Query 015104
Match_columns 413
No_of_seqs 234 out of 651
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 03:09:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015104.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015104hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2753 Uncharacterized conser 100.0 1E-70 2.2E-75 526.3 21.3 368 6-392 1-373 (378)
2 KOG2908 26S proteasome regulat 100.0 7.7E-64 1.7E-68 481.4 14.0 359 14-393 2-373 (380)
3 KOG3250 COP9 signalosome, subu 99.8 1.1E-21 2.4E-26 178.7 7.4 161 224-393 27-189 (258)
4 KOG0687 26S proteasome regulat 99.6 8.5E-16 1.8E-20 148.7 10.6 244 118-375 123-375 (393)
5 PF01399 PCI: PCI domain; Int 99.6 6E-16 1.3E-20 128.0 3.2 102 257-359 1-105 (105)
6 smart00088 PINT motif in prote 99.5 7.3E-15 1.6E-19 118.8 4.4 86 292-380 3-88 (88)
7 smart00753 PAM PCI/PINT associ 99.5 7.3E-15 1.6E-19 118.8 4.4 86 292-380 3-88 (88)
8 COG5187 RPN7 26S proteasome re 99.4 3.4E-13 7.4E-18 129.1 10.3 222 133-363 149-380 (412)
9 KOG1464 COP9 signalosome, subu 99.0 6.6E-10 1.4E-14 106.2 8.4 189 192-393 245-437 (440)
10 KOG2581 26S proteasome regulat 98.7 5.6E-08 1.2E-12 97.2 8.9 163 176-356 248-420 (493)
11 KOG0686 COP9 signalosome, subu 97.9 3.5E-05 7.6E-10 77.6 8.8 242 135-384 186-441 (466)
12 KOG1498 26S proteasome regulat 97.7 8.7E-05 1.9E-09 74.5 7.7 201 174-397 209-426 (439)
13 KOG2688 Transcription-associat 97.6 6.9E-05 1.5E-09 76.0 5.5 187 160-363 190-388 (394)
14 KOG1463 26S proteasome regulat 97.3 0.0017 3.7E-08 64.4 10.7 185 171-360 203-391 (411)
15 KOG1497 COP9 signalosome, subu 97.3 0.0016 3.5E-08 64.0 9.5 163 217-393 222-389 (399)
16 COG5600 Transcription-associat 97.1 0.0011 2.5E-08 66.4 6.5 179 172-365 217-409 (413)
17 PF10602 RPN7: 26S proteasome 96.2 0.0097 2.1E-07 54.5 6.1 110 118-235 55-170 (177)
18 COG5159 RPN6 26S proteasome re 95.8 0.09 1.9E-06 51.5 10.6 160 192-359 220-388 (421)
19 KOG2582 COP9 signalosome, subu 95.2 1.1 2.4E-05 45.3 16.2 315 35-372 22-373 (422)
20 COG5071 RPN5 26S proteasome re 94.7 0.029 6.3E-07 55.1 3.6 86 296-397 341-426 (439)
21 KOG2758 Translation initiation 93.6 0.062 1.3E-06 53.3 3.4 71 292-363 328-398 (432)
22 KOG1076 Translation initiation 90.5 0.32 6.9E-06 52.7 4.5 123 241-363 637-767 (843)
23 PF10075 PCI_Csn8: COP9 signal 88.0 0.36 7.7E-06 42.4 2.4 81 254-338 39-121 (143)
24 PF09012 FeoC: FeoC like trans 86.6 0.18 3.9E-06 38.7 -0.4 35 312-346 12-46 (69)
25 KOG2072 Translation initiation 84.3 6 0.00013 44.0 9.6 244 146-392 242-536 (988)
26 PF03399 SAC3_GANP: SAC3/GANP/ 82.5 2.2 4.7E-05 39.3 4.9 160 158-325 37-203 (204)
27 PF14938 SNAP: Soluble NSF att 81.4 10 0.00022 37.0 9.4 142 134-281 112-260 (282)
28 PF09756 DDRGK: DDRGK domain; 77.2 0.88 1.9E-05 42.2 0.4 59 300-359 100-158 (188)
29 PF02082 Rrf2: Transcriptional 77.0 2 4.2E-05 34.0 2.3 58 299-359 11-69 (83)
30 PF09339 HTH_IclR: IclR helix- 72.0 2.1 4.6E-05 30.6 1.3 46 300-345 4-49 (52)
31 COG3355 Predicted transcriptio 65.8 14 0.00031 32.0 5.2 78 312-393 40-120 (126)
32 PF08281 Sigma70_r4_2: Sigma-7 63.5 3.8 8.3E-05 29.3 1.2 28 313-340 25-52 (54)
33 PRK11179 DNA-binding transcrip 63.3 3.3 7.1E-05 36.7 0.9 35 312-346 21-55 (153)
34 TIGR02010 IscR iron-sulfur clu 62.9 6.2 0.00013 34.2 2.6 47 300-346 10-57 (135)
35 TIGR02944 suf_reg_Xantho FeS a 61.7 5.3 0.00011 34.2 1.9 36 312-347 23-58 (130)
36 PRK11920 rirA iron-responsive 60.6 5.4 0.00012 35.6 1.8 46 302-347 12-57 (153)
37 KOG3054 Uncharacterized conser 57.8 6.4 0.00014 37.7 1.8 47 312-358 212-258 (299)
38 PRK10857 DNA-binding transcrip 56.9 8.6 0.00019 34.7 2.5 49 298-346 8-57 (164)
39 KOG1861 Leucine permease trans 56.1 16 0.00034 38.4 4.5 169 151-329 322-493 (540)
40 PF09202 Rio2_N: Rio2, N-termi 55.3 9.5 0.00021 30.5 2.2 53 297-349 7-59 (82)
41 PF05369 MtmB: Monomethylamine 55.0 15 0.00032 38.0 4.0 69 17-108 382-451 (457)
42 COG1522 Lrp Transcriptional re 52.6 6 0.00013 34.5 0.7 40 313-352 21-60 (154)
43 PRK11169 leucine-responsive tr 52.6 9.1 0.0002 34.3 1.9 35 312-346 26-60 (164)
44 PF13730 HTH_36: Helix-turn-he 52.5 16 0.00035 26.1 2.9 48 297-344 7-55 (55)
45 smart00344 HTH_ASNC helix_turn 52.4 6.4 0.00014 32.3 0.9 35 312-346 15-49 (108)
46 smart00346 HTH_ICLR helix_turn 52.0 8.7 0.00019 30.2 1.6 48 300-347 6-53 (91)
47 smart00347 HTH_MARR helix_turn 51.6 20 0.00044 28.1 3.7 43 313-355 23-65 (101)
48 TIGR00738 rrf2_super rrf2 fami 50.1 14 0.0003 31.5 2.6 35 312-346 23-57 (132)
49 PF04545 Sigma70_r4: Sigma-70, 47.4 13 0.00028 26.2 1.7 28 313-340 19-46 (50)
50 smart00550 Zalpha Z-DNA-bindin 46.0 9.6 0.00021 29.0 0.9 33 314-346 22-54 (68)
51 PF01022 HTH_5: Bacterial regu 44.8 21 0.00045 24.9 2.4 33 313-345 14-46 (47)
52 PF08784 RPA_C: Replication pr 44.0 19 0.00042 29.4 2.4 52 298-350 49-101 (102)
53 PF13412 HTH_24: Winged helix- 43.7 16 0.00034 25.4 1.6 34 312-345 15-48 (48)
54 PRK10870 transcriptional repre 43.5 49 0.0011 30.0 5.3 52 312-363 69-120 (176)
55 PRK14165 winged helix-turn-hel 42.9 30 0.00064 32.9 3.8 48 312-359 19-66 (217)
56 PF13404 HTH_AsnC-type: AsnC-t 42.8 5.1 0.00011 27.7 -1.0 22 312-333 15-36 (42)
57 PRK10141 DNA-binding transcrip 42.7 24 0.00051 30.1 2.8 77 313-396 29-105 (117)
58 COG1959 Predicted transcriptio 42.5 21 0.00045 31.7 2.6 47 301-347 11-58 (150)
59 PF10668 Phage_terminase: Phag 41.7 13 0.00029 27.9 1.0 24 312-335 20-43 (60)
60 PRK03573 transcriptional regul 41.1 46 0.001 28.7 4.6 50 314-363 46-95 (144)
61 cd04761 HTH_MerR-SF Helix-Turn 38.7 30 0.00064 23.7 2.4 47 315-374 1-47 (49)
62 PF01978 TrmB: Sugar-specific 38.6 15 0.00033 27.6 0.9 37 312-348 20-56 (68)
63 PF09218 DUF1959: Domain of un 38.5 33 0.00071 29.3 3.0 41 318-384 17-57 (117)
64 TIGR02337 HpaR homoprotocatech 37.9 54 0.0012 27.2 4.4 50 312-361 40-89 (118)
65 TIGR03879 near_KaiC_dom probab 37.2 15 0.00032 28.8 0.7 31 313-343 31-61 (73)
66 PF08220 HTH_DeoR: DeoR-like h 36.4 16 0.00034 26.8 0.7 40 303-343 4-43 (57)
67 cd00090 HTH_ARSR Arsenical Res 34.7 36 0.00079 24.7 2.5 36 315-350 21-56 (78)
68 PF12840 HTH_20: Helix-turn-he 34.1 25 0.00055 25.8 1.5 35 312-346 22-56 (61)
69 PRK12537 RNA polymerase sigma 33.6 24 0.00053 31.6 1.6 28 313-340 148-175 (182)
70 smart00418 HTH_ARSR helix_turn 32.6 50 0.0011 23.2 2.9 35 313-347 9-43 (66)
71 PF12802 MarR_2: MarR family; 31.9 24 0.00051 25.6 1.0 40 313-352 20-59 (62)
72 cd00092 HTH_CRP helix_turn_hel 31.7 33 0.00072 25.0 1.8 35 312-346 23-57 (67)
73 PF01325 Fe_dep_repress: Iron 31.6 26 0.00057 26.0 1.2 44 301-345 10-53 (60)
74 PF07106 TBPIP: Tat binding pr 31.3 99 0.0021 27.7 5.2 80 311-393 13-97 (169)
75 PF13601 HTH_34: Winged helix 31.0 27 0.00059 27.5 1.3 41 313-353 13-53 (80)
76 COG1595 RpoE DNA-directed RNA 30.9 27 0.00058 31.4 1.4 30 312-341 141-170 (182)
77 smart00419 HTH_CRP helix_turn_ 28.5 36 0.00078 23.0 1.4 32 314-345 8-39 (48)
78 PF14938 SNAP: Soluble NSF att 28.3 3.8E+02 0.0083 25.8 9.2 123 133-266 152-277 (282)
79 PRK11014 transcriptional repre 28.1 50 0.0011 28.6 2.6 36 312-347 23-58 (141)
80 PRK09191 two-component respons 28.0 1.9E+02 0.0042 26.8 6.9 29 313-341 103-131 (261)
81 PF04539 Sigma70_r3: Sigma-70 27.8 29 0.00063 26.6 1.0 27 312-338 18-44 (78)
82 PF14964 DUF4507: Domain of un 27.8 6.8E+02 0.015 25.7 11.6 122 33-172 15-142 (362)
83 PRK06759 RNA polymerase factor 27.4 34 0.00073 29.5 1.4 28 313-340 121-148 (154)
84 TIGR02999 Sig-70_X6 RNA polyme 27.4 34 0.00073 30.5 1.4 28 313-340 149-176 (183)
85 smart00345 HTH_GNTR helix_turn 27.4 70 0.0015 22.4 2.9 33 313-345 18-51 (60)
86 PF13424 TPR_12: Tetratricopep 27.3 83 0.0018 23.5 3.5 63 143-206 12-74 (78)
87 TIGR02431 pcaR_pcaU beta-ketoa 27.3 41 0.00089 32.0 2.1 46 300-345 10-55 (248)
88 PF10255 Paf67: RNA polymerase 27.0 2.2E+02 0.0047 29.7 7.4 187 139-336 122-343 (404)
89 PRK09642 RNA polymerase sigma 26.8 35 0.00077 29.7 1.4 28 313-340 121-148 (160)
90 PRK12523 RNA polymerase sigma 26.7 35 0.00076 30.3 1.4 28 313-340 134-161 (172)
91 PRK04214 rbn ribonuclease BN/u 26.6 80 0.0017 32.7 4.2 76 311-393 307-391 (412)
92 PF13384 HTH_23: Homeodomain-l 26.4 28 0.0006 24.2 0.5 29 314-342 17-45 (50)
93 TIGR02983 SigE-fam_strep RNA p 26.3 37 0.0008 29.6 1.5 27 314-340 126-152 (162)
94 PF03979 Sigma70_r1_1: Sigma-7 26.3 21 0.00045 28.3 -0.2 38 304-342 12-52 (82)
95 PF13463 HTH_27: Winged helix 26.2 73 0.0016 23.3 2.9 41 312-352 16-56 (68)
96 PRK09651 RNA polymerase sigma 26.1 37 0.0008 30.2 1.4 29 313-341 134-162 (172)
97 PRK12529 RNA polymerase sigma 25.6 38 0.00082 30.4 1.4 28 313-340 142-169 (178)
98 PRK09047 RNA polymerase factor 25.3 39 0.00084 29.3 1.4 28 313-340 121-148 (161)
99 PRK12514 RNA polymerase sigma 25.3 42 0.00091 29.9 1.6 27 314-340 145-171 (179)
100 PF07389 DUF1500: Protein of u 25.2 44 0.00096 27.0 1.5 30 313-344 47-77 (100)
101 smart00421 HTH_LUXR helix_turn 24.9 44 0.00096 23.0 1.4 25 315-339 19-43 (58)
102 PF04967 HTH_10: HTH DNA bindi 24.8 50 0.0011 24.1 1.6 29 312-340 21-49 (53)
103 PRK09954 putative kinase; Prov 24.7 34 0.00073 34.4 1.0 37 312-348 15-51 (362)
104 PF10007 DUF2250: Uncharacteri 24.5 39 0.00085 27.6 1.2 27 319-345 26-52 (92)
105 PF14947 HTH_45: Winged helix- 24.5 64 0.0014 25.0 2.4 42 313-358 18-59 (77)
106 PRK09638 RNA polymerase sigma 24.4 37 0.00081 30.0 1.1 28 314-341 142-169 (176)
107 smart00422 HTH_MERR helix_turn 24.4 75 0.0016 23.4 2.7 47 315-373 1-47 (70)
108 PF05331 DUF742: Protein of un 24.3 50 0.0011 28.1 1.8 40 304-346 48-87 (114)
109 KOG3252 Uncharacterized conser 24.2 5.9E+02 0.013 23.8 9.5 94 254-359 96-190 (217)
110 TIGR02947 SigH_actino RNA poly 24.0 43 0.00094 30.2 1.5 28 313-340 146-173 (193)
111 PF04510 DUF577: Family of unk 23.6 1.4E+02 0.003 27.4 4.6 52 48-108 39-90 (174)
112 PRK07037 extracytoplasmic-func 23.4 44 0.00095 29.1 1.4 35 313-349 124-158 (163)
113 PRK10163 DNA-binding transcrip 23.1 49 0.0011 32.1 1.7 57 300-358 26-82 (271)
114 PRK15090 DNA-binding transcrip 23.1 54 0.0012 31.4 2.1 46 300-346 15-60 (257)
115 PRK12522 RNA polymerase sigma 23.1 47 0.001 29.4 1.5 28 313-340 134-161 (173)
116 PRK15431 ferrous iron transpor 23.0 38 0.00082 26.9 0.8 34 312-345 14-47 (78)
117 PF08221 HTH_9: RNA polymerase 22.9 46 0.001 24.9 1.2 34 312-345 25-58 (62)
118 PF10771 DUF2582: Protein of u 22.9 87 0.0019 23.9 2.7 44 312-357 20-63 (65)
119 PRK12547 RNA polymerase sigma 22.9 46 0.001 29.2 1.4 28 313-340 127-154 (164)
120 PHA02763 hypothetical protein; 22.7 81 0.0018 25.5 2.6 50 314-365 52-102 (102)
121 TIGR03643 conserved hypothetic 22.7 40 0.00087 26.2 0.8 32 304-337 5-36 (72)
122 cd07377 WHTH_GntR Winged helix 22.7 1.2E+02 0.0025 21.7 3.4 33 313-345 23-56 (66)
123 PRK12520 RNA polymerase sigma 22.6 47 0.001 30.0 1.4 27 314-340 147-173 (191)
124 PRK12530 RNA polymerase sigma 22.3 48 0.001 30.0 1.4 28 313-340 149-176 (189)
125 PRK12527 RNA polymerase sigma 22.2 49 0.0011 28.8 1.4 35 313-349 120-154 (159)
126 PRK12513 RNA polymerase sigma 22.2 49 0.0011 29.9 1.4 28 313-340 154-181 (194)
127 PF13542 HTH_Tnp_ISL3: Helix-t 22.1 49 0.0011 23.1 1.2 24 315-338 28-51 (52)
128 cd06170 LuxR_C_like C-terminal 21.9 55 0.0012 22.6 1.4 26 314-339 15-40 (57)
129 PRK09645 RNA polymerase sigma 21.8 51 0.0011 29.0 1.5 28 313-340 133-160 (173)
130 PRK12525 RNA polymerase sigma 21.4 51 0.0011 29.1 1.4 28 313-340 133-160 (168)
131 PRK08301 sporulation sigma fac 21.2 55 0.0012 30.7 1.6 28 313-340 197-224 (234)
132 smart00420 HTH_DEOR helix_turn 20.9 44 0.00096 22.8 0.7 33 313-345 13-45 (53)
133 PRK11569 transcriptional repre 20.9 56 0.0012 31.7 1.7 46 300-345 29-74 (274)
134 PRK12511 RNA polymerase sigma 20.8 55 0.0012 29.6 1.5 51 313-367 126-176 (182)
135 PF10985 DUF2805: Protein of u 20.5 47 0.001 25.9 0.8 31 304-336 4-34 (73)
136 PF13518 HTH_28: Helix-turn-he 20.5 61 0.0013 22.4 1.4 33 316-349 14-46 (52)
No 1
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=100.00 E-value=1e-70 Score=526.28 Aligned_cols=368 Identities=42% Similarity=0.720 Sum_probs=337.3
Q ss_pred CCCCCCcceeeeeecccccccccCCcchhHHHHHHHHHHHhhhhhhhhhhHHHH-HhhhhhhhhccCCCCcchhheeeeh
Q 015104 6 PTSEEDPALAVVRFTSELAWADAGPEAAEEQVNRLCLEAQESMVMGRWMDLASL-MLTSADLMFSKVSDKDLECIFTVIC 84 (413)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~e~~~~~~~~e~l~~~klw~qLt~~-l~~~~~~~~~~~~dke~e~~~n~i~ 84 (413)
+||+|+|+++..+|..+++|.++|+..+++|.. .+..+ .|.+++.. +++.|+.+++. |+|++||++|+|+
T Consensus 1 ~~~~e~P~f~dis~~~Ql~elr~yl~~~eaeis---~e~~~-----kgl~~~l~~ii~~c~v~~k~-~ekdle~vlnsi~ 71 (378)
T KOG2753|consen 1 PTSEEVPVFADISFEEQLAELRAYLKKLEAEIS---EEASE-----KGLEEDLLMIIEACDVLAKI-PEKDLECVLNSIV 71 (378)
T ss_pred CCCccCceEEEecHHHHHHHHHHHHhhcCcccc---hhhhc-----cCHHHHHHHHHHHhHHhhcC-CcchHHHHHHHHH
Confidence 689999999999999999999999999999888 22222 46555555 44547776655 9999999999999
Q ss_pred hcccCCCChhHHHHHHHHHHhhhhcCCCCC-cchhHHHHHHHhhhhcCc-chhhHHHHHHHhHhhcCccccccccchhch
Q 015104 85 NLVTKPESLDEVHEMTKLISGKIIQQPNDK-PAMRLKILFNLYNLLENP-YSRFFVYMKALNLAVNGKVTEHIIPSFKKI 162 (413)
Q Consensus 85 ~lv~~~~~~~~~l~~v~~l~~~~~~~~~~~-~~~~l~~L~~Lfn~l~~~-~~r~~v~~~il~~a~~~~~~~~~~~~l~~~ 162 (413)
+++...+ +++..++++.+|+++.+++++. +.+||++|++|||.++.+ +.|+.||++++++|..++.+..+.+.++.+
T Consensus 72 sLi~~~~-~e~~e~~v~a~~ekva~q~n~~~~~l~L~vLsnLfn~~d~~~~aR~~Vy~~lv~la~~~~~~~~i~~~lk~~ 150 (378)
T KOG2753|consen 72 SLIKNAP-PEKVEEMVKAICEKVAKQPNDKTASLRLQVLSNLFNGVDKPTPARYQVYMSLVTLAASCKLIEYIVPNLKQL 150 (378)
T ss_pred HHHHhCC-HHHhHHHHHHHHHHHhcCccCCCcccHHHHHHHHHhccCCCchHHHHHHHHHHHHHhhcceeeeecccHHHH
Confidence 9998875 9999999999999999988765 779999999999999875 589999999999999999999999999999
Q ss_pred HHHHhhhccCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCCccchhhHHHHHHHHHHHhhhcCCCccccc-c
Q 015104 163 DSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQCD-L 241 (413)
Q Consensus 163 ~~~L~~w~~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii~aL~~~~i~~fe-L 241 (413)
++|+++|+++.+.+|.+|++++++++.++. .+++.+++..||+||+.+++ ++|++.|.+|++.|+.+|++|.|| |
T Consensus 151 ~~~lkew~~~vedqrel~r~v~~al~~~k~-~~~s~kvmt~lLgtyt~dna---s~AredA~rcV~~av~dP~~F~fD~L 226 (378)
T KOG2753|consen 151 DDWLKEWNISVEDQRELLRAVHKALKDNKS-VDESSKVMTELLGTYTEDNA---SEAREDAMRCVVEAVKDPKIFLFDHL 226 (378)
T ss_pred HHHHHhCCCCHHHHHHHHHHHHHHHHhcch-hhhHHHHHHHHHHHhcccch---hHHHHHHHHHHHHHHcCCceeccchh
Confidence 999999999999999999999999998754 78999999999999999875 578999999999999999999996 9
Q ss_pred CCCccccccccchhhhHHHHHHHHHHHhhcccchhccccchhhhhhcCCcchhHHhhhhhhhhhccCCCCCCCcchhhhh
Q 015104 242 LDMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIK 321 (413)
Q Consensus 242 L~~p~v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~l~~~~~~~KirLLaL~~L~~~~~r~isy~~Ia 321 (413)
+.+|+|++|+++ .+|+||.||.+|.+++|.+|.+.|++|+.++|++|+.+.+||||||||+||.. +++|||++|+
T Consensus 227 l~L~pV~qLE~d----~i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KMRLLTlm~LA~e-s~eisy~~l~ 301 (378)
T KOG2753|consen 227 LTLPPVKQLEGD----LIHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKMRLLTLMSLAEE-SNEISYDTLA 301 (378)
T ss_pred ccCchHHHhccc----hHHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHHHHHHHHHHhcc-CCCCCHHHHH
Confidence 999999999986 49999999999999999999999999999999999999999999999999996 8999999999
Q ss_pred hccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHHhhhhhh-hhhHHHHHHHhh
Q 015104 322 DTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLRTKLSTW-RANVANVISTIQ 392 (413)
Q Consensus 322 ~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~~rL~~W-~~~v~~~~~~v~ 392 (413)
++|+|.+||||.|||+||++|+|+|||||++++|+|+++++|+||++||+.|+++|..| ++++.++.+...
