Query 014533
Match_columns 423
No_of_seqs 252 out of 1080
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 06:04:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014533.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014533hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0774 Transcription factor P 100.0 2.2E-29 4.8E-34 243.3 16.4 205 171-409 26-249 (334)
2 KOG0773 Transcription factor M 99.9 1.9E-26 4E-31 229.6 -0.9 238 170-411 46-302 (342)
3 PF03790 KNOX1: KNOX1 domain ; 99.8 1.2E-19 2.6E-24 134.1 3.4 44 174-217 1-44 (45)
4 PF05920 Homeobox_KN: Homeobox 99.6 3.6E-16 7.8E-21 113.1 4.3 40 366-405 1-40 (40)
5 cd00086 homeodomain Homeodomai 99.5 1.5E-13 3.3E-18 102.8 6.9 58 349-409 1-58 (59)
6 smart00389 HOX Homeodomain. DN 99.4 3.8E-13 8.2E-18 100.2 6.6 55 350-407 2-56 (56)
7 PF00046 Homeobox: Homeobox do 99.4 4.4E-13 9.4E-18 101.0 5.6 57 349-408 1-57 (57)
8 KOG0775 Transcription factor S 99.4 1E-13 2.2E-18 135.7 1.7 72 328-408 160-233 (304)
9 PF03791 KNOX2: KNOX2 domain ; 99.3 1.5E-12 3.2E-17 99.4 4.9 39 231-269 3-52 (52)
10 PF03792 PBC: PBC domain; Int 99.1 7.5E-10 1.6E-14 104.1 11.8 143 171-347 24-190 (191)
11 KOG0487 Transcription factor A 98.8 3E-09 6.5E-14 106.6 3.5 59 349-410 236-294 (308)
12 TIGR01565 homeo_ZF_HD homeobox 98.8 1.1E-08 2.5E-13 79.8 5.1 53 348-403 1-57 (58)
13 KOG0843 Transcription factor E 98.7 1.8E-08 3.8E-13 94.4 4.4 62 347-411 101-162 (197)
14 KOG0489 Transcription factor z 98.6 1.9E-08 4.2E-13 98.5 3.9 65 348-415 159-223 (261)
15 KOG0493 Transcription factor E 98.6 5.2E-08 1.1E-12 95.8 5.0 62 348-412 246-307 (342)
16 KOG3802 Transcription factor O 98.6 3.6E-08 7.7E-13 101.4 4.0 62 347-411 293-354 (398)
17 KOG0485 Transcription factor N 98.5 1.2E-07 2.6E-12 91.2 6.4 59 348-409 104-162 (268)
18 COG5576 Homeodomain-containing 98.5 8.9E-08 1.9E-12 87.9 4.5 64 346-412 49-112 (156)
19 KOG0850 Transcription factor D 98.5 7.7E-08 1.7E-12 93.0 4.0 59 349-410 123-181 (245)
20 KOG0483 Transcription factor H 98.5 9.2E-08 2E-12 90.9 4.2 59 348-409 50-108 (198)
21 KOG0842 Transcription factor t 98.5 7.5E-08 1.6E-12 96.7 3.2 59 348-409 153-211 (307)
22 KOG0488 Transcription factor B 98.3 4.1E-07 8.8E-12 91.6 4.6 59 348-409 172-230 (309)
23 KOG0491 Transcription factor B 98.3 3.5E-07 7.6E-12 84.9 2.8 61 345-408 97-157 (194)
24 KOG0484 Transcription factor P 98.3 6.2E-07 1.3E-11 77.9 3.5 64 342-408 11-74 (125)
25 KOG2251 Homeobox transcription 98.2 1E-06 2.2E-11 84.8 4.4 58 348-408 37-94 (228)
26 KOG0492 Transcription factor M 98.2 9.1E-07 2E-11 84.8 3.2 66 340-408 136-201 (246)
27 KOG0848 Transcription factor C 98.1 7.8E-07 1.7E-11 87.9 0.7 57 352-411 203-259 (317)
28 KOG0494 Transcription factor C 98.0 3.7E-06 8.1E-11 82.9 4.3 56 352-410 145-200 (332)
29 KOG4577 Transcription factor L 98.0 2.5E-06 5.5E-11 85.1 2.3 71 341-414 160-230 (383)
30 KOG0486 Transcription factor P 98.0 3.4E-06 7.4E-11 84.9 2.8 58 349-409 113-170 (351)
31 KOG0847 Transcription factor, 97.7 1.9E-05 4.1E-10 76.5 2.6 68 347-417 166-233 (288)
32 KOG1168 Transcription factor A 97.7 9.9E-06 2.1E-10 81.0 0.7 70 342-414 303-372 (385)
33 KOG2252 CCAAT displacement pro 97.7 5.5E-05 1.2E-09 80.9 5.5 55 349-406 421-475 (558)
34 KOG0490 Transcription factor, 97.6 2.6E-05 5.7E-10 72.7 2.1 63 345-410 57-119 (235)
35 KOG0849 Transcription factor P 97.5 6.1E-05 1.3E-09 77.2 3.8 60 348-410 176-235 (354)
36 KOG0773 Transcription factor M 97.4 6.6E-05 1.4E-09 75.5 2.5 67 348-415 95-161 (342)
37 KOG0844 Transcription factor E 97.3 8.7E-05 1.9E-09 74.9 1.6 55 352-409 185-239 (408)
38 PF11569 Homez: Homeodomain le 96.8 0.00095 2.1E-08 52.2 2.8 43 360-405 10-52 (56)
39 PF03789 ELK: ELK domain ; In 96.5 0.0017 3.8E-08 41.9 2.0 22 326-347 1-22 (22)
40 KOG0490 Transcription factor, 94.7 0.024 5.2E-07 52.9 3.0 60 349-411 154-213 (235)
41 KOG1146 Homeobox protein [Gene 91.0 0.18 3.9E-06 59.5 3.5 60 348-410 903-962 (1406)
42 PF04218 CENP-B_N: CENP-B N-te 82.2 1.9 4.1E-05 32.8 3.6 47 349-403 1-47 (53)
43 KOG3623 Homeobox transcription 79.9 3.4 7.3E-05 46.9 5.9 52 360-414 568-619 (1007)
44 PF01527 HTH_Tnp_1: Transposas 73.2 6.2 0.00013 30.7 4.3 46 350-403 2-48 (76)
45 cd06171 Sigma70_r4 Sigma70, re 71.3 6.3 0.00014 27.3 3.6 46 354-407 10-55 (55)
46 PF08281 Sigma70_r4_2: Sigma-7 65.8 11 0.00023 27.7 4.0 44 354-405 10-53 (54)
47 cd00569 HTH_Hin_like Helix-tur 64.4 12 0.00026 23.0 3.6 40 352-399 3-42 (42)
48 PF04545 Sigma70_r4: Sigma-70, 62.6 9.2 0.0002 27.9 3.0 47 354-408 4-50 (50)
49 KOG4511 Uncharacterized conser 59.9 27 0.00058 35.8 6.6 69 178-267 49-127 (335)
50 PRK06759 RNA polymerase factor 51.5 18 0.00039 31.4 3.5 47 354-408 106-152 (154)
51 TIGR02937 sigma70-ECF RNA poly 48.1 20 0.00044 29.7 3.2 48 354-409 110-157 (158)
52 PRK09644 RNA polymerase sigma 44.6 25 0.00055 31.1 3.5 50 353-410 107-156 (165)
