cols=173 Identities=43% Similarity=0.728 Sum_probs=154.7
Q ss_pred HHHHHHhhhcCCCcC-----hHHHH---HhhCCChh---hHHHHHHhhhh-------HHHHHHHHHhhccccchhhHHHH
Q psy11709 301 LLTFMQLAETKTEMS-----FDMIQ---KELDLNPN---QIEAFIIDGKI-------AAKVMIELLSTYTAENASQARED 362 (474)
Q Consensus 301 LLtL~~La~~~~~ls-----y~~Ia---~~l~i~~~---eVE~~VI~aI~-------aglv~~klL~t~~~~~~~ea~~~ 362 (474)
.++++++|.+.+.+. ++.|. +.++++.+ ++=.+|=+|++ +..++.+||.||+.+|+++|++.
T Consensus 127 y~~lv~la~~~~~~~~i~~~lk~~~~~lkew~~~vedqrel~r~v~~al~~~k~~~~s~kvmt~lLgtyt~dnas~Ared 206 (378)
T KOG2753|consen 127 YMSLVTLAASCKLIEYIVPNLKQLDDWLKEWNISVEDQRELLRAVHKALKDNKSVDESSKVMTELLGTYTEDNASEARED 206 (378)
T ss_pred HHHHHHHHhhcceeeeecccHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHhcccchhHHHHH
Confidence 467777787744443 34444 67888864 45556667774 44699999999999999999999
Q ss_pred HHHHHHHHhcCCCeeecccccCCccccccccccHHHHHHHHhhCChhhHHHHHHhchHhHhhhcCCCHHHHHHHHHHHHH
Q psy11709 363 AQACILAALADPNTFLLHPLLTLKPVKFLEGELIHDLLNIFVSEKVNTYQDFYKQHKEYIVNKLGLDHQENLRKMRLLTF 442 (474)
Q Consensus 363 a~~li~~Al~~p~vy~F~eLl~~p~v~~L~~~~l~~LL~iF~~G~~~~y~~~~~~~~~~~~~~~~l~~~~~~~KirlLtL 442 (474)
|.+||+.|+.+|+.|.||+|+.+|+|+.|+++.+|+||.||.+|.+++|..|.+.|++++ .++|++++++.+|||||||
T Consensus 207 A~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~i~qLL~IF~s~~L~aYveF~~~N~~Fv-qs~gl~~E~~~~KMRLLTl 285 (378)
T KOG2753|consen 207 AMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDLIHQLLKIFVSGKLDAYVEFVAANSGFV-QSQGLVHEQNMAKMRLLTL 285 (378)
T ss_pred HHHHHHHHHcCCceeccchhccCchHHHhccchHHHHHHHHHhcchHHHHHHHHhChHHH-HHhcccHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999997 9999999999999999999
Q ss_pred HHhHhcCCCCCHHHHHhhcCCChhhhhhhccC
Q psy11709 443 MQLAETKTEMSFDMIQKELDLNPNQIEAFIID 474 (474)
Q Consensus 443 ~~La~~~r~lsy~~Ia~~l~i~~~eVE~lVId 474 (474)
|+||..+++|||++|++.|+|.+||||.||||
T Consensus 286 m~LA~es~eisy~~l~k~LqI~edeVE~fVId 317 (378)
T KOG2753|consen 286 MSLAEESNEISYDTLAKELQINEDEVELFVID 317 (378)
T ss_pred HHHhccCCCCCHHHHHHHhccCHHHHHHHHHH
Confidence 99999999999999999999999999999997
No 4
>KOG2908|consensus
Probab=99.83 E-value=4.1e-21 Score=190.71 Aligned_cols=127 Identities=22% Similarity=0.332 Sum_probs=112.0
Q ss_pred HHHHhhccccchh--hHHHHHHHHHHHHhcCCCeeecccccCCcccccccc---ccHHHHHHHHhhCChhhHHHHHHhch
Q psy11709 345 IELLSTYTAENAS--QAREDAQACILAALADPNTFLLHPLLTLKPVKFLEG---ELIHDLLNIFVSEKVNTYQDFYKQHK 419 (474)
Q Consensus 345 ~klL~t~~~~~~~--ea~~~a~~li~~Al~~p~vy~F~eLl~~p~v~~L~~---~~l~~LL~iF~~G~~~~y~~~~~~~~ 419 (474)
.++|+.-+.++-+ +.++.|..++.+|+.|+++||||||+.||+..+|.| .|++++|.+|+.||+..|+..+..+.
T Consensus 181 L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~ 260 (380)
T KOG2908|consen 181 LLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWG 260 (380)
T ss_pred HHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhc
Confidence 3455544444443 777999999999999999999999999999999999 49999999999999999999998886
Q ss_pred HhHhhhcCCCHHHHHHHHHHHHHHHhHhc----CCCCCHHHHHhhcCCChhhhhhhcc
Q psy11709 420 EYIVNKLGLDHQENLRKMRLLTFMQLAET----KTEMSFDMIQKELDLNPNQIEAFII 473 (474)
Q Consensus 420 ~~~~~~~~l~~~~~~~KirlLtL~~La~~----~r~lsy~~Ia~~l~i~~~eVE~lVI 473 (474)
++ +.++-++..+.+|||+|||+++||. .|.+||++||++++||.+|||.+||
T Consensus 261 ~~--p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVM 316 (380)
T KOG2908|consen 261 KQ--PDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELLVM 316 (380)
T ss_pred cC--chHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHHHHH
Confidence 64 4555568899999999999999996 7999999999999999999999986
No 5
>KOG3250|consensus
Probab=99.49 E-value=1.5e-14 Score=135.63 Aligned_cols=104 Identities=23% Similarity=0.311 Sum_probs=94.5
Q ss_pred HHHHHHHHhcCCCeeecccccCCcccccccc---ccHHHHHHHHhhCChhhHHHHHHhchHhHhhhcCCCHHHHHHHHHH
Q psy11709 363 AQACILAALADPNTFLLHPLLTLKPVKFLEG---ELIHDLLNIFVSEKVNTYQDFYKQHKEYIVNKLGLDHQENLRKMRL 439 (474)
Q Consensus 363 a~~li~~Al~~p~vy~F~eLl~~p~v~~L~~---~~l~~LL~iF~~G~~~~y~~~~~~~~~~~~~~~~l~~~~~~~Kirl 439 (474)
-..+|.+|+.+|++|.|||||.+|+|.+|.+ +.+++||++|++|||.||....-..|.+ ...++.|++-
T Consensus 26 l~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~aea~rlp~L--------s~~q~~kLk~ 97 (258)
T KOG3250|consen 26 LEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAEALRLPKL--------SLAQLNKLKH 97 (258)
T ss_pred HHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhhhhcCCCC--------CHHHHHhhhc
Confidence 5789999999999999999999999999987 4999999999999999999876555554 4678899999
Q ss_pred HHHHHhHhcCCCCCHHHHHhhcCCCh-hhhhhhccC
Q psy11709 440 LTFMQLAETKTEMSFDMIQKELDLNP-NQIEAFIID 474 (474)
Q Consensus 440 LtL~~La~~~r~lsy~~Ia~~l~i~~-~eVE~lVId 474 (474)
++.+++|+..+.|+|..+.+.+.+.. .|||++||+
T Consensus 98 ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~iie 133 (258)
T KOG3250|consen 98 LTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLIIE 133 (258)
T ss_pred ceehhhhhhchhhhHHHHHhhccCCchhHHHHHHHH
Confidence 99999999999999999999999976 699999984
No 6
>KOG3250|consensus
Probab=99.33 E-value=3.1e-12 Score=120.19 Aligned_cols=116 Identities=23% Similarity=0.273 Sum_probs=101.5
Q ss_pred HHHHHHHHHcCCCcccchhhcCCchhhhcccc---cHHHHHHHHhhCChhHHHHHHhhchHhHHhhcCCCHHHHHHHHHH
Q psy11709 225 AQACILAALADPNTFLLHPLLTLKPVKFLEGE---LIHDLLNIFVAEKVNTYQDFYKQHKEYIVNKLGLDHQENLRKMRL 301 (474)
Q Consensus 225 A~~~i~~aL~~p~~f~f~~Ll~~p~v~~L~~~---~l~~LL~iF~~g~l~~y~~f~~~~~~~~~~~~~l~~~~l~~KirL 301 (474)
-..+|..|+.+|++|-|+||+.+|.|..|.++ .+++||.+|.+|++.+|..-...-|. |+ .....|++-
T Consensus 26 l~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~aea~rlp~-------Ls-~~q~~kLk~ 97 (258)
T KOG3250|consen 26 LEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAEALRLPK-------LS-LAQLNKLKH 97 (258)
T ss_pred HHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhhhhcCCC-------CC-HHHHHhhhc
Confidence 45689999999999999999999999999875 69999999999999999864333232 22 456789999
Q ss_pred HHHHHhhhcCCCcChHHHHHhhCCC-hhhHHHHHHhhhhHHHHHHHHH
Q psy11709 302 LTFMQLAETKTEMSFDMIQKELDLN-PNQIEAFIIDGKIAAKVMIELL 348 (474)
Q Consensus 302 LtL~~La~~~~~lsy~~Ia~~l~i~-~~eVE~~VI~aI~aglv~~klL 348 (474)
++..++|+..+.|||..+.+.+... ..|+|.+||+|++++++.||+-
T Consensus 98 ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~iieamya~IlrGkld 145 (258)
T KOG3250|consen 98 LTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILRGKLD 145 (258)
T ss_pred ceehhhhhhchhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHHhhHH
Confidence 9999999999999999999999996 5899999999999999999983
No 7
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=98.89 E-value=1.2e-09 Score=92.21 Aligned_cols=90 Identities=20% Similarity=0.346 Sum_probs=79.4
Q ss_pred cHHHHHHHHhhCChhHHHHHHhhc-hHhHHhhcCCCH--HHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHHHH
Q psy11709 257 LIHDLLNIFVAEKVNTYQDFYKQH-KEYIVNKLGLDH--QENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAF 333 (474)
Q Consensus 257 ~l~~LL~iF~~g~l~~y~~f~~~~-~~~~~~~~~l~~--~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~ 333 (474)
|+.+|+++|.+|++..|..+...+ +.++ .+.++.. +.+.+|+|..+|.+++..-+.+++++|++.++++.++||.|
T Consensus 2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~-~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~ 80 (105)
T PF01399_consen 2 PYSELLRAFRSGDLQEFEEFLEKHSESLF-KDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESI 80 (105)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHTCHHHH-HCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHH-cCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHH
Confidence 688999999999999999999998 7776 5556544 78999999999999999999999999999999999999999
Q ss_pred HHhhhhHHHHHHHH
Q psy11709 334 IIDGKIAAKVMIEL 347 (474)
Q Consensus 334 VI~aI~aglv~~kl 347 (474)
|+++|..|.+.|++
T Consensus 81 l~~~I~~~~i~~~I 94 (105)
T PF01399_consen 81 LIDLISNGLIKAKI 94 (105)
T ss_dssp HHHHHHTTSSEEEE
T ss_pred HHHHHHCCCEEEEE
Confidence 99999999877543
No 8
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=98.53 E-value=1.3e-07 Score=79.77 Aligned_cols=80 Identities=24% Similarity=0.403 Sum_probs=68.9
Q ss_pred ccHHHHHHHHhhCChhhHHHHHHhc-hHhHhhhcCCC--HHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChhhhhh
Q psy11709 394 ELIHDLLNIFVSEKVNTYQDFYKQH-KEYIVNKLGLD--HQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEA 470 (474)
Q Consensus 394 ~~l~~LL~iF~~G~~~~y~~~~~~~-~~~~~~~~~l~--~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~eVE~ 470 (474)
+|+++|+++|..|++.+|..+.+.+ +.+. .+.++. .+.+.+|+|..+|..++...+.+++++|++.++++.++||.
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~-~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~ 79 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLF-KDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVES 79 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHH-HCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHH-cCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHH
Confidence 4889999999999999999999999 5553 443433 48999999999999999999999999999999999999999
Q ss_pred hccC
Q psy11709 471 FIID 474 (474)
Q Consensus 471 lVId 474 (474)
||++
T Consensus 80 ~l~~ 83 (105)
T PF01399_consen 80 ILID 83 (105)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 9864
No 9
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=97.86 E-value=7.1e-06 Score=67.62 Aligned_cols=56 Identities=21% Similarity=0.342 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHHHHH
Q psy11709 292 HQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVMIEL 347 (474)
Q Consensus 292 ~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~~kl 347 (474)
.+.+.+|+|..++.+++...+.++|++|++.++++.++||.||+++|..|.+.|++
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~I 58 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 35789999999999999999999999999999999999999999999999887665
No 10
>smart00753 PAM PCI/PINT associated module.
Probab=97.86 E-value=7.1e-06 Score=67.62 Aligned_cols=56 Identities=21% Similarity=0.342 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHHHHH
Q psy11709 292 HQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVMIEL 347 (474)
Q Consensus 292 ~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~~kl 347 (474)
.+.+.+|+|..++.+++...+.++|++|++.++++.++||.||+++|..|.+.|++
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~I 58 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKI 58 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEE
Confidence 35789999999999999999999999999999999999999999999999887665
No 11
>KOG2581|consensus
Probab=97.83 E-value=0.0011 Score=68.73 Aligned_cols=139 Identities=13% Similarity=0.146 Sum_probs=90.6
Q ss_pred ccchHHHHHHHHHHhcccCCCChhhHHHHHHHH--HHHHHcCCCc--ccchhhcCCchhhhcccc--cHHHHHHHHhhCC
Q psy11709 196 CSKTELAAKVMIELLSTYTAENASQAREDAQAC--ILAALADPNT--FLLHPLLTLKPVKFLEGE--LIHDLLNIFVAEK 269 (474)
Q Consensus 196 ~~~~~~ay~~~l~~L~t~~~~~~~e~~~~A~~~--i~~aL~~p~~--f~f~~Ll~~p~v~~L~~~--~l~~LL~iF~~g~ 269 (474)
..++..|-++++..++.-+..-+--.++...+| ++.-|.+|.- -.| ..|. ++.+ ++|+|=++.-.||
T Consensus 260 qldYssA~~~~~qa~rkapq~~alGf~q~v~k~~ivv~ll~geiPers~F----~Qp~---~~ksL~~Yf~Lt~AVr~gd 332 (493)
T KOG2581|consen 260 QLDYSSALEYFLQALRKAPQHAALGFRQQVNKLMIVVELLLGEIPERSVF----RQPG---MRKSLRPYFKLTQAVRLGD 332 (493)
T ss_pred hcchhHHHHHHHHHHHhCcchhhhhHHHHHHHHHHHHHHHcCCCcchhhh----cCcc---HHHHHHHHHHHHHHHHHhh
Confidence 457788888888877755542221222333333 3333444321 112 1222 3334 7999999999999
Q ss_pred hhHHHHHHhhchHhHHhhcCC-------CHHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChh-hHHHHHHhhhhHH
Q psy11709 270 VNTYQDFYKQHKEYIVNKLGL-------DHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPN-QIEAFIIDGKIAA 341 (474)
Q Consensus 270 l~~y~~f~~~~~~~~~~~~~l-------~~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~-eVE~~VI~aI~ag 341 (474)
++.|..-..+++..+ ..-|. .+..+..=||.++|. =.-||+.+||+.|+++.+ ++|.+|=+||+-|
T Consensus 333 lkkF~~~leq~k~~f-~~D~ty~LivRLR~NVIkTgIR~ISls-----YSRISl~DIA~kL~l~Seed~EyiVakAIRDG 406 (493)
T KOG2581|consen 333 LKKFNETLEQFKDKF-QADGTYTLIVRLRHNVIKTGIRKISLS-----YSRISLQDIAKKLGLNSEEDAEYIVAKAIRDG 406 (493)
T ss_pred HHHHHHHHHHHHHHH-hhCCcchHHHHHHHHHHHHhhhheeee-----eeeccHHHHHHHhcCCCchhHHHHHHHHHHhc
Confidence 999999888876555 33232 344445555544432 467899999999999875 5999999999999
Q ss_pred HHHHHH
Q psy11709 342 KVMIEL 347 (474)
Q Consensus 342 lv~~kl 347 (474)
++++++
T Consensus 407 vIea~I 412 (493)
T KOG2581|consen 407 VIEAKI 412 (493)
T ss_pred cceeee
Confidence 999765
No 12
>smart00753 PAM PCI/PINT associated module.