T Consensus 302 k~LqI~edeVE~fVIdaI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~kL~aw~k~~~stv~~~l~ 373 (378)
T KOG2753|consen 302 KELQINEDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRDKLAAWGKQNLSTVRENLQ 373 (378)
T ss_pred HHhccCHHHHHHHHHHHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHHHHHHHHHhhhhHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999 666666655544
No 2
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.7e-64 Score=481.42 Aligned_cols=359 Identities=16% Similarity=0.213 Sum_probs=309.7
Q ss_pred eeeeeecccccccccCCcchhHHHHHHHHHHHhhhhhhhhhhHHHHHhhh-hhhhhccCCCCcchhheeeehhcccCCCC
Q 015104 14 LAVVRFTSELAWADAGPEAAEEQVNRLCLEAQESMVMGRWMDLASLMLTS-ADLMFSKVSDKDLECIFTVICNLVTKPES 92 (413)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~a~~e~~~~~~~~e~l~~~klw~qLt~~l~~~-~~~~~~~~~dke~e~~~n~i~~lv~~~~~ 92 (413)
..+++|+.+++.. |+|++++.|..+|+||++|+|||||.++..+ .+++|..+| .+-.+|..| +..++.
T Consensus 2 ~~~~~~L~~~~~~------a~~~l~~ew~~leeLy~eKLW~QLt~~l~~fvd~~~f~~~~--~~l~lY~NF---vsefe~ 70 (380)
T KOG2908|consen 2 MNAPDYLQTQLKS------ANPSLAAEWDRLEELYEEKLWHQLTLALVDFVDDPPFQAGD--LLLQLYLNF---VSEFET 70 (380)
T ss_pred CcHHHHHHHHHhh------cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccch--HHHHHHHHH---HHHHhh
Confidence 4578999999988 8999999999999999999999999999887 666676533 445566665 346666
Q ss_pred hhHHHHHHHHHHhhhhcCCCCCcchhHHHHHHHhhhhcC-cchhhHHHHHHHhHhh---cCccccccccchhchHHHHhh
Q 015104 93 LDEVHEMTKLISGKIIQQPNDKPAMRLKILFNLYNLLEN-PYSRFFVYMKALNLAV---NGKVTEHIIPSFKKIDSFLKE 168 (413)
Q Consensus 93 ~~~~l~~v~~l~~~~~~~~~~~~~~~l~~L~~Lfn~l~~-~~~r~~v~~~il~~a~---~~~~~~~~~~~l~~~~~~L~~ 168 (413)
..|.+++|+ ++..+.++. .+....+++|..+-+.+.. +.+.+.+| -..+.|+ .-||+..+++.|++.++.|++
T Consensus 71 kINplslve-i~l~~~~~~-~D~~~al~~Le~i~~~~~~~~e~~av~~-~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~ 147 (380)
T KOG2908|consen 71 KINPLSLVE-ILLVVSEQI-SDKDEALEFLEKIIEKLKEYKEPDAVIY-ILTEIARLKLEINDLKEIKKLLDDLKSMLDS 147 (380)
T ss_pred ccChHHHHH-HHHHHHHHh-ccHHHHHHHHHHHHHHHHhhccchhHHH-HHHHHHHHHHhcccHHHHHHHHHHHHHHHhc
Confidence 678999998 444555543 4678999999999998864 23333333 3333333 458999999999999999998
Q ss_pred hc-cCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCCccchhhHHHHHHHHHHHhhhcCCCcccc-ccCCCcc
Q 015104 169 WN-IDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQC-DLLDMPA 246 (413)
Q Consensus 169 w~-~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii~aL~~~~i~~f-eLL~~p~ 246 (413)
.+ +++.+|..||+..+.||+. .|+++.||+.+|+||+|.+.++++ .++.++.|++++++||+|+++||| |||.||+
T Consensus 148 ~~~v~~~Vh~~fY~lssqYyk~-~~d~a~yYr~~L~YL~~~d~~~l~-~se~~~lA~~L~~aALLGe~iyNfGELL~HPi 225 (380)
T KOG2908|consen 148 LDGVTSNVHSSFYSLSSQYYKK-IGDFASYYRHALLYLGCSDIDDLS-ESEKQDLAFDLSLAALLGENIYNFGELLAHPI 225 (380)
T ss_pred ccCCChhhhhhHHHHHHHHHHH-HHhHHHHHHHHHHHhccccccccC-HHHHHHHHHHHHHHHHhccccccHHHHHhhHH
Confidence 77 6666999999999999998 689999999999999999988874 578889999999999999999999 9999999
Q ss_pred ccccccchhhhHHHHHHHHHHHhhcccchhccccc---hhhhhhcCCcchhHHhhhhhhhhhccCCC---CCCCcchhhh
Q 015104 247 IGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGN---SALLKSYGLVHEDCIAKMRLMSLVDLGSN---ESGQIPYGLI 320 (413)
Q Consensus 247 v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~---~~~l~~~~l~~~~~~~KirLLaL~~L~~~---~~r~isy~~I 320 (413)
+.+|+|+ ++.||+++|.+|+.||+..|++....+ |++-+ +...+.+|||||||+++||. +.|.+||++|
T Consensus 226 lesL~gT-~~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~----~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~I 300 (380)
T KOG2908|consen 226 LESLKGT-NREWLKDLLIAFNSGDLKRFESLKGVWGKQPDLAS----NEDFLLQKIRLLALIEITFSRPANERTLSFKEI 300 (380)
T ss_pred HHHhcCC-cHHHHHHHHHHhccCCHHHHHHHHHHhccCchHHH----HHHHHHHHHHHHHHHHHHhcCcchhccccHHHH
Confidence 9999996 899999999999999999999987543 44433 25577899999999999996 5799999999
Q ss_pred hhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHHhhhhhhhhhHHHHHHHhhh
Q 015104 321 KDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLRTKLSTWRANVANVISTIQA 393 (413)
Q Consensus 321 a~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~~rL~~W~~~v~~~~~~v~~ 393 (413)
|++++||.++||++||||++.|||+|.||||+|+|+++|||||+++++|+..|++|++.|+++|+++...|++
T Consensus 301 a~~tkip~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~ 373 (380)
T KOG2908|consen 301 AEATKIPNKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEH 373 (380)
T ss_pred HHHhCCCHHHHHHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999997
No 3
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.85 E-value=1.1e-21 Score=178.68 Aligned_cols=161 Identities=23% Similarity=0.335 Sum_probs=143.6
Q ss_pred HHHHHhhhcCCCcccc-ccCCCccccccccchhhhHHHHHHHHHHHhhcccchhccccchhhhhhcCCcchhHHhhhhhh
Q 015104 224 VRTIIEFVKSPDMFQC-DLLDMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLM 302 (413)
Q Consensus 224 ~~lii~aL~~~~i~~f-eLL~~p~v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~l~~~~~~~KirLL 302 (413)
-.+|..|+.+|++|.| ||+.+|.|.+|.++ .++.+++||.+|++|+|.+|..-... ++-.....+-|++-+
T Consensus 27 ~~lIsqale~P~vf~F~ELl~l~nv~qlae~-~dsa~lrlL~lFa~Gt~~Dy~aea~r-------lp~Ls~~q~~kLk~l 98 (258)
T KOG3250|consen 27 EELISQALEAPGVFVFGELLILPNVVQLAEP-IDSAYLRLLELFAYGTYRDYSAEALR-------LPKLSLAQLNKLKHL 98 (258)
T ss_pred HHHHHHHhcCCCeeeHHHHHhhhhHHHHccc-ccHHHHHHHHHHhcCchhhhhhhhhc-------CCCCCHHHHHhhhcc
Confidence 4567889999999999 99999999999874 78899999999999999999753211 111245567899999
Q ss_pred hhhccCCCCCCCcchhhhhhccccCc-chhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHHhhhhhhh
Q 015104 303 SLVDLGSNESGQIPYGLIKDTLQINN-DEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLRTKLSTWR 381 (413)
Q Consensus 303 aL~~L~~~~~r~isy~~Ia~~l~i~~-~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~~rL~~W~ 381 (413)
+..++++. .+.|+|..+.+.+.+.. -++|++||.|+.++++.|||||.+|+++|.|+..|.+.+.++.+|.-.|++|+
T Consensus 99 tV~slas~-~k~lpy~~Ll~~l~~~nvrelEd~iieamya~IlrGkldqr~q~leV~faigRdlr~k~i~nm~~TL~~w~ 177 (258)
T KOG3250|consen 99 TVVSLASF-EKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILRGKLDQRNQTLEVDFAIGRDLRSKDIDNMKYTLDEWC 177 (258)
T ss_pred eehhhhhh-chhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHHhhHHhhcceEeechhhcccccHhHHHHHHHHHHHHH
Confidence 99999987 68999999999998864 79999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHhhh
Q 015104 382 ANVANVISTIQA 393 (413)
Q Consensus 382 ~~v~~~~~~v~~ 393 (413)
+.+.+++-.|++
T Consensus 178 ~~cenvL~~ie~ 189 (258)
T KOG3250|consen 178 EGCENVLFGIEA 189 (258)
T ss_pred HHHHHHHHHHHh
Confidence 999999999875
No 4
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=99.64 E-value=8.5e-16 Score=148.66 Aligned_cols=244 Identities=17% Similarity=0.226 Sum_probs=192.0
Q ss_pred hHHHHHHHhhhhcCcchhhHHHHHHHhHhhcCccccccccchhchHHHHhh---hccCchhhhHHHHHHHHhhhhcccCc
Q 015104 118 RLKILFNLYNLLENPYSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKE---WNIDIKDKRALFLGIANVLKESRSSS 194 (413)
Q Consensus 118 ~l~~L~~Lfn~l~~~~~r~~v~~~il~~a~~~~~~~~~~~~l~~~~~~L~~---w~~~~~~~~~~y~~~~~~l~~~~~~~ 194 (413)
.++.+.-.|..--+-..|.+|++.+++++-..+|.+.+...++.+++.+++ |+. ++|.+.|.+++.+..++ |
T Consensus 123 a~~~~~~t~~ktvs~g~kiDVvf~~iRlglfy~D~~lV~~~iekak~liE~GgDWeR--rNRlKvY~Gly~msvR~---F 197 (393)
T KOG0687|consen 123 ALEALRKTYEKTVSLGHKIDVVFYKIRLGLFYLDHDLVTESIEKAKSLIEEGGDWER--RNRLKVYQGLYCMSVRN---F 197 (393)
T ss_pred HHHHHHHHHHHHhhcccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhCCChhh--hhhHHHHHHHHHHHHHh---H
Confidence 334444444432222569999999999999999999999999999999986 987 99999999999988763 9
Q ss_pred hhhHHHHHHHhhhccCCccchhhHHHHHHHHHHHhhhcCCCcccc--ccCCCccccccccchhhhHHHHHHHHHHHhhcc
Q 015104 195 KDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQC--DLLDMPAIGQLENDAKYASVYQLLKIFLTQRLD 272 (413)
Q Consensus 195 ~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii~aL~~~~i~~f--eLL~~p~v~~L~~~~~~~~l~~LL~~f~~G~l~ 272 (413)
++|..+++..++||+..++.+.+. .+.++++.++..-+.-+. .++..|.|...-. .-+.+.+++..+..++++
T Consensus 198 k~Aa~Lfld~vsTFtS~El~~Y~~---~v~Ytv~~g~i~leR~dlktKVi~~~Evl~vl~--~l~~~~q~l~SLY~C~Y~ 272 (393)
T KOG0687|consen 198 KEAADLFLDSVSTFTSYELMSYET---FVRYTVITGLIALERVDLKTKVIKCPEVLEVLH--KLPSVSQLLNSLYECDYS 272 (393)
T ss_pred HHHHHHHHHHcccccceecccHHH---HHHHHHHHhhheeccchHHhhhcCcHHHHHHhh--cCchHHHHHHHHHhccHH
Confidence 999999999999999988876664 456666666655555454 3788888855432 356899999999999999
Q ss_pred cchhccc-cchhhhhhcCC--cchhH-HhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccc
Q 015104 273 GYLEFQA-GNSALLKSYGL--VHEDC-IAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKM 348 (413)
Q Consensus 273 ~f~~~~~-~~~~~l~~~~l--~~~~~-~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkI 348 (413)
+|..... -....++...+ .|-.+ .|-||..++.++..+ +|.++.+.+|+++||+.+.++.-+-+.|..|-+.|||
T Consensus 273 ~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLES-Yrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckI 351 (393)
T KOG0687|consen 273 DFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLES-YRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKI 351 (393)
T ss_pred HHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeee
Confidence 9875442 22223333222 35544 799999999999998 9999999999999999999999999999999999999
Q ss_pred cccccEEEEecccccccchhhHHHHHh
Q 015104 349 DQMNQVVIVRRCTERVFGQHQWQTLRT 375 (413)
Q Consensus 349 DQv~~~v~vt~v~~R~~~~~q~~~L~~ 375 (413)
|.|||+|.+++.... ..|.+..-.
T Consensus 352 DrVnGVVEtNrpD~K---N~qyq~vik 375 (393)
T KOG0687|consen 352 DRVNGVVETNRPDEK---NAQYQAVIK 375 (393)
T ss_pred ecccceeecCCcccc---chHHHHHHh
Confidence 999999999986654 334444433
No 5
>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=99.58 E-value=6e-16 Score=128.04 Aligned_cols=102 Identities=27% Similarity=0.382 Sum_probs=90.3
Q ss_pred hHHHHHHHHHHHhhcccchhccccc-hhhhhhcCCc--chhHHhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhh
Q 015104 257 ASVYQLLKIFLTQRLDGYLEFQAGN-SALLKSYGLV--HEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEK 333 (413)
Q Consensus 257 ~~l~~LL~~f~~G~l~~f~~~~~~~-~~~l~~~~l~--~~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~ 333 (413)
+|+++|+.+|..||+..|.++...+ +.++.+.++. .+.+.+++|..++.+++.. ++++++++|++.++++.++||.
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~-y~~i~~~~ia~~l~~~~~~vE~ 79 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKP-YSSISISEIAKALQLSEEEVES 79 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC--SEEEHHHHHHHHTCCHHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHH-hcccchHHHHHHhccchHHHHH
Confidence 4899999999999999999998887 6666655543 3678999999999999997 8999999999999999999999
Q ss_pred HHhhhhhhccccccccccccEEEEec
Q 015104 334 WVVKARTAKLMDCKMDQMNQVVIVRR 359 (413)
Q Consensus 334 lvi~aI~~gLI~gkIDQv~~~v~vt~ 359 (413)
+|+++|..|+|+|+|||++|+|+++|
T Consensus 80 ~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 80 ILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHHHHHHCCCEEEEEECCCCEEEecC
Confidence 99999999999999999999999986
No 6
>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=99.52 E-value=7.3e-15 Score=118.77 Aligned_cols=86 Identities=26% Similarity=0.288 Sum_probs=82.1
Q ss_pred chhHHhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHH
Q 015104 292 HEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQ 371 (413)
Q Consensus 292 ~~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~ 371 (413)
.+.+.+|+|..++.++++. +++|+|++|++.++++.++||.+|+++|..|.|.|+|||.+++|.+++..+|. .++|.
T Consensus 3 ~~~l~~~~~~~~l~~l~~~-y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~~ 79 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEP-YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPLA 79 (88)
T ss_pred HHHHHHHHHHHHHHHHhHH-hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hhHHH
Confidence 3467899999999999998 89999999999999999999999999999999999999999999999999998 78999
Q ss_pred HHHhhhhhh
Q 015104 372 TLRTKLSTW 380 (413)
Q Consensus 372 ~L~~rL~~W 380 (413)
.+.++|..|
T Consensus 80 ~~~~~l~~~ 88 (88)
T smart00088 80 QFAETLKKL 88 (88)
T ss_pred HHHHHhhcC
Confidence 999999988
No 7
>smart00753 PAM PCI/PINT associated module.
Probab=99.52 E-value=7.3e-15 Score=118.77 Aligned_cols=86 Identities=26% Similarity=0.288 Sum_probs=82.1
Q ss_pred chhHHhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHH
Q 015104 292 HEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQ 371 (413)
Q Consensus 292 ~~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~ 371 (413)
.+.+.+|+|..++.++++. +++|+|++|++.++++.++||.+|+++|..|.|.|+|||.+++|.+++..+|. .++|.