53 PRK09646 RNA polymerase sigma 44.5 22 0.00048 32.6 3.1 50 354-411 142-191 (194)
54 PRK09642 RNA polymerase sigma 43.4 27 0.00058 30.7 3.4 49 354-410 106-154 (160)
55 PRK12514 RNA polymerase sigma 43.1 24 0.00052 31.6 3.1 48 354-409 129-176 (179)
56 PRK11924 RNA polymerase sigma 42.3 25 0.00054 30.8 3.0 48 354-409 125-172 (179)
57 PRK06811 RNA polymerase factor 41.2 30 0.00066 31.5 3.5 49 353-409 130-178 (189)
58 PRK00118 putative DNA-binding 41.2 29 0.00064 30.3 3.2 47 354-408 17-63 (104)
59 PRK03975 tfx putative transcri 39.7 33 0.00071 31.5 3.4 48 352-408 4-51 (141)
60 PRK09652 RNA polymerase sigma 39.2 30 0.00065 30.4 3.1 48 354-409 128-175 (182)
61 TIGR02985 Sig70_bacteroi1 RNA 38.7 34 0.00074 29.3 3.2 48 354-409 113-160 (161)
62 TIGR02999 Sig-70_X6 RNA polyme 37.1 37 0.00081 30.3 3.4 48 354-409 134-181 (183)
63 TIGR02989 Sig-70_gvs1 RNA poly 36.8 40 0.00086 29.3 3.4 48 353-408 110-157 (159)
64 TIGR02939 RpoE_Sigma70 RNA pol 36.5 27 0.0006 31.3 2.4 49 354-410 138-186 (190)
65 PF13443 HTH_26: Cro/C1-type H 36.2 29 0.00063 26.0 2.2 23 380-402 12-34 (63)
66 PF11288 DUF3089: Protein of u 36.0 14 0.0003 36.0 0.4 46 155-205 93-138 (207)
67 smart00421 HTH_LUXR helix_turn 35.3 86 0.0019 21.9 4.4 47 354-409 3-49 (58)
68 PRK12526 RNA polymerase sigma 34.6 38 0.00082 31.5 3.1 49 354-410 153-201 (206)
69 PRK12541 RNA polymerase sigma 33.2 44 0.00095 29.4 3.1 49 353-409 111-159 (161)
70 TIGR02983 SigE-fam_strep RNA p 33.2 48 0.001 29.0 3.4 50 354-411 110-159 (162)
71 PRK09648 RNA polymerase sigma 32.4 47 0.001 30.1 3.2 48 354-409 139-186 (189)
72 PRK05602 RNA polymerase sigma 32.3 41 0.00088 30.4 2.8 49 355-411 129-177 (186)
73 PRK12512 RNA polymerase sigma 31.9 47 0.001 29.9 3.1 50 354-411 131-180 (184)
74 PRK09047 RNA polymerase factor 31.3 57 0.0012 28.4 3.5 50 353-410 105-154 (161)
75 PRK12546 RNA polymerase sigma 31.0 44 0.00096 30.9 2.9 49 354-410 113-161 (188)
76 PF13518 HTH_28: Helix-turn-he 30.7 50 0.0011 23.6 2.6 24 381-404 15-38 (52)
77 PRK13919 putative RNA polymera 30.7 52 0.0011 29.6 3.2 48 354-409 135-182 (186)
78 PRK12547 RNA polymerase sigma 30.6 50 0.0011 29.3 3.1 49 354-410 112-160 (164)
79 PRK12515 RNA polymerase sigma 30.4 53 0.0012 29.8 3.3 49 354-410 131-179 (189)
80 PRK09639 RNA polymerase sigma 30.1 53 0.0011 28.8 3.1 47 354-409 112-158 (166)
81 PF12362 DUF3646: DNA polymera 30.1 41 0.00088 29.9 2.3 20 174-193 89-108 (117)
82 PRK12519 RNA polymerase sigma 29.9 40 0.00086 30.6 2.4 48 354-409 141-188 (194)
83 PRK12530 RNA polymerase sigma 29.6 53 0.0012 30.1 3.1 48 354-409 134-181 (189)
84 PRK12524 RNA polymerase sigma 28.7 55 0.0012 30.0 3.1 49 354-410 136-184 (196)
85 PRK12537 RNA polymerase sigma 28.6 59 0.0013 29.4 3.2 48 354-409 133-180 (182)
86 PF13730 HTH_36: Helix-turn-he 28.2 2.1E+02 0.0045 20.9 5.6 49 354-405 2-52 (55)
87 TIGR02948 SigW_bacill RNA poly 28.0 54 0.0012 29.3 2.8 48 354-409 136-183 (187)
88 PRK09649 RNA polymerase sigma 27.7 67 0.0015 29.3 3.4 51 353-411 129-179 (185)
89 TIGR02954 Sig70_famx3 RNA poly 27.5 64 0.0014 28.6 3.2 48 354-409 119-166 (169)
90 PRK15369 two component system 27.3 1.5E+02 0.0033 25.4 5.5 48 354-410 149-196 (211)
91 TIGR02980 SigBFG RNA polymeras 27.0 65 0.0014 30.3 3.3 47 354-408 178-224 (227)
92 TIGR02959 SigZ RNA polymerase 26.9 67 0.0015 28.8 3.2 49 354-410 100-148 (170)
93 PRK12536 RNA polymerase sigma 26.7 68 0.0015 29.0 3.3 48 354-409 129-176 (181)
94 PRK12532 RNA polymerase sigma 26.7 65 0.0014 29.4 3.2 49 354-410 136-184 (195)
95 PRK12516 RNA polymerase sigma 26.1 65 0.0014 29.6 3.1 50 354-411 116-165 (187)
96 PRK12520 RNA polymerase sigma 26.0 73 0.0016 29.0 3.4 48 354-409 131-178 (191)
97 PRK12523 RNA polymerase sigma 25.9 77 0.0017 28.3 3.4 49 353-409 118-166 (172)
98 PRK07037 extracytoplasmic-func 25.9 71 0.0015 28.0 3.1 49 353-409 108-156 (163)
99 PRK09641 RNA polymerase sigma 25.1 71 0.0015 28.5 3.0 48 354-409 136-183 (187)
100 PRK12531 RNA polymerase sigma 25.0 66 0.0014 29.5 2.9 51 353-411 140-190 (194)
101 PRK12542 RNA polymerase sigma 24.1 77 0.0017 28.6 3.1 48 354-409 122-169 (185)
102 PF10668 Phage_terminase: Phag 23.9 61 0.0013 25.9 2.1 22 379-400 23-44 (60)
103 TIGR02479 FliA_WhiG RNA polyme 23.9 76 0.0016 29.9 3.1 48 354-409 175-222 (224)
104 PRK06986 fliA flagellar biosyn 23.8 68 0.0015 30.5 2.8 48 354-409 184-231 (236)
105 cd00669 Asp_Lys_Asn_RS_core As 23.7 68 0.0015 31.9 2.9 39 166-204 196-238 (269)
106 PRK12533 RNA polymerase sigma 23.5 82 0.0018 30.1 3.3 49 354-410 134-182 (216)
107 PRK09637 RNA polymerase sigma 23.5 77 0.0017 29.0 3.0 48 354-409 106-153 (181)
108 PRK12538 RNA polymerase sigma 23.3 64 0.0014 31.1 2.6 49 354-410 171-219 (233)
109 PRK07670 RNA polymerase sigma 23.1 80 0.0017 30.4 3.2 47 354-408 201-247 (251)
110 PRK08583 RNA polymerase sigma 23.0 81 0.0017 30.4 3.2 48 354-409 205-252 (257)