Probab=96.83 E-value=0.0011 Score=54.40 Aligned_cols=45 Identities=27% Similarity=0.409 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChhhhhhhccC
Q psy11709 430 HQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIID 474 (474)
Q Consensus 430 ~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~eVE~lVId 474 (474)
.+.+.+|+|..++..++...+.++|++|++.++++.++||.||++
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~ 47 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSK 47 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHH
Confidence 467899999999999999999999999999999999999999874
No 13
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=96.83 E-value=0.0011 Score=54.40 Aligned_cols=45 Identities=27% Similarity=0.409 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChhhhhhhccC
Q psy11709 430 HQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIID 474 (474)
Q Consensus 430 ~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~eVE~lVId 474 (474)
.+.+.+|+|..++..++...+.++|++|++.++++.++||.||++
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~ 47 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSK 47 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHH
Confidence 467899999999999999999999999999999999999999874
No 14
>KOG1464|consensus
Probab=94.55 E-value=0.5 Score=47.35 Aligned_cols=141 Identities=15% Similarity=0.293 Sum_probs=92.1
Q ss_pred ccchHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHH--HcCCCcccchhhcCCchhhhccccc----HHHHHHHHhhCC
Q psy11709 196 CSKTELAAKVMIELLSTYTAENASQAREDAQACILAA--LADPNTFLLHPLLTLKPVKFLEGEL----IHDLLNIFVAEK 269 (474)
Q Consensus 196 ~~~~~~ay~~~l~~L~t~~~~~~~e~~~~A~~~i~~a--L~~p~~f~f~~Ll~~p~v~~L~~~~----l~~LL~iF~~g~ 269 (474)
.|+.++|..-.......|+.+.. ..+-.+.+-.+.| |--.++--||.= -.+-.+++| .-+|+.++-..+
T Consensus 244 eg~fe~AhTDFFEAFKNYDEsGs-pRRttCLKYLVLANMLmkS~iNPFDsQ----EAKPyKNdPEIlAMTnlv~aYQ~Nd 318 (440)
T KOG1464|consen 244 EGEFEKAHTDFFEAFKNYDESGS-PRRTTCLKYLVLANMLMKSGINPFDSQ----EAKPYKNDPEILAMTNLVAAYQNND 318 (440)
T ss_pred cchHHHHHhHHHHHHhcccccCC-cchhHHHHHHHHHHHHHHcCCCCCccc----ccCCCCCCHHHHHHHHHHHHHhccc
Confidence 35667776666666666765432 2333333333322 222223233311 112233432 578999999999
Q ss_pred hhHHHHHHhhch------HhHHhhcCCCHHHHHHHHHHHHHHHhhhc--CCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 270 VNTYQDFYKQHK------EYIVNKLGLDHQENLRKMRLLTFMQLAET--KTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 270 l~~y~~f~~~~~------~~~~~~~~l~~~~l~~KirLLtL~~La~~--~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
+.+|+...++|. .|+.+ ..+.+.+++|--.|..|..- +--||| |+++|+|++.|||.+++.+|--.
T Consensus 319 I~eFE~Il~~~~~~IM~DpFIRe----h~EdLl~niRTQVLlkLIkPYt~i~Ipf--is~~Lnv~~~dV~~LLV~~ILD~ 392 (440)
T KOG1464|consen 319 IIEFERILKSNRSNIMDDPFIRE----HIEDLLRNIRTQVLLKLIKPYTNIGIPF--ISKELNVPEADVESLLVSCILDD 392 (440)
T ss_pred HHHHHHHHHhhhccccccHHHHH----HHHHHHHHHHHHHHHHHhccccccCchh--hHhhcCCCHHHHHHHHHHHHhcc
Confidence 999999988763 35523 24789999999999999987 445555 99999999999999999999655
Q ss_pred HHHHHH
Q psy11709 342 KVMIEL 347 (474)
Q Consensus 342 lv~~kl 347 (474)
-+.|++
T Consensus 393 ~i~g~I 398 (440)
T KOG1464|consen 393 TIDGRI 398 (440)
T ss_pred ccccch
Confidence 455543
No 15
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=92.41 E-value=16 Score=38.32 Aligned_cols=213 Identities=17% Similarity=0.102 Sum_probs=117.6
Q ss_pred hhhHHHHHHHHHhccCCC-C----cchHHH-H---HHHHHHHHhcCchhHHHhhHHHHHHhhhcCCCCHHHHH-----HH
Q psy11709 105 GPVTLRVLWLLFQSLEPT-S----PMRYHV-Y---YHLVQIAQNADQIKSVFKDVDHLKQQFSQCPPSNEQMQ-----KL 170 (474)
Q Consensus 105 ~~~~l~~L~~lfn~l~~~-s----~~r~~v-~---~~il~~a~~~~~~~~l~~~l~~l~~~l~~w~~~~~~~~-----~l 170 (474)
-+.+=|.++..||..-++ + |.+... | ..+.++.-+-+.++.+...++..+. ..--+++...++ ++
T Consensus 146 l~~~sr~l~R~Fn~il~dR~p~ln~skk~g~y~iaNlL~~iY~Rl~~~~l~~n~lka~~~-vs~~Di~~~~~sq~v~f~Y 224 (413)
T COG5600 146 LSKISRLLTRMFNSILNDRSPALNPSKKVGLYYIANLLFQIYLRLGRFKLCENFLKASKE-VSMPDISEYQKSQVVVFHY 224 (413)
T ss_pred HHHHHHHHHHHHHHhcCCcCccCChhhHHHHHHHHHHHHHHHHHhccHHHHHHHHHhccc-ccccccchhhhcceeehhh
Confidence 345668888889886543 2 233222 2 2334555566777777666664433 222223322222 23
Q ss_pred HHHHHHHHHHhHHHHHHhhhhccccccchHHHHHHHHH-HhcccCCCChhhHHHHHHHHHHHHHcCCCcccchhhcCCch
Q psy11709 171 LRLLHQALLASKQYRLLRMQTKSSLCSKTELAAKVMIE-LLSTYTAENASQAREDAQACILAALADPNTFLLHPLLTLKP 249 (474)
Q Consensus 171 y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ay~~~l~-~L~t~~~~~~~e~~~~A~~~i~~aL~~p~~f~f~~Ll~~p~ 249 (474)
|+-+.-.+.+ +..+||-.+.. ++.|-.... -.....+.=.+..+|.-... |+
T Consensus 225 YLG~~~l~~e-----------------n~heA~~~L~~aFl~c~~l~~-~n~~rIl~~~ipt~Llv~~~---------~P 277 (413)
T COG5600 225 YLGIYYLLNE-----------------NFHEAFLHLNEAFLQCPWLIT-RNRKRILPYYIPTSLLVNKF---------PP 277 (413)
T ss_pred HHHHHHHHHH-----------------hHHHHHHHHHHHHHhChhhhh-cchheehhHHhhHHHHhCCC---------CC
Confidence 4444433332 33445544444 554433111 01122333344444443322 23
Q ss_pred hh-hccc----ccHHHHHHHHhhCChhHHHHHHhhchHhHHhhcCCCHHHHHHHHHHHHHHHhhhc-------CCCcChH
Q psy11709 250 VK-FLEG----ELIHDLLNIFVAEKVNTYQDFYKQHKEYIVNKLGLDHQENLRKMRLLTFMQLAET-------KTEMSFD 317 (474)
Q Consensus 250 v~-~L~~----~~l~~LL~iF~~g~l~~y~~f~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La~~-------~~~lsy~ 317 (474)
++ .|+. +.+--|..+..+|++++|.....+|..++ -+.|+ +-.+..+.++++.-.|.-. +..+|++
T Consensus 278 tk~~L~r~~~~s~~~~LvkavrsGni~~~~~~l~~ner~~-~~~~l-~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~s 355 (413)
T COG5600 278 TKDLLERFKRCSVYSPLVKAVRSGNIEDFDLALSRNERKF-AKRGL-YLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLS 355 (413)
T ss_pred chHHHHhccccchhHHHHHHHHcCCHHHHHHHHHHhHHHH-HHcch-HHHHHhhccHHHHHHHHHHHHhhccccccCcHH
Confidence 33 2333 24677889999999999999999998888 56666 3345566666666555543 3344555
Q ss_pred H--HHHhhCCCh-----hhHHHHHHhhhhHHHHHHHH
Q psy11709 318 M--IQKELDLNP-----NQIEAFIIDGKIAAKVMIEL 347 (474)
Q Consensus 318 ~--Ia~~l~i~~-----~eVE~~VI~aI~aglv~~kl 347 (474)
- |+.++...+ ++||-.+..+|..|.+.|-+
T Consensus 356 il~~~~qls~~dn~~~~~~VEciL~tlI~~G~lrgYi 392 (413)
T COG5600 356 ILLIVLQLSAIDNFHSFKEVECILVTLIGLGLLRGYI 392 (413)
T ss_pred HHHHHHHccCCCcccChHHHHHHHHHHHhhhhhhhee
Confidence 4 455444433 58999999999999877654
No 16
>KOG0687|consensus
Probab=91.69 E-value=18 Score=37.37 Aligned_cols=211 Identities=14% Similarity=0.113 Sum_probs=135.1
Q ss_pred HHHHHHHHhccCCCCcchHHHHHHHHHHHHhcCchhHHHhhHHHHHHhhhcCC-CCHHHHHHHHHHHHHHHHHhHHHHHH
Q psy11709 109 LRVLWLLFQSLEPTSPMRYHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQCP-PSNEQMQKLLRLLHQALLASKQYRLL 187 (474)
Q Consensus 109 l~~L~~lfn~l~~~s~~r~~v~~~il~~a~~~~~~~~l~~~l~~l~~~l~~w~-~~~~~~~~ly~~i~~~~~~~~~~~~~ 187 (474)
+..+...|..--.. ..|..|+..+++++--.++.+.+...++..+..+.+=+ -+-.-+-+.|.-++-...
T Consensus 124 ~~~~~~t~~ktvs~-g~kiDVvf~~iRlglfy~D~~lV~~~iekak~liE~GgDWeRrNRlKvY~Gly~msv-------- 194 (393)
T KOG0687|consen 124 LEALRKTYEKTVSL-GHKIDVVFYKIRLGLFYLDHDLVTESIEKAKSLIEEGGDWERRNRLKVYQGLYCMSV-------- 194 (393)
T ss_pred HHHHHHHHHHHhhc-ccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhCCChhhhhhHHHHHHHHHHHH--------
Confidence 34444444332222 57888888999999999999999999999999887411 122334444666654433
Q ss_pred hhhhccccccchHHHHHHHHHHhcccCCCCh---hhHHHHHHHHHHHHHcCCCcccchhhcCCchhhhccc--ccHHHHH
Q psy11709 188 RMQTKSSLCSKTELAAKVMIELLSTYTAENA---SQAREDAQACILAALADPNTFLLHPLLTLKPVKFLEG--ELIHDLL 262 (474)
Q Consensus 188 ~~~~~~~~~~~~~~ay~~~l~~L~t~~~~~~---~e~~~~A~~~i~~aL~~p~~f~f~~Ll~~p~v~~L~~--~~l~~LL 262 (474)
.++.+|....+.-++||+.-+. +.....++=+..-+|--|++ =.-.+..|-|...-. +++.+++
T Consensus 195 ---------R~Fk~Aa~Lfld~vsTFtS~El~~Y~~~v~Ytv~~g~i~leR~dl--ktKVi~~~Evl~vl~~l~~~~q~l 263 (393)
T KOG0687|consen 195 ---------RNFKEAADLFLDSVSTFTSYELMSYETFVRYTVITGLIALERVDL--KTKVIKCPEVLEVLHKLPSVSQLL 263 (393)
T ss_pred ---------HhHHHHHHHHHHHcccccceecccHHHHHHHHHHHhhheeccchH--HhhhcCcHHHHHHhhcCchHHHHH
Confidence 3688899999999999998655 34555555555555544432 122555555554333 2566777
Q ss_pred HHHhhCChhHHHHHH----hhc--hHhHHhhcCCCHHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHHHHHHh
Q psy11709 263 NIFVAEKVNTYQDFY----KQH--KEYIVNKLGLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIID 336 (474)
Q Consensus 263 ~iF~~g~l~~y~~f~----~~~--~~~~~~~~~l~~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~VI~ 336 (474)
.-+-.-+.++|-.-. .++ ++.+ ++=......|-||+.+-.++-.+=|.++.+-.|++.+++++=++.=+=+
T Consensus 264 ~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~---l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDreL~r 340 (393)
T KOG0687|consen 264 NSLYECDYSDFFNDLAAVEAKQLKDDRY---LGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDRELGR 340 (393)
T ss_pred HHHHhccHHHHHHHHHHHHHHhhccchh---cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHhHHHH
Confidence 766666666554221 111 1111 0101356789999999999999999999999999999998755544444
Q ss_pred hhhHHH
Q psy11709 337 GKIAAK 342 (474)
Q Consensus 337 aI~agl 342 (474)
=|-+|.
T Consensus 341 FI~~gr 346 (393)
T KOG0687|consen 341 FIAAGR 346 (393)
T ss_pred hhccCc
Confidence 444543
No 17
>KOG2688|consensus
Probab=89.68 E-value=2.5 Score=44.54 Aligned_cols=212 Identities=13% Similarity=0.105 Sum_probs=128.2
Q ss_pred hHHHHHHHHHhccCCC-------CcchHHHH--HHHHHHHHhcCchhHHHhhHHHH---HHhhhcCCCCHHHHHHHHHHH
Q psy11709 107 VTLRVLWLLFQSLEPT-------SPMRYHVY--YHLVQIAQNADQIKSVFKDVDHL---KQQFSQCPPSNEQMQKLLRLL 174 (474)
Q Consensus 107 ~~l~~L~~lfn~l~~~-------s~~r~~v~--~~il~~a~~~~~~~~l~~~l~~l---~~~l~~w~~~~~~~~~ly~~i 174 (474)
.+-+.+...|+..-++ +.-....| ..+.++..+-+....+++-+..+ ..|...|..+.-..-.+|.-.
T Consensus 134 ~~s~~i~~~f~~cl~d~~~~~~~~kk~~~~~i~n~lf~Iyfri~~~~L~k~l~ra~~~~~~~~~~~~l~~~v~y~YylGr 213 (394)
T KOG2688|consen 134 AASRTISRLFSSCLSDRRADLEESKKVAMLYIVNQLFQIYFRIEKLLLCKNLIRAFDQSGSDISDFPLAQLVVYHYYLGR 213 (394)
T ss_pred HHHHHHHHHHHHHhCccccccccchhhHHHHHHHHHHHHHHHHhhHHHhHHHHHHhhccccchhhcccccceeeeeeeee
Confidence 4455666777765433 12222333 24445666666666666555533 356677777765555555553
Q ss_pred HHHHHHhHHHHHHhhhhccccccchHHHHHHHHHHhcccCCCChhhHHHHHHHHHHHHHcCCCcccchhhcCCchhhhcc
Q psy11709 175 HQALLASKQYRLLRMQTKSSLCSKTELAAKVMIELLSTYTAENASQAREDAQACILAALADPNTFLLHPLLTLKPVKFLE 254 (474)
Q Consensus 175 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ay~~~l~~L~t~~~~~~~e~~~~A~~~i~~aL~~p~~f~f~~Ll~~p~v~~L~ 254 (474)
...+.. +..+|+..+..........-....+-...=++...+ ..+. +|-..-|.
T Consensus 214 ~a~~~~-----------------d~~~A~~~L~~af~~cp~~~~~n~~~iliylip~~~------llg~---~Pt~~lL~ 267 (394)
T KOG2688|consen 214 YAMFES-----------------DFLNAFLQLNEAFRLCPDLLLKNKRLILIYLIPTGL------LLGR---IPTKELLD 267 (394)
T ss_pred ehhhhh-----------------hHHHHHHHHHHHHHhCcHHHHhhhhhHHHHHhHHHH------Hhcc---CcchhhHh
Confidence 333332 445555555544332222212222222222222111 1111 35555554
Q ss_pred c---ccHHHHHHHHhhCChhHHHHHHhhchHhHHhhcCCCHHHHHHHHHHHHHHHhhhc-------CCCcChHHHHHhhC
Q psy11709 255 G---ELIHDLLNIFVAEKVNTYQDFYKQHKEYIVNKLGLDHQENLRKMRLLTFMQLAET-------KTEMSFDMIQKELD 324 (474)
Q Consensus 255 ~---~~l~~LL~iF~~g~l~~y~~f~~~~~~~~~~~~~l~~~~l~~KirLLtL~~La~~-------~~~lsy~~Ia~~l~ 324 (474)
. +.+-.|.++.-+|++..|....+.|..++ -..|+- -...|.++++.-.|..+ +..+|++.+-.+++
T Consensus 268 ~~~~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f-~~~gi~--l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~ 344 (394)
T KOG2688|consen 268 FYTLDKYSPLVQAVRSGNLRLFDLALADNERFF-IRSGIY--LTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQ 344 (394)
T ss_pred HhhHHhHHHHHHHHHhccHHHHHHHHhhhHHHH-HHhccH--HHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHh
Confidence 3 25778999999999999999999998888 666652 24455888988888776 57999999999998
Q ss_pred CCh------hhHHHHHHhhhhHHHHHHHH
Q psy11709 325 LNP------NQIEAFIIDGKIAAKVMIEL 347 (474)
Q Consensus 325 i~~------~eVE~~VI~aI~aglv~~kl 347 (474)
... +|||-.+...|..|.+.|-+
T Consensus 345 ~~~~~~~~~deveciLa~lI~~G~ikgYi 373 (394)
T KOG2688|consen 345 FSGVTDVDLDEVECILANLIDLGRIKGYI 373 (394)
T ss_pred hcCCCCCchhhHHHHHHhhhhhccccchh
Confidence 753 78999999999998776543
No 18
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=87.80 E-value=19 Score=36.69 Aligned_cols=184 Identities=15% Similarity=0.200 Sum_probs=113.2
Q ss_pred cchHHHHHHHHHHHHhcCchhHHHhhHHHHHHhhhc-CCCCHHHHHHHHHHHHHHHHHhHHHHHHhhhhccccccchHHH
Q psy11709 124 PMRYHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQ-CPPSNEQMQKLLRLLHQALLASKQYRLLRMQTKSSLCSKTELA 202 (474)
Q Consensus 124 ~~r~~v~~~il~~a~~~~~~~~l~~~l~~l~~~l~~-w~~~~~~~~~ly~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~a 202 (474)
.+...||..++.++--.++...+...|+.++..+.. .+-+-.-+-+.|.-++-.... ++.+|
T Consensus 149 g~KiDv~l~kiRlg~~y~d~~vV~e~lE~~~~~iEkGgDWeRrNRyK~Y~Gi~~m~~R-----------------nFkeA 211 (412)
T COG5187 149 GLKIDVFLCKIRLGLIYGDRKVVEESLEVADDIIEKGGDWERRNRYKVYKGIFKMMRR-----------------NFKEA 211 (412)
T ss_pred ccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhCCCHHhhhhHHHHHHHHHHHHH-----------------hhHHH
Confidence 477899999999999999999999999999888863 111222333446666644444 67889
Q ss_pred HHHHHHHhcccCCCCh---hhHHHHHHHHHHHHHcCCCcccc-hhhcCCchhhhcccc-----cHHHHHHHHhhCChh-H
Q psy11709 203 AKVMIELLSTYTAENA---SQAREDAQACILAALADPNTFLL-HPLLTLKPVKFLEGE-----LIHDLLNIFVAEKVN-T 272 (474)
Q Consensus 203 y~~~l~~L~t~~~~~~---~e~~~~A~~~i~~aL~~p~~f~f-~~Ll~~p~v~~L~~~-----~l~~LL~iF~~g~l~-~ 272 (474)
...+..-|.||+..+. +.+...|.-|.. ++-.-+ +. ..++..|-|-++-++ .+.+|..-+-.-|.. .