T Consensus 3 ~~~l~~~~~~~~l~~l~~~-y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~~ 79 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEP-YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPLA 79 (88)
T ss_pred HHHHHHHHHHHHHHHHhHH-hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hhHHH
Confidence 3467899999999999998 89999999999999999999999999999999999999999999999999998 78999
Q ss_pred HHHhhhhhh
Q 015104 372 TLRTKLSTW 380 (413)
Q Consensus 372 ~L~~rL~~W 380 (413)
.+.++|..|
T Consensus 80 ~~~~~l~~~ 88 (88)
T smart00753 80 QFAETLKKL 88 (88)
T ss_pred HHHHHhhcC
Confidence 999999988
No 8
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=99.45 E-value=3.4e-13 Score=129.07 Aligned_cols=222 Identities=16% Similarity=0.219 Sum_probs=180.3
Q ss_pred chhhHHHHHHHhHhhcCccccccccchhchHHHHhh---hccCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhcc
Q 015104 133 YSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKE---WNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFS 209 (413)
Q Consensus 133 ~~r~~v~~~il~~a~~~~~~~~~~~~l~~~~~~L~~---w~~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~ 209 (413)
..+.+||+..++++-..+|...+...|+.++..++. |+. ++|.+.|..++.+..++ |+++..++...|+||+
T Consensus 149 g~KiDv~l~kiRlg~~y~d~~vV~e~lE~~~~~iEkGgDWeR--rNRyK~Y~Gi~~m~~Rn---FkeAa~Ll~d~l~tF~ 223 (412)
T COG5187 149 GLKIDVFLCKIRLGLIYGDRKVVEESLEVADDIIEKGGDWER--RNRYKVYKGIFKMMRRN---FKEAAILLSDILPTFE 223 (412)
T ss_pred ccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhCCCHHh--hhhHHHHHHHHHHHHHh---hHHHHHHHHHHhcccc
Confidence 469999999999999999999999999999999985 877 89999999999998874 8999999999999999
Q ss_pred CCccchhhHHHHHHHHHHHhhhcCCCcccc--ccCCCcccccccc-chhhhHHHHHHHHHHHhhcccc-hhccccchhhh
Q 015104 210 GEDAHTMDEAKEEAVRTIIEFVKSPDMFQC--DLLDMPAIGQLEN-DAKYASVYQLLKIFLTQRLDGY-LEFQAGNSALL 285 (413)
Q Consensus 210 ~~~~~~~~e~~~~a~~lii~aL~~~~i~~f--eLL~~p~v~~L~~-~~~~~~l~~LL~~f~~G~l~~f-~~~~~~~~~~l 285 (413)
..++.+.+. .+.++++..|..-+.-+. .+++.|.|-++-+ +..-+.+.+|...+..+|+..| .....-..+.+
T Consensus 224 S~El~sY~~---~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L 300 (412)
T COG5187 224 SSELISYSR---AVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSL 300 (412)
T ss_pred ccccccHHH---HHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhc
Confidence 888766554 356667777766566564 4889998765444 3356677888899999999954 33332222222
Q ss_pred hhcCC--cchhH-HhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccc
Q 015104 286 KSYGL--VHEDC-IAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTE 362 (413)
Q Consensus 286 ~~~~l--~~~~~-~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~ 362 (413)
..... .|..+ .+.||.-++.++... +|.++.+.+|+.+||+.+-|+.=+=+.|-.|-+.|.||.+||+|.+++...
T Consensus 301 ~~d~fl~rh~d~fvREMRrrvYaQlLES-Yr~lsl~sMA~tFgVSV~yvdrDLg~FIp~~~LncvIDRvnGvVetnrpde 379 (412)
T COG5187 301 QDDVFLGRHVDLFVREMRRRVYAQLLES-YRLLSLESMAQTFGVSVEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRPDE 379 (412)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHH-HHHhhHHHHHHHhCccHHHHhhhHHhhCCCCceeeeeecccceEeccCcch
Confidence 22111 25444 799999999999998 999999999999999999999999999999999999999999999998766
Q ss_pred c
Q 015104 363 R 363 (413)
Q Consensus 363 R 363 (413)
+
T Consensus 380 k 380 (412)
T COG5187 380 K 380 (412)
T ss_pred h
Confidence 3
No 9
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.03 E-value=6.6e-10 Score=106.15 Aligned_cols=189 Identities=13% Similarity=0.190 Sum_probs=139.0
Q ss_pred cCchhhHHHHHHHhhhccCCccchhhHHHHHHHHHHHhhhcC-CCccccccCCCccccccccchhhhHHHHHHHHHHHhh
Q 015104 192 SSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKS-PDMFQCDLLDMPAIGQLENDAKYASVYQLLKIFLTQR 270 (413)
Q Consensus 192 ~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii~aL~~-~~i~~feLL~~p~v~~L~~~~~~~~l~~LL~~f~~G~ 270 (413)
|.++++...+......|+.+.. +-+.....+++.+-.+- .+|--|| ...-+-.+++|+.-.+.+|+.++...|
T Consensus 245 g~fe~AhTDFFEAFKNYDEsGs---pRRttCLKYLVLANMLmkS~iNPFD---sQEAKPyKNdPEIlAMTnlv~aYQ~Nd 318 (440)
T KOG1464|consen 245 GEFEKAHTDFFEAFKNYDESGS---PRRTTCLKYLVLANMLMKSGINPFD---SQEAKPYKNDPEILAMTNLVAAYQNND 318 (440)
T ss_pred chHHHHHhHHHHHHhcccccCC---cchhHHHHHHHHHHHHHHcCCCCCc---ccccCCCCCCHHHHHHHHHHHHHhccc
Confidence 4566666666666666655321 22334455566654332 2332254 223333566788888999999999999
Q ss_pred cccchhccccchhhhhhcCC---cchhHHhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcccccc
Q 015104 271 LDGYLEFQAGNSALLKSYGL---VHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCK 347 (413)
Q Consensus 271 l~~f~~~~~~~~~~l~~~~l---~~~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gk 347 (413)
+.+|+.....|...+-..|. ..+.+++++|--.|+.|..+ +..|...-|+++|+||+.+||.+++.||-..-|+|+
T Consensus 319 I~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkP-Yt~i~Ipfis~~Lnv~~~dV~~LLV~~ILD~~i~g~ 397 (440)
T KOG1464|consen 319 IIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKP-YTNIGIPFISKELNVPEADVESLLVSCILDDTIDGR 397 (440)
T ss_pred HHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhcc-ccccCchhhHhhcCCCHHHHHHHHHHHHhccccccc
Confidence 99999988777544444443 14688999999999999998 888888889999999999999999999999999999
Q ss_pred ccccccEEEEecccccccchhhHHHHHhhhhhhhhhHHHHHHHhhh
Q 015104 348 MDQMNQVVIVRRCTERVFGQHQWQTLRTKLSTWRANVANVISTIQA 393 (413)
Q Consensus 348 IDQv~~~v~vt~v~~R~~~~~q~~~L~~rL~~W~~~v~~~~~~v~~ 393 (413)
|||+++.+..-.... -=..+.+.|+.|.++++++.+.|-+
T Consensus 398 Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~s 437 (440)
T KOG1464|consen 398 IDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVS 437 (440)
T ss_pred hHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999887654322 1123678899999999999887643
No 10
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=98.69 E-value=5.6e-08 Score=97.24 Aligned_cols=163 Identities=15% Similarity=0.266 Sum_probs=116.2
Q ss_pred hhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCCccchhhHHHHHHHHH--HHhhhcCCCccccccCCCccccccccc
Q 015104 176 KRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRT--IIEFVKSPDMFQCDLLDMPAIGQLEND 253 (413)
Q Consensus 176 ~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~l--ii~aL~~~~i~~feLL~~p~v~~L~~~ 253 (413)
|.-||.....+.+ .+|..+-++++..+.--+.. . .++ .++....+ ++.-|.+ +|-.-.+...|.++ +
T Consensus 248 RY~yY~GrIkaiq---ldYssA~~~~~qa~rkapq~-~-alG-f~q~v~k~~ivv~ll~g-eiPers~F~Qp~~~---k- 316 (493)
T KOG2581|consen 248 RYLYYLGRIKAIQ---LDYSSALEYFLQALRKAPQH-A-ALG-FRQQVNKLMIVVELLLG-EIPERSVFRQPGMR---K- 316 (493)
T ss_pred HHHHHHhhHHHhh---cchhHHHHHHHHHHHhCcch-h-hhh-HHHHHHHHHHHHHHHcC-CCcchhhhcCccHH---H-
Confidence 5556777776654 56888999998888866542 2 122 22233333 3333444 33222233455552 2
Q ss_pred hhhhHHHHHHHHHHHhhcccchhccccchhhhhhcC-------CcchhHHhhhhhhhhhccCCCCCCCcchhhhhhcccc
Q 015104 254 AKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYG-------LVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQI 326 (413)
Q Consensus 254 ~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~-------l~~~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i 326 (413)
.-.++++|=.+...||++.|.+..+++.+.+...| |.|..+..-||.++|. +..||+.+||+.|++
T Consensus 317 -sL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISls------YSRISl~DIA~kL~l 389 (493)
T KOG2581|consen 317 -SLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLS------YSRISLQDIAKKLGL 389 (493)
T ss_pred -HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeee------eeeccHHHHHHHhcC
Confidence 23578999999999999999999888877776655 2466667778888776 889999999999999
Q ss_pred Ccc-hhhhHHhhhhhhccccccccccccEEE
Q 015104 327 NND-EVEKWVVKARTAKLMDCKMDQMNQVVI 356 (413)
Q Consensus 327 ~~~-eVE~lvi~aI~~gLI~gkIDQv~~~v~ 356 (413)
+.+ ++|.+|-+||+.|+|+|+||--+|-+.
T Consensus 390 ~Seed~EyiVakAIRDGvIea~Id~~~g~m~ 420 (493)
T KOG2581|consen 390 NSEEDAEYIVAKAIRDGVIEAKIDHEDGFMQ 420 (493)
T ss_pred CCchhHHHHHHHHHHhccceeeeccccCcee
Confidence 864 599999999999999999999988444
No 11
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.93 E-value=3.5e-05 Score=77.64 Aligned_cols=242 Identities=14% Similarity=0.135 Sum_probs=151.9
Q ss_pred hhHHHHHHHhHhhcCccccccccchhchHHHHhh---hccCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCC
Q 015104 135 RFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKE---WNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGE 211 (413)
Q Consensus 135 r~~v~~~il~~a~~~~~~~~~~~~l~~~~~~L~~---w~~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~ 211 (413)
-.+.++..+.++--.++...+.....+.++..+. ..-...-+.+.+.++++...+ +++.+.++.+.. .|+.-
T Consensus 186 vInm~ln~i~VSI~~~nw~hv~sy~~~A~st~~~~~~~~q~v~~kl~C~agLa~L~lk---kyk~aa~~fL~~--~~~~~ 260 (466)
T KOG0686|consen 186 VINMCLNLILVSIYMGNWGHVLSYISKAESTPDANENLAQEVPAKLKCAAGLANLLLK---KYKSAAKYFLLA--EFDHC 260 (466)
T ss_pred HHHHHHHHHHHHHhhcchhhhhhHHHHHHhCchhhhhHHHhcCcchHHHHHHHHHHHH---HHHHHHHHHHhC--CCCcc
Confidence 3566677777777777777777777777776532 111123345556666664332 255555554432 12222
Q ss_pred ccchhhHHHHHHHHHHHhhhcCCCcccc--ccCCCccccccccchhhhHHHHHHHHHHHhhcccchhccccchh-hhhhc
Q 015104 212 DAHTMDEAKEEAVRTIIEFVKSPDMFQC--DLLDMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSA-LLKSY 288 (413)
Q Consensus 212 ~~~~~~e~~~~a~~lii~aL~~~~i~~f--eLL~~p~v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~-~l~~~ 288 (413)
+-...-...+.+++....||..=+.=.. ++...-.+..+-. -.+.+.++|..|.++.+..-.+...+..+ ++-+.
T Consensus 261 d~~~ivtpsdv~iYggLcALAtfdr~~Lk~~vi~n~~Fk~fle--l~Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~ 338 (466)
T KOG0686|consen 261 DYPEIVTPSDVAIYGGLCALATFDRQDLKLNVIKNESFKLFLE--LEPQLREILFKFYSSKYASCLELLREIKPRLLLDM 338 (466)
T ss_pred CccceecchhhHHHHhhHhhccCCHHHHHHHHHcchhhhhHHh--cChHHHHHHHHHhhhhHHHHHHHHHHhccceeech
Confidence 2111111235677777777754222111 2333333332211 12468899999999998887666554422 21111
Q ss_pred CC-cc-hhHHhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccc--
Q 015104 289 GL-VH-EDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERV-- 364 (413)
Q Consensus 289 ~l-~~-~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~-- 364 (413)
=| +| ..+..+||--+|++-..+ +-++.++.||.+++.++.+.|.-|+..|-.|.|+||||+-++++++.-...|.
T Consensus 339 yLaphVd~Ly~~IR~r~llqy~~p-y~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~~~en~~ 417 (466)
T KOG0686|consen 339 YLAPHVDNLYSLIRNRALLQYLSP-YSSADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDADSENAT 417 (466)
T ss_pred hcchhHHHHHHHHHHhhHHHhcCc-cccchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeecccccccch
Confidence 11 23 367899999999999987 88999999999999999999999999999999999999999999998775544
Q ss_pred ----cchhhHHHHHhhhhhhhhhH
Q 015104 365 ----FGQHQWQTLRTKLSTWRANV 384 (413)
Q Consensus 365 ----~~~~q~~~L~~rL~~W~~~v 384 (413)
+...+=-.++.|-.-|+..+
T Consensus 418 fe~~~~~~~~~~~~~kal~lr~~~ 441 (466)
T KOG0686|consen 418 FERVLPMGKRSQLEAKALLLRAAL 441 (466)
T ss_pred hhhcchhhHHHHHHHHHHHHHHHH
Confidence 33333334444445555443
No 12
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=8.7e-05 Score=74.53 Aligned_cols=201 Identities=16% Similarity=0.243 Sum_probs=133.7
Q ss_pred hhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCCccchhhHHHHHHHHHHH-hhhcCCCcccc-ccCCCccc-ccc
Q 015104 174 KDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTII-EFVKSPDMFQC-DLLDMPAI-GQL 250 (413)
Q Consensus 174 ~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii-~aL~~~~i~~f-eLL~~p~v-~~L 250 (413)
..+.+||.....+... -..|+...-.|=+-|+.....+-++.-......++ ..++.|..-.- +++..-.- +.|
T Consensus 209 ~lKlkyY~lmI~l~lh----~~~Yl~v~~~Yraiy~t~~vk~d~~kw~~vL~~iv~f~~LAp~dneQsdll~~is~dKkL 284 (439)
T KOG1498|consen 209 ELKLKYYELMIRLGLH----DRAYLNVCRSYRAIYDTGNVKEDPEKWIEVLRSIVSFCVLAPHDNEQSDLLARISNDKKL 284 (439)
T ss_pred HHHHHHHHHHHHhccc----ccchhhHHHHHHHHhcccccccChhhhhhhhhhheeEEeecCCCcHHHHHHHHHhccccc
Confidence 3466777776664322 13455666666666665443221222233444443 34455533212 45543222 234
Q ss_pred ccchhhhHHHHHHHHHHHhhcccchhccccchhhhhhcCC--------------cchhHHhhhhhhhhhccCCCCCCCcc
Q 015104 251 ENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGL--------------VHEDCIAKMRLMSLVDLGSNESGQIP 316 (413)
Q Consensus 251 ~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~l--------------~~~~~~~KirLLaL~~L~~~~~r~is 316 (413)
.+ .+..-++|..|.+|.+-.|..+.+++.+.+...++ ...-..+.||++|=. +..||
T Consensus 285 ~e---~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~y------YSrIt 355 (439)
T KOG1498|consen 285 SE---LPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKY------YSRIT 355 (439)
T ss_pred cc---CccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHH------Hhhcc
Confidence 33 45667899999999998887665555444443311 111235778887755 77899
Q ss_pred hhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHHhhhhhhhhhHHHHHHHhhhccc
Q 015104 317 YGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLRTKLSTWRANVANVISTIQATNK 396 (413)
Q Consensus 317 y~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~~rL~~W~~~v~~~~~~v~~~~~ 396 (413)
+..++.-++.|.++.|.++.+.+..|-+.||||+..|++....+ +.+.+-|..|..+++++...++.+.+
T Consensus 356 ~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~----------K~~~~~LneW~~nve~L~~ll~K~~H 425 (439)
T KOG1498|consen 356 LKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKV----------KDSNEILNEWASNVEKLLGLLEKVSH 425 (439)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEec----------ccHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999988753 34567799999999999999887665
Q ss_pred c
Q 015104 397 I 397 (413)
Q Consensus 397 ~ 397 (413)
+
T Consensus 426 L 426 (439)
T KOG1498|consen 426 L 426 (439)
T ss_pred H
Confidence 3
No 13
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=97.63 E-value=6.9e-05 Score=75.98 Aligned_cols=187 Identities=13% Similarity=0.106 Sum_probs=131.1
Q ss_pred hchHHHHhhhccCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCCccchhhHHHHHHHHHHHhhhcCCCcccc
Q 015104 160 KKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQC 239 (413)
Q Consensus 160 ~~~~~~L~~w~~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii~aL~~~~i~~f 239 (413)
+....+...|..+..+...||.+...++.. ++..++..+.......+..- ....+.....++-..+.-..
T Consensus 190 ~~~~~~~~~~~l~~~v~y~YylGr~a~~~~---d~~~A~~~L~~af~~cp~~~---~~n~~~iliylip~~~llg~---- 259 (394)
T KOG2688|consen 190 DQSGSDISDFPLAQLVVYHYYLGRYAMFES---DFLNAFLQLNEAFRLCPDLL---LKNKRLILIYLIPTGLLLGR---- 259 (394)
T ss_pred hccccchhhcccccceeeeeeeeeehhhhh---hHHHHHHHHHHHHHhCcHHH---HhhhhhHHHHHhHHHHHhcc----
Confidence 333367778888888899999997666654 36777777766655544321 12222334444443222111
Q ss_pred ccCCCccccccccchhhhHHHHHHHHHHHhhcccchhccccchhhhhhcCCcchhHHhhhhhhhhhccCCC------CCC
Q 015104 240 DLLDMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLGSN------ESG 313 (413)
Q Consensus 240 eLL~~p~v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~l~~~~~~~KirLLaL~~L~~~------~~r 313 (413)
+|-..-|..- .-..+-.|+.+...||+..|....+.|..++.+.|+- -.+.|.+++++-.|..+ +..
T Consensus 260 ----~Pt~~lL~~~-~~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~--l~l~~l~lv~yrnL~kkv~~~~~~~~ 332 (394)
T KOG2688|consen 260 ----IPTKELLDFY-TLDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGIY--LTLEKLPLVVYRNLFKKVIQLWGKTS 332 (394)
T ss_pred ----CcchhhHhHh-hHHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccH--HHhhhhhHHHHHHHHHHHHHHhCCCC
Confidence 3544444322 1235667899999999999999998888888876541 22455778877777654 356
Q ss_pred CcchhhhhhccccCc------chhhhHHhhhhhhccccccccccccEEEEeccccc
Q 015104 314 QIPYGLIKDTLQINN------DEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTER 363 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~------~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R 363 (413)
.+|++.+..+++... +|||-.+..+|..|.|+|.|+-..+++.++.-.|-
T Consensus 333 ~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~ikgYish~~~~~V~sK~~pf 388 (394)
T KOG2688|consen 333 QLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRIKGYISHQLQTLVFSKKDPF 388 (394)
T ss_pred CCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccccchhchhhheEEEecCCCC
Confidence 899999999988754 79999999999999999999999999999986654
No 14
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=0.0017 Score=64.45 Aligned_cols=185 Identities=14% Similarity=0.073 Sum_probs=120.4
Q ss_pred cCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCCccchhhHHHHHHHHHHHhhhcCCCcccc-ccCCCccccc
Q 015104 171 IDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQC-DLLDMPAIGQ 249 (413)
Q Consensus 171 ~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii~aL~~~~i~~f-eLL~~p~v~~ 249 (413)
.++..++.+=....-++.. ..+|+-+|.++...+..|+.-+-. ..|..-..+.+..-+-....=+. .++.......