111 PF01381 HTH_3: Helix-turn-hel 22.7 66 0.0014 23.3 2.0 21 382-402 13-33 (55)
112 PF00196 GerE: Bacterial regul 22.6 1.2E+02 0.0027 22.6 3.5 48 354-410 3-50 (58)
113 PRK09413 IS2 repressor TnpA; R 22.4 1.5E+02 0.0033 25.7 4.5 48 350-404 8-55 (121)
114 PRK12522 RNA polymerase sigma 22.3 90 0.0019 27.8 3.2 48 354-409 119-166 (173)
115 PF05821 NDUF_B8: NADH-ubiquin 22.3 75 0.0016 30.4 2.7 24 372-395 33-57 (179)
116 TIGR02943 Sig70_famx1 RNA poly 21.9 94 0.002 28.5 3.3 48 354-409 131-178 (188)
117 PRK09645 RNA polymerase sigma 21.6 96 0.0021 27.5 3.2 49 354-410 118-166 (173)
118 PRK09415 RNA polymerase factor 21.4 81 0.0018 28.5 2.7 47 354-408 127-173 (179)
119 PRK04217 hypothetical protein; 21.4 1.1E+02 0.0024 27.0 3.3 49 353-409 41-89 (110)
120 PRK12543 RNA polymerase sigma 21.3 1.1E+02 0.0023 27.7 3.4 47 354-408 117-163 (179)
121 PRK08295 RNA polymerase factor 20.9 94 0.002 28.4 3.1 46 354-408 155-200 (208)
122 PHA03397 vlf-1 very late expre 20.9 94 0.002 32.7 3.4 31 174-205 13-43 (363)
123 TIGR02947 SigH_actino RNA poly 20.8 48 0.001 30.2 1.1 48 354-409 131-178 (193)
124 PRK06288 RNA polymerase sigma 20.7 92 0.002 30.4 3.1 48 354-409 212-259 (268)
125 PRK12539 RNA polymerase sigma 20.6 1.1E+02 0.0023 27.8 3.3 49 354-410 131-179 (184)
126 TIGR02950 SigM_subfam RNA poly 20.6 42 0.00091 29.0 0.6 46 355-408 106-151 (154)
127 PRK09636 RNA polymerase sigma 20.4 1.2E+02 0.0025 30.0 3.8 51 354-412 115-165 (293)
128 PF07425 Pardaxin: Pardaxin; 20.4 51 0.0011 23.0 0.9 22 176-197 5-26 (33)
129 KOG4040 NADH:ubiquinone oxidor 20.4 60 0.0013 30.9 1.6 36 359-394 25-61 (186)
130 PF10281 Ish1: Putative stress 20.4 1.9E+02 0.0041 20.4 3.8 27 358-385 4-31 (38)
131 PF13551 HTH_29: Winged helix- 20.3 4.4E+02 0.0096 21.3 6.7 46 355-400 58-109 (112)
132 PRK12513 RNA polymerase sigma 20.3 45 0.00098 30.3 0.8 49 354-410 139-187 (194)
133 PF04967 HTH_10: HTH DNA bindi 20.2 2.4E+02 0.0051 21.8 4.6 47 355-402 1-47 (53)
134 PRK12528 RNA polymerase sigma 20.1 1.2E+02 0.0025 26.7 3.3 47 353-407 112-158 (161)
135 TIGR02941 Sigma_B RNA polymera 20.0 94 0.002 29.9 3.0 48 354-409 205-252 (255)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.96 E-value=2.2e-29 Score=243.26 Aligned_cols=205 Identities=24% Similarity=0.377 Sum_probs=175.8
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHhh-----hhccCCCcchhhHHHHHHHhHhHhhhhhhcCCCCC-------CCCCChH
Q 014533 171 WQNARYKAEILSHPLYEQLLSAHVAC-----LRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQG-------LVTDDKE 238 (423)
Q Consensus 171 ~e~e~lKAkI~sHPLYp~LL~AyIdC-----lKVGAPpdvv~rLd~~l~~s~~~~~~~sa~~~~~~-------~~gdDPE 238 (423)
|++.+.|.+|-|||+||.|.++.++. +.|....|+-+. |.++.++++|+...++.|+..+ ..|+..|
T Consensus 26 Deaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~-dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsd 104 (334)
T KOG0774|consen 26 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPP-DPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSD 104 (334)
T ss_pred chHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCC-ChHHHHHHHHHHHhcccCccccchhhhhccCCChHH
Confidence 56668999999999999999999994 444444443332 7788899999999998887642 2357899
Q ss_pred HHHHHHHHhhhHHH---HH-hhhhhHHHHHhhhhCCCCCCCCCCCCCCcchhcccCCCccCCCCCCCCCCCCCCCCCCch
Q 014533 239 LDQFMQHVRVHAME---AV-MACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSLEGPDTMGFGPLIPTE 314 (423)
Q Consensus 239 LDQFMe~lr~pf~E---A~-~Fc~~IEsQL~sL~g~s~~eg~g~~~Sdded~~~~sd~~~~~g~~~~~ds~~f~pi~p~~ 314 (423)
+++-+..+|..+.+ ++ .+|+++.+.+.+|.. +.+.++||.+.+
T Consensus 105 YR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~---------------------------------eQsr~RPi~~ke 151 (334)
T KOG0774|consen 105 YRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLR---------------------------------EQSRTRPIMPKE 151 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---------------------------------HhcccCCCCHHH
Confidence 99999888876532 22 589999999999985 233689999999
Q ss_pred hhhHH--HHHHHHHHHHHHHhhhhhHHHhHHHHHhh-ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCC
Q 014533 315 SERSL--MERVRQELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQ 391 (423)
Q Consensus 315 ~er~~--m~r~~~ELK~~Lk~ky~~~i~~lree~~k-kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs 391 (423)
.||++ |.+.|.-++..|++..|..+..||.+++. +|||++|+|.++.||..||+.|..+|||+++.|++||++||++
T Consensus 152 ~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnIt 231 (334)
T KOG0774|consen 152 IERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNIT 231 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCce
Confidence 99885 89999999999999999999999999996 6778899999999999999999999999999999999999999
Q ss_pred hhhhhhhhhhhhhhcccC
Q 014533 392 LKQINNWFINQRKRNWHS 409 (423)
Q Consensus 392 ~kQV~NWFiN~RkR~kK~ 409 (423)
..||+|||.|+|.|.||.