T Consensus 212 a~Ll~d~l~tF~S~El~sY~~~vrYa~~~Gl--~~leR~-diktki~dspevl~vi~~~e~l~sl~~l~~SLy~cdY~~~ 288 (412)
T COG5187 212 AILLSDILPTFESSELISYSRAVRYAIFCGL--LRLERR-DIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYGGD 288 (412)
T ss_pred HHHHHHHhccccccccccHHHHHHHHHHhhh--heeehh-hhhhhhcCCHHHHHhccchhhhhhHHHHHHHHHHhccchh
Confidence 9999999999998765 234344433332 222111 22 235555544443222 244444443333443 2
Q ss_pred HHH----HHhhc-hH-hHHhhcCCCHHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHH
Q psy11709 273 YQD----FYKQH-KE-YIVNKLGLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIE 331 (474)
Q Consensus 273 y~~----f~~~~-~~-~~~~~~~l~~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE 331 (474)
|.. |++.- |. |+ |-..+...+-||.=.-+++-.+=|.++.+..|++++++++=|+
T Consensus 289 F~~ll~~~~n~L~~d~fl----~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~yvd 349 (412)
T COG5187 289 FMNLLYLFCNSLQDDVFL----GRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVEYVD 349 (412)
T ss_pred hHHHHHHHHhhccchHHH----HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHHHHh
Confidence 221 11211 22 22 1123556788998899999998899999999999999976444
No 19
>KOG1497|consensus
Probab=86.91 E-value=41 Score=34.79 Aligned_cols=115 Identities=19% Similarity=0.260 Sum_probs=74.8
Q ss_pred hhHHHHHHHHHHHHHcCCCcccc-hhhcCCchhhhcccccHHHHHH-----HHhh-CChhHHHHHHhhchHhHHhhcCC-
Q psy11709 219 SQAREDAQACILAALADPNTFLL-HPLLTLKPVKFLEGELIHDLLN-----IFVA-EKVNTYQDFYKQHKEYIVNKLGL- 290 (474)
Q Consensus 219 ~e~~~~A~~~i~~aL~~p~~f~f-~~Ll~~p~v~~L~~~~l~~LL~-----iF~~-g~l~~y~~f~~~~~~~~~~~~~l- 290 (474)
-++...|..|.+-|..+|....| ..|..-|.++.+ +.|.+++ -|.. .+++.|..|..-|...- ...|.
T Consensus 222 ~~aL~~a~~CtlLA~~gpqrsr~Latlfkder~~~l---~~y~ileKmyl~riI~k~el~ef~~~L~pHQka~-~~dgss 297 (399)
T KOG1497|consen 222 LEALKKALQCTLLASAGPQRSRMLATLFKDERCQKL---PAYGILEKMYLERIIRKEELQEFEAFLQPHQKAH-TMDGSS 297 (399)
T ss_pred HHHHHHhHhheeecCCChHHHHHHHHHhcCcccccc---cchHHHHHHHHHHHhcchhHHHHHHHhcchhhhc-ccCcch
Confidence 46777788899999999988654 555555665555 4444443 3343 47889988875553211 11222
Q ss_pred --CHHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHHHHHHhhhhHHH
Q psy11709 291 --DHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAAK 342 (474)
Q Consensus 291 --~~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~agl 342 (474)
+...+.+ -||++.+|- ..+||+++++-++||.+.+|..+=+-|..|-
T Consensus 298 il~ra~~Eh--Nlls~Skly---~nisf~~Lg~ll~i~~ekaekiaa~MI~qeR 346 (399)
T KOG1497|consen 298 ILDRAVIEH--NLLSASKLY---NNISFEELGALLKIDAEKAEKIAAQMITQER 346 (399)
T ss_pred hhhhHHHHH--hHHHHHHHH---HhccHHHHHHHhCCCHHHHHHHHHHHHhHHH
Confidence 2222222 345555544 4689999999999999999999888877763
No 20
>KOG2582|consensus
Probab=85.14 E-value=46 Score=34.99 Aligned_cols=257 Identities=18% Similarity=0.234 Sum_probs=126.3
Q ss_pred hHHHHHHHHHHHHhccChHH---HHHHHHHHHHHHhcccC-CCChhhHHHHHHHHHhccCCCCcchHHHH-HHHHHHHHh
Q psy11709 65 DIESVLNSIVSMLVLINPER---AENLILAFSEKLSKASD-AKLGPVTLRVLWLLFQSLEPTSPMRYHVY-YHLVQIAQN 139 (474)
Q Consensus 65 e~e~~~nlli~ll~~~~~~~---~~~~v~~l~~~l~~~~~-~~~~~~~l~~L~~lfn~l~~~s~~r~~v~-~~il~~a~~ 139 (474)
+.|-.+-++-+-+.+-+.++ +...+-.+|.-++...- ...|..-++++.+.-..+.+.+. |.... .-+++++-+
T Consensus 74 ~~~~li~~~~~FV~~~n~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~~~~-qlT~~H~~l~~~~L~ 152 (422)
T KOG2582|consen 74 DPETLIELLNDFVDENNGEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQPSNG-QLTSIHADLLQLCLE 152 (422)
T ss_pred CHHHHHHHHHHHHHhcChHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhccCcc-chhhhHHHHHHHHHH
Confidence 44555555555554445442 12222244444432111 12333335555555555444422 22221 235566777
Q ss_pred cCchhHHHhhHH-HHHHhhhcCCCCHHHHHHHHHHHHHHHHHhHHHHHHhhhhccccccchHHHHHHHHHHhccc-CCCC
Q psy11709 140 ADQIKSVFKDVD-HLKQQFSQCPPSNEQMQKLLRLLHQALLASKQYRLLRMQTKSSLCSKTELAAKVMIELLSTY-TAEN 217 (474)
Q Consensus 140 ~~~~~~l~~~l~-~l~~~l~~w~~~~~~~~~ly~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ay~~~l~~L~t~-~~~~ 217 (474)
.+++....|.++ ++... ++.++-.+.+++ +.+-||.. |--++ .++.+.| .++ |-.|. ++.-
T Consensus 153 ak~y~~~~p~ld~divei---~~~n~h~~~k~f-L~Y~yYgg--------~icig--lk~fe~A-l~~--~e~~v~~Pa~ 215 (422)
T KOG2582|consen 153 AKDYASVLPYLDDDIVEI---CKANPHLDPKYF-LLYLYYGG--------MICIG--LKRFERA-LYL--LEICVTTPAM 215 (422)
T ss_pred hhcccccCCccchhHHHH---hccCCCCCHHHH-HHHHHhcc--------eeeec--cccHHHH-HHH--HHHHHhcchh
Confidence 777766666666 33222 222333333432 23334433 11111 2344444 111 11222 2322
Q ss_pred h-h-hHHHHHHHHHHHHHc-CCCcccchhhcCCchhhhccc-c-cHHHHHHHHhhCChhHHHHHHhhchHhHHhhcCC--
Q psy11709 218 A-S-QAREDAQACILAALA-DPNTFLLHPLLTLKPVKFLEG-E-LIHDLLNIFVAEKVNTYQDFYKQHKEYIVNKLGL-- 290 (474)
Q Consensus 218 ~-~-e~~~~A~~~i~~aL~-~p~~f~f~~Ll~~p~v~~L~~-~-~l~~LL~iF~~g~l~~y~~f~~~~~~~~~~~~~l-- 290 (474)
+ + ...|.-.+.+.-.|. --.+|.++.=....+....+. + ++++++.++..+.-.+.+....+|.+-+.++.+.
T Consensus 216 ~vs~~hlEaYkkylLvsLI~~GK~~ql~k~ts~~~~r~~K~ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l 295 (422)
T KOG2582|consen 216 AVSHIHLEAYKKYLLVSLILTGKVFQLPKNTSQNAGRFFKPMSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGL 295 (422)
T ss_pred HHHHHHHHHHHHHHHHHhhhcCceeeccccchhhhHHhcccCCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHH
Confidence 2 2 222333444443433 333444443332222222332 2 8999999999999888888877765433133221
Q ss_pred CH--HHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCC-hhhHHHHHHhhhhHHH
Q psy11709 291 DH--QENLRKMRLLTFMQLAETKTEMSFDMIQKELDLN-PNQIEAFIIDGKIAAK 342 (474)
Q Consensus 291 ~~--~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~-~~eVE~~VI~aI~agl 342 (474)
-. -.-..|=|++.|... --+++.++||+..++. .+|||+.|+.-|..|-
T Consensus 296 ~k~av~sl~k~nI~rltkt---F~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~ 347 (422)
T KOG2582|consen 296 AKQAVSSLYKKNIQRLTKT---FLSLSLSDIASRVQLASAQEVEKYILQMIEDGE 347 (422)
T ss_pred HHHHHHHHHHHHHHHHHHH---HHHhhHHHHHHHHHhcchHHHHHHHHHHhccCc
Confidence 11 123345555555444 4578999999988876 4899999999999884
No 21
>KOG1464|consensus
Probab=84.52 E-value=1.5 Score=44.04 Aligned_cols=75 Identities=17% Similarity=0.451 Sum_probs=62.4
Q ss_pred cHHHHHHHHhhCChhhHHHHHHhchH------hHhhhcCCCHHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChhhh
Q psy11709 395 LIHDLLNIFVSEKVNTYQDFYKQHKE------YIVNKLGLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQI 468 (474)
Q Consensus 395 ~l~~LL~iF~~G~~~~y~~~~~~~~~------~~~~~~~l~~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~eV 468 (474)
..-+|+.+....|+.+|+....+|.. ++.. +.+.+++++|---|+.|..--..|...-|+++|.||+.||
T Consensus 306 AMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIRe----h~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~~~dV 381 (440)
T KOG1464|consen 306 AMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIRE----HIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVPEADV 381 (440)
T ss_pred HHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHH----HHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCCHHHH
Confidence 44567888889999999999988753 3322 2589999999999999999877777778999999999999
Q ss_pred hhhcc
Q psy11709 469 EAFII 473 (474)
Q Consensus 469 E~lVI 473 (474)
|.+++
T Consensus 382 ~~LLV 386 (440)
T KOG1464|consen 382 ESLLV 386 (440)
T ss_pred HHHHH
Confidence 99875
No 22
>KOG2758|consensus
Probab=81.26 E-value=14 Score=38.20 Aligned_cols=91 Identities=23% Similarity=0.399 Sum_probs=63.7
Q ss_pred cHHHHHH-HHhhCChhHHHHHHhhchHhHHhhcCCC--HHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHHHH
Q psy11709 257 LIHDLLN-IFVAEKVNTYQDFYKQHKEYIVNKLGLD--HQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAF 333 (474)
Q Consensus 257 ~l~~LL~-iF~~g~l~~y~~f~~~~~~~~~~~~~l~--~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~ 333 (474)
|+-+.|. .|..-|+++-+.-..+....+..++=|. -+.-..-.|++-+-..|-=+..|+.+-+|+.|+.+.+|.|.|
T Consensus 290 PiteFl~clyvn~DFdgAq~kl~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErw 369 (432)
T KOG2758|consen 290 PITEFLECLYVNYDFDGAQKKLRECEEVLVNDFFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERW 369 (432)
T ss_pred cHHHHHHHHhhccchHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHH
Confidence 5555554 3445566665544433332221111110 134567789998888888899999999999999999999999
Q ss_pred HHhhhhHHHHHHHH
Q psy11709 334 IIDGKIAAKVMIEL 347 (474)
Q Consensus 334 VI~aI~aglv~~kl 347 (474)
+++.|+...+.+|.
T Consensus 370 ivnlIr~~rl~Aki 383 (432)
T KOG2758|consen 370 IVNLIRTARLDAKI 383 (432)
T ss_pred HHHHHHHhhhhhhh
Confidence 99999998777654
No 23
>KOG0686|consensus
Probab=79.26 E-value=32 Score=36.57 Aligned_cols=90 Identities=10% Similarity=0.179 Sum_probs=71.4
Q ss_pred cHHHHHHHHhhCChhHHHHHHhhch-HhHHhhcCC--CHHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHHHH
Q psy11709 257 LIHDLLNIFVAEKVNTYQDFYKQHK-EYIVNKLGL--DHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAF 333 (474)
Q Consensus 257 ~l~~LL~iF~~g~l~~y~~f~~~~~-~~~~~~~~l--~~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~ 333 (474)
.+.++|..|.++.++.--....+.+ .++ =+.=| ..+.+-.|||==+|.+-...=..++++.+|.+.+.++...|.=
T Consensus 307 qlr~il~~fy~sky~~cl~~L~~~k~~ll-LD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~ 385 (466)
T KOG0686|consen 307 QLREILFKFYSSKYASCLELLREIKPRLL-LDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESE 385 (466)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHhcccee-echhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHH
Confidence 5889999999999887776665543 221 00111 2367889999999998888778899999999999999999999
Q ss_pred HHhhhhHHHHHHHH
Q psy11709 334 IIDGKIAAKVMIEL 347 (474)
Q Consensus 334 VI~aI~aglv~~kl 347 (474)
|+.-|-.|.+.||.
T Consensus 386 l~~LI~~~~i~~rI 399 (466)
T KOG0686|consen 386 LLELILEGKISGRI 399 (466)
T ss_pred HHHHHHccchheee
Confidence 99999999999875
No 24
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=76.49 E-value=50 Score=30.89 Aligned_cols=163 Identities=12% Similarity=0.157 Sum_probs=91.2
Q ss_pred CchhHHHhhHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHhHHHHHHhhhhccccccchHHHHHHHHHHhcccCCC----
Q psy11709 141 DQIKSVFKDVDHLKQQFSQCPPSNEQMQKLLRLLHQALLASKQYRLLRMQTKSSLCSKTELAAKVMIELLSTYTAE---- 216 (474)
Q Consensus 141 ~~~~~l~~~l~~l~~~l~~w~~~~~~~~~ly~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ay~~~l~~L~t~~~~---- 216 (474)
...+-+...+..+.+=+.-.++..+....+|..++..+.. .++.++.-+++-.+...|..-
T Consensus 29 ~~y~fi~drlRsiRqDl~vQ~~~~~~~i~v~E~~ar~~i~---------------~~d~~qf~~c~~~L~~lY~~~~~~~ 93 (204)
T PF03399_consen 29 DDYNFIWDRLRSIRQDLTVQNIENDFAIKVYERIARFAIE---------------SGDLEQFNQCLSQLKELYDDLRDLP 93 (204)
T ss_dssp CHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHHT-
T ss_pred hhhHHHHHHhHHHHhhHHHHhcCCHHHHHHHHHHHHHHhh---------------cCCHHHHHHHHHHHHHHHHhhccCC
Confidence 3466777777777777777777777788888888888776 455555555555555555431
Q ss_pred Ch-hhHHHHHHHHHHHHHcCCCcccchh-hcCCchhhhcccc---cHHHHHHHHhhCChhHHHHHH--hhchHhHHhhcC
Q psy11709 217 NA-SQAREDAQACILAALADPNTFLLHP-LLTLKPVKFLEGE---LIHDLLNIFVAEKVNTYQDFY--KQHKEYIVNKLG 289 (474)
Q Consensus 217 ~~-~e~~~~A~~~i~~aL~~p~~f~f~~-Ll~~p~v~~L~~~---~l~~LL~iF~~g~l~~y~~f~--~~~~~~~~~~~~ 289 (474)
.. .+..=.+..++.....++. -+|.. +..+|.- ...++ -..++...+..|++..|-... .+.|... ...