T Consensus 203 cpPqlQa~lDLqSGIlha~-ekDykTafSYFyEAfEgf~s~~~~--v~A~~sLKYMlLcKIMln~~ddv~~lls~K~~l~ 279 (411)
T KOG1463|consen 203 CPPQLQATLDLQSGILHAA-EKDYKTAFSYFYEAFEGFDSLDDD--VKALTSLKYMLLCKIMLNLPDDVAALLSAKLALK 279 (411)
T ss_pred cCHHHHHHHHHhccceeec-ccccchHHHHHHHHHccccccCCc--HHHHHHHHHHHHHHHHhcCHHHHHHHHhhHHHHh
Confidence 3444444443333333333 357899999999999989763321 12222222222221111111112 2444333322
Q ss_pred cccchhhhHHHHHHHHHHHhhcccchhccccchhhhhhcCCc--ch-hHHhhhhhhhhhccCCCCCCCcchhhhhhcccc
Q 015104 250 LENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLV--HE-DCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQI 326 (413)
Q Consensus 250 L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~l~--~~-~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i 326 (413)
+.+ +....+...-++|..-++++|+.....++.-+...++. |- .+...|-=--|+.+..+ +..+-.+-||+-.|+
T Consensus 280 y~g-~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEP-yS~Vei~hIA~~IGl 357 (411)
T KOG1463|consen 280 YAG-RDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEP-YSRVEISHIAEVIGL 357 (411)
T ss_pred ccC-cchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCc-hhhhhHHHHHHHHCC
Confidence 444 46677888889999999999998888887766665542 21 22233333356667776 888999999999999
Q ss_pred CcchhhhHHhhhhhhccccccccccccEEEEecc
Q 015104 327 NNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRC 360 (413)
Q Consensus 327 ~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v 360 (413)
+...||.=+-+.|-.+.+.|.+||-+|++.|.--
T Consensus 358 ~~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e 391 (411)
T KOG1463|consen 358 DVPQVEKKLSQMILDKKFYGTLDQGEGCLIVFEE 391 (411)
T ss_pred CcHHHHHHHHHHHHHHHhhcccccCCCeEEEeCC
Confidence 9999999999999999999999999999998753
No 15
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.25 E-value=0.0016 Score=64.05 Aligned_cols=163 Identities=18% Similarity=0.270 Sum_probs=99.7
Q ss_pred hHHHHHHHHHHHhhhcCCCcccc--ccCCCccccccccchhhhHHHH--HHHHHHHhhcccchhccccchhhhhhcCCcc
Q 015104 217 DEAKEEAVRTIIEFVKSPDMFQC--DLLDMPAIGQLENDAKYASVYQ--LLKIFLTQRLDGYLEFQAGNSALLKSYGLVH 292 (413)
Q Consensus 217 ~e~~~~a~~lii~aL~~~~i~~f--eLL~~p~v~~L~~~~~~~~l~~--LL~~f~~G~l~~f~~~~~~~~~~l~~~~l~~ 292 (413)
-++-.-|..|.+.|.-||-+-.+ .+..-|.++.+. -|+-+-. |=.+....+++.|..+...|...-...|...
T Consensus 222 ~~aL~~a~~CtlLA~~gpqrsr~Latlfkder~~~l~---~y~ileKmyl~riI~k~el~ef~~~L~pHQka~~~dgssi 298 (399)
T KOG1497|consen 222 LEALKKALQCTLLASAGPQRSRMLATLFKDERCQKLP---AYGILEKMYLERIIRKEELQEFEAFLQPHQKAHTMDGSSI 298 (399)
T ss_pred HHHHHHhHhheeecCCChHHHHHHHHHhcCccccccc---chHHHHHHHHHHHhcchhHHHHHHHhcchhhhcccCcchh
Confidence 44556677777777778776555 355556665552 1222211 1224445668888877654422111122211
Q ss_pred -hhHHhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHH
Q 015104 293 -EDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQ 371 (413)
Q Consensus 293 -~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~ 371 (413)
..-...--++++.+| +..+||+++.+-++||...+|..+-+.|..|.++|.|||.++.++..-+.+ ..||.
T Consensus 299 l~ra~~EhNlls~Skl----y~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~~e~----l~~wd 370 (399)
T KOG1497|consen 299 LDRAVIEHNLLSASKL----YNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFEDREE----LPQWD 370 (399)
T ss_pred hhhHHHHHhHHHHHHH----HHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecchhh----hhhhh
Confidence 111112234444444 456999999999999999999999999999999999999999999875222 34454
Q ss_pred HHHhhhhhhhhhHHHHHHHhhh
Q 015104 372 TLRTKLSTWRANVANVISTIQA 393 (413)
Q Consensus 372 ~L~~rL~~W~~~v~~~~~~v~~ 393 (413)
. ....-++.|+++.+.|..
T Consensus 371 k---qi~sl~~qvNki~~~i~~ 389 (399)
T KOG1497|consen 371 K---QIQSLCNQVNKILDKISH 389 (399)
T ss_pred H---HHHHHHHHHHHHHHHHHH
Confidence 3 233345556666665554
No 16
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=97.07 E-value=0.0011 Score=66.37 Aligned_cols=179 Identities=17% Similarity=0.147 Sum_probs=112.4
Q ss_pred CchhhhHHHHHHHHhhhhcccCchhhHHHHHH-HhhhccCCccchhhHHHHHHHHHHHhhhcCCCccccccCCCcccccc
Q 015104 172 DIKDKRALFLGIANVLKESRSSSKDSFKFLTK-YLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQCDLLDMPAIGQL 250 (413)
Q Consensus 172 ~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~-yL~t~~~~~~~~~~e~~~~a~~lii~aL~~~~i~~feLL~~p~v~~L 250 (413)
+..+.-.||++++..+.++ +.++|-.+.. +++|-... + ...+..+-..+..+|.-...+ |-..-|
T Consensus 217 sq~v~f~YYLG~~~l~~en---~heA~~~L~~aFl~c~~l~---~-~n~~rIl~~~ipt~Llv~~~~-------Ptk~~L 282 (413)
T COG5600 217 SQVVVFHYYLGIYYLLNEN---FHEAFLHLNEAFLQCPWLI---T-RNRKRILPYYIPTSLLVNKFP-------PTKDLL 282 (413)
T ss_pred cceeehhhHHHHHHHHHHh---HHHHHHHHHHHHHhChhhh---h-cchheehhHHhhHHHHhCCCC-------CchHHH
Confidence 4456678999999888763 3445555444 56654321 1 111223344444455433332 222334
Q ss_pred ccchhhhHHHHHHHHHHHhhcccchhccccchhhhhhcCCcchhHHhhhhhhhhhccCCC------CCCCcchhhhhhcc
Q 015104 251 ENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLGSN------ESGQIPYGLIKDTL 324 (413)
Q Consensus 251 ~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~l~~~~~~~KirLLaL~~L~~~------~~r~isy~~Ia~~l 324 (413)
+..+.-+.+--|..+..+||+++|....++|..++.+.|+ +-.+..+.++++.-.|..+ ++..+|++-+...+
T Consensus 283 ~r~~~~s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l-~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~ 361 (413)
T COG5600 283 ERFKRCSVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGL-YLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVL 361 (413)
T ss_pred HhccccchhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcch-HHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHH
Confidence 4332233455678999999999999999888888887775 2233344444444443322 23445666555555
Q ss_pred ccC-------cchhhhHHhhhhhhccccccccccccEEEEeccccccc
Q 015104 325 QIN-------NDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVF 365 (413)
Q Consensus 325 ~i~-------~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~ 365 (413)
+++ .++||-.+..+|..|+++|.|.-..+++.++.-.|-.+
T Consensus 362 qls~~dn~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~pFp~ 409 (413)
T COG5600 362 QLSAIDNFHSFKEVECILVTLIGLGLLRGYISHSRRTVVFSKKDPFPV 409 (413)
T ss_pred HccCCCcccChHHHHHHHHHHHhhhhhhheecccceEEEEecCCCCCC
Confidence 554 26899999999999999999999999999998776543
No 17
>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=96.23 E-value=0.0097 Score=54.50 Aligned_cols=110 Identities=15% Similarity=0.259 Sum_probs=86.1
Q ss_pred hHHHHHHHhhhhcCcchhhHHHHHHHhHhhcCccccccccchhchHHHHhh---hccCchhhhHHHHHHHHhhhhcccCc
Q 015104 118 RLKILFNLYNLLENPYSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKE---WNIDIKDKRALFLGIANVLKESRSSS 194 (413)
Q Consensus 118 ~l~~L~~Lfn~l~~~~~r~~v~~~il~~a~~~~~~~~~~~~l~~~~~~L~~---w~~~~~~~~~~y~~~~~~l~~~~~~~ 194 (413)
.++.....+..-..+..+.++++.+++++-..++...+.+.+.+++..++. |+. ..+.++|.+++.+..+ +|
T Consensus 55 A~k~y~~~~~~~~~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~~~--~nrlk~~~gL~~l~~r---~f 129 (177)
T PF10602_consen 55 ALKAYSRARDYCTSPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGGDWER--RNRLKVYEGLANLAQR---DF 129 (177)
T ss_pred HHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccchHHH--HHHHHHHHHHHHHHhc---hH
Confidence 334443333332234668889999999999999999999999999999987 765 7888999999997654 59
Q ss_pred hhhHHHHHHHhhhccC---CccchhhHHHHHHHHHHHhhhcCCC
Q 015104 195 KDSFKFLTKYLATFSG---EDAHTMDEAKEEAVRTIIEFVKSPD 235 (413)
Q Consensus 195 ~~~y~~~l~yL~t~~~---~~~~~~~e~~~~a~~lii~aL~~~~ 235 (413)
..+.+.++..+.+|+. .++.+ ..+.|+..++.||.+-+
T Consensus 130 ~~AA~~fl~~~~t~~~~~~~el~s---~~d~a~Y~~l~aLat~~ 170 (177)
T PF10602_consen 130 KEAAELFLDSLSTFTSLQYTELIS---YNDFAIYGGLCALATLD 170 (177)
T ss_pred HHHHHHHHccCcCCCCCchhhhcC---HHHHHHHHHHHHHHhCC
Confidence 9999999999999986 55543 44789999999987643
No 18
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=95.78 E-value=0.09 Score=51.55 Aligned_cols=160 Identities=15% Similarity=0.139 Sum_probs=104.4
Q ss_pred cCchhhHHHHHHHhhhccCCccchhhHHHHHHHHHHHhhhcCCCccc----c-ccCCCcc-ccccccchhhhHHHHHHHH
Q 015104 192 SSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEFVKSPDMFQ----C-DLLDMPA-IGQLENDAKYASVYQLLKI 265 (413)
Q Consensus 192 ~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii~aL~~~~i~~----f-eLL~~p~-v~~L~~~~~~~~l~~LL~~ 265 (413)
.+|.-+|.++...+..|+.-+.. .+|-.-..++ |++.-+.| . .+|.... +..+.+ .....+...-++
T Consensus 220 ~dyktA~SYF~Ea~Egft~l~~d--~kAc~sLkYm----lLSkIMlN~~~evk~vl~~K~t~~~y~~-r~I~am~avaea 292 (421)
T COG5159 220 RDYKTASSYFIEALEGFTLLKMD--VKACVSLKYM----LLSKIMLNRREEVKAVLRNKNTLKHYDD-RMIRAMLAVAEA 292 (421)
T ss_pred ccchhHHHHHHHHHhccccccch--HHHHHHHHHH----HHHHHHHhhHHHHHHHHccchhHhhhhh-hhHHHHHHHHHH
Confidence 56889999999999999874321 2222222222 33322223 2 2333222 223333 234567777788
Q ss_pred HHHhhcccchhccccchhhhhhcCC--cchhH-HhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhc
Q 015104 266 FLTQRLDGYLEFQAGNSALLKSYGL--VHEDC-IAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAK 342 (413)
Q Consensus 266 f~~G~l~~f~~~~~~~~~~l~~~~l--~~~~~-~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~g 342 (413)
|.+-++.+|....+.+.+-+.+.++ +|-.. ..-+-=--|+..+.+ ...+..+-||+-+|++..+||.=+-+.|-.+
T Consensus 293 ~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEP-fs~VeishIa~viGldt~qvEgKLsqMILDK 371 (421)
T COG5159 293 FGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEP-FSVVEISHIADVIGLDTNQVEGKLSQMILDK 371 (421)
T ss_pred hCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCc-ceeeehhHHHHHhcccHHHHHHHHHHHHHHH
Confidence 9999999999877666554443332 12111 111111235566666 7788899999999999999999999999999
Q ss_pred cccccccccccEEEEec
Q 015104 343 LMDCKMDQMNQVVIVRR 359 (413)
Q Consensus 343 LI~gkIDQv~~~v~vt~ 359 (413)
.+.|.+||.+|.+.|.-
T Consensus 372 ifyG~LDqg~gcLivy~ 388 (421)
T COG5159 372 IFYGTLDQGDGCLIVYG 388 (421)
T ss_pred HHHhhhccCCceEEEeC
Confidence 99999999999999975
No 19
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.21 E-value=1.1 Score=45.31 Aligned_cols=315 Identities=13% Similarity=0.188 Sum_probs=159.0
Q ss_pred HHHHHHHHHHHhhhhhhhhhhHHHHHhhhhhh-------hhc-----cCCC--CcchhheeeehhcccCCCChhHHH---
Q 015104 35 EQVNRLCLEAQESMVMGRWMDLASLMLTSADL-------MFS-----KVSD--KDLECIFTVICNLVTKPESLDEVH--- 97 (413)
Q Consensus 35 ~e~~~~~~~~e~l~~~klw~qLt~~l~~~~~~-------~~~-----~~~d--ke~e~~~n~i~~lv~~~~~~~~~l--- 97 (413)
.|+++...+-+++.+++ |..+-.-|.. +++ .+. +.|. .+.|..+-++-++|.+= +. .++
T Consensus 22 ~eL~~~i~~~~ell~k~-~~~~~~~L~~-ld~~~hSlgml~~l~~~f~~~~~~~~~~~li~~~~~FV~~~-n~-eqlr~a 97 (422)
T KOG2582|consen 22 GELAELIVKSKELLAKN-SSDLDAVLLH-LDPQVHSLGMLAVLKVKFHTPSANPDPETLIELLNDFVDEN-NG-EQLRLA 97 (422)
T ss_pred HHHHHHHHhhHHHHHhC-cchHHHHHHh-cCccccchhhhhhhhccccCcccCCCHHHHHHHHHHHHHhc-Ch-HHHhhH
Confidence 57778888888888877 7776653322 221 000 1111 24444444444444432 11 122
Q ss_pred -----HHHHHHHhhhhcCCCCCcchhHHHHHHHhhhhcCcchhhH-HHHHHHhHhhcCccccccccchh-chHHHHhhhc
Q 015104 98 -----EMTKLISGKIIQQPNDKPAMRLKILFNLYNLLENPYSRFF-VYMKALNLAVNGKVTEHIIPSFK-KIDSFLKEWN 170 (413)
Q Consensus 98 -----~~v~~l~~~~~~~~~~~~~~~l~~L~~Lfn~l~~~~~r~~-v~~~il~~a~~~~~~~~~~~~l~-~~~~~L~~w~ 170 (413)
.+|+.+.+.+.+ ...|..-++++.+.-..+.+...++. +---++.++-..+++....|.++ .+... ..
T Consensus 98 s~~f~~lc~~l~~~~~~--~~~p~~gi~ii~~av~k~~~~~~qlT~~H~~l~~~~L~ak~y~~~~p~ld~divei---~~ 172 (422)
T KOG2582|consen 98 SEIFFPLCHDLTEAVVK--KNKPLRGIRIIMQAVDKMQPSNGQLTSIHADLLQLCLEAKDYASVLPYLDDDIVEI---CK 172 (422)
T ss_pred HHHHHHHHHHHHHHHHh--cCCccccchHHHHHHHHhccCccchhhhHHHHHHHHHHhhcccccCCccchhHHHH---hc
Confidence 344444444432 23343334444444443322111111 11123444555567777777776 33222 12
Q ss_pred cCchhhhHHHHHHHHhhh-----hcccCchhhHHHHHHHhhhccCCccchhhHHHHHHHHH--HHhhhcCCCccccccCC
Q 015104 171 IDIKDKRALFLGIANVLK-----ESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRT--IIEFVKSPDMFQCDLLD 243 (413)
Q Consensus 171 ~~~~~~~~~y~~~~~~l~-----~~~~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~l--ii~aL~~~~i~~feLL~ 243 (413)
-++....+++.. +.||. .. ++++.| +..|-.|.+... .+......+|++- .+.-+....+|..+=-.
T Consensus 173 ~n~h~~~k~fL~-Y~yYgg~icigl-k~fe~A---l~~~e~~v~~Pa-~~vs~~hlEaYkkylLvsLI~~GK~~ql~k~t 246 (422)
T KOG2582|consen 173 ANPHLDPKYFLL-YLYYGGMICIGL-KRFERA---LYLLEICVTTPA-MAVSHIHLEAYKKYLLVSLILTGKVFQLPKNT 246 (422)
T ss_pred cCCCCCHHHHHH-HHHhcceeeecc-ccHHHH---HHHHHHHHhcch-hHHHHHHHHHHHHHHHHHhhhcCceeeccccc
Confidence 234455554433 33332 21 234333 223333332211 1122223344432 22223333444332111
Q ss_pred CccccccccchhhhHHHHHHHHHHHhhcccchhccccchh-hhhhcC--Ccch--hHHhhhhhhhhhccCCCCCCCcchh
Q 015104 244 MPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSA-LLKSYG--LVHE--DCIAKMRLMSLVDLGSNESGQIPYG 318 (413)
Q Consensus 244 ~p~v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~-~l~~~~--l~~~--~~~~KirLLaL~~L~~~~~r~isy~ 318 (413)
..++..+.+. -..++++++.++..+.-.+.+....++.+ |.++.+ +-.. ...-|=|++.+.... -+++.+
T Consensus 247 s~~~~r~~K~-ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF----~sLsL~ 321 (422)
T KOG2582|consen 247 SQNAGRFFKP-MSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTF----LSLSLS 321 (422)
T ss_pred hhhhHHhccc-CCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHH----HHhhHH
Confidence 2233223221 33488999999999988877777655544 333322 2122 123455555555443 469999
Q ss_pred hhhhccccC-cchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHH
Q 015104 319 LIKDTLQIN-NDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQT 372 (413)
Q Consensus 319 ~Ia~~l~i~-~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~ 372 (413)
+||+..++. .+|||..|+..|..|-|-++|| |-|..+.--...-+++-.+.