T Consensus 232 vsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 232 VSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred ehhhccccccceeehhhh
Confidence 999999999999999983
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.91 E-value=1.9e-26 Score=229.63 Aligned_cols=238 Identities=22% Similarity=0.303 Sum_probs=157.6
Q ss_pred chhhHHHHHHHhhCCChHHHHHHHHhhhhccCCCcchhhHHHHHHHhHhHhhhhhhcCCC-C--CCCCCChHHHHHHHH-
Q 014533 170 NWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAG-Q--GLVTDDKELDQFMQH- 245 (423)
Q Consensus 170 ~~e~e~lKAkI~sHPLYp~LL~AyIdClKVGAPpdvv~rLd~~l~~s~~~~~~~sa~~~~-~--~~~gdDPELDQFMe~- 245 (423)
......+|..+.+||||..++.||+.|++++++.+.+.+++............+...... . ..-+.+++++.||..
T Consensus 46 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~ 125 (342)
T KOG0773|consen 46 MVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKL 125 (342)
T ss_pred ccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHH
Confidence 455566799999999999999999999999999999887655443332222222111100 0 123478899988832
Q ss_pred ----------HhhhH--HHHHhhhhhHHHHHhhhhCCCCCCCCCCCCCCcchhcccCCCccCCCCC-CCCCCCCCCCCCC
Q 014533 246 ----------VRVHA--MEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSL-EGPDTMGFGPLIP 312 (423)
Q Consensus 246 ----------lr~pf--~EA~~Fc~~IEsQL~sL~g~s~~eg~g~~~Sdded~~~~sd~~~~~g~~-~~~ds~~f~pi~p 312 (423)
+.... ++++.++++++..+...++.++....+.....++++... ...+.+ ...+..++.+...
T Consensus 126 ~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~q~~~~~~~~~~~~~~~ 201 (342)
T KOG0773|consen 126 EKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEK----AIGGQLSSSEELLGESEQDD 201 (342)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhcc----cccccccccccccccccccc
Confidence 11122 689999999999999988766554444332222221100 000000 0001111111111
Q ss_pred chhhhHHH--HHHHHHHHHHHHhhhhhHHHhHHHHHhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCC
Q 014533 313 TESERSLM--ERVRQELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGL 390 (423)
Q Consensus 313 ~~~er~~m--~r~~~ELK~~Lk~ky~~~i~~lree~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgL 390 (423)
.+.+...+ .+....++..+.+.+..++.....+..++|+++.||+.++.+|+.||.+|+.||||++.+|..||++|||
T Consensus 202 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGL 281 (342)
T KOG0773|consen 202 SEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGL 281 (342)
T ss_pred cccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCC
Confidence 11111111 2234556666666666556666666778889999999999999999999999999999999999999999
Q ss_pred ChhhhhhhhhhhhhhcccCCC
Q 014533 391 QLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 391 s~kQV~NWFiN~RkR~kK~n~ 411 (423)
+..||+|||||+|+|.|++..
T Consensus 282 s~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 282 SRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CcccCCchhhhcccccCCchH
Confidence 999999999999999999876
No 3
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.77 E-value=1.2e-19 Score=134.12 Aligned_cols=44 Identities=43% Similarity=0.744 Sum_probs=40.9
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhhccCCCcchhhHHHHHHHhH
Q 014533 174 ARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQ 217 (423)
Q Consensus 174 e~lKAkI~sHPLYp~LL~AyIdClKVGAPpdvv~rLd~~l~~s~ 217 (423)
+.|||+|++|||||+||+|||+|+|||||+|++++||++..+++
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~~ 44 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAESQ 44 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Confidence 47999999999999999999999999999999999999887654
No 4
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.62 E-value=3.6e-16 Score=113.08 Aligned_cols=40 Identities=53% Similarity=1.020 Sum_probs=36.5
Q ss_pred HHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 014533 366 WWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 405 (423)
Q Consensus 366 Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR 405 (423)
||..|..+|||+++||..||++|||+.+||+|||+|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 9999999999999999999999999999999999999998
No 5
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.46 E-value=1.5e-13 Score=102.79 Aligned_cols=58 Identities=28% Similarity=0.567 Sum_probs=54.3
Q ss_pred ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 349 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 349 kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
++++..|++++..+|+.||.. +|||+..++..||..|||+.+||.+||.|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 356789999999999999999 8999999999999999999999999999999998864
No 6
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.42 E-value=3.8e-13 Score=100.24 Aligned_cols=55 Identities=27% Similarity=0.531 Sum_probs=51.3
Q ss_pred cCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 014533 350 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 407 (423)
Q Consensus 350 RKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~k 407 (423)
+.+..|++++..+|+.||.. +|||+.+++..||..+||+.+||.+||+|+|+|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQK---NPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 45677999999999999998 78999999999999999999999999999999864
No 7
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.39 E-value=4.4e-13 Score=100.98 Aligned_cols=57 Identities=33% Similarity=0.740 Sum_probs=54.1
Q ss_pred ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 349 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 349 kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
||+|..|++++..+|+.+|.. +|||+.+++..||..+||+..||.+||.|+|.+.|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQE---NPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHH---SSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHH---hccccccccccccccccccccccccCHHHhHHHhCc
Confidence 577889999999999999998 899999999999999999999999999999999874
No 8
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.38 E-value=1e-13 Score=135.72 Aligned_cols=72 Identities=31% Similarity=0.649 Sum_probs=61.6