T Consensus 94 ~~~~~~ef~~y~lL~~l~~~~~-~~~~~~l~~l~~~-~~~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~-~~l- 169 (204)
T PF03399_consen 94 PSPNEAEFIAYYLLYLLCQNNI-PDFHMELELLPSE-ILSSPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLF-ACL- 169 (204)
T ss_dssp --TTHHHHHHHHHHHTT-T----THHHHHHTTS-HH-HHTSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHH-HHH-
T ss_pred CCCCHHHHHHHHHHHHHHcccc-hHHHHHHHHCchh-hhcCHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHH-HHH-
Confidence 11 1222223333332223322 23322 3333321 12222 256888999999999988877 4434332 110
Q ss_pred CCHHHHHHHHHHHHHHHhhhcCCC-cChHHHHHhhC
Q psy11709 290 LDHQENLRKMRLLTFMQLAETKTE-MSFDMIQKELD 324 (474)
Q Consensus 290 l~~~~l~~KirLLtL~~La~~~~~-lsy~~Ia~~l~ 324 (474)
-+....++|.-++..++.+-+. +|-+.+++-|+
T Consensus 170 --~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 170 --MERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp --HGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred --HHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 1236779999999999998666 88888877554
No 25
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=73.22 E-value=4.8 Score=36.10 Aligned_cols=74 Identities=12% Similarity=0.114 Sum_probs=50.6
Q ss_pred cHHHHHHHHhhCChhhHHHHHHhc--hHhHhhhcCCCHHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChhhhhhhc
Q psy11709 395 LIHDLLNIFVSEKVNTYQDFYKQH--KEYIVNKLGLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAFI 472 (474)
Q Consensus 395 ~l~~LL~iF~~G~~~~y~~~~~~~--~~~~~~~~~l~~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~eVE~lV 472 (474)
.+..|.+.+..|++.+|-...+.+ +..+ .. ..+.+..++|-=.+-.+...-+.|+-+++++-||++++|++.++
T Consensus 43 ~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~-~~---~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~ 118 (143)
T PF10075_consen 43 AIWSLGQALWEGDYSKFWQALRSNPWSPDY-KP---FVPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKFI 118 (143)
T ss_dssp HHHHHHHHHHTT-HHHHHHHS-TT----HH-HH---TSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHhccchHHH-HH---HHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHH
Confidence 567888999999999998766654 1221 11 13456777777776666677799999999999999988888775
No 26
>KOG2581|consensus
Probab=72.91 E-value=9.4 Score=40.45 Aligned_cols=73 Identities=18% Similarity=0.245 Sum_probs=53.1
Q ss_pred cHHHHHHHHhhCChhhHHHHHHhchHhHhhhc------CCCHHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChh-h
Q psy11709 395 LIHDLLNIFVSEKVNTYQDFYKQHKEYIVNKL------GLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPN-Q 467 (474)
Q Consensus 395 ~l~~LL~iF~~G~~~~y~~~~~~~~~~~~~~~------~l~~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~-e 467 (474)
++++|=++.-.||++.|+....++.+.+..+- -|.+...+.=||.++| .-+-||+.+||+.|+++.+ +
T Consensus 320 ~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISl-----sYSRISl~DIA~kL~l~Seed 394 (493)
T KOG2581|consen 320 PYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISL-----SYSRISLQDIAKKLGLNSEED 394 (493)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheee-----eeeeccHHHHHHHhcCCCchh
Confidence 89999999999999999999888876542221 0123334444444433 3577999999999999875 5
Q ss_pred hhhhc
Q psy11709 468 IEAFI 472 (474)
Q Consensus 468 VE~lV 472 (474)
+|.+|
T Consensus 395 ~EyiV 399 (493)
T KOG2581|consen 395 AEYIV 399 (493)
T ss_pred HHHHH
Confidence 99876
No 27
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=72.42 E-value=63 Score=30.15 Aligned_cols=94 Identities=18% Similarity=0.134 Sum_probs=68.3
Q ss_pred cchHHHHHHHHHHHHhcCchhHHHhhHHHHHHhhhcCCCCHHHHH--HHHHHHHHHHHHhHHHHHHhhhhccccccchHH
Q psy11709 124 PMRYHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQCPPSNEQMQ--KLLRLLHQALLASKQYRLLRMQTKSSLCSKTEL 201 (474)
Q Consensus 124 ~~r~~v~~~il~~a~~~~~~~~l~~~l~~l~~~l~~w~~~~~~~~--~ly~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 (474)
..+..++..+++++-..++...+...+.+.+..++. +.+.+.+. +.|..++... .+++..
T Consensus 70 ~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~-~~d~~~~nrlk~~~gL~~l~-----------------~r~f~~ 131 (177)
T PF10602_consen 70 GHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEK-GGDWERRNRLKVYEGLANLA-----------------QRDFKE 131 (177)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhc-cchHHHHHHHHHHHHHHHHH-----------------hchHHH
Confidence 466788889999999999999999999999999887 33333333 3355554332 568899
Q ss_pred HHHHHHHHhcccCC---CChhhHHHHHHHHHHHHHcC
Q psy11709 202 AAKVMIELLSTYTA---ENASQAREDAQACILAALAD 235 (474)
Q Consensus 202 ay~~~l~~L~t~~~---~~~~e~~~~A~~~i~~aL~~ 235 (474)
|.+..+.-+.+|+. .+.-...+.|.=.++.||..
T Consensus 132 AA~~fl~~~~t~~~~~~~el~s~~d~a~Y~~l~aLat 168 (177)
T PF10602_consen 132 AAELFLDSLSTFTSLQYTELISYNDFAIYGGLCALAT 168 (177)
T ss_pred HHHHHHccCcCCCCCchhhhcCHHHHHHHHHHHHHHh
Confidence 99999999999986 34434567777777777654
No 28
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; 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: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=69.85 E-value=5.3 Score=29.31 Aligned_cols=29 Identities=14% Similarity=0.202 Sum_probs=22.4
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhh
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKI 339 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ 339 (474)
-..+||++||+.++++...|..++-+|.+
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 35689999999999999999999988875
No 29
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=68.47 E-value=27 Score=31.15 Aligned_cols=76 Identities=13% Similarity=0.145 Sum_probs=51.5
Q ss_pred cHHHHHHHHhhCChhHHHHHHhhc---hHhHHhhcCCCHHHHHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhhHHHH
Q psy11709 257 LIHDLLNIFVAEKVNTYQDFYKQH---KEYIVNKLGLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAF 333 (474)
Q Consensus 257 ~l~~LL~iF~~g~l~~y~~f~~~~---~~~~~~~~~l~~~~l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~ 333 (474)
.+..|.+.+-.|++.+|-...+++ +.+. . ..+.+..++|-=.+-.+...=..|+-+.+++-|+++++|++.|
T Consensus 43 ~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~-~----~v~~~~~~iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~ 117 (143)
T PF10075_consen 43 AIWSLGQALWEGDYSKFWQALRSNPWSPDYK-P----FVPGFEDTIRERIAHLISKAYSSISLSDLAEMLGLSEEELEKF 117 (143)
T ss_dssp HHHHHHHHHHTT-HHHHHHHS-TT----HHH-H----TSTTHHHHHHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHH
T ss_pred HHHHHHHHHHCCCHHHHHHHHHhccchHHHH-H----HHHHHHHHHHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHH
Confidence 367788888899988887765554 2222 1 1244667777666666666678999999999999999999998
Q ss_pred HHhh
Q psy11709 334 IIDG 337 (474)
Q Consensus 334 VI~a 337 (474)
+.+-
T Consensus 118 ~~~~ 121 (143)
T PF10075_consen 118 IKSR 121 (143)
T ss_dssp HHHH
T ss_pred HHHc
Confidence 8764
No 30
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=66.45 E-value=2.7 Score=32.94 Aligned_cols=42 Identities=12% Similarity=0.240 Sum_probs=31.0
Q ss_pred HHHHHhhhcCCCcChHHHHHhhCCChhhHHHHHHhhhhHHHH
Q psy11709 302 LTFMQLAETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKV 343 (474)
Q Consensus 302 LtL~~La~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv 343 (474)
..+-+.-..++.+|+++||..++++.+.||..+=.=++.|.|
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I 44 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYI 44 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSC
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcE
Confidence 344455556899999999999999999999988777777744
No 31
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=61.08 E-value=5.3 Score=31.28 Aligned_cols=32 Identities=16% Similarity=0.385 Sum_probs=22.7
Q ss_pred HHHHHhHhcCCCCCHHHHHhhcCCChhhhhhh
Q psy11709 440 LTFMQLAETKTEMSFDMIQKELDLNPNQIEAF 471 (474)
Q Consensus 440 LtL~~La~~~r~lsy~~Ia~~l~i~~~eVE~l 471 (474)
..|.+....++.+|+++||..++++.+.||.+
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~m 34 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAM 34 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHH
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHH
Confidence 34455556689999999999999999877754
No 32
>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=53.46 E-value=20 Score=25.87 Aligned_cols=30 Identities=7% Similarity=0.182 Sum_probs=25.6
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
....||++||+.++++...|-.+.-+|+..
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 677899999999999999999988888753
No 33
>PF12397 U3snoRNP10: U3 small nucleolar RNA-associated protein 10 ; InterPro: IPR022125 This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with PF08146 from PFAM. This family is the protein associated with U3 snoRNA which is involved in the processing of pre-rRNA.
Probab=52.87 E-value=1.1e+02 Score=26.21 Aligned_cols=89 Identities=17% Similarity=0.204 Sum_probs=52.7
Q ss_pred hHHHHHHHHhhhhhhcCCChhhHHH-HHHHHHHHHhccChHHHHHHHHHHHHHHhcccCCCCh-hhHHHHHHHHHhccCC
Q psy11709 44 EDDLHKIIGVCDACFQDANEADIES-VLNSIVSMLVLINPERAENLILAFSEKLSKASDAKLG-PVTLRVLWLLFQSLEP 121 (474)
Q Consensus 44 ~~~l~ki~~~~~~~~~~~~eke~e~-~~nlli~ll~~~~~~~~~~~v~~l~~~l~~~~~~~~~-~~~l~~L~~lfn~l~~ 121 (474)
|+.+.+++......++..+..|+.. .|-++..+..+.+- ..+.+..+++.+.+....... ...+-.|..+++.-..
T Consensus 1 E~~l~~lLP~l~~~L~~s~~~d~~~a~ymIl~~La~k~~L--~~~~l~~l~~~i~~~~~~~~~~~~~l~~L~~l~q~q~~ 78 (121)
T PF12397_consen 1 EDILPRLLPFLLKGLKSSSSPDLQAAAYMILSVLASKVPL--SDEVLNALMESILKNWTQETVQRQALICLIVLCQSQEN 78 (121)
T ss_pred CcHHHHHHHHHHHHHccCCcHHHHHHHHHHHHHHHhhcCC--cHHHHHHHHHHHHhccccchhHHHHHHHHHHHHHcccc
Confidence 3567788888887776444557754 45555555555442 346677778888765443334 5677777888866533
Q ss_pred CCcchHHHHHHHH
Q psy11709 122 TSPMRYHVYYHLV 134 (474)
Q Consensus 122 ~s~~r~~v~~~il 134 (474)
....--.++.++.
T Consensus 79 ~~~lp~~~~~~l~ 91 (121)
T PF12397_consen 79 VDSLPRKVFKALL 91 (121)
T ss_pred cccCCHHHHHHHH
Confidence 3333344555444
No 34
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=51.18 E-value=2.6e+02 Score=27.74 Aligned_cols=137 Identities=15% Similarity=0.121 Sum_probs=76.7
Q ss_pred HHHHHHHHHHHhc-CchhHHHhhHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHhHHHHHHhhhhccccccchHHHHHHH
Q psy11709 128 HVYYHLVQIAQNA-DQIKSVFKDVDHLKQQFSQCPPSNEQMQKLLRLLHQALLASKQYRLLRMQTKSSLCSKTELAAKVM 206 (474)
Q Consensus 128 ~v~~~il~~a~~~-~~~~~l~~~l~~l~~~l~~w~~~~~~~~~ly~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ay~~~ 206 (474)
.++..+-++.... ++.+.......+.-.+...-+ .+.....++.-+++++.. .+++++|....
T Consensus 115 ~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~---------------l~~y~~A~~~~ 178 (282)
T PF14938_consen 115 KCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYAR---------------LGRYEEAIEIY 178 (282)
T ss_dssp HHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHH---------------TT-HHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHH---------------hCCHHHHHHHH
Confidence 3444455555555 555555555556666666554 556667777778877777 77888887777
Q ss_pred HHHhcccCCCCh--hhHHHHHHHHHHHHHcCCCcccc----hhhcCC-chhhhc-ccccHHHHHHHHhhCChhHHHHHHh
Q psy11709 207 IELLSTYTAENA--SQAREDAQACILAALADPNTFLL----HPLLTL-KPVKFL-EGELIHDLLNIFVAEKVNTYQDFYK 278 (474)
Q Consensus 207 l~~L~t~~~~~~--~e~~~~A~~~i~~aL~~p~~f~f----~~Ll~~-p~v~~L-~~~~l~~LL~iF~~g~l~~y~~f~~ 278 (474)
-+....+...+. -.+++.....++--|...+.-.- ++.... |....= +..-+.+|+..|..||.+.|.+-..
T Consensus 179 e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~~s~E~~~~~~l~~A~~~~D~e~f~~av~ 258 (282)
T PF14938_consen 179 EEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFASSREYKFLEDLLEAYEEGDVEAFTEAVA 258 (282)
T ss_dssp HHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTSTTSHHHHHHHHHHHHHHTT-CCCHHHHCH
T ss_pred HHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCCCcHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 666654443332 24666666666666665443221 111111 111110 0114899999999999999987654
Q ss_pred hc
Q psy11709 279 QH 280 (474)
Q Consensus 279 ~~ 280 (474)
..
T Consensus 259 ~~ 260 (282)
T PF14938_consen 259 EY 260 (282)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 35
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=50.68 E-value=18 Score=25.66 Aligned_cols=25 Identities=16% Similarity=0.311 Sum_probs=17.7
Q ss_pred hhcCCCcChHHHHHhhCCChhhHHH
Q psy11709 308 AETKTEMSFDMIQKELDLNPNQIEA 332 (474)
Q Consensus 308 a~~~~~lsy~~Ia~~l~i~~~eVE~ 332 (474)
-..+...||.+||+.++++...|-.
T Consensus 12 Lq~d~r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 12 LQEDGRRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp HHH-TTS-HHHHHHHHTS-HHHHHH
T ss_pred HHHcCCccHHHHHHHHCcCHHHHHH
Confidence 3446789999999999999887643
No 36
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=44.77 E-value=23 Score=27.48 Aligned_cols=23 Identities=13% Similarity=0.349 Sum_probs=21.3
Q ss_pred CCCcChHHHHHhhCCChhhHHHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAF 333 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~ 333 (474)
++.+++.+||+.|+|++..|-.|
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHH
Confidence 68999999999999999998877
No 37
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=44.17 E-value=1.4e+02 Score=22.78 Aligned_cols=70 Identities=11% Similarity=0.081 Sum_probs=50.7
Q ss_pred hHHHHHHHHHHHHhcCchhHHHhhHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHhHHHHHHhhhhccccccchHHHHHH
Q psy11709 126 RYHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQCPPSNEQMQKLLRLLHQALLASKQYRLLRMQTKSSLCSKTELAAKV 205 (474)
Q Consensus 126 r~~v~~~il~~a~~~~~~~~l~~~l~~l~~~l~~w~~~~~~~~~ly~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ay~~ 205 (474)
...+|..+-.+....|.++...+.+++.-+.....+-+.......|.-++.++.. .|+.++|-++
T Consensus 4 ~a~~~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~---------------~g~~~~A~~~ 68 (78)
T PF13424_consen 4 TANAYNNLARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYR---------------LGDYEEALEY 68 (78)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHH---------------TTHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH---------------cCCHHHHHHH
Confidence 3456666777777888888887777766666666655555678889999999998 8898988666
Q ss_pred HHHHh
Q psy11709 206 MIELL 210 (474)
Q Consensus 206 ~l~~L 210 (474)
.-+.+
T Consensus 69 ~~~al 73 (78)
T PF13424_consen 69 YQKAL 73 (78)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 55544
No 38
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=43.93 E-value=27 Score=24.80 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=17.3
Q ss_pred HhHhcCCCCCHHHHHhhcCCChhhh
Q psy11709 444 QLAETKTEMSFDMIQKELDLNPNQI 468 (474)
Q Consensus 444 ~La~~~r~lsy~~Ia~~l~i~~~eV 468 (474)
.+-..+...||.+||+.+|++...|
T Consensus 10 ~~Lq~d~r~s~~~la~~lglS~~~v 34 (42)
T PF13404_consen 10 RLLQEDGRRSYAELAEELGLSESTV 34 (42)
T ss_dssp HHHHH-TTS-HHHHHHHHTS-HHHH
T ss_pred HHHHHcCCccHHHHHHHHCcCHHHH
Confidence 3334467799999999999998765
No 39
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=43.79 E-value=36 Score=30.14 Aligned_cols=74 Identities=15% Similarity=0.139 Sum_probs=50.4
Q ss_pred HHHHHHHHhhhc--CCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHH---HHHHhhccccchhhHHHHHHHHHHHHhcC
Q psy11709 299 MRLLTFMQLAET--KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVM---IELLSTYTAENASQAREDAQACILAALAD 373 (474)
Q Consensus 299 irLLtL~~La~~--~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~---~klL~t~~~~~~~ea~~~a~~li~~Al~~ 373 (474)
.-+.+++.||.. ++.++-++||+.++||..-|+..+=+--++|+|. |+- .-|.... ...+....-|..|+.+
T Consensus 9 YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~-Ggy~l~~--~~~~Itl~dv~~a~eg 85 (135)
T TIGR02010 9 YAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPG-GGYQLGR--PAEDISVADIIDAVDE 85 (135)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCC-CCEeccC--CHHHCcHHHHHHHhCC
Confidence 446677777765 4579999999999999999999999988999775 110 1122211 2334445566677766
Q ss_pred CC
Q psy11709 374 PN 375 (474)
Q Consensus 374 p~ 375 (474)
+.