T Consensus 322 dIA~~vQLa~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~n 373 (422)
T KOG2582|consen 322 DIASRVQLASAQEVEKYILQMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHEN 373 (422)
T ss_pred HHHHHHHhcchHHHHHHHHHHhccCceEEEec---ceEEEecCcccCCCHHHHhh
Confidence 999977775 4899999999999999999999 77777765555666655553
No 20
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=94.70 E-value=0.029 Score=55.13 Aligned_cols=86 Identities=13% Similarity=0.323 Sum_probs=73.4
Q ss_pred HhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHHh
Q 015104 296 IAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLRT 375 (413)
Q Consensus 296 ~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~~ 375 (413)
.+.+|+++=- +..|+...|..-++.|+.+.|..+.+....|.+.|||+|..+++.....+ +..+
T Consensus 341 EHN~RvI~~y------YSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~----------n~~~ 404 (439)
T COG5071 341 EHNIRVIANY------YSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSQ----------NVQE 404 (439)
T ss_pred HhhHhHHHHH------hhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEecCccceEEeeccc----------cHHH
Confidence 4666766532 67899999999999999999999999999999999999999999876432 4456
Q ss_pred hhhhhhhhHHHHHHHhhhcccc
Q 015104 376 KLSTWRANVANVISTIQATNKI 397 (413)
Q Consensus 376 rL~~W~~~v~~~~~~v~~~~~~ 397 (413)
.|..|.++|..++..++..+++
T Consensus 405 ~lneW~~NV~ellgklek~~HL 426 (439)
T COG5071 405 QLNEWGSNVTELLGKLEKVRHL 426 (439)
T ss_pred HHHHhcccHHHHHHHHHHHhHH
Confidence 7999999999999999988773
No 21
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=93.61 E-value=0.062 Score=53.30 Aligned_cols=71 Identities=20% Similarity=0.355 Sum_probs=63.4
Q ss_pred chhHHhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEeccccc
Q 015104 292 HEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTER 363 (413)
Q Consensus 292 ~~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R 363 (413)
-+..++..|++-+-.+|.- +..||.+-+|+.|+.+++|.|.|+++.|+...|++|||..-|.|.+...++-
T Consensus 328 l~~F~E~ARl~ifEtfCRI-HqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~~~s 398 (432)
T KOG2758|consen 328 LDEFLENARLLIFETFCRI-HQCITIDMLADKLNMDPEEAERWIVNLIRTARLDAKIDSKLGHVVMGHPTVS 398 (432)
T ss_pred HHHHHHHHHHHHHHHHHHH-HHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhhhhhccccCceeecCCCCC
Confidence 4567889999999888876 5789999999999999999999999999999999999999999998765543
No 22
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=90.46 E-value=0.32 Score=52.67 Aligned_cols=123 Identities=14% Similarity=0.154 Sum_probs=87.7
Q ss_pred cCCCccccccccchhh--hHHHHHHHHHHHhhcccchhccccch---hhhhhcCCcchhHHhhhhhhhhhccCCC---CC
Q 015104 241 LLDMPAIGQLENDAKY--ASVYQLLKIFLTQRLDGYLEFQAGNS---ALLKSYGLVHEDCIAKMRLMSLVDLGSN---ES 312 (413)
Q Consensus 241 LL~~p~v~~L~~~~~~--~~l~~LL~~f~~G~l~~f~~~~~~~~---~~l~~~~l~~~~~~~KirLLaL~~L~~~---~~ 312 (413)
.|.+..-+++.|.|+. .-+..-=+++..||+.+-.+|.-.+- +++....-....+.++|+--+|-...|+ -+
T Consensus 637 ~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y 716 (843)
T KOG1076|consen 637 QLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSVY 716 (843)
T ss_pred HHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 4444455556554332 23445567888999988777643321 1121100012344688888887777665 36
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEeccccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTER 363 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R 363 (413)
.++|.+.+|+-+.+|+..|-..|-+.|...=|.+++||+.++|.++++.|-
T Consensus 717 ~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrvE~s 767 (843)
T KOG1076|consen 717 DSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVMHRVEPS 767 (843)
T ss_pred hhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEEeeccch
Confidence 789999999999999999999999999999999999999999999998774
No 23
>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=88.05 E-value=0.36 Score=42.36 Aligned_cols=81 Identities=12% Similarity=0.159 Sum_probs=53.0
Q ss_pred hhhhHHHHHHHHHHHhhcccchhccccc--hhhhhhcCCcchhHHhhhhhhhhhccCCCCCCCcchhhhhhccccCcchh
Q 015104 254 AKYASVYQLLKIFLTQRLDGYLEFQAGN--SALLKSYGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEV 331 (413)
Q Consensus 254 ~~~~~l~~LL~~f~~G~l~~f~~~~~~~--~~~l~~~~l~~~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eV 331 (413)
+.-..+..|...+-.|++.+|-.....+ ++.+.. ....+..++|--.+--+... +.+|+.+.+++-||++++++
T Consensus 39 ~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~---~v~~~~~~iR~~i~~~i~~a-Y~sIs~~~la~~Lg~~~~el 114 (143)
T PF10075_consen 39 PEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKP---FVPGFEDTIRERIAHLISKA-YSSISLSDLAEMLGLSEEEL 114 (143)
T ss_dssp TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHH---TSTTHHHHHHHHHHHHHHHH--SEE-HHHHHHHTTS-HHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHH---HHHHHHHHHHHHHHHHHHHH-HhHcCHHHHHHHhCCCHHHH
Confidence 4566788899999999999988765543 122221 13445566665555444444 78999999999999998899
Q ss_pred hhHHhhh
Q 015104 332 EKWVVKA 338 (413)
Q Consensus 332 E~lvi~a 338 (413)
+.++.+-
T Consensus 115 ~~~~~~~ 121 (143)
T PF10075_consen 115 EKFIKSR 121 (143)
T ss_dssp HHHHHHH
T ss_pred HHHHHHc
Confidence 9888764
No 24
>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=86.56 E-value=0.18 Score=38.71 Aligned_cols=35 Identities=11% Similarity=0.191 Sum_probs=29.8
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
.+.+|+++||.+|+++++.||..+=.-++.|.|+-
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~ 46 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRK 46 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEE
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence 57899999999999999999999999999998873
No 25
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=84.32 E-value=6 Score=43.97 Aligned_cols=244 Identities=14% Similarity=0.165 Sum_probs=122.6
Q ss_pred hhcCccccccccchhchHHHHhhhc--cCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhc-cC-CccchhhHHHH
Q 015104 146 AVNGKVTEHIIPSFKKIDSFLKEWN--IDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATF-SG-EDAHTMDEAKE 221 (413)
Q Consensus 146 a~~~~~~~~~~~~l~~~~~~L~~w~--~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~-~~-~~~~~~~e~~~ 221 (413)
|...+.-...-.+++.+...+.--. .-+.--..||..++.++-.+ |++---...+++|...+ +. .++ +.++.+.
T Consensus 242 Ai~lELWQEAyrSiEDIhgLm~lSKrtPkp~~laNYY~KL~~VF~~s-gn~LfHAaAw~k~f~l~k~~~K~~-Tqde~q~ 319 (988)
T KOG2072|consen 242 AIELELWQEAYRSIEDIHGLMKLSKRTPKPSTLANYYEKLAKVFWKS-GNPLFHAAAWLKLFKLYKNMNKNL-TQDELQR 319 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHhc-CcHHHHHHHHHHHHHHHHHhcccc-cHHHHHH
Confidence 3333444444445555555444222 22345677888888887764 43211112233344333 11 233 4577888
Q ss_pred HHHHHHHhhhcCCCccc---c-ccCCCcccc-----------ccccch-hhhHHHHHHH----HHHHhhcccchhcccc-
Q 015104 222 EAVRTIIEFVKSPDMFQ---C-DLLDMPAIG-----------QLENDA-KYASVYQLLK----IFLTQRLDGYLEFQAG- 280 (413)
Q Consensus 222 ~a~~lii~aL~~~~i~~---f-eLL~~p~v~-----------~L~~~~-~~~~l~~LL~----~f~~G~l~~f~~~~~~- 280 (413)
.|-..+.++|.-|-.+. + -++..+... .|...| ...-+.+++. .+...++.+.-.+++.
T Consensus 320 ~as~VlLaaLSIP~~~~~~~~~r~~e~e~~~~ek~~rla~LL~L~~~PTR~~ll~e~v~~gV~~~v~qe~kdLY~iLEve 399 (988)
T KOG2072|consen 320 MASRVLLAALSIPIPDARSDSARLIEIEDIGKEKNLRLANLLGLPAPPTRKGLLKEAVREGVLSKVDQEVKDLYNILEVE 399 (988)
T ss_pred HHHHHHHHHhcCCCCCcccccccccccccchhhHHHHHHHHhCCCCCccHHHHHHHHHHhccHhhhhHHHHHHHHHHHhc
Confidence 89999999998884443 2 134333320 011111 1111222211 1222222222222211
Q ss_pred -ch-----------hhhhhcCCcchhHH---hhhhhhhhhccCCCCCCCcchhhhhhccc-cCcchhhhHHhhhhhhccc
Q 015104 281 -NS-----------ALLKSYGLVHEDCI---AKMRLMSLVDLGSNESGQIPYGLIKDTLQ-INNDEVEKWVVKARTAKLM 344 (413)
Q Consensus 281 -~~-----------~~l~~~~l~~~~~~---~KirLLaL~~L~~~~~r~isy~~Ia~~l~-i~~~eVE~lvi~aI~~gLI 344 (413)
|| +.++..| .+.+++ ++.-++-|..-++.-+.+|+|+.+.+-.- ++.-++|.++|+|-..+-+
T Consensus 400 F~PL~l~k~lq~ll~~ls~~~-~~~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v 478 (988)
T KOG2072|consen 400 FHPLKLCKKLQPLLDKLSESP-DKSQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDV 478 (988)
T ss_pred CCHHHHHHHHHHHHHHHHcCC-CccccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccce
Confidence 12 1122111 123333 44444444433333466888888877422 3567999999999999999
Q ss_pred cccccccccEEEEec---cccccc---c----hhhHHHHHhhhhhhhhhHHHHHHHhh
Q 015104 345 DCKMDQMNQVVIVRR---CTERVF---G----QHQWQTLRTKLSTWRANVANVISTIQ 392 (413)
Q Consensus 345 ~gkIDQv~~~v~vt~---v~~R~~---~----~~q~~~L~~rL~~W~~~v~~~~~~v~ 392 (413)
.-+||-..++|.... ...++= | .---+.+++.|..-.+.+..+...+.
T Consensus 479 ~iriDH~~~~v~FgsDl~~s~~~~~~eg~~lqs~~sE~ir~~L~~m~~~L~~~~e~~d 536 (988)
T KOG2072|consen 479 SIRIDHESNSVSFGSDLFLSKEEDEPEGPELQSMPSEGIRSQLTAMAESLSKVVEELD 536 (988)
T ss_pred eEEeccccceeeeccccccccccccCCCchhhcCchHhHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999872 211111 1 11134455556665556555555554
No 26
>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=82.45 E-value=2.2 Score=39.26 Aligned_cols=160 Identities=14% Similarity=0.175 Sum_probs=79.7
Q ss_pred chhchHHHHhhhccCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCC--ccchhhHHHHHHHHHHHhhhcCCC
Q 015104 158 SFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGE--DAHTMDEAKEEAVRTIIEFVKSPD 235 (413)
Q Consensus 158 ~l~~~~~~L~~w~~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~--~~~~~~e~~~~a~~lii~aL~~~~ 235 (413)
.+..+..=+.--++.......+|..++..+-.. ++..++-+.+......|... ...+..+..=.++.++ ..+....
T Consensus 37 rlRsiRqDl~vQ~~~~~~~i~v~E~~ar~~i~~-~d~~qf~~c~~~L~~lY~~~~~~~~~~~~~ef~~y~lL-~~l~~~~ 114 (204)
T PF03399_consen 37 RLRSIRQDLTVQNIENDFAIKVYERIARFAIES-GDLEQFNQCLSQLKELYDDLRDLPPSPNEAEFIAYYLL-YLLCQNN 114 (204)
T ss_dssp HHHHHHHHHHHTT--SHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHT---TTHHHHHHHHHH-HTT-T--
T ss_pred HhHHHHhhHHHHhcCCHHHHHHHHHHHHHHhhc-CCHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHH-HHHHccc
Confidence 333333333333445555677777777766543 33333333333333333221 0011122222344433 3443332
Q ss_pred cccc--ccCCCccccccccchhhhHHHHHHHHHHHhhcccchhcc--ccchhhhhhcCCcchhHHhhhhhhhhhccCCCC
Q 015104 236 MFQC--DLLDMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQ--AGNSALLKSYGLVHEDCIAKMRLMSLVDLGSNE 311 (413)
Q Consensus 236 i~~f--eLL~~p~v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~--~~~~~~l~~~~l~~~~~~~KirLLaL~~L~~~~ 311 (413)
.-.| .+...|. .+.+++...-..++..++..||+..|.... .+.|.+... .-+....+||..++..++..
T Consensus 115 ~~~~~~~l~~l~~--~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~---l~~~~~~~iR~~al~~i~~a- 188 (204)
T PF03399_consen 115 IPDFHMELELLPS--EILSSPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLFAC---LMERFFNRIRLRALQSISKA- 188 (204)
T ss_dssp -THHHHHHTTS-H--HHHTSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHH---HHGGGHHHHHHHHHHHHHHH-
T ss_pred chHHHHHHHHCch--hhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHH---HHHHHHHHHHHHHHHHHHHH-
Confidence 2233 3333432 133344556677899999999999998876 333333221 12346789999999999876
Q ss_pred CCC-cchhhhhhccc
Q 015104 312 SGQ-IPYGLIKDTLQ 325 (413)
Q Consensus 312 ~r~-isy~~Ia~~l~ 325 (413)
++. +|.+.+++-|+
T Consensus 189 y~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 189 YRSSIPLSFLAELLG 203 (204)
T ss_dssp S-T-EEHHHHHHHTT
T ss_pred cCCCCCHHHHHHHcC
Confidence 666 88888877654
No 27
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=81.35 E-value=10 Score=36.97 Aligned_cols=142 Identities=11% Similarity=0.115 Sum_probs=86.4
Q ss_pred hhhHHHHHHHhHhhcC-ccccccccchhchHHHHhhhccCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCCc
Q 015104 134 SRFFVYMKALNLAVNG-KVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGED 212 (413)
Q Consensus 134 ~r~~v~~~il~~a~~~-~~~~~~~~~l~~~~~~L~~w~~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~~ 212 (413)
.=+.++..+-++-... ++.+.......++-.+...=+ .......++..++.++... +++.++....-+....+....
T Consensus 112 ~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~-~~~~a~~~~~~~A~l~~~l-~~y~~A~~~~e~~~~~~l~~~ 189 (282)
T PF14938_consen 112 QAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG-SPHSAAECLLKAADLYARL-GRYEEAIEIYEEVAKKCLENN 189 (282)
T ss_dssp HHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHT-T-HHHHHHHHHHHHHTCCCHC
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC-ChhhHHHHHHHHHHHHHHh-CCHHHHHHHHHHHHHHhhccc
Confidence 3355555555555555 666666666666666665444 4566678888888888774 678888888777666554333
Q ss_pred cchhhHHHHHHHHHHHhhhcCCCccc----c-ccCC-CccccccccchhhhHHHHHHHHHHHhhcccchhccccc
Q 015104 213 AHTMDEAKEEAVRTIIEFVKSPDMFQ----C-DLLD-MPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGN 281 (413)
Q Consensus 213 ~~~~~e~~~~a~~lii~aL~~~~i~~----f-eLL~-~p~v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~ 281 (413)
+.. ..+++..+..++.-|...+.-. | +... .|.+ .++.++.-+.+|+.+|..||.+.|.+.....
T Consensus 190 l~~-~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F---~~s~E~~~~~~l~~A~~~~D~e~f~~av~~~ 260 (282)
T PF14938_consen 190 LLK-YSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSF---ASSREYKFLEDLLEAYEEGDVEAFTEAVAEY 260 (282)
T ss_dssp TTG-HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTS---TTSHHHHHHHHHHHHHHTT-CCCHHHHCHHH
T ss_pred ccc-hhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCC---CCcHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 321 2355666677776666555432 2 1221 2433 3345788899999999999999998765443
No 28
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=77.24 E-value=0.88 Score=42.15 Aligned_cols=59 Identities=5% Similarity=0.126 Sum_probs=41.1
Q ss_pred hhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEec
Q 015104 300 RLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRR 359 (413)
Q Consensus 300 rLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~ 359 (413)
-|-.+++.+.. .+.+...++|..+|+...+|-.-|-.....|.|.|-||.-..-|+||-
T Consensus 100 lL~~Fi~yIK~-~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~ 158 (188)
T PF09756_consen 100 LLQEFINYIKE-HKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISE 158 (188)
T ss_dssp HHHHHHHHHHH--SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---
T ss_pred HHHHHHHHHHH-cceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecH
Confidence 34445555554 689999999999999999999999999999999999999888888883
No 29
>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=77.04 E-value=2 Score=34.04 Aligned_cols=58 Identities=16% Similarity=0.229 Sum_probs=41.6
Q ss_pred hhhhhhhccCCC-CCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEec
Q 015104 299 MRLMSLVDLGSN-ESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRR 359 (413)
Q Consensus 299 irLLaL~~L~~~-~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~ 359 (413)
+|+|..+ +.. ..+.+|-++||+.+++|+..|+..+=+.-..|+|+.+ -..++-....+
T Consensus 11 l~~l~~l--a~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~-~G~~GGy~L~~ 69 (83)
T PF02082_consen 11 LRILLYL--ARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS-RGRGGGYRLAR 69 (83)
T ss_dssp HHHHHHH--HCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE-TSTTSEEEESS
T ss_pred HHHHHHH--HhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec-CCCCCceeecC
Confidence 3444444 433 2345999999999999999999999999999998654 24466666665
No 30
>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=72.03 E-value=2.1 Score=30.64 Aligned_cols=46 Identities=11% Similarity=0.244 Sum_probs=35.3
Q ss_pred hhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 300 RLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 300 rLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
|-+.+++......+.++..+|++.+|+|..-|-.++-.....|+|+
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 4455666655434568999999999999999999988888888764
No 31
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=65.76 E-value=14 Score=31.98 Aligned_cols=78 Identities=12% Similarity=0.226 Sum_probs=59.9
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccc-ccc-ccccEEEEecccccccchhhHH-HHHhhhhhhhhhHHHHH
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC-KMD-QMNQVVIVRRCTERVFGQHQWQ-TLRTKLSTWRANVANVI 388 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g-kID-Qv~~~v~vt~v~~R~~~~~q~~-~L~~rL~~W~~~v~~~~ 388 (413)
++.++-++||+.++.+..-|..-|=+.+..|||.= +.. .-.|-.++..+ .+.+++. .+...|+.|.+++.+.+
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~----i~~ee~k~~i~~~l~~w~~~~~~~i 115 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKP----IDPEEIKKKILKDLDEWYDKMKQLI 115 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEec----CCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999943 333 23334445433 3345544 57788999999999998
Q ss_pred HHhhh
Q 015104 389 STIQA 393 (413)
Q Consensus 389 ~~v~~ 393 (413)
+..+.
T Consensus 116 ~~~~~ 120 (126)
T COG3355 116 EEFEK 120 (126)
T ss_pred HHHhc
Confidence 88765
No 32
>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=63.53 E-value=3.8 Score=29.27 Aligned_cols=28 Identities=25% Similarity=0.438 Sum_probs=21.7
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
...||++||+.+|+++..|..++-+|..
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 3589999999999999999999988864
No 33
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=63.28 E-value=3.3 Score=36.73 Aligned_cols=35 Identities=14% Similarity=0.324 Sum_probs=32.9
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
+...||++||+.+|+++..|-.=+=+....|.|+|
T Consensus 21 d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 21 NARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 56799999999999999999999999999999985
No 34
>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=62.95 E-value=6.2 Score=34.21 Aligned_cols=47 Identities=26% Similarity=0.376 Sum_probs=38.6
Q ss_pred hhhhhhccCCC-CCCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 300 RLMSLVDLGSN-ESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 300 rLLaL~~L~~~-~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
-+.+++.|+.. +.+.+|-++||+.+++|...|+..+-+.-.+|+|..
T Consensus 10 Al~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 10 AVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 35556666654 245799999999999999999999999999999974
No 35
>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=61.67 E-value=5.3 Score=34.21 Aligned_cols=36 Identities=19% Similarity=0.174 Sum_probs=33.2
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhcccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCK 347 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gk 347 (413)
.+.+|..+|++.+++|..-|...+-+.-..|+|.+.
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 467999999999999999999999999999999764
No 36
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=60.63 E-value=5.4 Score=35.55 Aligned_cols=46 Identities=13% Similarity=-0.003 Sum_probs=36.5
Q ss_pred hhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcccccc
Q 015104 302 MSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCK 347 (413)
Q Consensus 302 LaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gk 347 (413)
.+|+.|+..+.+.+|-++||+..+||...++..+-+.-.+|+|+..
T Consensus 12 r~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~ 57 (153)
T PRK11920 12 RMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETV 57 (153)
T ss_pred HHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence 3444444433456899999999999999999999999999998654
No 37
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=57.82 E-value=6.4 Score=37.73 Aligned_cols=47 Identities=9% Similarity=0.202 Sum_probs=42.2
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEe
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVR 358 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt 358 (413)
++.++++++|.++|+-..++=.=+=..+..|+|.|-||.-.+-++|+
T Consensus 212 nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 212 NKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred cCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 68999999999999987766667777888999999999999999998
No 38
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=56.89 E-value=8.6 Score=34.74 Aligned_cols=49 Identities=20% Similarity=0.382 Sum_probs=39.7
Q ss_pred hhhhhhhhccCCC-CCCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 298 KMRLMSLVDLGSN-ESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 298 KirLLaL~~L~~~-~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
..-|.+++.+++. +.+.+|-++||+.+++|..-|+..+-+.-.+|||..
T Consensus 8 ~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 8 RYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 3445555555554 245799999999999999999999999999999985
No 39
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=56.12 E-value=16 Score=38.41 Aligned_cols=169 Identities=13% Similarity=0.131 Sum_probs=96.9
Q ss_pred cccccccchhchHHHHhhhccCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCCccchhhHHHHHHHHHHHhh
Q 015104 151 VTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGEDAHTMDEAKEEAVRTIIEF 230 (413)
Q Consensus 151 ~~~~~~~~l~~~~~~L~~w~~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~~~~~~~e~~~~a~~lii~a 230 (413)
+...+..+++.+..-|.=-.+-..-...+|..-|.+.-+ +|+..+|=++--..-.-|.. ... ....+++.+-++-.