Q ss_pred HHHHHhhhh--hHHHhHHHHHhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 014533 328 KHELKQGYK--EKIVDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 405 (423)
Q Consensus 328 K~~Lk~ky~--~~i~~lree~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR 405 (423)
|+.+++||. +.||+-.+...+.|-| .+.+|++||.. +|||++++|++||+.|||+..||.|||.|+|.|
T Consensus 160 KYRvRrKfPlPrTIWDGEet~yCFKek------SR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR 230 (304)
T KOG0775|consen 160 KYRVRRKFPLPRTIWDGEETVYCFKEK------SRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQR 230 (304)
T ss_pred cceeeccCCCCCccccCceeeeehhHh------hHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence 566677776 6778777766665443 88999999997 999999999999999999999999999999999
Q ss_pred ccc
Q 014533 406 NWH 408 (423)
Q Consensus 406 ~kK 408 (423)
.|-
T Consensus 231 DRa 233 (304)
T KOG0775|consen 231 DRA 233 (304)
T ss_pred hhh
Confidence 883
No 9
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.33 E-value=1.5e-12 Score=99.44 Aligned_cols=39 Identities=49% Similarity=0.652 Sum_probs=35.8
Q ss_pred CCCCCChHHHHHH-----------HHHhhhHHHHHhhhhhHHHHHhhhhC
Q 014533 231 GLVTDDKELDQFM-----------QHVRVHAMEAVMACWEIEQSLQSLTG 269 (423)
Q Consensus 231 ~~~gdDPELDQFM-----------e~lr~pf~EA~~Fc~~IEsQL~sL~g 269 (423)
+++|+|||||||| ++|.+||.||++|||+||+||++|||
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPFQEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4689999999999 46889999999999999999999985
No 10
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=99.10 E-value=7.5e-10 Score=104.08 Aligned_cols=143 Identities=22% Similarity=0.305 Sum_probs=110.5
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHhh-----hhccCCCcchhhHHHHHHHhHhHhhhhhhcCCCCCC------CC-----
Q 014533 171 WQNARYKAEILSHPLYEQLLSAHVAC-----LRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQGL------VT----- 234 (423)
Q Consensus 171 ~e~e~lKAkI~sHPLYp~LL~AyIdC-----lKVGAPpdvv~rLd~~l~~s~~~~~~~sa~~~~~~~------~g----- 234 (423)
||+.++|.+|.+||+||.|.+++|+- +++..+.+..+. |+++.++++|+...++.||+.+. .|
T Consensus 24 Deaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~-dpQl~RLDNML~AEGV~gPe~~~~~~~~~~~~~~~~ 102 (191)
T PF03792_consen 24 DEAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPP-DPQLMRLDNMLLAEGVAGPEKGGRAAAAAAGTAADN 102 (191)
T ss_pred hHHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCC-chhhhhhhcchhhhcCcCCCCcccchhhhhccCccc
Confidence 46699999999999999999999984 334444333222 77888899999999888875421 11
Q ss_pred --CChHHHHHHHHHhhhHHHHH----hhhhhHHHHHhhhhCCCCCCCCCCCCCCcchhcccCCCccCCCCCCCCCCCCCC
Q 014533 235 --DDKELDQFMQHVRVHAMEAV----MACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSLEGPDTMGFG 308 (423)
Q Consensus 235 --dDPELDQFMe~lr~pf~EA~----~Fc~~IEsQL~sL~g~s~~eg~g~~~Sdded~~~~sd~~~~~g~~~~~ds~~f~ 308 (423)
+.+++..-+-.+|.-|.+.+ .+|+++...+.+|.. +.+.|+
T Consensus 103 ~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLr---------------------------------eQs~~R 149 (191)
T PF03792_consen 103 SIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLLR---------------------------------EQSEFR 149 (191)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHH---------------------------------HhcccC
Confidence 34688888877776554332 578888888888874 223699
Q ss_pred CCCCchhhhHH--HHHHHHHHHHHHHhhhhhHHHhHHHHHh
Q 014533 309 PLIPTESERSL--MERVRQELKHELKQGYKEKIVDIREEIL 347 (423)
Q Consensus 309 pi~p~~~er~~--m~r~~~ELK~~Lk~ky~~~i~~lree~~ 347 (423)
||++.+.|+++ |.++|.-+..+||++.|+.+..||..|+
T Consensus 150 PIs~keiE~m~~~i~~Kf~~iq~qLKQstCEaVm~LRsRfl 190 (191)
T PF03792_consen 150 PISPKEIERMVNIIHRKFSKIQMQLKQSTCEAVMILRSRFL 190 (191)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999985 7999999999999999999999998775
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.79 E-value=3e-09 Score=106.63 Aligned_cols=59 Identities=22% Similarity=0.342 Sum_probs=53.7
Q ss_pred ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 349 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 349 kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
+|||-.++|.++..|+.-|.-+. |.|++-|.+|++.++||.+||..||+|+|+|.||-+
T Consensus 236 RKKRcPYTK~QtlELEkEFlfN~---YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLFNM---YITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccCCchHHHHHHHHHHHHHHH---HHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 44566899999999988888744 999999999999999999999999999999999966
No 12
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=98.76 E-value=1.1e-08 Score=79.78 Aligned_cols=53 Identities=19% Similarity=0.437 Sum_probs=49.9
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPY----PTEEDKARLVQETGLQLKQINNWFINQR 403 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PY----PSe~eK~~LA~~TgLs~kQV~NWFiN~R 403 (423)
+||.|++|+.+++..|+..|.. .+| |+..++..||..+||+..+|.+||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~---~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEK---LGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHH---cCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4788899999999999999998 889 9999999999999999999999999954
No 13
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.67 E-value=1.8e-08 Score=94.43 Aligned_cols=62 Identities=19% Similarity=0.297 Sum_probs=56.3
Q ss_pred hhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 347 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 347 ~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
.-||.|+.|+.++...|+..|.. +-|-.-.||.+||+.++|++.||.+||+|+|.|+|+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 34677889999999999999998 669999999999999999999999999999999998543
No 14
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.64 E-value=1.9e-08 Score=98.53 Aligned_cols=65 Identities=23% Similarity=0.293 Sum_probs=58.5
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCCc
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTST 415 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s~~~ 415 (423)
.||.|..|+..++..|+.-|.- +.|.++..|.+||..+.|++.||.+||+|+|+|.||.+.-.+.