T Consensus 86 ~~ 87 (135)
T TIGR02010 86 SV 87 (135)
T ss_pred CC
Confidence 53
No 40
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=42.96 E-value=2.9e+02 Score=32.48 Aligned_cols=162 Identities=12% Similarity=0.109 Sum_probs=88.7
Q ss_pred hHHHHHHHHhhhhhhcCCChhhHHHHHHHHHHHHhcc-C-h-HHHHHHHHHHHHHH---hcccCCCChhhHHHHHHHHHh
Q psy11709 44 EDDLHKIIGVCDACFQDANEADIESVLNSIVSMLVLI-N-P-ERAENLILAFSEKL---SKASDAKLGPVTLRVLWLLFQ 117 (474)
Q Consensus 44 ~~~l~ki~~~~~~~~~~~~eke~e~~~nlli~ll~~~-~-~-~~~~~~v~~l~~~l---~~~~~~~~~~~~l~~L~~lfn 117 (474)
...+.+|+..=+.-++..+-+-+.-+|.+|+..+..+ + . ...-..+..|+..| ++......+.....+|..+++
T Consensus 444 ~~iI~RIrk~~hpsLa~~NK~Kl~~f~~vLlq~i~~la~~~~~~~~~~ld~L~~~L~~Laq~~p~~~a~~~r~~L~~~~~ 523 (840)
T PF04147_consen 444 PTIIQRIRKCYHPSLAEGNKEKLQVFFGVLLQHILYLASQDSPPPFEVLDSLIPHLYDLAQKYPEEAAECFREVLKEMQK 523 (840)
T ss_pred hHHHHHHHHhCCCCCCcchHHHHHHHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555544334345566667777777777555554 1 1 11122233333332 322111234455566777766
Q ss_pred ccCCC---------CcchHHHHHHHHHHHHhcC-ch-hHHHhhHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHhHHHHH
Q psy11709 118 SLEPT---------SPMRYHVYYHLVQIAQNAD-QI-KSVFKDVDHLKQQFSQCPPSNEQMQKLLRLLHQALLASKQYRL 186 (474)
Q Consensus 118 ~l~~~---------s~~r~~v~~~il~~a~~~~-~~-~~l~~~l~~l~~~l~~w~~~~~~~~~ly~~i~~~~~~~~~~~~ 186 (474)
.+... +..+--||.+++...-.+. .. ..+.|.+=-+..||.++.+.+-..-.....++..+.. |--
T Consensus 524 ~~~~~~l~~~~~~~P~l~~Lvllklv~~lFPTSD~~HpVVTPalllm~~~L~q~~v~s~~di~~GlfL~~l~l~---y~~ 600 (840)
T PF04147_consen 524 RFRKGALKPKERSWPSLSDLVLLKLVGTLFPTSDFRHPVVTPALLLMSEYLSQCRVRSLRDIASGLFLCTLLLE---YQS 600 (840)
T ss_pred HHhhhcccccCCCCCChhHHHHHHHHHHhcCcccccCcchhHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH---HHH
Confidence 65541 2346677777777665444 44 4557888899999999998665443333444444433 222
Q ss_pred HhhhhccccccchHHHHHHHHHHhcccCC
Q psy11709 187 LRMQTKSSLCSKTELAAKVMIELLSTYTA 215 (474)
Q Consensus 187 ~~~~~~~~~~~~~~~ay~~~l~~L~t~~~ 215 (474)
++ .....++..|+...|.++.+
T Consensus 601 ~S-------KR~vPEvinFL~~~L~~~~p 622 (840)
T PF04147_consen 601 LS-------KRFVPEVINFLLGLLLLLVP 622 (840)
T ss_pred Hh-------cccChHHHHHHHHHHHHhCC
Confidence 22 55667777777777766654
No 41
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=42.13 E-value=27 Score=26.49 Aligned_cols=31 Identities=16% Similarity=0.373 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChh
Q psy11709 433 NLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPN 466 (474)
Q Consensus 433 ~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~ 466 (474)
..||+++|.++ ...+.+++++||+.++++..
T Consensus 4 i~rq~~Ll~~L---~~~~~~~~~ela~~l~~S~r 34 (59)
T PF08280_consen 4 IKRQLKLLELL---LKNKWITLKELAKKLNISER 34 (59)
T ss_dssp HHHHHHHHHHH---HHHTSBBHHHHHHHCTS-HH
T ss_pred HHHHHHHHHHH---HcCCCCcHHHHHHHHCCCHH
Confidence 45666665554 44899999999999999974
No 42
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=41.85 E-value=30 Score=27.27 Aligned_cols=24 Identities=17% Similarity=0.322 Sum_probs=19.4
Q ss_pred CCCcChHHHHHhhCCChhhHHHHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFI 334 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~V 334 (474)
+|.-+-++||+.++++.++|..+.
T Consensus 18 gr~Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 18 GREPTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp SS--BHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCHHHHHHHHcccHHHHHHHH
Confidence 899999999999999999999765
No 43
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; 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: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=41.13 E-value=17 Score=26.57 Aligned_cols=24 Identities=17% Similarity=0.265 Sum_probs=17.0
Q ss_pred CCCCCHHHHHhhcCCChhhhhhhc
Q psy11709 449 KTEMSFDMIQKELDLNPNQIEAFI 472 (474)
Q Consensus 449 ~r~lsy~~Ia~~l~i~~~eVE~lV 472 (474)
-...||++||+.++++...|..++
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l 47 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRL 47 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHH
Confidence 356899999999999999887664
No 44
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=40.54 E-value=74 Score=27.29 Aligned_cols=31 Identities=16% Similarity=0.240 Sum_probs=23.8
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
...+|++|||+.++|+-.-|-.++-+|...-
T Consensus 31 ~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L 61 (101)
T PF04297_consen 31 EEDLSLSEIAEELGISRQAVYDSIKRAEKKL 61 (101)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 6789999999999999999999999887543
No 45
>PF07389 DUF1500: Protein of unknown function (DUF1500); InterPro: IPR009974 This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, they are around 100 residues in length. The function of this family is unknown.
Probab=40.02 E-value=46 Score=27.72 Aligned_cols=31 Identities=16% Similarity=0.308 Sum_probs=25.2
Q ss_pred hcCCCcChHHHHHhhCCC-hhhHHHHHHhhhhHH
Q psy11709 309 ETKTEMSFDMIQKELDLN-PNQIEAFIIDGKIAA 341 (474)
Q Consensus 309 ~~~~~lsy~~Ia~~l~i~-~~eVE~~VI~aI~ag 341 (474)
..-..++|.+|-+. .| ++.||.|||+.+.-|
T Consensus 44 tr~~vi~Fd~iVr~--mpNes~v~qWV~dtln~i 75 (100)
T PF07389_consen 44 TRCAVIPFDDIVRT--MPNESRVKQWVIDTLNDI 75 (100)
T ss_pred HhhccccHHHHHHh--CCCHHHHHHHHHHHHHhH
Confidence 33457899999997 54 469999999999877
No 46
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=39.49 E-value=28 Score=28.07 Aligned_cols=32 Identities=13% Similarity=0.121 Sum_probs=28.5
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAK 342 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~agl 342 (474)
...+||.|||+.+++|..-|..++-.-.++|.
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~ 61 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHLKGETKAGG 61 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcCcccch
Confidence 47889999999999999999999887777774
No 47
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=39.16 E-value=26 Score=28.22 Aligned_cols=43 Identities=19% Similarity=0.223 Sum_probs=31.6
Q ss_pred HHHHHhhhc--CCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHH
Q psy11709 302 LTFMQLAET--KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVM 344 (474)
Q Consensus 302 LtL~~La~~--~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~ 344 (474)
-.++-|+.. ++.++-.+||+.+++|..-|+..+=+=.++|++.
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeE
Confidence 344445554 4459999999999999999999888877888654
No 48
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=38.77 E-value=49 Score=26.65 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=20.5
Q ss_pred CCCCCHHHHHhhcCCChhhhhhhc
Q psy11709 449 KTEMSFDMIQKELDLNPNQIEAFI 472 (474)
Q Consensus 449 ~r~lsy~~Ia~~l~i~~~eVE~lV 472 (474)
...+||++||+.++++..-|..++
T Consensus 30 ~eGlS~kEIAe~LGIS~~TVk~~l 53 (73)
T TIGR03879 30 EAGKTASEIAEELGRTEQTVRNHL 53 (73)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 478999999999999998777654
No 49
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=38.47 E-value=36 Score=31.40 Aligned_cols=31 Identities=10% Similarity=0.201 Sum_probs=27.8
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
-..+||+|||+.++||..-|..++-.|...-
T Consensus 141 ~~gls~~EIA~~l~i~~~tVks~l~ra~~~l 171 (182)
T COG1595 141 LEGLSYEEIAEILGISVGTVKSRLHRARKKL 171 (182)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3689999999999999999999999988654
No 50
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=37.87 E-value=35 Score=31.41 Aligned_cols=30 Identities=20% Similarity=0.143 Sum_probs=26.9
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
-..+||++||+.+++|..-|..++.+|.+.
T Consensus 147 ~~~~s~~eIA~~lgis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 147 VDGCSHAEIAQRLGAPLGTVKAWIKRSLKA 176 (182)
T ss_pred HcCCCHHHHHHHHCCChhhHHHHHHHHHHH
Confidence 367899999999999999999999998864
No 51
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=37.84 E-value=28 Score=27.38 Aligned_cols=23 Identities=17% Similarity=0.296 Sum_probs=18.3
Q ss_pred CCCCCHHHHHhhcCCChhhhhhh
Q psy11709 449 KTEMSFDMIQKELDLNPNQIEAF 471 (474)
Q Consensus 449 ~r~lsy~~Ia~~l~i~~~eVE~l 471 (474)
+|.-|.++||+.|+++.++|..+
T Consensus 18 gr~Pt~eEiA~~lgis~~~v~~~ 40 (78)
T PF04539_consen 18 GREPTDEEIAEELGISVEEVREL 40 (78)
T ss_dssp SS--BHHHHHHHHTS-HHHHHHH
T ss_pred CCCCCHHHHHHHHcccHHHHHHH
Confidence 79999999999999999998765
No 52
>PF07389 DUF1500: Protein of unknown function (DUF1500); InterPro: IPR009974 This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, they are around 100 residues in length. The function of this family is unknown.
Probab=37.15 E-value=23 Score=29.45 Aligned_cols=29 Identities=21% Similarity=0.442 Sum_probs=22.5
Q ss_pred HhHhcCCCCCHHHHHhhcCCCh-hhhhhhccC
Q psy11709 444 QLAETKTEMSFDMIQKELDLNP-NQIEAFIID 474 (474)
Q Consensus 444 ~La~~~r~lsy~~Ia~~l~i~~-~eVE~lVId 474 (474)
.+..+-..++|.+|-+. +|. +.||+||||
T Consensus 41 rlftr~~vi~Fd~iVr~--mpNes~v~qWV~d 70 (100)
T PF07389_consen 41 RLFTRCAVIPFDDIVRT--MPNESRVKQWVID 70 (100)
T ss_pred HHHHhhccccHHHHHHh--CCCHHHHHHHHHH
Confidence 34445567899999999 665 589999986
No 53
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=35.43 E-value=6.8e+02 Score=28.01 Aligned_cols=71 Identities=17% Similarity=0.234 Sum_probs=44.9
Q ss_pred chHHHHHHHHhhhhhhcCCChhhHHHHHHHHHHHHhccChHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHhc
Q psy11709 43 IEDDLHKIIGVCDACFQDANEADIESVLNSIVSMLVLINPERAENLILAFSEKLSKASDAKLGPVTLRVLWLLFQS 118 (474)
Q Consensus 43 ~~~~l~ki~~~~~~~~~~~~eke~e~~~nlli~ll~~~~~~~~~~~v~~l~~~l~~~~~~~~~~~~l~~L~~lfn~ 118 (474)
-.+.+.||+.+..-++......|+..+-+.+++++.. ++...+..++..+....+ .....|-++|.-|-..
T Consensus 90 ~~~~v~kvaDvL~QlL~tdd~~E~~~v~~sL~~ll~~----d~k~tL~~lf~~i~~~~~-~de~~Re~~lkFl~~k 160 (556)
T PF05918_consen 90 NPEHVSKVADVLVQLLQTDDPVELDAVKNSLMSLLKQ----DPKGTLTGLFSQIESSKS-GDEQVRERALKFLREK 160 (556)
T ss_dssp --T-HHHHHHHHHHHTT---HHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHH---H-S-HHHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHHHHHhcccHHHHHHHHHHHHHHHhc----CcHHHHHHHHHHHHhccc-CchHHHHHHHHHHHHH
Confidence 3577899999988888755558999999999999987 456777888888863221 2344565555544433
No 54
>PF13518 HTH_28: Helix-turn-helix domain
Probab=35.14 E-value=63 Score=22.97 Aligned_cols=27 Identities=15% Similarity=0.223 Sum_probs=24.2
Q ss_pred ChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 315 SFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 315 sy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
|+.+||+.++|+...|..|+-.--..|
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 999999999999999999997766655
No 55
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=34.61 E-value=65 Score=26.14 Aligned_cols=42 Identities=19% Similarity=0.309 Sum_probs=27.2
Q ss_pred HHHHHHhhhcCCCcChHHHHHhhC---CChhhHHHHHHhhhhHHH
Q psy11709 301 LLTFMQLAETKTEMSFDMIQKELD---LNPNQIEAFIIDGKIAAK 342 (474)
Q Consensus 301 LLtL~~La~~~~~lsy~~Ia~~l~---i~~~eVE~~VI~aI~agl 342 (474)
+-.|+..+..++.+||++|..+|. ++.++++.++-.--..|+
T Consensus 9 i~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 9 IKKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 344777777788899999999987 456677777666666664
No 56
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=34.19 E-value=48 Score=26.92 Aligned_cols=32 Identities=25% Similarity=0.511 Sum_probs=21.8
Q ss_pred HHHHHhHhcCCCCCHHHHHhhcC---CChhhhhhh
Q psy11709 440 LTFMQLAETKTEMSFDMIQKELD---LNPNQIEAF 471 (474)
Q Consensus 440 LtL~~La~~~r~lsy~~Ia~~l~---i~~~eVE~l 471 (474)
-.|+..+.+.+.|||++|..+|. ++.+++|.+
T Consensus 10 ~~Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i 44 (82)
T PF03979_consen 10 KKLIEKGKKKGYLTYDEINDALPEDDLDPEQIDEI 44 (82)
T ss_dssp HHHHHHHHHHSS-BHHHHHHH-S-S---HHHHHHH
T ss_pred HHHHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHH
Confidence 34778888888999999999998 444566654
No 57
>KOG2758|consensus
Probab=33.10 E-value=65 Score=33.44 Aligned_cols=80 Identities=25% Similarity=0.447 Sum_probs=55.3
Q ss_pred cHHHHHHH-HhhCChhhHHHHHHhchHhHhhhcCCC--HHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChhhhhhh
Q psy11709 395 LIHDLLNI-FVSEKVNTYQDFYKQHKEYIVNKLGLD--HQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQIEAF 471 (474)
Q Consensus 395 ~l~~LL~i-F~~G~~~~y~~~~~~~~~~~~~~~~l~--~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~eVE~l 471 (474)
|+-+.|+. +..-|+++-+.-..+-.+.+..+.-+- -+.-++-.|++-+-..|.-+..||.+.+|+.|.++.+|.|.|
T Consensus 290 PiteFl~clyvn~DFdgAq~kl~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErw 369 (432)
T KOG2758|consen 290 PITEFLECLYVNYDFDGAQKKLRECEEVLVNDFFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERW 369 (432)
T ss_pred cHHHHHHHHhhccchHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHH
Confidence 33344443 455666666655444444332332221 245667889999999999999999999999999999999999
Q ss_pred ccC
Q psy11709 472 IID 474 (474)
Q Consensus 472 VId 474 (474)
++|
T Consensus 370 ivn 372 (432)
T KOG2758|consen 370 IVN 372 (432)
T ss_pred HHH
Confidence 874
No 58
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=32.65 E-value=50 Score=29.11 Aligned_cols=29 Identities=10% Similarity=0.016 Sum_probs=25.8
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
...||.|||+.+++|..-|..++-+|++.
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46899999999999999999999887753
No 59
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=32.41 E-value=43 Score=25.32 Aligned_cols=32 Identities=16% Similarity=0.362 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhhhcCCCcChHHHHHhhCCChhh
Q psy11709 295 NLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQ 329 (474)
Q Consensus 295 l~~KirLLtL~~La~~~~~lsy~~Ia~~l~i~~~e 329 (474)
..+|++||.+. .+++.+++.+||+.++++..-
T Consensus 4 i~rq~~Ll~~L---~~~~~~~~~ela~~l~~S~rt 35 (59)
T PF08280_consen 4 IKRQLKLLELL---LKNKWITLKELAKKLNISERT 35 (59)
T ss_dssp HHHHHHHHHHH---HHHTSBBHHHHHHHCTS-HHH
T ss_pred HHHHHHHHHHH---HcCCCCcHHHHHHHHCCCHHH
Confidence 45666666554 448999999999999999753
No 60
>PF13518 HTH_28: Helix-turn-helix domain
Probab=31.90 E-value=57 Score=23.21 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=21.9
Q ss_pred HHhHhcCCCCCHHHHHhhcCCChhhhhhhc
Q psy11709 443 MQLAETKTEMSFDMIQKELDLNPNQIEAFI 472 (474)
Q Consensus 443 ~~La~~~r~lsy~~Ia~~l~i~~~eVE~lV 472 (474)
+.+... .. |+.++|+.++|+...|-.|+
T Consensus 6 v~~~~~-g~-s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 6 VELYLE-GE-SVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HHHHHc-CC-CHHHHHHHHCCCHhHHHHHH
Confidence 444443 34 99999999999988888886
No 61
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=31.76 E-value=1.9e+02 Score=30.75 Aligned_cols=118 Identities=8% Similarity=0.113 Sum_probs=68.0
Q ss_pred CCChhhHHHHHHHHHHHHhccChHH-----HHHHHHHHHHHHhcccCCCChhhHHHHHHHHHhccCCC-CcchHHHHHHH
Q psy11709 60 DANEADIESVLNSIVSMLVLINPER-----AENLILAFSEKLSKASDAKLGPVTLRVLWLLFQSLEPT-SPMRYHVYYHL 133 (474)
Q Consensus 60 ~~~eke~e~~~nlli~ll~~~~~~~-----~~~~v~~l~~~l~~~~~~~~~~~~l~~L~~lfn~l~~~-s~~r~~v~~~i 133 (474)
+.+..-+.-+|.++..++...+.+. ..+++..++..+.++...++. ..-.+|..+|..++.. +-.|-.+...+
T Consensus 101 e~~WpHL~~vY~il~~~i~~~~~~~~~~~i~~~fi~~Ll~l~~S~D~rER~-~lk~~l~~iy~k~~~~r~~Ir~~i~~~~ 179 (409)
T PF01603_consen 101 EPSWPHLQLVYEILLRFIESPPFDPAKKYIDQKFIKKLLELFDSPDPRERD-YLKTILHRIYGKFPNLRSFIRKSINNIF 179 (409)
T ss_dssp -TTHHHHHHHHHHHHHHHTSTT--CCTTTS-HHHHHHHHHTTTSSTHHHHH-HHHHHHHHHHHH-TTTHHHHHHHHHHHH
T ss_pred ccccHhHHHHHHHHHHHHHCccccHHHHHcCHHHHHHHHHHcCCCCHHHHH-HHHHHHHHHHHHhhhhHHHHHHHHHHHH
Confidence 3444556788998888888764321 235555666655433211222 3357788888877654 33555555566
Q ss_pred HHHHHhcCchhHHHhhHHHHHHhhhcCCCCH-HHHHHHH-HHHHHHH
Q psy11709 134 VQIAQNADQIKSVFKDVDHLKQQFSQCPPSN-EQMQKLL-RLLHQAL 178 (474)
Q Consensus 134 l~~a~~~~~~~~l~~~l~~l~~~l~~w~~~~-~~~~~ly-~~i~~~~ 178 (474)
.++.........+.+.|+=+...++++.+.- ++|..++ +++.-.+
T Consensus 180 ~~fi~e~~~~~gI~elLeil~sii~gf~~plk~eh~~fl~~vllPLh 226 (409)
T PF01603_consen 180 YRFIYETERHNGIAELLEILGSIINGFAVPLKEEHKQFLRKVLLPLH 226 (409)
T ss_dssp HHHHHTTS--STHHHHHHHHHHHHTT--SS--HHHHHHHHHTTGGGG
T ss_pred HHHhcCcccccCHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHHHHh
Confidence 6677667777888888888889999888443 5677665 4444333
No 62
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=31.67 E-value=70 Score=22.57 Aligned_cols=26 Identities=8% Similarity=0.188 Sum_probs=22.7
Q ss_pred CcChHHHHHhhCCChhhHHHHHHhhh
Q psy11709 313 EMSFDMIQKELDLNPNQIEAFIIDGK 338 (474)
Q Consensus 313 ~lsy~~Ia~~l~i~~~eVE~~VI~aI 338 (474)
..++.+||+.++++..-|..++-.+.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46999999999999999999887664
No 63
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=31.42 E-value=39 Score=26.20 Aligned_cols=23 Identities=13% Similarity=0.349 Sum_probs=20.4
Q ss_pred CCCCCHHHHHhhcCCChhhhhhh
Q psy11709 449 KTEMSFDMIQKELDLNPNQIEAF 471 (474)
Q Consensus 449 ~r~lsy~~Ia~~l~i~~~eVE~l 471 (474)
++.+++.+||+.|+|++..|-.|
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHH
Confidence 67999999999999999887665
No 64
>KOG2688|consensus
Probab=30.87 E-value=1.5e+02 Score=31.54 Aligned_cols=74 Identities=12% Similarity=0.280 Sum_probs=56.7
Q ss_pred cHHHHHHHHhhCChhhHHHHHHhchHhHhhhcCCCHHHHHHHHHHHHHHHhHhc-------CCCCCHHHHHhhcCCCh--
Q psy11709 395 LIHDLLNIFVSEKVNTYQDFYKQHKEYIVNKLGLDHQENLRKMRLLTFMQLAET-------KTEMSFDMIQKELDLNP-- 465 (474)
Q Consensus 395 ~l~~LL~iF~~G~~~~y~~~~~~~~~~~~~~~~l~~~~~~~KirlLtL~~La~~-------~r~lsy~~Ia~~l~i~~-- 465 (474)
.+-.|+++..+|++..|....+.|..++ -..|+- -...|.++++.-.|..+ +..+|++.+..+++...