T Consensus 322 ~Y~y~CdQ~KSiRQDLTVQ~IrneFTveVYEtHARIALE-kGD~~EfNQCQtQLk~LY~e-gip--g~~~EF~AYriLY~ 397 (540)
T KOG1861|consen 322 NYAYLCDQFKSIRQDLTVQRIRNEFTVEVYETHARIALE-KGDLEEFNQCQTQLKALYSE-GIP--GAYLEFTAYRILYY 397 (540)
T ss_pred cHHHHHHHHHHHhhhhhhheeccceeeeeehhhhHHHHh-cCCHHHHHHHHHHHHHHHcc-CCC--CchhhHHHHHHHHH
Confidence 455555555555554543344444456778888887777 57777776554433333322 111 11334555545544
Q ss_pred hcCCCccccccCC-Cccc-cccccchhhhHHHHHHHHHHHhhcccchhccccchhhhhhcCCcchhHHhhhhhhhhhccC
Q 015104 231 VKSPDMFQCDLLD-MPAI-GQLENDAKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLG 308 (413)
Q Consensus 231 L~~~~i~~feLL~-~p~v-~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~l~~~~~~~KirLLaL~~L~ 308 (413)
+...+.- |++. +..+ ..++.++--.-.+++=.+...|||-.|..+...-|.+ . |..-+.++.+.|..+|.=+|
T Consensus 398 i~tkN~~--di~sll~~lt~E~ked~~V~hAL~vR~A~~~GNY~kFFrLY~~AP~M-~--~yLmdlF~erER~~Al~ii~ 472 (540)
T KOG1861|consen 398 IFTKNYP--DILSLLRDLTEEDKEDEAVAHALEVRSAVTLGNYHKFFRLYLTAPNM-S--GYLMDLFLERERKKALTIIC 472 (540)
T ss_pred HHhcCch--HHHHHHHhccHhhccCHHHHHHHHHHHHHHhccHHHHHHHHhhcccc-h--hHHHHHHHHHHHHHHHHHHH
Confidence 4433221 2111 0111 1122222223355777788999999998876444432 1 22345668899999999999
Q ss_pred CCCCC-CcchhhhhhccccCcc
Q 015104 309 SNESG-QIPYGLIKDTLQINND 329 (413)
Q Consensus 309 ~~~~r-~isy~~Ia~~l~i~~~ 329 (413)
.. +| +||++-|++.+....-
T Consensus 473 Ks-yrP~i~~~fi~~~laf~~~ 493 (540)
T KOG1861|consen 473 KS-YRPTITVDFIASELAFDSM 493 (540)
T ss_pred HH-cCCCccHHHHhhhhhhchH
Confidence 87 77 8999999998887653
No 40
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=55.32 E-value=9.5 Score=30.48 Aligned_cols=53 Identities=21% Similarity=0.386 Sum_probs=43.8
Q ss_pred hhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcccccccc
Q 015104 297 AKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMD 349 (413)
Q Consensus 297 ~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkID 349 (413)
.-.|+|.-+++.-+++.-+|.+.|.+..+++..+|+.-+-+.+..|||.-+.-
T Consensus 7 ~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~ 59 (82)
T PF09202_consen 7 EDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNK 59 (82)
T ss_dssp HHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-S
T ss_pred HHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCC
Confidence 45788999999887778899999999999999999999999999999987443
No 41
>PF05369 MtmB: Monomethylamine methyltransferase MtmB; InterPro: IPR008031 Monomethylamine methyltransferase of the archaebacterium Methanosarcina barkeri contains a novel amino acid, pyrrolysine, encoded by the termination codon UAG []. The structure of the enzyme reveals a homohexamer comprised of individual subunits with a TIM barrel fold. MtmB initiates the metabolism of monomethylamine by catalysing the transfer of the methyl group from monomethylamine to the corrinoid cofactor of MtmC.; GO: 0008168 methyltransferase activity
Probab=55.01 E-value=15 Score=38.05 Aligned_cols=69 Identities=20% Similarity=0.231 Sum_probs=52.0
Q ss_pred eeecccccccccCCcchhHHHHHHHHHHHhhhhhhhhhhHHHHHhhhhhhhhccC-CCCcchhheeeehhcccCCCChhH
Q 015104 17 VRFTSELAWADAGPEAAEEQVNRLCLEAQESMVMGRWMDLASLMLTSADLMFSKV-SDKDLECIFTVICNLVTKPESLDE 95 (413)
Q Consensus 17 ~~~~~~~~~~~~~~~~a~~e~~~~~~~~e~l~~~klw~qLt~~l~~~~~~~~~~~-~dke~e~~~n~i~~lv~~~~~~~~ 95 (413)
+||.+|.+.+-++-+++ +++.++..+=.+|+++ |+.. ..|+|+.+|++- .+.+.++
T Consensus 382 arfmaEva~a~a~~~ls--evN~i~~~i~~~Ye~~----------------~~~~p~Gk~F~EcYdv~-----t~~Pt~E 438 (457)
T PF05369_consen 382 ARFMAEVARAVAGMDLS--EVNDILDKIVAKYEKN----------------YSSAPKGKPFQECYDVN-----TMQPTDE 438 (457)
T ss_pred HHHHHHHHHHHhcccHH--HHHHHHHHHHHHhhhc----------------cccCCCCCChHHHhccc-----ccCCcHH
Confidence 48999999887776666 7888999888888864 3333 358998899976 3567788
Q ss_pred HHHHHHHHHhhhh
Q 015104 96 VHEMTKLISGKII 108 (413)
Q Consensus 96 ~l~~v~~l~~~~~ 108 (413)
.+++.+.+..++.
T Consensus 439 Y~~~Y~~~~k~l~ 451 (457)
T PF05369_consen 439 YMNVYDKAKKELE 451 (457)
T ss_pred HHHHHHHHHHHHH
Confidence 8888887766554
No 42
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=52.61 E-value=6 Score=34.53 Aligned_cols=40 Identities=5% Similarity=0.158 Sum_probs=34.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhccccccccccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMN 352 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~ 352 (413)
..+||.+||+.+|+|...|=.-|=+....|+|+|.-=.++
T Consensus 21 ~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~ 60 (154)
T COG1522 21 ARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLD 60 (154)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEEC
Confidence 4599999999999999999999999999999988644444
No 43
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=52.56 E-value=9.1 Score=34.31 Aligned_cols=35 Identities=9% Similarity=0.134 Sum_probs=32.8
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
+..+||.+||+.+|++..-|-.=+=+....|.|+|
T Consensus 26 d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 26 DGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 57899999999999999999999999999999986
No 44
>PF13730 HTH_36: Helix-turn-helix domain
Probab=52.48 E-value=16 Score=26.05 Aligned_cols=48 Identities=15% Similarity=0.240 Sum_probs=36.4
Q ss_pred hhhhhhhhhccCCCCCCC-cchhhhhhccccCcchhhhHHhhhhhhccc
Q 015104 297 AKMRLMSLVDLGSNESGQ-IPYGLIKDTLQINNDEVEKWVVKARTAKLM 344 (413)
Q Consensus 297 ~KirLLaL~~L~~~~~r~-isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI 344 (413)
.|+-++.|.+.+..+... -|++.||+.+|++..-|...+-+....|+|
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 456666777777542223 379999999999999999888888888775
No 45
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=52.45 E-value=6.4 Score=32.28 Aligned_cols=35 Identities=9% Similarity=0.191 Sum_probs=32.3
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
+..+|+.+|++.+|++...|-..+-+....|+|++
T Consensus 15 ~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 15 DARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 35699999999999999999999999999999985
No 46
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=52.05 E-value=8.7 Score=30.24 Aligned_cols=48 Identities=8% Similarity=0.206 Sum_probs=37.5
Q ss_pred hhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcccccc
Q 015104 300 RLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCK 347 (413)
Q Consensus 300 rLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gk 347 (413)
|.+.++++.....+.++..+|++.++++..-|-..+-.....|+|...
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 334445544432257999999999999999999999999999999753
No 47
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=51.62 E-value=20 Score=28.15 Aligned_cols=43 Identities=9% Similarity=0.131 Sum_probs=36.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEE
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVV 355 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v 355 (413)
+.++..+|++.++++...|-..|-+....|+|.-.-++.++..
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~ 65 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRS 65 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCe
Confidence 4689999999999999999999999999999987777654433
No 48
>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=50.08 E-value=14 Score=31.49 Aligned_cols=35 Identities=23% Similarity=0.300 Sum_probs=32.1
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
...+|.++||+.+++|...|...+-+....|+|..
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~ 57 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVES 57 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 34799999999999999999999999999999975
No 49
>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=47.43 E-value=13 Score=26.16 Aligned_cols=28 Identities=18% Similarity=0.240 Sum_probs=23.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
...||++||+.+|++..-|-.+.-+|+.
T Consensus 19 ~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp ST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 4689999999999999999888888764
No 50
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=46.04 E-value=9.6 Score=29.04 Aligned_cols=33 Identities=9% Similarity=0.001 Sum_probs=30.9
Q ss_pred CcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
.++-.+||+++|++...|...+-+....|+|.-
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 499999999999999999999999999999865
No 51
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=44.82 E-value=21 Score=24.90 Aligned_cols=33 Identities=21% Similarity=0.388 Sum_probs=28.2
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
+..+..+|++.++++...|-+-+=.....|+|+
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 678999999999999999988888888888874
No 52
>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=43.96 E-value=19 Score=29.39 Aligned_cols=52 Identities=12% Similarity=0.183 Sum_probs=40.3
Q ss_pred hhhhhhhhcc-CCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccc
Q 015104 298 KMRLMSLVDL-GSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQ 350 (413)
Q Consensus 298 KirLLaL~~L-~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQ 350 (413)
+-+++.++.- +.. ..=++.++|++.|+++.++|+.-|=..+..|.|=-.||.
T Consensus 49 ~~~Vl~~i~~~~~~-~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 49 QDKVLNFIKQQPNS-EEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHHHC-----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred HHHHHHHHHhcCCC-CCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 4556666666 333 345999999999999999999999999999999888875
No 53
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=43.73 E-value=16 Score=25.38 Aligned_cols=34 Identities=18% Similarity=0.338 Sum_probs=28.3
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
+..+|-.+||+.+|++..-|-..+=+....|+|+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 3569999999999999999999999999898874
No 54
>PRK10870 transcriptional repressor MprA; Provisional
Probab=43.45 E-value=49 Score=29.99 Aligned_cols=52 Identities=8% Similarity=0.065 Sum_probs=44.0
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEeccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTER 363 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R 363 (413)
...++..+|++.++++..-|=..|=+....|+|.-.-|..++....-..++.
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~ 120 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEK 120 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHH
Confidence 4679999999999999999999999999999999999988876655444443
No 55
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=42.89 E-value=30 Score=32.85 Aligned_cols=48 Identities=4% Similarity=0.079 Sum_probs=42.2
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEec
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRR 359 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~ 359 (413)
...+|..+||+.++++..-+=..|-+.-..|+|.-..+...+.+.+|-
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTe 66 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITE 66 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECH
Confidence 457999999999999999999999999999999999887777777763
No 56
>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=42.75 E-value=5.1 Score=27.73 Aligned_cols=22 Identities=18% Similarity=0.480 Sum_probs=16.1
Q ss_pred CCCcchhhhhhccccCcchhhh
Q 015104 312 SGQIPYGLIKDTLQINNDEVEK 333 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~ 333 (413)
+...||.+||+.+|++...|-.
T Consensus 15 d~r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 15 DGRRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp -TTS-HHHHHHHHTS-HHHHHH
T ss_pred cCCccHHHHHHHHCcCHHHHHH
Confidence 4678999999999999877643
No 57
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=42.71 E-value=24 Score=30.14 Aligned_cols=77 Identities=8% Similarity=0.105 Sum_probs=53.2
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHHhhhhhhhhhHHHHHHHhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLRTKLSTWRANVANVISTIQ 392 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~~rL~~W~~~v~~~~~~v~ 392 (413)
+..+..+|++.++++..-|-+-+=..-.+|||..+-+.......+. |.+ .+.+..+-+ ..|......+...++
T Consensus 29 ~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~---~~~--~~~~~~~~~--~~w~~~~~~l~~~l~ 101 (117)
T PRK10141 29 GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLS---PHI--PAWAAKIIE--QAWLCEQEDVQAIVR 101 (117)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEEC---chH--HHHHHHHHH--HHHHHHHHHHHHHHH
Confidence 5689999999999999888888888888999988877554444443 321 122222222 268888877777777
Q ss_pred hccc
Q 015104 393 ATNK 396 (413)
Q Consensus 393 ~~~~ 396 (413)
+..+
T Consensus 102 ~l~~ 105 (117)
T PRK10141 102 NLAR 105 (117)
T ss_pred HHhc
Confidence 6544
No 58
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=42.53 E-value=21 Score=31.72 Aligned_cols=47 Identities=26% Similarity=0.263 Sum_probs=37.9
Q ss_pred hhhhhccCCCC-CCCcchhhhhhccccCcchhhhHHhhhhhhcccccc
Q 015104 301 LMSLVDLGSNE-SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCK 347 (413)
Q Consensus 301 LLaL~~L~~~~-~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gk 347 (413)
+.+|+.|+... .+.+|-++||+..+||+.-++.++-+.-.+|||+..
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~ 58 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSV 58 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEee
Confidence 44555666541 337889999999999999999999999999999654
No 59
>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=41.73 E-value=13 Score=27.93 Aligned_cols=24 Identities=25% Similarity=0.573 Sum_probs=20.9
Q ss_pred CCCcchhhhhhccccCcchhhhHH
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWV 335 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lv 335 (413)
.+.+++.+||+.|||++..|-.|=
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHh
Confidence 578999999999999998887663
No 60
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=41.14 E-value=46 Score=28.66 Aligned_cols=50 Identities=8% Similarity=0.043 Sum_probs=43.3
Q ss_pred CcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEeccccc
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTER 363 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R 363 (413)
.++-.+|++.++++..-|=..|-+....|+|.=.-|..++....-..+++
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~ 95 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEK 95 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChH
Confidence 46789999999999999999999999999999999988887766655554
No 61
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.71 E-value=30 Score=23.72 Aligned_cols=47 Identities=11% Similarity=0.192 Sum_probs=33.6
Q ss_pred cchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHH
Q 015104 315 IPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLR 374 (413)
Q Consensus 315 isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~ 374 (413)
+|-.++|+.+||+..-|..| +..|++.+.-+.. .+|.|+.+++..|+
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~----~~~g~l~~~~~~~---------~~~~y~~~~v~~l~ 47 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYY----ERIGLLSPARTEG---------GYRLYSDADLERLR 47 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCCC---------CCEEeCHHHHHHhh
Confidence 35678999999999999999 4567776432221 35678888877664
No 62
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=38.64 E-value=15 Score=27.56 Aligned_cols=37 Identities=16% Similarity=0.169 Sum_probs=33.4
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKM 348 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkI 348 (413)
.+..|-.+||+.+++|...|-..+=+....|+|+-.-
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 4789999999999999999999999999999996543
No 63
>PF09218 DUF1959: Domain of unknown function (DUF1959); InterPro: IPR012056 [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster []. Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family [, ]. Members of this subgroup include: Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli CO-induced hydrogenase (Coo) from Rhodospirillum rubrum Mbh hydrogenase from Pyrococcus furiosus Eha and Ehb hydrogenases from Methanothermobacter species Ech hydrogenase from Methanosarcina barkeri Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA IPR011306 from INTERPRO, EhaB IPR011314 from INTERPRO, EhaC IPR011316 from INTERPRO, EhaD IPR011308 from INTERPRO, EhaE IPR011317 from INTERPRO, EhaF IPR011313 from INTERPRO, EhaG IPR011311 from INTERPRO, EhaI IPR011318 from INTERPRO, EhaK IPR011319 from INTERPRO, EhaL IPR011305 from INTERPRO) and four hydrophobic subunits (EhaM, EhaR IPR014502 from INTERPRO, EhS, EhT) []. The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. This entry represents proteins that are predicted to be the hydrophilic EhaM subunits of Eha-type energy-converting [NiFe] hydrogenase complexes.; PDB: 1NXH_B.
Probab=38.49 E-value=33 Score=29.28 Aligned_cols=41 Identities=10% Similarity=0.158 Sum_probs=32.5
Q ss_pred hhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHHhhhhhhhhhH
Q 015104 318 GLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLRTKLSTWRANV 384 (413)
Q Consensus 318 ~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~~rL~~W~~~v 384 (413)
-.|+++||||.++|+..+|+. ++..-.++|+.|.++|+-.+
T Consensus 17 ~plSk~lgi~~ee~~~ili~~--------------------------~DmssLe~lhar~E~Ak~~c 57 (117)
T PF09218_consen 17 IPLSKELGISIEEFIDILIEK--------------------------LDMSSLENLHARYEQAKMGC 57 (117)
T ss_dssp TTTTTTGGGTHHHHHHHHHHH--------------------------S-HHHHHHHHHHHHTTHHHH
T ss_pred HHHHHHhCcCHHHHHHHHHHh--------------------------cChHHHHhccHHHHHHhhhh
Confidence 357899999999999999985 45567778888888887654
No 64
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=37.90 E-value=54 Score=27.24 Aligned_cols=50 Identities=10% Similarity=0.090 Sum_probs=41.3
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEeccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCT 361 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~ 361 (413)
+..++..+|++.++++..-|=..|-+....|+|...-|..++....-..+
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT 89 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLT 89 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEEC
Confidence 35789999999999999999999999999999999988777654443333
No 65
>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=37.16 E-value=15 Score=28.77 Aligned_cols=31 Identities=13% Similarity=0.019 Sum_probs=25.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhcc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKL 343 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gL 343 (413)
..+||++||+.+++|+.-|..++-+-.+.|.
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~ 61 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETKAGG 61 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcccch
Confidence 5689999999999999999988876555554
No 66
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=36.42 E-value=16 Score=26.81 Aligned_cols=40 Identities=10% Similarity=0.238 Sum_probs=29.4
Q ss_pred hhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcc
Q 015104 303 SLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKL 343 (413)
Q Consensus 303 aL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gL 343 (413)
.++++... .+.++.+++|+.++|+..-+-.-+.+.-..|+
T Consensus 4 ~Il~~l~~-~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~ 43 (57)
T PF08220_consen 4 QILELLKE-KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGL 43 (57)
T ss_pred HHHHHHHH-cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 34444444 57899999999999998777776666655555
No 67
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=34.71 E-value=36 Score=24.73 Aligned_cols=36 Identities=14% Similarity=0.302 Sum_probs=32.3
Q ss_pred cchhhhhhccccCcchhhhHHhhhhhhccccccccc
Q 015104 315 IPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQ 350 (413)
Q Consensus 315 isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQ 350 (413)
+++.+|++.++++...+-..+-.....|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 999999999999999999999888899999876555
No 68
>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=34.07 E-value=25 Score=25.79 Aligned_cols=35 Identities=20% Similarity=0.325 Sum_probs=30.4
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
.+..+..+|++.++++...+-+-+=.....|+|+.
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 46899999999999999999999888889999875
No 69
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=33.58 E-value=24 Score=31.65 Aligned_cols=28 Identities=14% Similarity=0.216 Sum_probs=25.6
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||++||+.+|+|..-|...+.+|..
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 4689999999999999999999999864
No 70
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=32.63 E-value=50 Score=23.23 Aligned_cols=35 Identities=20% Similarity=0.353 Sum_probs=30.5
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhcccccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCK 347 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gk 347 (413)
+.+++.+|++.++++...|-..+=+....|++.-.
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 56899999999999999888888888889999743
No 71
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=31.88 E-value=24 Score=25.55 Aligned_cols=40 Identities=15% Similarity=0.245 Sum_probs=33.5
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhccccccccccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMN 352 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~ 352 (413)
..++..+|++.++++..-|-..|=+....|+|.-.-|.-+
T Consensus 20 ~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 20 EELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp SGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 3599999999999999999999999999999987666544
No 72
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=31.65 E-value=33 Score=25.04 Aligned_cols=35 Identities=14% Similarity=0.149 Sum_probs=31.3
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
...+|..+||+.++++..-|...+-+....|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 45799999999999999999999999999988864
No 73
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=31.59 E-value=26 Score=26.03 Aligned_cols=44 Identities=16% Similarity=0.291 Sum_probs=33.5
Q ss_pred hhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 301 LMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 301 LLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
|.++..+... ...++-.+||+.+++++.-|=..+=+.-..|+|+
T Consensus 10 L~~Iy~l~~~-~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 10 LKAIYELSEE-GGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHHC-TSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcC-CCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 3344444444 5789999999999999988888888888888875
No 74
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=31.34 E-value=99 Score=27.69 Aligned_cols=80 Identities=11% Similarity=0.090 Sum_probs=58.2
Q ss_pred CCCCcchhhhhhccc--cCcchhhhHHhhhhhhccccccccccccEEEEecccccccc---hhhHHHHHhhhhhhhhhHH
Q 015104 311 ESGQIPYGLIKDTLQ--INNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFG---QHQWQTLRTKLSTWRANVA 385 (413)
Q Consensus 311 ~~r~isy~~Ia~~l~--i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~---~~q~~~L~~rL~~W~~~v~ 385 (413)
.+|..|..+|...|+ ++-..|...+=.....|.|.+|. -|.-.|.++....|+ .++...|...+....+.+.