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence 6788889999999999998877 6699999999999999999999999999999999987654443
No 15
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.58 E-value=5.2e-08 Score=95.78 Aligned_cols=62 Identities=34% Similarity=0.466 Sum_probs=56.5
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 412 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s 412 (423)
.||.|.-|+.++.+-|+.-|.++. |.|+.-|+.||.++||.+.||..||+|+|.++||..-+
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR---YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR---YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh---hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence 356778899999999999999955 99999999999999999999999999999999996543
No 16
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.58 E-value=3.6e-08 Score=101.36 Aligned_cols=62 Identities=16% Similarity=0.412 Sum_probs=58.7
Q ss_pred hhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 347 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 347 ~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
.|||||..+.-.++..|+..|.+ ||-|+-+|.-.||++.+|.+..|++||+|+|.|.|+.++
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 56677789999999999999998 999999999999999999999999999999999999888
No 17
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.55 E-value=1.2e-07 Score=91.22 Aligned_cols=59 Identities=20% Similarity=0.322 Sum_probs=54.6
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
|||.|..|+..++..|+.-|.... |.+-.||..||.++.|++.||..||+|+|.|-|+.
T Consensus 104 KKktRTvFSraQV~qLEs~Fe~kr---YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 104 KKKTRTVFSRAQVFQLESTFELKR---YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred cccchhhhhHHHHHHHHHHHHHHh---hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 677788999999999999999966 99999999999999999999999999999987763
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.52 E-value=8.9e-08 Score=87.94 Aligned_cols=64 Identities=19% Similarity=0.337 Sum_probs=58.3
Q ss_pred HhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 014533 346 ILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 412 (423)
Q Consensus 346 ~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s 412 (423)
...+++|.+.+..+..+|+..|.. +|||+..+|..|+..++|+++-|..||+|+|.+.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 345778889999999999999998 9999999999999999999999999999999999986553
No 19
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.51 E-value=7.7e-08 Score=92.98 Aligned_cols=59 Identities=20% Similarity=0.306 Sum_probs=53.7
Q ss_pred ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 349 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 349 kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
+|.|+.++.-+.+.|.+-|++ ..|.--.||.+||..+||++.||..||+|+|-|.||..
T Consensus 123 RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 345678999999999999998 77999999999999999999999999999999998843
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.50 E-value=9.2e-08 Score=90.92 Aligned_cols=59 Identities=29% Similarity=0.440 Sum_probs=53.7
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.++|+.+|+.+++..|+.=|..|. |-.+++|..||++.||++.||.+||+|+|.|-|.+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~---~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEK---KLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred cccccccccHHHHHHhHHhhcccc---ccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 456778899999999999999966 88889999999999999999999999999998764
No 21
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.47 E-value=7.5e-08 Score=96.67 Aligned_cols=59 Identities=17% Similarity=0.351 Sum_probs=53.2
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
|||+|--|++-++-.|++=|.+.. |-+--||+.||..++||..||..||+|+|-|-|+.
T Consensus 153 kRKrRVLFSqAQV~ELERRFrqQR---YLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~ 211 (307)
T KOG0842|consen 153 KRKRRVLFSQAQVYELERRFRQQR---YLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQ 211 (307)
T ss_pred ccccccccchhHHHHHHHHHHhhh---ccccHhHHHHHHhcCCCchheeeeeecchhhhhhh
Confidence 444555799999999999999955 99999999999999999999999999999998874
No 22
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.34 E-value=4.1e-07 Score=91.61 Aligned_cols=59 Identities=20% Similarity=0.392 Sum_probs=52.3
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
++|.|..|+-.++..|+.-|..-. |.+..||..||...||+-.||..||+|+|.|-|+.
T Consensus 172 ~RksRTaFT~~Ql~~LEkrF~~QK---YLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 172 RRKSRTAFSDHQLFELEKRFEKQK---YLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred cccchhhhhHHHHHHHHHHHHHhh---cccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence 344567899999999999999844 99999999999999999999999999988877664
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.30 E-value=3.5e-07 Score=84.90 Aligned_cols=61 Identities=18% Similarity=0.361 Sum_probs=54.0
Q ss_pred HHhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 345 EILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 345 e~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
...++|-|..|+..+...|+.-|+... |-+-.|+.+||...+|+++||..||+|+|+++||
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~Qr---YLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQR---YLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhh---hcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 334455667899999999999999744 9999999999999999999999999999999998
No 24
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.27 E-value=6.2e-07 Score=77.93 Aligned_cols=64 Identities=16% Similarity=0.287 Sum_probs=57.1
Q ss_pred HHHHHhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 342 IREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 342 lree~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
+-+..+.+|-|..|+..+...|+..|.+ .-||..-.|++||.+..|++-.|++||+|+|.+.+|
T Consensus 11 l~ekrKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK 74 (125)
T KOG0484|consen 11 LTEKRKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK 74 (125)
T ss_pred hhHHHHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence 4445555667889999999999999998 569999999999999999999999999999999987
No 25
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.23 E-value=1e-06 Score=84.84 Aligned_cols=58 Identities=19% Similarity=0.359 Sum_probs=53.2
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
.+|-|+.|+..+..+|+.-|.+ .-||+...+++||.+++|.+.+|.+||.|+|.+-++
T Consensus 37 qRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~ 94 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRR 94 (228)
T ss_pred cccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhH
Confidence 3456789999999999999998 669999999999999999999999999999988776
No 26
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.20 E-value=9.1e-07 Score=84.78 Aligned_cols=66 Identities=15% Similarity=0.275 Sum_probs=60.4
Q ss_pred HhHHHHHhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 340 VDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 340 ~~lree~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
..||+....+|.|..|+..+...|+.=|.+ -.|-+.+||.+++....|+..||..||+|+|.|.|+
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 457777778888999999999999999998 459999999999999999999999999999999886
No 27
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.10 E-value=7.8e-07 Score=87.86 Aligned_cols=57 Identities=23% Similarity=0.328 Sum_probs=50.5
Q ss_pred CCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 352 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 352 rgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
|-.++..++-.|+.-|-- .+|.|..-|.+||..+||+++||..||+|+|.|.+|-|.
T Consensus 203 RvVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred eEEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 456888899999887755 889999999999999999999999999999999988653
No 28
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.05 E-value=3.7e-06 Score=82.89 Aligned_cols=56 Identities=20% Similarity=0.296 Sum_probs=51.1
Q ss_pred CCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 352 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 352 rgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
|+.|+..+...|+.-|.+ --||..--|+.||.+|+|.+..|.+||+|+|.|-+|..