T Consensus 273 ~~~~lv~aVr~Gnl~~f~~al~~~E~~f-~~~gi~--l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~ 349 (394)
T KOG2688|consen 273 KYSPLVQAVRSGNLRLFDLALADNERFF-IRSGIY--LTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVT 349 (394)
T ss_pred hHHHHHHHHHhccHHHHHHHHhhhHHHH-HHhccH--HHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCC
Confidence 5566789999999999999999998875 443332 24556889888887764 57999999999998754
Q ss_pred ----hhhhhh
Q psy11709 466 ----NQIEAF 471 (474)
Q Consensus 466 ----~eVE~l 471 (474)
+|||-.
T Consensus 350 ~~~~deveci 359 (394)
T KOG2688|consen 350 DVDLDEVECI 359 (394)
T ss_pred CCchhhHHHH
Confidence 477743
No 65
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=30.48 E-value=76 Score=22.53 Aligned_cols=27 Identities=7% Similarity=0.074 Sum_probs=22.9
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhh
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGK 338 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI 338 (474)
...++.+||+.++++..-|+.++-++.
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 347999999999999999999876554
No 66
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=29.81 E-value=57 Score=29.08 Aligned_cols=29 Identities=7% Similarity=0.149 Sum_probs=25.8
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
..+||++||+.+++|.+-|..++-+|...
T Consensus 125 ~g~s~~eIA~~lgis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 125 EDLSEAQVAEALGISVGTVKSRLSRALAR 153 (162)
T ss_pred hcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 36899999999999999999999888754
No 67
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=29.74 E-value=58 Score=29.68 Aligned_cols=29 Identities=10% Similarity=0.049 Sum_probs=25.8
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
..+||+|||+.+++|+.-|...+-+|...
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 57899999999999999999988887754
No 68
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.34 E-value=61 Score=28.87 Aligned_cols=30 Identities=13% Similarity=0.135 Sum_probs=26.4
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
-..+||+|||+.+++|..-|...+-+|...
T Consensus 120 ~~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 120 LEEKSYQEIALQEKIEVKTVEMKLYRARKW 149 (160)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 367899999999999999999998887754
No 69
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=29.02 E-value=63 Score=28.68 Aligned_cols=30 Identities=7% Similarity=0.087 Sum_probs=26.7
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||++||+.+++|..-|...+-+|++.-
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATHAL 150 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 578999999999999999999988887654
No 70
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=28.79 E-value=64 Score=28.02 Aligned_cols=73 Identities=16% Similarity=0.142 Sum_probs=46.2
Q ss_pred HHHHHHhhhc--CCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHHHHH--HhhccccchhhHHHHHHHHHHHHhcCCC
Q psy11709 301 LLTFMQLAET--KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVMIEL--LSTYTAENASQAREDAQACILAALADPN 375 (474)
Q Consensus 301 LLtL~~La~~--~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~~kl--L~t~~~~~~~ea~~~a~~li~~Al~~p~ 375 (474)
|..+.-++.. +..++-++||+.+++|..-|...+-.-.++|++...- -.-|... ....+....-|..++.++.
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~--~~~~~itl~~I~~~~e~~~ 87 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLA--RPPEEITVGDVVRAVEGPL 87 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCC--CCHHHCCHHHHHHHHcCcC
Confidence 3444444433 4589999999999999999999998888888765110 0112221 1333444555666776553
No 71
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=28.73 E-value=84 Score=28.58 Aligned_cols=32 Identities=6% Similarity=0.252 Sum_probs=28.0
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAK 342 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~agl 342 (474)
-..+||+|||+.++++..-|...+-+|++.-.
T Consensus 133 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 133 LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 36789999999999999999999988886653
No 72
>KOG2582|consensus
Probab=28.62 E-value=1.2e+02 Score=32.05 Aligned_cols=80 Identities=16% Similarity=0.355 Sum_probs=53.8
Q ss_pred ccHHHHHHHHhhCChhhHHHHHHhchHhHhhhcCCC-HHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCCh-hhhhhh
Q psy11709 394 ELIHDLLNIFVSEKVNTYQDFYKQHKEYIVNKLGLD-HQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNP-NQIEAF 471 (474)
Q Consensus 394 ~~l~~LL~iF~~G~~~~y~~~~~~~~~~~~~~~~l~-~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~-~eVE~l 471 (474)
.++++++++...+.-.+.+....+|.+-+.++.+.- .-++..=+..=.+..|...--+++.++||+..++.. +|||..
T Consensus 259 ~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~ 338 (422)
T KOG2582|consen 259 NPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKY 338 (422)
T ss_pred chHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHH
Confidence 389999999999999989988888765332432111 112233333334445555556799999999888865 689888
Q ss_pred cc
Q psy11709 472 II 473 (474)
Q Consensus 472 VI 473 (474)
|+
T Consensus 339 Il 340 (422)
T KOG2582|consen 339 IL 340 (422)
T ss_pred HH
Confidence 75
No 73
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=28.61 E-value=46 Score=27.84 Aligned_cols=44 Identities=14% Similarity=0.249 Sum_probs=31.5
Q ss_pred HHHHHHHHHh-hhcCCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 298 KMRLLTFMQL-AETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 298 KirLLtL~~L-a~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
+-++|.++.- +....=++.++|++.|+++.++|+.-|=.-+..|
T Consensus 49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG 93 (102)
T PF08784_consen 49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEG 93 (102)
T ss_dssp HHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 4566777777 5556779999999999999999887766655555
No 74
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=28.52 E-value=61 Score=29.43 Aligned_cols=30 Identities=13% Similarity=0.313 Sum_probs=26.6
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||.|||+.++++..-|...+-+|++.-
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 578999999999999999999998887654
No 75
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=28.22 E-value=53 Score=26.44 Aligned_cols=27 Identities=11% Similarity=0.074 Sum_probs=20.6
Q ss_pred HHHHHHHhHhcCCCCCHHHHHhhcCCC
Q psy11709 438 RLLTFMQLAETKTEMSFDMIQKELDLN 464 (474)
Q Consensus 438 rlLtL~~La~~~r~lsy~~Ia~~l~i~ 464 (474)
+++..+.-.-.++..||.+||+.++.|
T Consensus 4 ~V~~~v~~IP~G~v~TYg~iA~~~g~p 30 (79)
T cd06445 4 RVWEALRQIPYGEVTTYGQIAKLAGTP 30 (79)
T ss_pred HHHHHHhcCCCCCcCcHHHHHHHHCCC
Confidence 344444444568999999999999997
No 76
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=28.16 E-value=63 Score=29.46 Aligned_cols=29 Identities=10% Similarity=0.289 Sum_probs=24.7
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
...||++||+.+++++.-|...+-+|.+.
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRRSLLK 172 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHHHHHH
Confidence 45899999999999999998888777654
No 77
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=28.01 E-value=8.5e+02 Score=26.88 Aligned_cols=146 Identities=16% Similarity=0.198 Sum_probs=72.1
Q ss_pred HHhcCchhHHHhhHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHhHHHHHHhhhhccccccchHHHHHHHHHHhcccCCC
Q psy11709 137 AQNADQIKSVFKDVDHLKQQFSQCPPSNEQMQKLLRLLHQALLASKQYRLLRMQTKSSLCSKTELAAKVMIELLSTYTAE 216 (474)
Q Consensus 137 a~~~~~~~~l~~~l~~l~~~l~~w~~~~~~~~~ly~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~ay~~~l~~L~t~~~~ 216 (474)
|...+........++.+++-++.-+.. -.+|..=+.+++. .|+..+|+..+=..-. .+..
T Consensus 201 Aqhyd~~g~~~~Al~~Id~aI~htPt~----~ely~~KarilKh---------------~G~~~~Aa~~~~~Ar~-LD~~ 260 (517)
T PF12569_consen 201 AQHYDYLGDYEKALEYIDKAIEHTPTL----VELYMTKARILKH---------------AGDLKEAAEAMDEARE-LDLA 260 (517)
T ss_pred HHHHHHhCCHHHHHHHHHHHHhcCCCc----HHHHHHHHHHHHH---------------CCCHHHHHHHHHHHHh-CChh
Confidence 333333334446666666666654433 3477888888887 8888888766544322 2222
Q ss_pred Ch------------hhHHHHHHHHHHHHHcCCCcccchhhcCCchhhhcccccHHHHHHHHh-hCC----hhHHHHHHhh
Q psy11709 217 NA------------SQAREDAQACILAALADPNTFLLHPLLTLKPVKFLEGELIHDLLNIFV-AEK----VNTYQDFYKQ 279 (474)
Q Consensus 217 ~~------------~e~~~~A~~~i~~aL~~p~~f~f~~Ll~~p~v~~L~~~~l~~LL~iF~-~g~----l~~y~~f~~~ 279 (474)
|- ....+.|.+.+-.+.+.+. -...+|..+..+=.+ .+-=..+. .|+ +..|....+.
T Consensus 261 DRyiNsK~aKy~LRa~~~e~A~~~~~~Ftr~~~-~~~~~L~~mQc~Wf~-----~e~a~a~~r~~~~~~ALk~~~~v~k~ 334 (517)
T PF12569_consen 261 DRYINSKCAKYLLRAGRIEEAEKTASLFTREDV-DPLSNLNDMQCMWFE-----TECAEAYLRQGDYGLALKRFHAVLKH 334 (517)
T ss_pred hHHHHHHHHHHHHHCCCHHHHHHHHHhhcCCCC-CcccCHHHHHHHHHH-----HHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 10 1123556666665555543 112223333322111 11222222 233 3344444444
Q ss_pred chHhHHhhcCCCHHHHHHHHHHHHHHHhhh
Q psy11709 280 HKEYIVNKLGLDHQENLRKMRLLTFMQLAE 309 (474)
Q Consensus 280 ~~~~~~~~~~l~~~~l~~KirLLtL~~La~ 309 (474)
+..+..+++.. |..|.|||.+=+-++|--
T Consensus 335 f~~~~~DQfDF-H~Yc~RK~t~r~Y~~~L~ 363 (517)
T PF12569_consen 335 FDDFEEDQFDF-HSYCLRKMTLRAYVDMLR 363 (517)
T ss_pred HHHHhcccccH-HHHHHhhccHHHHHHHHH
Confidence 44444222222 677999997766666654
No 78
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=27.64 E-value=77 Score=25.36 Aligned_cols=45 Identities=11% Similarity=0.132 Sum_probs=34.7
Q ss_pred HHHHHHHhhhcC-CCcChHHHHHhhCCChhhHHHHHHhhhhHHHHH
Q psy11709 300 RLLTFMQLAETK-TEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVM 344 (474)
Q Consensus 300 rLLtL~~La~~~-~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~ 344 (474)
|.+.++++...+ +.++..+|++.++++..-|-..+-.-...|.+.
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 445556655554 789999999999999998888887777777654
No 79
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=27.43 E-value=96 Score=24.92 Aligned_cols=37 Identities=11% Similarity=0.304 Sum_probs=29.7
Q ss_pred HHHhhhcCCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 304 FMQLAETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 304 L~~La~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
+++||-.+| .||+.|...+|+++.||=.+.=+-++.+
T Consensus 5 iIeMAweDR-tpFeaI~~~fGL~E~eVi~lMR~~lk~~ 41 (72)
T TIGR03643 5 IIEMAWEDR-TPFEAIEQQFGLSEKEVIKLMRQNLKPS 41 (72)
T ss_pred HHHHHHccC-CCHHHHHHHHCCCHHHHHHHHHhhcChh
Confidence 456666555 4999999999999999988877777766
No 80
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=27.35 E-value=67 Score=29.77 Aligned_cols=30 Identities=7% Similarity=0.128 Sum_probs=26.6
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||.+||+.+++|..-|...+-+|.+.-
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 175 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRKQL 175 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 578999999999999999999988887643
No 81
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=27.01 E-value=67 Score=29.48 Aligned_cols=29 Identities=17% Similarity=0.296 Sum_probs=25.5
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
..+||+|||+.+++|+.-|...+-+|+..
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~~ 170 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYVT 170 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 56899999999999999999988877654
No 82
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=26.51 E-value=71 Score=29.53 Aligned_cols=30 Identities=13% Similarity=0.256 Sum_probs=26.1
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||++||+.+++|..-|...+-+|.+.-
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 175 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRARMRL 175 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 468999999999999999999988887653
No 83
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=26.34 E-value=91 Score=28.87 Aligned_cols=79 Identities=10% Similarity=0.074 Sum_probs=53.9
Q ss_pred HHHHHHHHHhhhc--CCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHHHHH--HhhccccchhhHHHHHHHHHHHHhcC
Q psy11709 298 KMRLLTFMQLAET--KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVMIEL--LSTYTAENASQAREDAQACILAALAD 373 (474)
Q Consensus 298 KirLLtL~~La~~--~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~~kl--L~t~~~~~~~ea~~~a~~li~~Al~~ 373 (474)
..-|.+++.+|+. ++.+|-++||+.+++|..=++..+-+--++|+|...- =.-|... ....++...=|+.|+.+
T Consensus 8 ~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~La--r~p~~Itl~dIl~aieg 85 (164)
T PRK10857 8 RYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLG--KDASSIAVGEVISAVDE 85 (164)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeecc--CCHHHCCHHHHHHHHcC
Confidence 3456667777765 4579999999999999999999998888999776100 0112221 14445566677788887
Q ss_pred CCeee
Q psy11709 374 PNTFL 378 (474)
Q Consensus 374 p~vy~ 378 (474)
|....