T Consensus 13 qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~---~GKqkiY~~~Q~~~~~~s~eel~~ld~ei~~L~~el~ 89 (169)
T PF07106_consen 13 QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKE---YGKQKIYFANQDELEVPSPEELAELDAEIKELREELA 89 (169)
T ss_pred cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeee---ecceEEEeeCccccCCCCchhHHHHHHHHHHHHHHHH
Confidence 378899999999995 66678888888888889998885 455566666655554 6677777777777777766
Q ss_pred HHHHHhhh
Q 015104 386 NVISTIQA 393 (413)
Q Consensus 386 ~~~~~v~~ 393 (413)
.+...+..
T Consensus 90 ~l~~~~k~ 97 (169)
T PF07106_consen 90 ELKKEVKS 97 (169)
T ss_pred HHHHHHHH
Confidence 66655544
No 75
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=31.02 E-value=27 Score=27.51 Aligned_cols=41 Identities=12% Similarity=0.272 Sum_probs=33.0
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhcccccccccccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQ 353 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~ 353 (413)
+.++|.+|++.++++...+-.-+=+.-..|+|+.+-.-..+
T Consensus 13 ~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 13 EEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp SEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 67999999999999999999999999999999877554443
No 76
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=30.88 E-value=27 Score=31.42 Aligned_cols=30 Identities=23% Similarity=0.305 Sum_probs=26.3
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhh
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTA 341 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~ 341 (413)
...+||++||+.+|||..-|...+-+|...
T Consensus 141 ~~gls~~EIA~~l~i~~~tVks~l~ra~~~ 170 (182)
T COG1595 141 LEGLSYEEIAEILGISVGTVKSRLHRARKK 170 (182)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 356999999999999999999999998543
No 77
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=28.50 E-value=36 Score=23.00 Aligned_cols=32 Identities=13% Similarity=0.232 Sum_probs=29.0
Q ss_pred CcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
.++..+||+.++++...|-..+-+....|+|.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 47889999999999999999999999999886
No 78
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=28.29 E-value=3.8e+02 Score=25.81 Aligned_cols=123 Identities=17% Similarity=0.095 Sum_probs=61.3
Q ss_pred chhhHHHHHHHhHhhcCccccccccchhchHHHHhhhccC-chhhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccCC
Q 015104 133 YSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNID-IKDKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSGE 211 (413)
Q Consensus 133 ~~r~~v~~~il~~a~~~~~~~~~~~~l~~~~~~L~~w~~~-~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~~ 211 (413)
.....++..+..+....++++.....++++-...-+-++. ...+.-++..+.-+|.. |+...+-+.+-+|....+.
T Consensus 152 ~~a~~~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~--~D~v~A~~~~~~~~~~~~~- 228 (282)
T PF14938_consen 152 HSAAECLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAM--GDYVAARKALERYCSQDPS- 228 (282)
T ss_dssp HHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHT--T-HHHHHHHHHHHGTTSTT-
T ss_pred hhHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHc--CCHHHHHHHHHHHHhhCCC-
Confidence 4456667677777666777766666665443332111111 12344445555555553 6677777777777764332
Q ss_pred ccchhhHHHHHHHHHHHhhhcCCCcccc-c-cCCCccccccccchhhhHHHHHHHHH
Q 015104 212 DAHTMDEAKEEAVRTIIEFVKSPDMFQC-D-LLDMPAIGQLENDAKYASVYQLLKIF 266 (413)
Q Consensus 212 ~~~~~~e~~~~a~~lii~aL~~~~i~~f-e-LL~~p~v~~L~~~~~~~~l~~LL~~f 266 (413)
-. +..|. ....-++.|....+.=.| + +-..+.+..| ++|...+|...
T Consensus 229 F~-~s~E~--~~~~~l~~A~~~~D~e~f~~av~~~d~~~~l-----d~w~~~~l~~~ 277 (282)
T PF14938_consen 229 FA-SSREY--KFLEDLLEAYEEGDVEAFTEAVAEYDSISRL-----DNWKTKMLLKI 277 (282)
T ss_dssp ST-TSHHH--HHHHHHHHHHHTT-CCCHHHHCHHHTTSS--------HHHHHHHHHH
T ss_pred CC-CcHHH--HHHHHHHHHHHhCCHHHHHHHHHHHcccCcc-----HHHHHHHHHHH
Confidence 11 11332 245556667766554334 2 3334445444 35887777543
No 79
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=28.07 E-value=50 Score=28.64 Aligned_cols=36 Identities=6% Similarity=0.099 Sum_probs=29.5
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhcccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCK 347 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gk 347 (413)
...+|-++||+.++||..-|+..+-+.-..|+|+.+
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~ 58 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAV 58 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEe
Confidence 346788899999999988888888888888888654
No 80
>PRK09191 two-component response regulator; Provisional
Probab=28.05 E-value=1.9e+02 Score=26.80 Aligned_cols=29 Identities=17% Similarity=0.188 Sum_probs=25.6
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTA 341 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~ 341 (413)
..+||++||+.+|+|+.-|...+-+|+..
T Consensus 103 ~~~s~~eIA~~l~~s~~tV~~~l~ra~~~ 131 (261)
T PRK09191 103 EGFSVEEAAEILGVDPAEAEALLDDARAE 131 (261)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46899999999999999999999888653
No 81
>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=27.81 E-value=29 Score=26.55 Aligned_cols=27 Identities=19% Similarity=0.196 Sum_probs=21.0
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhh
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKA 338 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~a 338 (413)
.|.-|.++||+.+|++.++|..++-.+
T Consensus 18 gr~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 18 GREPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp SS--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 588999999999999999999877544
No 82
>PF14964 DUF4507: Domain of unknown function (DUF4507)
Probab=27.78 E-value=6.8e+02 Score=25.69 Aligned_cols=122 Identities=10% Similarity=0.141 Sum_probs=80.4
Q ss_pred hhHHHHHHHHHHHhhhhhh----hhhhHHHHHhhhhhhhhccCCCCcchhheeeehhcccCCCChhHHHHHHHHHHhhhh
Q 015104 33 AEEQVNRLCLEAQESMVMG----RWMDLASLMLTSADLMFSKVSDKDLECIFTVICNLVTKPESLDEVHEMTKLISGKII 108 (413)
Q Consensus 33 a~~e~~~~~~~~e~l~~~k----lw~qLt~~l~~~~~~~~~~~~dke~e~~~n~i~~lv~~~~~~~~~l~~v~~l~~~~~ 108 (413)
.|.-..+....+|.+...+ .-.+.+..|++ +.+|...+++...+. ++ ++.+.+.+++.+|.-+.
T Consensus 15 fp~~a~e~L~~le~l~~~r~~~~~~~~~~~~lie--efiF~~~~~r~~~~~---------~l-n~lQELQLleiL~~yF~ 82 (362)
T PF14964_consen 15 FPSCAKEALSQLEKLCRSRGPSPNQQDELMELIE--EFIFQEPDDRGSQRK---------RL-NALQELQLLEILCDYFQ 82 (362)
T ss_pred hHHHHHHHHHHHHHHHhccCCccccchHHHHHHH--HHHhcCchhccCCCC---------CC-CHHHHHHHHHHHHHHHc
Confidence 3445556677777555543 45556666655 445655444433321 22 34467788888887765
Q ss_pred cCCCCCcchhHHHHHHHhhhhcCc--chhhHHHHHHHhHhhcCccccccccchhchHHHHhhhccC
Q 015104 109 QQPNDKPAMRLKILFNLYNLLENP--YSRFFVYMKALNLAVNGKVTEHIIPSFKKIDSFLKEWNID 172 (413)
Q Consensus 109 ~~~~~~~~~~l~~L~~Lfn~l~~~--~~r~~v~~~il~~a~~~~~~~~~~~~l~~~~~~L~~w~~~ 172 (413)
. ..+...|..+...||..-.++ ..|..++.+++.+|...+ ..+.|+-+--||..-+-+
T Consensus 83 ~--~~~d~~r~~iF~~LF~~~~~~~~~~R~~lL~kLVS~AIa~~----~~~VL~~a~~Wmqq~g~~ 142 (362)
T PF14964_consen 83 E--QSDDAVRYAIFDSLFGGQGDDADESRMSLLSKLVSMAIALP----CVPVLNCAATWMQQLGCS 142 (362)
T ss_pred c--cCCHHHHHHHHHHHcCCCCCchhhHHHHHHHHHHHHHHhcc----cHHHHHHHHHHHHHcCCC
Confidence 3 255678999999998865432 349999999999998765 347788889999985543
No 83
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=27.45 E-value=34 Score=29.47 Aligned_cols=28 Identities=14% Similarity=-0.060 Sum_probs=25.0
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
...|+++||+.+|+|..-|...+-+|+.
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3589999999999999999999988864
No 84
>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=27.44 E-value=34 Score=30.51 Aligned_cols=28 Identities=21% Similarity=0.138 Sum_probs=25.0
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||++||+.+|+|+.-|...+-+|..
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999988754
No 85
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=27.41 E-value=70 Score=22.43 Aligned_cols=33 Identities=9% Similarity=0.181 Sum_probs=29.3
Q ss_pred CCc-chhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 313 GQI-PYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 313 r~i-sy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
..+ |..+||+.++++..-|...+-+.-..|+|.
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 457 899999999999999999999988888875
No 86
>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=27.31 E-value=83 Score=23.50 Aligned_cols=63 Identities=8% Similarity=0.077 Sum_probs=39.5
Q ss_pred HhHhhcCccccccccchhchHHHHhhhccCchhhhHHHHHHHHhhhhcccCchhhHHHHHHHhh
Q 015104 143 LNLAVNGKVTEHIIPSFKKIDSFLKEWNIDIKDKRALFLGIANVLKESRSSSKDSFKFLTKYLA 206 (413)
Q Consensus 143 l~~a~~~~~~~~~~~~l~~~~~~L~~w~~~~~~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~ 206 (413)
-.+-...|+++...+.++++-+.....+-+.......|..++.++.. .|+++++.++.-+.+.
T Consensus 12 a~~~~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~-~g~~~~A~~~~~~al~ 74 (78)
T PF13424_consen 12 ARVYRELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYR-LGDYEEALEYYQKALD 74 (78)
T ss_dssp HHHHHHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHH-TTHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH-cCCHHHHHHHHHHHHh
Confidence 33334456677776666665555444443334557788888998887 4777777777766654
No 87
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=27.28 E-value=41 Score=32.00 Aligned_cols=46 Identities=4% Similarity=0.148 Sum_probs=37.4
Q ss_pred hhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 300 RLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 300 rLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
|-+.++++.....+.++..+|++.+|+|..-+-.++-.....|.+.
T Consensus 10 ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4455555544324679999999999999999999999999999987
No 88
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=27.02 E-value=2.2e+02 Score=29.68 Aligned_cols=187 Identities=13% Similarity=0.165 Sum_probs=92.2
Q ss_pred HHHHHhHhhc---CccccccccchhchHHHHhh--hccCch-hhhHHHHHHHHhhhhcccCchhhHHHHHHHhhhccC--
Q 015104 139 YMKALNLAVN---GKVTEHIIPSFKKIDSFLKE--WNIDIK-DKRALFLGIANVLKESRSSSKDSFKFLTKYLATFSG-- 210 (413)
Q Consensus 139 ~~~il~~a~~---~~~~~~~~~~l~~~~~~L~~--w~~~~~-~~~~~y~~~~~~l~~~~~~~~~~y~~~l~yL~t~~~-- 210 (413)
|.+++.+.+- -||+....+.++.++---.. |.+..- +.--+|-+.+-++-+.=.+.-..+..++.|++....
T Consensus 122 YFSligLlRvh~LLGDY~~Alk~l~~idl~~~~l~~~V~~~~is~~YyvGFaylMlrRY~DAir~f~~iL~yi~r~k~~~ 201 (404)
T PF10255_consen 122 YFSLIGLLRVHCLLGDYYQALKVLENIDLNKKGLYTKVPACHISTYYYVGFAYLMLRRYADAIRTFSQILLYIQRTKNQY 201 (404)
T ss_pred HHHHHHHHHHHHhccCHHHHHHHhhccCcccchhhccCcchheehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3355555543 48888877777654431111 333222 223344444444332112233344555666665541
Q ss_pred -Ccc---chhhHHHHHHHHHH-HhhhcCCCccccccCCCccccccccchhhhHHHHHHHHHHHhhcccchhccc-cchhh
Q 015104 211 -EDA---HTMDEAKEEAVRTI-IEFVKSPDMFQCDLLDMPAIGQLENDAKYASVYQLLKIFLTQRLDGYLEFQA-GNSAL 284 (413)
Q Consensus 211 -~~~---~~~~e~~~~a~~li-i~aL~~~~i~~feLL~~p~v~~L~~~~~~~~l~~LL~~f~~G~l~~f~~~~~-~~~~~ 284 (413)
... +...-..+..+.++ +.-.+.|.. ++-.+...|+. + ..+=+.-..+||++.|+++.. .-|.|
T Consensus 202 ~~~~~q~d~i~K~~eqMyaLlAic~~l~p~~-----lde~i~~~lke--k---y~ek~~kmq~gd~~~f~elF~~acPKF 271 (404)
T PF10255_consen 202 HQRSYQYDQINKKNEQMYALLAICLSLCPQR-----LDESISSQLKE--K---YGEKMEKMQRGDEEAFEELFSFACPKF 271 (404)
T ss_pred ccccchhhHHHhHHHHHHHHHHHHHHhCCCC-----CCHHHHHHHHH--H---HHHHHHHHHccCHHHHHHHHHhhCCCc
Confidence 100 00011112222222 222234533 33344455543 2 335566778999999997743 44666
Q ss_pred hhhc-CCc---------chhH-----------HhhhhhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHh
Q 015104 285 LKSY-GLV---------HEDC-----------IAKMRLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVV 336 (413)
Q Consensus 285 l~~~-~l~---------~~~~-----------~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi 336 (413)
+... +.. .+.. .+-..+-+|-+...= +.+|+.+.+|.-++++++++-..++
T Consensus 272 Isp~~pp~~~~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~lRSyLKL-Ytti~l~KLA~fl~vd~~~lr~~Ll 343 (404)
T PF10255_consen 272 ISPVSPPDYDGPSQNKNKEPYRRQLKLFLDEVKQQQKLPTLRSYLKL-YTTIPLEKLASFLDVDEEELRSQLL 343 (404)
T ss_pred cCCCCCCCcccccchhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHHh-hcCCCHHHHHHHcCCCHHHHHHHHH
Confidence 6643 210 0222 222333344444333 7789999999999998886655554
No 89
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.84 E-value=35 Score=29.66 Aligned_cols=28 Identities=25% Similarity=0.208 Sum_probs=25.1
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||++||+.+|+|+.-|...+-+|..
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999988854
No 90
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=26.73 E-value=35 Score=30.25 Aligned_cols=28 Identities=11% Similarity=0.218 Sum_probs=25.1
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||.+||+.+|+|..-|...+-+|+.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999988865
No 91
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=26.56 E-value=80 Score=32.72 Aligned_cols=76 Identities=8% Similarity=0.098 Sum_probs=49.6
Q ss_pred CCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHHHhhh---------hhhh
Q 015104 311 ESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTLRTKL---------STWR 381 (413)
Q Consensus 311 ~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L~~rL---------~~W~ 381 (413)
+.+.+|-++|++.+++|.++|+.++=+..+.|+|. +-++ +. |+--|+.+.=....+-+++ ..|.
T Consensus 307 ~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~-~~~~--g~----~~l~rd~~~itL~dv~~~~~~~~~~~~~~~~~ 379 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGYDELGELLCELARIGLLR-RGER--GQ----WVLARDLDSVPLAELYELFVLRPLPCRDDHVG 379 (412)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeE-ecCC--Cc----eEecCCHHhCcHHHHHHhCCCCcCCCccchHH
Confidence 35689999999999999999999999999999996 3221 21 4444444332222222222 2566
Q ss_pred hhHHHHHHHhhh
Q 015104 382 ANVANVISTIQA 393 (413)
Q Consensus 382 ~~v~~~~~~v~~ 393 (413)
.+++++++.+++
T Consensus 380 ~~~~~~l~~~~~ 391 (412)
T PRK04214 380 QAADAALTQLRQ 391 (412)
T ss_pred HHHHHHHHHHHH
Confidence 666666655543
No 92
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=26.40 E-value=28 Score=24.22 Aligned_cols=29 Identities=17% Similarity=0.320 Sum_probs=18.7
Q ss_pred CcchhhhhhccccCcchhhhHHhhhhhhc
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKARTAK 342 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI~~g 342 (413)
-.|..+||+.+|++..-|-.|+-+.-..|
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 36999999999999999999988776666
No 93
>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=26.31 E-value=37 Score=29.57 Aligned_cols=27 Identities=15% Similarity=0.241 Sum_probs=24.8
Q ss_pred CcchhhhhhccccCcchhhhHHhhhhh
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
.+|+++||+.+|+|.+-|...+-+|..
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 589999999999999999999998854
No 94
>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=26.28 E-value=21 Score=28.28 Aligned_cols=38 Identities=18% Similarity=0.440 Sum_probs=21.2
Q ss_pred hhccCCCCCCCcchhhhhhccc---cCcchhhhHHhhhhhhc
Q 015104 304 LVDLGSNESGQIPYGLIKDTLQ---INNDEVEKWVVKARTAK 342 (413)
Q Consensus 304 L~~L~~~~~r~isy~~Ia~~l~---i~~~eVE~lvi~aI~~g 342 (413)
|+....+ .+.|||++|.+.|. ++++.++.++-..-..|
T Consensus 12 Li~~gK~-~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~g 52 (82)
T PF03979_consen 12 LIEKGKK-KGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEG 52 (82)
T ss_dssp HHHHHHH-HSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT-
T ss_pred HHHHHhh-cCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCC
Confidence 4444444 56899999999976 33456666555444444
No 95
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=26.17 E-value=73 Score=23.31 Aligned_cols=41 Identities=17% Similarity=0.289 Sum_probs=31.6
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMN 352 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~ 352 (413)
.+.++..+|++.++++...|-..|=+.+..|+|+=.=|..+
T Consensus 16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d 56 (68)
T PF13463_consen 16 DGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHD 56 (68)
T ss_dssp TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSC
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCc
Confidence 57899999999999999999999999999999954444433
No 96
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=26.12 E-value=37 Score=30.18 Aligned_cols=29 Identities=28% Similarity=0.425 Sum_probs=25.8
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTA 341 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~ 341 (413)
...||++||+.+|++..-|...+-+|+..
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 56899999999999999999999888653
No 97
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=25.55 E-value=38 Score=30.35 Aligned_cols=28 Identities=21% Similarity=0.230 Sum_probs=24.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||++||+.+|+|+.-|...+-+|+.
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3589999999999999999999888765
No 98
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=25.34 E-value=39 Score=29.27 Aligned_cols=28 Identities=7% Similarity=0.099 Sum_probs=24.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||++||+.+|+|+.-|...+-+|+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3589999999999999999999888754
No 99
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=25.25 E-value=42 Score=29.85 Aligned_cols=27 Identities=7% Similarity=0.343 Sum_probs=24.1
Q ss_pred CcchhhhhhccccCcchhhhHHhhhhh
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..||++||+.+|+++.-|...+-+|..
T Consensus 145 g~s~~eIA~~lgis~~tV~~~l~Rar~ 171 (179)
T PRK12514 145 GLSYKELAERHDVPLNTMRTWLRRSLL 171 (179)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 489999999999999999999888743
No 100
>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=25.18 E-value=44 Score=27.05 Aligned_cols=30 Identities=27% Similarity=0.563 Sum_probs=23.7
Q ss_pred CCcchhhhhhccccC-cchhhhHHhhhhhhccc
Q 015104 313 GQIPYGLIKDTLQIN-NDEVEKWVVKARTAKLM 344 (413)
Q Consensus 313 r~isy~~Ia~~l~i~-~~eVE~lvi~aI~~gLI 344 (413)
-.++|.+|-+. .| ++.||+|||+.+..|..