T Consensus 145 RTiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred cchhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 678999999999999998 44999999999999999999999999999998876643
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.01 E-value=2.5e-06 Score=85.11 Aligned_cols=71 Identities=21% Similarity=0.431 Sum_probs=61.8
Q ss_pred hHHHHHhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCC
Q 014533 341 DIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTS 414 (423)
Q Consensus 341 ~lree~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s~~ 414 (423)
.|..+-..||.|..++..+...|+.-|.. .|-|.+--|++|+.+|||+.+.|++||+|+|.+.|+-..-++
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 44556678999999999999999998876 899999999999999999999999999999998877544433
No 30
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=97.99 E-value=3.4e-06 Score=84.89 Aligned_cols=58 Identities=19% Similarity=0.374 Sum_probs=52.4
Q ss_pred ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 349 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 349 kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
+|.|.-|+..+.+.|+.||..+. ||+.+.|+++|--|+|++..|++||.|+|.+-+|.
T Consensus 113 rrQrthFtSqqlqele~tF~rNr---ypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 113 RRQRTHFTSQQLQELEATFQRNR---YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhHHHHHHHHHHHHhhcc---CCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 44566899999999999999955 99999999999999999999999999999887664
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.71 E-value=1.9e-05 Score=76.47 Aligned_cols=68 Identities=22% Similarity=0.351 Sum_probs=57.4
Q ss_pred hhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCCccc
Q 014533 347 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTSTVL 417 (423)
Q Consensus 347 ~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s~~~~~ 417 (423)
.||+.|..|+..++..|+.-|.+ ..||--.++.+||...|+++.||.+||+|+|.+-+|+..---.+.
T Consensus 166 ~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasa 233 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASA 233 (288)
T ss_pred cccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhc
Confidence 45666778999999999999998 559999999999999999999999999999988777655443333
No 32
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.71 E-value=9.9e-06 Score=81.02 Aligned_cols=70 Identities=20% Similarity=0.373 Sum_probs=59.6
Q ss_pred HHHHHhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCC
Q 014533 342 IREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTS 414 (423)
Q Consensus 342 lree~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s~~ 414 (423)
+-..--|||||..+-..-++.|+++|.. -|-|+-+....+|++..|.+..|++||+|+|.+.|+-.-|++
T Consensus 303 l~~~~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa~ 372 (385)
T KOG1168|consen 303 LLPGGEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSAT 372 (385)
T ss_pred ccCccccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhhc
Confidence 3333447888888888889999999998 899999999999999999999999999999999988554443
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.66 E-value=5.5e-05 Score=80.90 Aligned_cols=55 Identities=22% Similarity=0.371 Sum_probs=51.4
Q ss_pred ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhc
Q 014533 349 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRN 406 (423)
Q Consensus 349 kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~ 406 (423)
||.|-.|+..+++.|...|.+ +|||+.++-+.|+.+++|...-|.|||-|+|+|.
T Consensus 421 KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 421 KKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 455668999999999999999 8899999999999999999999999999999994
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.61 E-value=2.6e-05 Score=72.70 Aligned_cols=63 Identities=13% Similarity=0.145 Sum_probs=56.8
Q ss_pred HHhhccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 345 EILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 345 e~~kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.+.++|.|..|+..+...|+.-|.. .+||....++.||..+++++..|.+||+|+|.+.++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 4456777889999999999999998 58999999999999999999999999999999988754
No 35
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.55 E-value=6.1e-05 Score=77.25 Aligned_cols=60 Identities=25% Similarity=0.465 Sum_probs=54.7
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.+|+|..|+..+...|..+|.. .|||....|+.||.++||+...|..||.|+|.|.+|-.
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3445678999999999999998 88999999999999999999999999999999888866
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.44 E-value=6.6e-05 Score=75.50 Aligned_cols=67 Identities=31% Similarity=0.525 Sum_probs=61.2
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCCc
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTST 415 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s~~~ 415 (423)
..+++++++.+. ..|+.|...|..+|||++.++..|+..++|+.-||++||+|.|+|.++.+..+..
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~ 161 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWG 161 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCC
Confidence 455778999999 9999999999999999999999999999999999999999999999998776543
No 37
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.32 E-value=8.7e-05 Score=74.85 Aligned_cols=55 Identities=16% Similarity=0.276 Sum_probs=47.4
Q ss_pred CCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 352 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 352 rgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
|.-|+.+++--|+.-|++ --|-++-.|.+||..++|.+.-|.+||+|+|+|.|+.
T Consensus 185 RTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 356888888888777766 3488999999999999999999999999999999873
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.82 E-value=0.00095 Score=52.16 Aligned_cols=43 Identities=21% Similarity=0.502 Sum_probs=31.2
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 014533 360 TSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 405 (423)
Q Consensus 360 ~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR 405 (423)
++.|+.+|..|. +..+.+-..|+.+++|+..||..||.-++.+
T Consensus 10 ~~pL~~Yy~~h~---~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHK---QLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT-------TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcC---CccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 455999999955 8899999999999999999999999876543
No 39
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=96.53 E-value=0.0017 Score=41.89 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=20.6
Q ss_pred HHHHHHHhhhhhHHHhHHHHHh
Q 014533 326 ELKHELKQGYKEKIVDIREEIL 347 (423)
Q Consensus 326 ELK~~Lk~ky~~~i~~lree~~ 347 (423)
|||.+|+++|+++|+++|+||+
T Consensus 1 ELK~~LlrkY~g~i~~Lr~Ef~ 22 (22)
T PF03789_consen 1 ELKHQLLRKYSGYISSLRQEFS 22 (22)
T ss_pred CHHHHHHHHHhHhHHHHHHHhC
Confidence 6899999999999999999984
No 40
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=94.71 E-value=0.024 Score=52.93 Aligned_cols=60 Identities=27% Similarity=0.518 Sum_probs=50.5
Q ss_pred ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 349 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 349 kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
++.+..+...+...|..-|.. .+||....+..|+..+|++...|.+||+|+|.+.++...