T Consensus 86 ~~~~~ 90 (164)
T PRK10857 86 SVDAT 90 (164)
T ss_pred CCccc
Confidence 75543
No 84
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=26.32 E-value=75 Score=28.63 Aligned_cols=30 Identities=7% Similarity=0.039 Sum_probs=26.4
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||++||+.++++..-|...+-+|.+.-
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 156 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARNRL 156 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 678999999999999999999988887653
No 85
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=26.27 E-value=76 Score=28.29 Aligned_cols=31 Identities=16% Similarity=0.277 Sum_probs=26.6
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
-..+||++||+.+++|+.-|...+-+|.+.-
T Consensus 119 ~~~~s~~eIA~~lgis~~tv~~~l~ra~~~L 149 (159)
T PRK12527 119 LEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149 (159)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4678999999999999999998888777653
No 86
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=25.89 E-value=75 Score=28.79 Aligned_cols=31 Identities=10% Similarity=0.099 Sum_probs=27.4
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
-...||++||+.++++..-|...+-+|.+.-
T Consensus 133 ~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~L 163 (173)
T PRK12522 133 YEQYSYKEMSEILNIPIGTVKYRLNYAKKQM 163 (173)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 3678999999999999999999998887665
No 87
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=25.77 E-value=75 Score=30.54 Aligned_cols=31 Identities=10% Similarity=-0.034 Sum_probs=27.0
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
-..+||+|||+.+++|..-|...+-+|++.-
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~rA~~~L 226 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEKRIIKRL 226 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4688999999999999999999988887643
No 88
>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=25.59 E-value=75 Score=22.36 Aligned_cols=22 Identities=23% Similarity=0.492 Sum_probs=17.9
Q ss_pred HHHHHhhCCChhhHHHHHHhhh
Q psy11709 317 DMIQKELDLNPNQIEAFIIDGK 338 (474)
Q Consensus 317 ~~Ia~~l~i~~~eVE~~VI~aI 338 (474)
.+|++.++++..+|..|.++|=
T Consensus 17 ~~L~~~tgls~~Qi~~WF~NaR 38 (40)
T PF05920_consen 17 EELAKQTGLSRKQISNWFINAR 38 (40)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHHhH
Confidence 4678889999999999999874
No 89
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.39 E-value=77 Score=29.41 Aligned_cols=30 Identities=17% Similarity=0.370 Sum_probs=26.4
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||+|||+.+++|+.-|...+-+|.+.-
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~RAr~~L 178 (189)
T PRK12530 149 LELSSEQICQECDISTSNLHVLLYRARLQL 178 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 478999999999999999999988887543
No 90
>PF03635 Vps35: Vacuolar protein sorting-associated protein 35 ; InterPro: IPR005378 The movement of lipid and protein components between intracellular organelles requires the regulated interactions of many molecules. Vacuolar protein sorting-associated protein (Vps)5 is a yeast protein that is a subunit of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. Sorting nexin (SNX) 1 and SNX2 are its mammalian orthologs []. To carry out its biological functions, Vps5 forms the retromer complex with at least four other proteins: Vps17, Vps26, Vps29, and Vps35.Vps35 contains a central region of weaker sequence similarity, thought to indicate the presence of at least three domains [].; PDB: 2R17_C.
Probab=24.89 E-value=5.4e+02 Score=29.90 Aligned_cols=158 Identities=16% Similarity=0.244 Sum_probs=76.2
Q ss_pred ChhhHHHHHHHHHHHHhccChH---------------HHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHhccCCCCcch
Q psy11709 62 NEADIESVLNSIVSMLVLINPE---------------RAENLILAFSEKLSKASDAKLGPVTLRVLWLLFQSLEPTSPMR 126 (474)
Q Consensus 62 ~eke~e~~~nlli~ll~~~~~~---------------~~~~~v~~l~~~l~~~~~~~~~~~~l~~L~~lfn~l~~~s~~r 126 (474)
+..+++.+|.++--++...+.. +-++.+.+++.-+. ++.+..-+++|..+.+.+....+.|
T Consensus 450 t~e~v~~ll~li~pLi~d~~d~~~~~~~~~~~~eef~eeQ~~varliHLi~----~~D~d~~~~iL~~~rk~~~~Gg~~r 525 (762)
T PF03635_consen 450 TPEEVDNLLELISPLIKDQDDQPSSEPDLKEDSEEFAEEQELVARLIHLIR----SDDPDQQFEILNIARKHFGNGGPKR 525 (762)
T ss_dssp -----------------------------------TCCCHHHHHHHHHHCT----TSSHHHHHHHHHHHHHHHCTT-SSS
T ss_pred CHHHHHHHHHHHHHHhhCCCCCCCccccccCchHHHHHHHHHHHHHHHHhc----CCCHHHHHHHHHHHHHHHHhCCCce
Confidence 4578899999888887654210 12455566666543 2368888999999999988765555
Q ss_pred H------HHHHHHHHHHHhcCchh-----------------HHHhhHHH---HHHhhhcCCCCHHHHHHHHHHHHHHHHH
Q psy11709 127 Y------HVYYHLVQIAQNADQIK-----------------SVFKDVDH---LKQQFSQCPPSNEQMQKLLRLLHQALLA 180 (474)
Q Consensus 127 ~------~v~~~il~~a~~~~~~~-----------------~l~~~l~~---l~~~l~~w~~~~~~~~~ly~~i~~~~~~ 180 (474)
. -|| ..++++++....+ .++..+.. .-.-|..-...++..=++|...+.+...
T Consensus 526 i~~TlP~LIf-~~lkL~r~~~~~~~~~~~~~~~~~~~~~~~~~~kifkfi~~~i~~L~~~~~~~~lalkL~Lq~A~~AD~ 604 (762)
T PF03635_consen 526 IRYTLPPLIF-AALKLARRIKDLKQKYPNNAIKDDDEDWEKKCKKIFKFIHQCISALYQIHPSSELALKLYLQAAIVADQ 604 (762)
T ss_dssp HHHHCHHHHH-HHHHHHHHHHCCC---------CT-TTHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHH
T ss_pred eeeeHHHHHH-HHHHHHHHHHHhhccchhhccccchhhHHHHHHHHHHHHHHHHHHHHhccCchhhhHHHHHHHHHHHHh
Confidence 3 223 3445554432211 11222222 2222223333456677778888877777
Q ss_pred hHHHHHHhhhhccccccchHHHHHHHHHHhcccCCC-ChhhHHHHHHHHHHHHHcCCCcc
Q psy11709 181 SKQYRLLRMQTKSSLCSKTELAAKVMIELLSTYTAE-NASQAREDAQACILAALADPNTF 239 (474)
Q Consensus 181 ~~~~~~~~~~~~~~~~~~~~~ay~~~l~~L~t~~~~-~~~e~~~~A~~~i~~aL~~p~~f 239 (474)
.+..+-+|.+....+..|..+ +-+.++-.|.-.++.+|..-..|
T Consensus 605 ---------------~~~e~iaYEFf~QAf~iYEE~IsDSk~Q~~aL~~ii~tL~~~r~~ 649 (762)
T PF03635_consen 605 ---------------CGLEEIAYEFFSQAFTIYEEEISDSKAQFQALTLIIGTLQKTRSF 649 (762)
T ss_dssp ---------------H--TTHHHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHCC----
T ss_pred ---------------hCcHHHHHHHHHHHHHHHHhhccchHHHHHHHHHHHHHHHHhcCC
Confidence 777778999999988888652 11345667888888888555443
No 91
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=24.86 E-value=65 Score=25.90 Aligned_cols=33 Identities=21% Similarity=0.331 Sum_probs=22.4
Q ss_pred HHHHHHhHhc--CCCCCHHHHHhhcCCChhhhhhh
Q psy11709 439 LLTFMQLAET--KTEMSFDMIQKELDLNPNQIEAF 471 (474)
Q Consensus 439 lLtL~~La~~--~r~lsy~~Ia~~l~i~~~eVE~l 471 (474)
+-.++-|+.. .+.+|-++||+.+++|..-|+..
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~ki 45 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKI 45 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHH
Confidence 3445555654 44599999999999999876643
No 92
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=24.55 E-value=83 Score=27.40 Aligned_cols=43 Identities=21% Similarity=0.244 Sum_probs=34.7
Q ss_pred HHHHHhhhc-CCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHH
Q psy11709 302 LTFMQLAET-KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVM 344 (474)
Q Consensus 302 LtL~~La~~-~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~ 344 (474)
..|+.|+.. ++.++..+|++.+++|..-|...+=+-.++|++.
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~ 56 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVT 56 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 334444544 5679999999999999999999988888889775
No 93
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=24.45 E-value=1.2e+02 Score=24.51 Aligned_cols=37 Identities=11% Similarity=0.301 Sum_probs=29.2
Q ss_pred HHHhhhcCCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 304 FMQLAETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 304 L~~La~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
+++||-.+| .||+.|....|+++.||=.+.=+-++.+
T Consensus 4 iIeMAweDR-tpFeaI~~qfGl~E~eVi~lMR~~Lk~~ 40 (73)
T PF10985_consen 4 IIEMAWEDR-TPFEAIERQFGLSEKEVIKLMRKELKPS 40 (73)
T ss_pred HHHHHHccC-CCHHHHHHHHCCCHHHHHHHHHhhcChh
Confidence 455666555 4999999999999999988777777666
No 94
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.39 E-value=81 Score=28.11 Aligned_cols=28 Identities=21% Similarity=0.332 Sum_probs=24.2
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhh
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKI 339 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ 339 (474)
..+||+|||+.+++|..-|...+-+|++
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5789999999999999999988666654
No 95
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=24.26 E-value=85 Score=29.17 Aligned_cols=29 Identities=14% Similarity=0.310 Sum_probs=25.2
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
...||++||+.++++..-|..++-+|.+.
T Consensus 157 ~~~s~~EIA~~Lgis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMRDGLIR 185 (194)
T ss_pred cCCCHHHHHHHhCCChHhHHHHHHHHHHH
Confidence 55899999999999999999988777654
No 96
>KOG1060|consensus
Probab=24.06 E-value=8.9e+02 Score=28.40 Aligned_cols=119 Identities=18% Similarity=0.278 Sum_probs=67.7
Q ss_pred HHHHhhhhhhcCCChhhHHHHHHHHHHHHhccChHHHHHHHHHHHHHHhcccCCCChhhHHHHHHHHHhccCCC--Ccch
Q psy11709 49 KIIGVCDACFQDANEADIESVLNSIVSMLVLINPERAENLILAFSEKLSKASDAKLGPVTLRVLWLLFQSLEPT--SPMR 126 (474)
Q Consensus 49 ki~~~~~~~~~~~~eke~e~~~nlli~ll~~~~~~~~~~~v~~l~~~l~~~~~~~~~~~~l~~L~~lfn~l~~~--s~~r 126 (474)
+-++.|+......+ +.+.|-++.++.+.+.--..+.|.-| ..+.+ ..|....++|+.|+..++.- +.+|
T Consensus 414 ~AiGrCA~~~~sv~----~tCL~gLv~Llsshde~Vv~eaV~vI-k~Llq----~~p~~h~~ii~~La~lldti~vp~AR 484 (968)
T KOG1060|consen 414 KAIGRCASRIGSVT----DTCLNGLVQLLSSHDELVVAEAVVVI-KRLLQ----KDPAEHLEILFQLARLLDTILVPAAR 484 (968)
T ss_pred HHHHHHHHhhCchh----hHHHHHHHHHHhcccchhHHHHHHHH-HHHHh----hChHHHHHHHHHHHHHhhhhhhhhhh
Confidence 33445554444344 57889999999887533333443333 33333 25778889999999988753 4577
Q ss_pred HHHHHHHHHHHHhcCchhHHHhhHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHH
Q psy11709 127 YHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQCPPSNEQMQKLLRLLHQALLA 180 (474)
Q Consensus 127 ~~v~~~il~~a~~~~~~~~l~~~l~~l~~~l~~w~~~~~~~~~ly~~i~~~~~~ 180 (474)
..+..-+-+++.. ....+...+..+-+-+.+ -.++.+-+++.+.+..|..
T Consensus 485 A~IiWLige~~e~--vpri~PDVLR~laksFs~--E~~evKlQILnL~aKLyl~ 534 (968)
T KOG1060|consen 485 AGIIWLIGEYCEI--VPRIAPDVLRKLAKSFSD--EGDEVKLQILNLSAKLYLT 534 (968)
T ss_pred ceeeeeehhhhhh--cchhchHHHHHHHHhhcc--ccchhhHHHHHhhhhheEe
Confidence 7766645555544 233334444433322221 2445566667777766643
No 97
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=23.97 E-value=81 Score=30.99 Aligned_cols=30 Identities=10% Similarity=0.241 Sum_probs=27.3
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||+|||+.++|+..-|+..+-+|.+.-
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RAr~~L 205 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQARERL 205 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 678999999999999999999999998754
No 98
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=23.97 E-value=86 Score=28.31 Aligned_cols=30 Identities=13% Similarity=0.068 Sum_probs=26.0
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||.|||+.+++|+.-|...+-+|.+.-
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYALRAL 162 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 478999999999999999999888887543
No 99
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=23.68 E-value=5.3e+02 Score=23.04 Aligned_cols=30 Identities=10% Similarity=0.293 Sum_probs=26.0
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
-...||+|||+.+++|..-|...+-+|++.
T Consensus 132 ~eg~s~~EIA~~l~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 132 LEGLTYVEIGERLGVSLSRIHQYMVEAFKC 161 (168)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 478899999999999999998888777754
No 100
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=23.67 E-value=1.2e+02 Score=21.71 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=20.9
Q ss_pred cChHHHHHhhCCChhhHHHHHHhh
Q psy11709 314 MSFDMIQKELDLNPNQIEAFIIDG 337 (474)
Q Consensus 314 lsy~~Ia~~l~i~~~eVE~~VI~a 337 (474)
.|+.+||+.++++.+-|..++-+.
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 799999999999999998876543
No 101
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=23.64 E-value=72 Score=22.69 Aligned_cols=29 Identities=17% Similarity=0.172 Sum_probs=18.7
Q ss_pred CcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 313 EMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 313 ~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
-.|..+||+.++++..-|-.|+=+--..|
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 67999999999999999999986655555
No 102
>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
Probab=23.61 E-value=1.7e+02 Score=28.11 Aligned_cols=51 Identities=10% Similarity=0.166 Sum_probs=36.4
Q ss_pred HHHHHHHhhCChhhHHHHHHhchHhHhhhcCCCHHHHHHHHHHHHHHHhHhc
Q psy11709 397 HDLLNIFVSEKVNTYQDFYKQHKEYIVNKLGLDHQENLRKMRLLTFMQLAET 448 (474)
Q Consensus 397 ~~LL~iF~~G~~~~y~~~~~~~~~~~~~~~~l~~~~~~~KirlLtL~~La~~ 448 (474)
+.+...|..|...||..+.+.-...+ ...--.+.++.+|+|++-+++=...
T Consensus 18 ~~~c~aFR~~r~~dFr~~rdi~e~ll-~~~~~~~a~~~k~l~i~QfLsRI~e 68 (200)
T cd00280 18 HSACRAFREGRYEDFRRTRDIAEALL-VGPLKLTATQLKTLRIMQFLSRIAE 68 (200)
T ss_pred HHHHHHHHccChHHHHHHHHHHHHHH-hccccccccchhHhHHHHHHHHHHc
Confidence 45788999999999999887665554 2211124567899999988875554
No 103
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=23.59 E-value=7.2e+02 Score=24.91 Aligned_cols=129 Identities=11% Similarity=0.091 Sum_probs=0.0
Q ss_pred ChhhHHHHHHhhhhHHHHH-----HHHHhhccccchhhHHHHHHHHHHHHhcCCCeeecccccCCccccccccccHHHHH
Q psy11709 326 NPNQIEAFIIDGKIAAKVM-----IELLSTYTAENASQAREDAQACILAALADPNTFLLHPLLTLKPVKFLEGELIHDLL 400 (474)
Q Consensus 326 ~~~eVE~~VI~aI~aglv~-----~klL~t~~~~~~~ea~~~a~~li~~Al~~p~vy~F~eLl~~p~v~~L~~~~l~~LL 400 (474)
+.+++..||.+-.+.--+. ..++....+.|.........+++.-+..+.+....+++-. .|... ....++|.
T Consensus 131 ~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~--~v~~~-~~~if~l~ 207 (326)
T PRK07452 131 DTEGLKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKA--LVSNT-TQNSLQLA 207 (326)
T ss_pred cHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHH--HhccC-cCcHHHHH
Q ss_pred HHHhhCChhhHHHHHH------hchHhHhhhcCCCHHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCC
Q psy11709 401 NIFVSEKVNTYQDFYK------QHKEYIVNKLGLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLN 464 (474)
Q Consensus 401 ~iF~~G~~~~y~~~~~------~~~~~~~~~~~l~~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~ 464 (474)
..+..|+..+...... .+|-.+ -..+.+.+|.|..+.....++.-+-++|++.++++
T Consensus 208 dai~~~~~~~A~~~l~~L~~~g~~p~~i-------l~~l~~~~r~l~~~k~~~~~G~~~~~~ia~~lgi~ 270 (326)
T PRK07452 208 DALLQGNTGKALALLDDLLDANEPALRI-------VATLTGQFRTWLWVKLLVESGERDVKVIAKAAGIG 270 (326)
T ss_pred HHHHCCCHHHHHHHHHHHHHCCCcHHHH-------HHHHHHHHHHHHHHHHHHHcCCCcHHHHHHHhCCC
No 104
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=23.29 E-value=95 Score=27.69 Aligned_cols=29 Identities=10% Similarity=0.329 Sum_probs=25.6
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhh
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKI 339 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ 339 (474)
-..+||.|||+.+++|..-|...+-+|.+
T Consensus 127 ~~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 127 VDGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36899999999999999999998888754
No 105
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.27 E-value=1.5e+02 Score=21.45 Aligned_cols=45 Identities=16% Similarity=0.179 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhhhc-CCCc-ChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 297 RKMRLLTFMQLAET-KTEM-SFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 297 ~KirLLtL~~La~~-~~~l-sy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
.|+-++.|++.+.+ +... |+++||+.++++.+-|-..+-+-...|
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G 53 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKG 53 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCc
Confidence 46667778888755 3333 799999999999888877766555554
No 106
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=22.82 E-value=87 Score=28.29 Aligned_cols=97 Identities=10% Similarity=0.101 Sum_probs=56.0
Q ss_pred hcCCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHHHHHHhhcccc-chhhHHHHHHHHHHHH---h--cCCCee-ec-c
Q psy11709 309 ETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVMIELLSTYTAE-NASQAREDAQACILAA---L--ADPNTF-LL-H 380 (474)
Q Consensus 309 ~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~~klL~t~~~~-~~~ea~~~a~~li~~A---l--~~p~vy-~F-~ 380 (474)
..+...||.+||+.++++...|-.=+=+-...|.+.+ |... +. .. ...-..| + ..|+.+ .+ .