T Consensus 47 ~vi~Fd~iVr~--mpNes~v~qWV~dtln~i~~ 77 (100)
T PF07389_consen 47 AVIPFDDIVRT--MPNESRVKQWVIDTLNDIMM 77 (100)
T ss_pred ccccHHHHHHh--CCCHHHHHHHHHHHHHhHhh
Confidence 36899999998 54 46999999998766543
No 101
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=24.90 E-value=44 Score=23.01 Aligned_cols=25 Identities=16% Similarity=0.214 Sum_probs=22.3
Q ss_pred cchhhhhhccccCcchhhhHHhhhh
Q 015104 315 IPYGLIKDTLQINNDEVEKWVVKAR 339 (413)
Q Consensus 315 isy~~Ia~~l~i~~~eVE~lvi~aI 339 (413)
.|+.+||+.++++..-|..++-++.
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 6999999999999999999887664
No 102
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=24.80 E-value=50 Score=24.14 Aligned_cols=29 Identities=17% Similarity=0.284 Sum_probs=23.6
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
-|.++..++|+.+||+..-+..-+=+|.+
T Consensus 21 PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 21 PRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 58999999999999998777766666543
No 103
>PRK09954 putative kinase; Provisional
Probab=24.75 E-value=34 Score=34.44 Aligned_cols=37 Identities=22% Similarity=0.175 Sum_probs=33.6
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKM 348 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkI 348 (413)
+..+|+.+||+.++++..-|-..+-+....|.|+|+-
T Consensus 15 ~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~ 51 (362)
T PRK09954 15 NPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKG 51 (362)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcE
Confidence 5689999999999999999999999999999998753
No 104
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=24.54 E-value=39 Score=27.62 Aligned_cols=27 Identities=26% Similarity=0.300 Sum_probs=24.6
Q ss_pred hhhhccccCcchhhhHHhhhhhhcccc
Q 015104 319 LIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 319 ~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
.||..+++|.++|+..+-+....|||+
T Consensus 26 ~ia~~l~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 26 SIARRLKIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 488899999999999999999999974
No 105
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=24.49 E-value=64 Score=25.02 Aligned_cols=42 Identities=12% Similarity=0.104 Sum_probs=32.1
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEe
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVR 358 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt 358 (413)
+..++.+|+..++++..-+...+=..+..|||++ .++...+|
T Consensus 18 ~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 18 GGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp T-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE----ETTEEEE-
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC----CCCEEEEC
Confidence 5678999999999999999999999999999933 56666666
No 106
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=24.44 E-value=37 Score=30.00 Aligned_cols=28 Identities=21% Similarity=0.215 Sum_probs=24.8
Q ss_pred CcchhhhhhccccCcchhhhHHhhhhhh
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKARTA 341 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI~~ 341 (413)
..||++||+.+|++..-|...+-+|+..
T Consensus 142 g~s~~eIA~~l~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 142 GYTYEEIAKMLNIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred CCCHHHHHHHHCCChhHHHHHHHHHHHH
Confidence 5899999999999999999998888543
No 107
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.37 E-value=75 Score=23.43 Aligned_cols=47 Identities=9% Similarity=0.158 Sum_probs=32.7
Q ss_pred cchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccchhhHHHH
Q 015104 315 IPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQHQWQTL 373 (413)
Q Consensus 315 isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~~q~~~L 373 (413)
+|-.++|+.+||+...+-.|. ..|++...-...+ ..|.|+..++..+
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~----~~gli~~~~~~~~--------g~r~y~~~dl~~l 47 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYE----RIGLLPPPIRTEG--------GYRLYSDEDLERL 47 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCC--------CCEecCHHHHHHH
Confidence 356789999999999999884 4788776422222 2467777776654
No 108
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=24.33 E-value=50 Score=28.12 Aligned_cols=40 Identities=18% Similarity=0.169 Sum_probs=33.6
Q ss_pred hhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 304 LVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 304 L~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
++++|. +.+|-+|||..+++|..-|--+|-+.+..|+|.-
T Consensus 48 Il~lC~---~~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 48 ILELCR---RPLSVAEIAARLGLPLGVVRVLVSDLADAGLVRV 87 (114)
T ss_pred HHHHHC---CCccHHHHHHhhCCCchhhhhhHHHHHhCCCEEE
Confidence 345554 3789999999999999999999999999998754
No 109
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.21 E-value=5.9e+02 Score=23.78 Aligned_cols=94 Identities=15% Similarity=0.172 Sum_probs=60.3
Q ss_pred hhhhHHHHHHHHHHHhhcccchhccccchhhhhhcCCcchhHHhhhhhhhhhccCCCCCCCcchhhhhhccccC-cchhh
Q 015104 254 AKYASVYQLLKIFLTQRLDGYLEFQAGNSALLKSYGLVHEDCIAKMRLMSLVDLGSNESGQIPYGLIKDTLQIN-NDEVE 332 (413)
Q Consensus 254 ~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~l~~~~l~~~~~~~KirLLaL~~L~~~~~r~isy~~Ia~~l~i~-~~eVE 332 (413)
.+...+++|=..+.+|+...|=.-.+.|++.++...==++.++.=++ -++++. +..|.=.-+|+.+|-. +.++|
T Consensus 96 e~~r~ii~L~~~LEt~~Fq~FW~~~~~N~~mle~itGFedsvr~yac--hvv~iT---yQkI~k~lLaellG~~sDs~le 170 (217)
T KOG3252|consen 96 EPFRSIIDLGDYLETCRFQQFWQEADENRDMLEGITGFEDSVRKYAC--HVVGIT---YQKIDKWLLAELLGGLSDSQLE 170 (217)
T ss_pred cchhHHHhHHHHHhhchHHHHhhhhccchHHhcCCCcHHHHHHHHHH--Hheech---HhhchHHHHHHhhCcccHHHHH
Confidence 36677888999999999999887777888887743111333322111 111111 2234444556666654 56999
Q ss_pred hHHhhhhhhccccccccccccEEEEec
Q 015104 333 KWVVKARTAKLMDCKMDQMNQVVIVRR 359 (413)
Q Consensus 333 ~lvi~aI~~gLI~gkIDQv~~~v~vt~ 359 (413)
.|+-+ .|.+.+.+|.+.|-.
T Consensus 171 ~~~~~-------~GW~a~e~G~ifv~~ 190 (217)
T KOG3252|consen 171 VWMTK-------YGWIADESGQIFVAS 190 (217)
T ss_pred HHHHH-------ccceecCCceEEEec
Confidence 99987 489999999777753
No 110
>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=24.03 E-value=43 Score=30.25 Aligned_cols=28 Identities=14% Similarity=0.172 Sum_probs=25.1
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||.+||+.+|+|+.-|...+-+|..
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~ 173 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRK 173 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999988854
No 111
>PF04510 DUF577: Family of unknown function (DUF577); InterPro: IPR007598 This is a family of Arabidopsis thaliana (Mouse-ear cress) proteins. Many of these members contain a repeated region.
Probab=23.60 E-value=1.4e+02 Score=27.36 Aligned_cols=52 Identities=17% Similarity=0.194 Sum_probs=33.0
Q ss_pred hhhhhhhhHHHHHhhhhhhhhccCCCCcchhheeeehhcccCCCChhHHHHHHHHHHhhhh
Q 015104 48 MVMGRWMDLASLMLTSADLMFSKVSDKDLECIFTVICNLVTKPESLDEVHEMTKLISGKII 108 (413)
Q Consensus 48 ~~~klw~qLt~~l~~~~~~~~~~~~dke~e~~~n~i~~lv~~~~~~~~~l~~v~~l~~~~~ 108 (413)
+.++.|++|-+=++ +. +.++++.+|.+|+.|-... ..+-..++.+.+..++.
T Consensus 39 ~~~~~W~eL~d~Il-------s~-~~~e~~kA~~IF~~L~~~l-~~efl~~~~~~L~~~~~ 90 (174)
T PF04510_consen 39 LQEGGWDELSDCIL-------SL-SENEPVKAFHIFICLPMPL-YGEFLIPFMENLLPEIS 90 (174)
T ss_pred cCCCCchhHHHHHH-------Hh-hccchHHHHHHHHhCCchh-hhhHHHHHHHHHHHHHH
Confidence 46677999996332 22 3568888999887755344 44445566666665554
No 112
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=23.42 E-value=44 Score=29.10 Aligned_cols=35 Identities=14% Similarity=-0.032 Sum_probs=27.8
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhcccccccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMD 349 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkID 349 (413)
...||++||+.+|+|..-|...+-+|+.. +++.+.
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~ra~~~--lr~~l~ 158 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIRDALVH--CRKCLD 158 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH--HHHHHh
Confidence 35899999999999999999998887543 444443
No 113
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=23.13 E-value=49 Score=32.10 Aligned_cols=57 Identities=11% Similarity=0.034 Sum_probs=40.4
Q ss_pred hhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEe
Q 015104 300 RLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVR 358 (413)
Q Consensus 300 rLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt 358 (413)
|-+.++++.....+.++..+|++.+++|..-|-.++-.....|.+.= |..++...+.
T Consensus 26 r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~--~~~~~~Y~lG 82 (271)
T PRK10163 26 RGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQ--DSQLGWWHIG 82 (271)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE--cCCCCeEEec
Confidence 44445555444245799999999999999999999999988888832 3334444433
No 114
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=23.10 E-value=54 Score=31.37 Aligned_cols=46 Identities=7% Similarity=0.175 Sum_probs=36.3
Q ss_pred hhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhccccc
Q 015104 300 RLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDC 346 (413)
Q Consensus 300 rLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~g 346 (413)
|.+.++++... .+.++..+|++.+|+|..-|-.++-.....|++.-
T Consensus 15 r~l~IL~~l~~-~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~ 60 (257)
T PRK15090 15 KVFGILQALGE-EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQ 60 (257)
T ss_pred HHHHHHHHhhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 44555555444 35799999999999999999999998888888754
No 115
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=23.06 E-value=47 Score=29.38 Aligned_cols=28 Identities=21% Similarity=0.226 Sum_probs=24.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
...||++||+.+|++..-|...+-+|..
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999988754
No 116
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=22.99 E-value=38 Score=26.88 Aligned_cols=34 Identities=12% Similarity=0.129 Sum_probs=30.6
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
++..+-.+|+..|+.|++-||..+-+-++.|.|+
T Consensus 14 ~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkve 47 (78)
T PRK15431 14 RGRMEAAQISQTLNTPQPMINAMLQQLESMGKAV 47 (78)
T ss_pred cCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 5788999999999999999999999988888775
No 117
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=22.94 E-value=46 Score=24.87 Aligned_cols=34 Identities=18% Similarity=0.218 Sum_probs=28.4
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
.+..|..+|.+.+++|.++|-.-++-.|+.|++.
T Consensus 25 ~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 25 RGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp C-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 4689999999999999999999999999998875
No 118
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=22.88 E-value=87 Score=23.89 Aligned_cols=44 Identities=14% Similarity=0.160 Sum_probs=27.4
Q ss_pred CCCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEE
Q 015104 312 SGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIV 357 (413)
Q Consensus 312 ~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~v 357 (413)
.+.+|+++|++.+++++.+|-.-+==..+-|-| .+++.++.++|
T Consensus 20 ~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI--~~~~~~~~~~v 63 (65)
T PF10771_consen 20 NGEWSVSELKKATGLSDKEVYLAIGWLARENKI--EFEEKNGELYV 63 (65)
T ss_dssp SSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSE--EEEEETTEEEE
T ss_pred CCCcCHHHHHHHhCcCHHHHHHHHHHHhccCce--eEEeeCCEEEE
Confidence 478999999999999988876533222334444 23455555554
No 119
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.87 E-value=46 Score=29.22 Aligned_cols=28 Identities=14% Similarity=0.134 Sum_probs=25.0
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||++||+.+|+++.-|...+-+|..
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999988854
No 120
>PHA02763 hypothetical protein; Provisional
Probab=22.75 E-value=81 Score=25.50 Aligned_cols=50 Identities=22% Similarity=0.391 Sum_probs=40.7
Q ss_pred CcchhhhhhccccCc-chhhhHHhhhhhhccccccccccccEEEEeccccccc
Q 015104 314 QIPYGLIKDTLQINN-DEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVF 365 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~-~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~ 365 (413)
.+|..-+++-++.+- +.||.|+-.| ..|=.-+||...=.+.|-|++.|-|
T Consensus 52 p~t~~~LsKYv~~SGFe~VEeWl~eA--rrLh~~~id~~ryeiivi~in~~~f 102 (102)
T PHA02763 52 PVTEYCLSKYVKFSGFENVEEWLNEA--RRLHNDKIDPERYEIIVIWINGRLF 102 (102)
T ss_pred CchHHHHHHHhhhcchhhHHHHHHHH--HHHhcCCCChhheEEEEEEEcCccC
Confidence 456666777777774 7899999998 6667889999999999999988754
No 121
>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=22.69 E-value=40 Score=26.23 Aligned_cols=32 Identities=16% Similarity=0.435 Sum_probs=22.9
Q ss_pred hhccCCCCCCCcchhhhhhccccCcchhhhHHhh
Q 015104 304 LVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVK 337 (413)
Q Consensus 304 L~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~ 337 (413)
+++||-. + ..||+.|..++|+++.||=.+.=+
T Consensus 5 iIeMAwe-D-RtpFeaI~~~fGL~E~eVi~lMR~ 36 (72)
T TIGR03643 5 IIEMAWE-D-RTPFEAIEQQFGLSEKEVIKLMRQ 36 (72)
T ss_pred HHHHHHc-c-CCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3455543 3 469999999999998887555433
No 122
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=22.68 E-value=1.2e+02 Score=21.71 Aligned_cols=33 Identities=12% Similarity=0.275 Sum_probs=28.8
Q ss_pred CCcc-hhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 313 GQIP-YGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 313 r~is-y~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
..++ -.+||+.++++..-|-..+-+.-..|+|.
T Consensus 23 ~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 23 DRLPSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3444 99999999999999999999999999885
No 123
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=22.57 E-value=47 Score=29.98 Aligned_cols=27 Identities=22% Similarity=0.195 Sum_probs=24.2
Q ss_pred CcchhhhhhccccCcchhhhHHhhhhh
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..||++||+.+|+|+.-|...+-+|..
T Consensus 147 g~s~~EIA~~lgis~~tV~~~l~Rar~ 173 (191)
T PRK12520 147 ELETEEICQELQITATNAWVLLYRARM 173 (191)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 589999999999999999999888743
No 124
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.28 E-value=48 Score=30.03 Aligned_cols=28 Identities=14% Similarity=0.162 Sum_probs=24.7
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||++||+.+|+|+.-|...+-+|..
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQECDISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3689999999999999999999888753
No 125
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.23 E-value=49 Score=28.78 Aligned_cols=35 Identities=26% Similarity=0.294 Sum_probs=28.2
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhcccccccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMD 349 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkID 349 (413)
..+||++||+.+|+|+.-|...+-+|... ++..|+
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra~~~--Lr~~l~ 154 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNAMKH--CRVRMR 154 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHH--HHHHHH
Confidence 46899999999999999999998888543 554444
No 126
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=22.15 E-value=49 Score=29.90 Aligned_cols=28 Identities=14% Similarity=0.188 Sum_probs=24.7
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
...||++||+.+|+|..-|...+-+|..
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 181 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQ 181 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999988888754
No 127
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.14 E-value=49 Score=23.11 Aligned_cols=24 Identities=8% Similarity=0.093 Sum_probs=21.0
Q ss_pred cchhhhhhccccCcchhhhHHhhh
Q 015104 315 IPYGLIKDTLQINNDEVEKWVVKA 338 (413)
Q Consensus 315 isy~~Ia~~l~i~~~eVE~lvi~a 338 (413)
.|+.+||+.+|++.+-|..++-++
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 799999999999999998877554
No 128
>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=21.89 E-value=55 Score=22.64 Aligned_cols=26 Identities=19% Similarity=0.138 Sum_probs=22.5
Q ss_pred CcchhhhhhccccCcchhhhHHhhhh
Q 015104 314 QIPYGLIKDTLQINNDEVEKWVVKAR 339 (413)
Q Consensus 314 ~isy~~Ia~~l~i~~~eVE~lvi~aI 339 (413)
..|+.+||+.++++..-|+.++-++.
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36999999999999999999977653
No 129
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.82 E-value=51 Score=29.03 Aligned_cols=28 Identities=18% Similarity=0.058 Sum_probs=24.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
...||++||+.+|+|+.-|...+-+|..
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYALR 160 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4689999999999999999999988853
No 130
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=21.44 E-value=51 Score=29.07 Aligned_cols=28 Identities=18% Similarity=0.331 Sum_probs=24.9
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
...||++||+.+|+|..-|...+-+|+.
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999998888765
No 131
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=21.21 E-value=55 Score=30.71 Aligned_cols=28 Identities=11% Similarity=0.095 Sum_probs=25.2
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhh
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKART 340 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~ 340 (413)
..+||++||+.+|+|..-|...+-+|+.
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999888854
No 132
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=20.94 E-value=44 Score=22.81 Aligned_cols=33 Identities=12% Similarity=0.243 Sum_probs=28.2
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
..++-.+|++.++++..-|...+-.....|+|.
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 468999999999999999988887777777765
No 133
>PRK11569 transcriptional repressor IclR; Provisional
Probab=20.90 E-value=56 Score=31.70 Aligned_cols=46 Identities=9% Similarity=0.221 Sum_probs=36.6
Q ss_pred hhhhhhccCCCCCCCcchhhhhhccccCcchhhhHHhhhhhhcccc
Q 015104 300 RLMSLVDLGSNESGQIPYGLIKDTLQINNDEVEKWVVKARTAKLMD 345 (413)
Q Consensus 300 rLLaL~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~ 345 (413)
|-+.++++.....+.++..+|++.+|+|..-|-.++-.....|++.
T Consensus 29 ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 29 RGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4444444444324679999999999999999999999999999985
No 134
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=20.83 E-value=55 Score=29.59 Aligned_cols=51 Identities=20% Similarity=0.182 Sum_probs=35.3
Q ss_pred CCcchhhhhhccccCcchhhhHHhhhhhhccccccccccccEEEEecccccccch
Q 015104 313 GQIPYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMDQMNQVVIVRRCTERVFGQ 367 (413)
Q Consensus 313 r~isy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkIDQv~~~v~vt~v~~R~~~~ 367 (413)
..+||++||+.+|+|+.-|...+.+|... ++..+++-. =..++...|++|-
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Rar~~--Lr~~~~~~~--~~~~~~~~~~~~~ 176 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRARAA--LRAFEEGTG--PARGRAHLRVVGG 176 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHHH--HHHHHHhcC--CCCCceeeeeecC
Confidence 46899999999999999999999988654 555555433 2223333445543
No 135
>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=20.51 E-value=47 Score=25.94 Aligned_cols=31 Identities=16% Similarity=0.420 Sum_probs=22.2
Q ss_pred hhccCCCCCCCcchhhhhhccccCcchhhhHHh
Q 015104 304 LVDLGSNESGQIPYGLIKDTLQINNDEVEKWVV 336 (413)
Q Consensus 304 L~~L~~~~~r~isy~~Ia~~l~i~~~eVE~lvi 336 (413)
+++||=. + ..||+.|...+|+++.||=.+.=
T Consensus 4 iIeMAwe-D-RtpFeaI~~qfGl~E~eVi~lMR 34 (73)
T PF10985_consen 4 IIEMAWE-D-RTPFEAIERQFGLSEKEVIKLMR 34 (73)
T ss_pred HHHHHHc-c-CCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455543 3 46999999999999888755433
No 136
>PF13518 HTH_28: Helix-turn-helix domain
Probab=20.50 E-value=61 Score=22.38 Aligned_cols=33 Identities=15% Similarity=0.282 Sum_probs=27.7
Q ss_pred chhhhhhccccCcchhhhHHhhhhhhcccccccc
Q 015104 316 PYGLIKDTLQINNDEVEKWVVKARTAKLMDCKMD 349 (413)
Q Consensus 316 sy~~Ia~~l~i~~~eVE~lvi~aI~~gLI~gkID 349 (413)
|+.++|+.+||+...|..|+-..-..| +.|-.+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~ 46 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGG-IEGLKP 46 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcC-HHHhcc
Confidence 999999999999999999998877766 345444
Done!