T Consensus 19 q~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~-----~~~~v~~-~~----lg~~~~a~v~v~v~~~~~~~~~~~ 88 (153)
T PRK11179 19 MENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG-----TRVDVNP-KQ----LGYDVCCFIGIILKSAKDYPSALA 88 (153)
T ss_pred HHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee-----EEEEECH-HH----cCCCEEEEEEEEEcccccHHHHHH
Confidence 3478899999999999999999888888888886652 1110 00 00 0000000 0 011111 11 1
Q ss_pred cccCCcccccccc-ccHHHHHHHHhhCChhhHHHHH
Q psy11709 381 PLLTLKPVKFLEG-ELIHDLLNIFVSEKVNTYQDFY 415 (474)
Q Consensus 381 eLl~~p~v~~L~~-~~l~~LL~iF~~G~~~~y~~~~ 415 (474)
.|-.+|.|.+... ++-|+++-.+...|.+++..+.
T Consensus 89 ~l~~~p~V~~~~~~tG~~dl~~~v~~~d~~~l~~~~ 124 (153)
T PRK11179 89 KLESLDEVVEAYYTTGHYSIFIKVMCRSIDALQHVL 124 (153)
T ss_pred HHhCCCCEEEEEEcccCCCEEEEEEECCHHHHHHHH
Confidence 2445666655543 4556666667778888887765
No 107
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=22.81 E-value=1.2e+02 Score=21.98 Aligned_cols=37 Identities=14% Similarity=0.292 Sum_probs=26.9
Q ss_pred HHHHHHHhhhc-CCCcChHHHHHhhCCChhhHHHHHHh
Q psy11709 300 RLLTFMQLAET-KTEMSFDMIQKELDLNPNQIEAFIID 336 (474)
Q Consensus 300 rLLtL~~La~~-~~~lsy~~Ia~~l~i~~~eVE~~VI~ 336 (474)
|-+.+++.... .+.++..+|++.+++|..-|-..+-.
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~t 41 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQT 41 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 55667776665 56689999999999998776665543
No 108
>KOG0212|consensus
Probab=22.72 E-value=1.1e+03 Score=26.49 Aligned_cols=110 Identities=22% Similarity=0.112 Sum_probs=61.6
Q ss_pred ceeecCChHHHHHHHHHHHHhhccc-cccccccCCchHHHHHHHHhhhhhhcCCChhhHHHHHHHHHHHHhccChHHHHH
Q psy11709 9 PVFIDLLLEDQALELRVYLKNLGAE-ISDEKSTKGIEDDLHKIIGVCDACFQDANEADIESVLNSIVSMLVLINPERAEN 87 (474)
Q Consensus 9 ~~~vd~~~~d~~~El~~yl~~~~~~-~~~~~~~~~~~~~l~ki~~~~~~~~~~~~eke~e~~~nlli~ll~~~~~~~~~~ 87 (474)
|...|.... .+.|+++-+.+.--. ++++... -+=+..+|+++....++...+.-=-++.|-+.++..+.+. +...
T Consensus 298 pc~s~~e~~-~i~~~a~~~n~~l~~l~s~~~~~--~~id~~~ii~vl~~~l~~~~~~tri~~L~Wi~~l~~~~p~-ql~~ 373 (675)
T KOG0212|consen 298 PCLSDTEEM-SIKEYAQMVNGLLLKLVSSERLK--EEIDYGSIIEVLTKYLSDDREETRIAVLNWIILLYHKAPG-QLLV 373 (675)
T ss_pred cCCCCCccc-cHHHHHHHHHHHHHHHHhhhhhc--cccchHHHHHHHHHHhhcchHHHHHHHHHHHHHHHhhCcc-hhhh
Confidence 333443333 677777766533222 2222111 1245678888888777655544447888988888877764 3444
Q ss_pred HHHHHHHHHhcccCCCChhhHHHHHHHHHhccCCC
Q psy11709 88 LILAFSEKLSKASDAKLGPVTLRVLWLLFQSLEPT 122 (474)
Q Consensus 88 ~v~~l~~~l~~~~~~~~~~~~l~~L~~lfn~l~~~ 122 (474)
+...+-..+.++-++......+..|+.+-+.-.+.
T Consensus 374 h~~~if~tLL~tLsd~sd~vvl~~L~lla~i~~s~ 408 (675)
T KOG0212|consen 374 HNDSIFLTLLKTLSDRSDEVVLLALSLLASICSSS 408 (675)
T ss_pred hccHHHHHHHHhhcCchhHHHHHHHHHHHHHhcCc
Confidence 44444455544444545556666666665555443
No 109
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=22.71 E-value=1.2e+02 Score=20.74 Aligned_cols=27 Identities=11% Similarity=0.234 Sum_probs=23.0
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhh
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGK 338 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI 338 (474)
...++.+||+.++++..-|-.|+-++.
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 557999999999999999988876654
No 110
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=22.65 E-value=94 Score=28.80 Aligned_cols=30 Identities=13% Similarity=0.114 Sum_probs=26.3
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||++||+.+++|..-|...+-+|...-
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Rar~~L 155 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 578999999999999999999988877653
No 111
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=22.62 E-value=90 Score=28.85 Aligned_cols=31 Identities=3% Similarity=0.055 Sum_probs=26.5
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
-...||.+||+.+++|..-|...+-+|.+.-
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3578999999999999999998888877543
No 112
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=22.47 E-value=7.1e+02 Score=24.34 Aligned_cols=128 Identities=15% Similarity=0.157 Sum_probs=72.0
Q ss_pred CCChhhHHHHHHhhhhH-HH-HH---HHHHhhccccchhhHHHHHHHHHHHHhcCCCeeecccccCCcccccccc----c
Q psy11709 324 DLNPNQIEAFIIDGKIA-AK-VM---IELLSTYTAENASQAREDAQACILAALADPNTFLLHPLLTLKPVKFLEG----E 394 (474)
Q Consensus 324 ~i~~~eVE~~VI~aI~a-gl-v~---~klL~t~~~~~~~ea~~~a~~li~~Al~~p~vy~F~eLl~~p~v~~L~~----~ 394 (474)
..+..++..||.+.+.. |+ +. ..++....+.|.........+++.-+ +.+. +....|..+-+ .
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~--~~~~------It~e~I~~~~~~~~~~ 181 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYA--PDGK------ITLEDVEEAVSDSARF 181 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhC--CCCC------CCHHHHHHHHhhhhcC
Confidence 34567788888776543 32 11 22222222333334444455554432 1111 23333333322 3
Q ss_pred cHHHHHHHHhhCChhhHHHHHHh------chHhHhhhcCCCHHHHHHHHHHHHHHHhHhcCCCCCHHHHHhhcCCChhh
Q psy11709 395 LIHDLLNIFVSEKVNTYQDFYKQ------HKEYIVNKLGLDHQENLRKMRLLTFMQLAETKTEMSFDMIQKELDLNPNQ 467 (474)
Q Consensus 395 ~l~~LL~iF~~G~~~~y~~~~~~------~~~~~~~~~~l~~~~~~~KirlLtL~~La~~~r~lsy~~Ia~~l~i~~~e 467 (474)
..++++..+..|+....-..... +|-.+ -..+.+.+|.|-.+....+.+. +.++|++.++++...
T Consensus 182 ~if~l~dal~~~~~~~a~~~l~~l~~~~~~~~~i-------l~~l~~~~~~L~~~k~~~~~~~-~~~~i~~~~~~~~~~ 252 (302)
T TIGR01128 182 NVFDLTDALLEGKAARALRILKGLLGEGEEPLIL-------LALLQRQLRLLLQLKRLAQQGG-PLAQLASKLGIWPYR 252 (302)
T ss_pred CHHHHHHHHHCCCHHHHHHHHHHHHHCCCcHHHH-------HHHHHHHHHHHHHHHHHHHcCC-CHHHHHHHcCCCHHH
Confidence 78899999999999765433322 12222 3578899999988876655443 789999999987543
No 113
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=22.38 E-value=91 Score=25.97 Aligned_cols=34 Identities=12% Similarity=0.232 Sum_probs=29.8
Q ss_pred CCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHH
Q psy11709 311 KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVM 344 (474)
Q Consensus 311 ~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~ 344 (474)
+..+|+.+||+.++++...|-..+-+-...|.+.
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 5679999999999999999999888888888655
No 114
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=22.12 E-value=98 Score=28.57 Aligned_cols=30 Identities=20% Similarity=0.206 Sum_probs=26.4
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||.+||+.++++..-|..++-+|++.-
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 185 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKL 185 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 468999999999999999999998887643
No 115
>COG1017 Hmp Hemoglobin-like flavoprotein [Energy production and conversion]
Probab=22.06 E-value=4.6e+02 Score=24.02 Aligned_cols=66 Identities=14% Similarity=0.203 Sum_probs=44.3
Q ss_pred HHHhccCCC-CcchHHHHHHHHHHHHhcCchhHHHhhHHHHHHhhhcCCCCHHH----HHHHHHHHHHHHH
Q psy11709 114 LLFQSLEPT-SPMRYHVYYHLVQIAQNADQIKSVFKDVDHLKQQFSQCPPSNEQ----MQKLLRLLHQALL 179 (474)
Q Consensus 114 ~lfn~l~~~-s~~r~~v~~~il~~a~~~~~~~~l~~~l~~l~~~l~~w~~~~~~----~~~ly~~i~~~~~ 179 (474)
++||.-... ...+-.+..+|+.+|+.-++++.+.+.++.+-.-=.+.++-++. ...++..|.+++.
T Consensus 41 niFN~~nQ~~G~Q~~aLA~ai~ayA~nIdnl~~l~~~v~rIa~KHvsl~I~pEhYpIVge~LL~aI~evlg 111 (150)
T COG1017 41 NIFNMANQKNGDQPKALANAILAYAKNIDNLEALLPVVERIAHKHVSLQIKPEHYPIVGEHLLAAIKEVLG 111 (150)
T ss_pred HHHhHhhhcccccHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHhcCCChhhccHHHHHHHHHHHHHhC
Confidence 677776544 33555667789999999999999999988776666666666553 3344444444443
No 116
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.96 E-value=1.5e+02 Score=29.87 Aligned_cols=30 Identities=3% Similarity=-0.013 Sum_probs=26.3
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||+|||+.+++++.-|...+-+|.+.-
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 186 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQRARATL 186 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 578999999999999999999888877554
No 117
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=21.72 E-value=1e+02 Score=28.71 Aligned_cols=30 Identities=3% Similarity=0.055 Sum_probs=26.6
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||.|||+.|+++..-|...+=+|.+.-
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar~~L 160 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRARQRL 160 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 678999999999999999999988887654
No 118
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=21.55 E-value=1e+02 Score=28.66 Aligned_cols=30 Identities=23% Similarity=0.228 Sum_probs=26.8
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
...||++||+.+++++.-|...+-+|...-
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (188)
T PRK12517 143 GGFSGEEIAEILDLNKNTVMTRLFRARNQL 172 (188)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 578999999999999999999998887654
No 119
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.55 E-value=1e+02 Score=28.14 Aligned_cols=30 Identities=13% Similarity=0.163 Sum_probs=26.4
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
...||.+||+.+++|..-|...+-+|.+.-
T Consensus 146 ~g~s~~eIA~~l~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 146 EGASIKETAAKLSMSEGAVRVALHRGLAAL 175 (184)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 478999999999999999999988887654
No 120
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=21.46 E-value=94 Score=23.34 Aligned_cols=35 Identities=11% Similarity=0.204 Sum_probs=25.3
Q ss_pred hcCCCcChHHHHHhhCCChhhHHHHHHhhhhHHHH
Q psy11709 309 ETKTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKV 343 (474)
Q Consensus 309 ~~~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv 343 (474)
..++..+..+|++.++++...+-.=+=.=.++|+|
T Consensus 20 ~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli 54 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLI 54 (61)
T ss_dssp HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 55899999999999999987766555444455543
No 121
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.43 E-value=98 Score=28.29 Aligned_cols=30 Identities=13% Similarity=0.091 Sum_probs=25.4
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||++||+.+++|..-|...+-+|...-
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~~~L 161 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAALKKL 161 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 567999999999999999998888776543
No 122
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.27 E-value=1e+02 Score=28.27 Aligned_cols=29 Identities=17% Similarity=0.108 Sum_probs=25.0
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
..+||++||+.+++|..-|...+-+|.+.
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGLKA 172 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 56899999999999999999888776654
No 123
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.24 E-value=1e+02 Score=29.63 Aligned_cols=29 Identities=14% Similarity=0.192 Sum_probs=25.7
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
..+||.|||+.++|++.-|...+-+|.+.
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~ 177 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRR 177 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 57899999999999999999998887654
No 124
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=21.20 E-value=1e+02 Score=27.47 Aligned_cols=29 Identities=3% Similarity=0.095 Sum_probs=25.4
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
...||++||+.++++..-|...+-+|.+.
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAIKK 165 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46899999999999999999888877754
No 125
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=21.16 E-value=91 Score=24.28 Aligned_cols=32 Identities=16% Similarity=0.159 Sum_probs=28.5
Q ss_pred CcChHHHHHhhCCChhhHHHHHHhhhhHHHHH
Q psy11709 313 EMSFDMIQKELDLNPNQIEAFIIDGKIAAKVM 344 (474)
Q Consensus 313 ~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~ 344 (474)
.++=.+||++++++...|...+.+-.+.|+|.
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 49999999999999999999998888888664
No 126
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.97 E-value=1.1e+02 Score=28.35 Aligned_cols=28 Identities=7% Similarity=0.001 Sum_probs=23.9
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhh
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKI 339 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ 339 (474)
..+||+|||+.+++|..-|...+-.|.+
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar~ 172 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARARD 172 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5789999999999999988888766654
No 127
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=20.92 E-value=98 Score=28.19 Aligned_cols=72 Identities=13% Similarity=0.021 Sum_probs=49.9
Q ss_pred HHHHHHhhhc-CCCcChHHHHHhhCCChhhHHHHHHhhhhHHHHHHHHHhhccccch-----hhHHHHHHHHHHHHhcCC
Q psy11709 301 LLTFMQLAET-KTEMSFDMIQKELDLNPNQIEAFIIDGKIAAKVMIELLSTYTAENA-----SQAREDAQACILAALADP 374 (474)
Q Consensus 301 LLtL~~La~~-~~~lsy~~Ia~~l~i~~~eVE~~VI~aI~aglv~~klL~t~~~~~~-----~ea~~~a~~li~~Al~~p 374 (474)
+-+|+-||.. ++.++-.+||+..+||..=++..+-.-.++|+|. +...... ....++...=|..|+.++
T Consensus 11 lr~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~-----S~rG~~GGy~La~~p~eItl~dIi~aveg~ 85 (153)
T PRK11920 11 IRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVE-----TVRGRNGGVRLGRPAADISLFDVVRVTEDS 85 (153)
T ss_pred HHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE-----eecCCCCCeeecCCHHHCcHHHHHHHHcCC
Confidence 4456666654 5568999999999999999999999999999766 2222111 134455566677788776
Q ss_pred Cee
Q psy11709 375 NTF 377 (474)
Q Consensus 375 ~vy 377 (474)
..+
T Consensus 86 ~~~ 88 (153)
T PRK11920 86 FSM 88 (153)
T ss_pred Cce
Confidence 443
No 128
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=20.68 E-value=1.1e+02 Score=27.94 Aligned_cols=29 Identities=17% Similarity=0.293 Sum_probs=24.9
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
...+|++||+.++++.+-|...+-+|.+.
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 56899999999999999998888776654
No 129
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=20.48 E-value=1.1e+02 Score=28.36 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=25.5
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
..+||++||+.+++|..-|...+-+|.+.
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRARLS 174 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 57899999999999999999888877654
No 130
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=20.48 E-value=89 Score=26.10 Aligned_cols=37 Identities=16% Similarity=0.384 Sum_probs=26.2
Q ss_pred HHHHHHHHHHh-HhcCCCCCHHHHHhhcCCChhhhhhh
Q psy11709 435 RKMRLLTFMQL-AETKTEMSFDMIQKELDLNPNQIEAF 471 (474)
Q Consensus 435 ~KirlLtL~~L-a~~~r~lsy~~Ia~~l~i~~~eVE~l 471 (474)
.+-++|.++.- +....=++.++|++.|+++.++|+.-
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~a 85 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKA 85 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHH
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHH
Confidence 35567777777 55567799999999999999877653
No 131
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=20.37 E-value=1.1e+02 Score=28.24 Aligned_cols=30 Identities=7% Similarity=0.041 Sum_probs=26.7
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
..+||++||+.++++..-|...+-+|.+.-
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr~~L 155 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRARSKL 155 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 678999999999999999999988887654
No 132
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=20.30 E-value=1.1e+02 Score=26.80 Aligned_cols=29 Identities=17% Similarity=0.349 Sum_probs=24.5
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
..+||++||+.+|+|+.-|...+=+|...
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKE 148 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 57899999999999999988887776543
No 133
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=20.15 E-value=1.1e+02 Score=27.48 Aligned_cols=29 Identities=3% Similarity=0.202 Sum_probs=25.1
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIA 340 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~a 340 (474)
..+||.+||+.++||..-|...+-+|...
T Consensus 134 ~g~s~~eiA~~lgis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45899999999999999999888777654
No 134
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=20.00 E-value=1.5e+02 Score=23.19 Aligned_cols=30 Identities=13% Similarity=0.272 Sum_probs=25.4
Q ss_pred CCcChHHHHHhhCCChhhHHHHHHhhhhHH
Q psy11709 312 TEMSFDMIQKELDLNPNQIEAFIIDGKIAA 341 (474)
Q Consensus 312 ~~lsy~~Ia~~l~i~~~eVE~~VI~aI~ag 341 (474)
.-.+|-+||+.++|...|+-....++-.|.
T Consensus 12 ~g~~FveIAr~~~i~a~e~a~~w~~Ve~Ak 41 (63)
T PF11242_consen 12 SGLSFVEIARKIGITAKEVAKAWAEVETAK 41 (63)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 346999999999999999988887776665
Done!