T Consensus 154 ~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 154 RRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 344556777777777777766 889999999999999999999999999999999987543
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.03 E-value=0.18 Score=59.47 Aligned_cols=60 Identities=20% Similarity=0.361 Sum_probs=53.7
Q ss_pred hccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 348 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 348 kkRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
++++|..+...+..+|+..|.... ||++++-+.|.+..+|....|..||+|.|.+.+|.-
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~---~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQR---TPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhcc---CChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 455667888889999999999855 999999999999999999999999999999999854
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=82.24 E-value=1.9 Score=32.82 Aligned_cols=47 Identities=15% Similarity=0.186 Sum_probs=31.5
Q ss_pred ccCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 014533 349 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQR 403 (423)
Q Consensus 349 kRKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~R 403 (423)
||+|..|+-+.+-.+-.-+.. .+ -+..||+.+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~---g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEE---GE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHC---TT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHc---CC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 466778887776555555554 22 588999999999999999999854
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=79.94 E-value=3.4 Score=46.90 Aligned_cols=52 Identities=27% Similarity=0.537 Sum_probs=45.8
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCCCC
Q 014533 360 TSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTS 414 (423)
Q Consensus 360 ~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s~~ 414 (423)
+.+|+.+|.. +++|++++-..+|.+.||...-|..||.+.+.....-+-+++
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 7888999888 889999999999999999999999999999988877553333
No 44
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=73.20 E-value=6.2 Score=30.73 Aligned_cols=46 Identities=17% Similarity=0.340 Sum_probs=30.6
Q ss_pred cCCCCCChHHHHHH-HHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhh
Q 014533 350 RRAGKLPGDTTSVL-KSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQR 403 (423)
Q Consensus 350 RKrgklpKea~~iL-k~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~R 403 (423)
++++.||.+.+..+ ...+.. ......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 45678888875554 444343 57788999999999999999988776
No 45
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=71.29 E-value=6.3 Score=27.27 Aligned_cols=46 Identities=13% Similarity=0.154 Sum_probs=35.2
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 407 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~k 407 (423)
.|+...+.++...+... ..-.++|+.+|++...|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 46777778887776432 23467899999999999999988887653
No 46
>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=65.79 E-value=11 Score=27.74 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=32.7
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 405 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR 405 (423)
.||...+.++...|.. .-.-.++|+.+|++...|.+|....|++
T Consensus 10 ~L~~~~r~i~~l~~~~--------g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ--------GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH--------CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 5788888888776554 3455689999999999999999998876
No 47
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=64.44 E-value=12 Score=23.00 Aligned_cols=40 Identities=10% Similarity=0.174 Sum_probs=27.8
Q ss_pred CCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 014533 352 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWF 399 (423)
Q Consensus 352 rgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWF 399 (423)
+..++.+.+..+..++.. .+ ....+|+.+|++...|.+|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 345666666666665543 22 35578899999999999985
No 48
>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=62.56 E-value=9.2 Score=27.92 Aligned_cols=47 Identities=11% Similarity=0.183 Sum_probs=36.7
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
.||+..+.+|...|.. ...-.++|+.+|++...|..+...+.++.|+
T Consensus 4 ~L~~~er~vi~~~y~~--------~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE--------GLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS--------T-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC--------CCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 5788888999887744 2335689999999999999999998888764
No 49
>KOG4511 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.94 E-value=27 Score=35.83 Aligned_cols=69 Identities=23% Similarity=0.295 Sum_probs=46.0
Q ss_pred HHHhhCCChHHHHHHHHhh--hhccCCCcchhhHHHHHHHhHhHhhhhhhcCCCCCCCCCChHHHHHHHHHhhhHH----
Q 014533 178 AEILSHPLYEQLLSAHVAC--LRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQGLVTDDKELDQFMQHVRVHAM---- 251 (423)
Q Consensus 178 AkI~sHPLYp~LL~AyIdC--lKVGAPpdvv~rLd~~l~~s~~~~~~~sa~~~~~~~~gdDPELDQFMe~lr~pf~---- 251 (423)
.=|+.|-=|..|+.-.++| .-||+-|+.... .+ . .+.+...-+|.+.+..|+.
T Consensus 49 ~y~~IH~EYk~LVd~lle~f~eevgi~p~qf~~---Ac-~-----------------~~~q~~~~h~~qv~lqp~lAA~d 107 (335)
T KOG4511|consen 49 VYIMIHKEYKQLVDTLLECFCEEVGITPTQFVA---AC-Q-----------------LFNQKDVSHQYQVALQPLLAAQD 107 (335)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHH---HH-h-----------------cccccchhHHHHHHHHHHHHhcc
Confidence 3578899999999999994 778988864321 11 0 1112223455565555543
Q ss_pred ----HHHhhhhhHHHHHhhh
Q 014533 252 ----EAVMACWEIEQSLQSL 267 (423)
Q Consensus 252 ----EA~~Fc~~IEsQL~sL 267 (423)
-+||-.+.||.||+.|
T Consensus 108 f~IFv~MM~qkNIElQLQAl 127 (335)
T KOG4511|consen 108 FNIFVPMMMQKNIELQLQAL 127 (335)
T ss_pred hhHHHHHHHHhhHHHHHHHH
Confidence 3467778999999997
No 50
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=51.47 E-value=18 Score=31.42 Aligned_cols=47 Identities=9% Similarity=0.067 Sum_probs=37.8
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
.||+..+.++..-|.... .-.++|+.+|++...|.+|....|++.++
T Consensus 106 ~L~~~~r~ii~l~~~~~~--------s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGK--------TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 588888888865554422 24589999999999999999999998876
No 51
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=48.12 E-value=20 Score=29.72 Aligned_cols=48 Identities=17% Similarity=0.230 Sum_probs=35.8
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||+..+.++..-+.. .| .-.++|+.+|+++..|.+|....+++.++.
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4667777777544333 12 345899999999999999999999988763
No 52
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=44.61 E-value=25 Score=31.12 Aligned_cols=50 Identities=14% Similarity=0.005 Sum_probs=40.6
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
..||...+.++..++..++ .-.++|..+|++...|.+|..-.|++.++-.
T Consensus 107 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHEL--------TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578888899987765533 3458999999999999999999999988744
No 53
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=44.51 E-value=22 Score=32.61 Aligned_cols=50 Identities=6% Similarity=-0.011 Sum_probs=40.1
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
.||...+.+|..-+... -.-.++|+.+|++...|.+++...|++.++...
T Consensus 142 ~L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 48888888887655542 234589999999999999999999999987653
No 54
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=43.36 E-value=27 Score=30.67 Aligned_cols=49 Identities=12% Similarity=0.176 Sum_probs=38.7
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
+||...+.++...+...+ .-.++|+.+|++...|.+.+.-+|++.++..
T Consensus 106 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEK--------SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 488888888876555422 2348999999999999999999999987643
No 55
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=43.06 E-value=24 Score=31.63 Aligned_cols=48 Identities=10% Similarity=0.227 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++...|...+ .-.++|+.+|++...|.+++.-.|++.++.
T Consensus 129 ~L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEGL--------SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 478788888877765522 245799999999999999999999998864
No 56
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=42.35 E-value=25 Score=30.83 Aligned_cols=48 Identities=10% Similarity=0.121 Sum_probs=37.2
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||+..+.++...+... -.-.++|+.+|++...|.+|+.-.|++.++.
T Consensus 125 ~L~~~~r~i~~l~~~~~--------~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG--------LSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 37777778876654432 2336899999999999999999999998763
No 57
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=41.23 E-value=30 Score=31.54 Aligned_cols=49 Identities=16% Similarity=0.198 Sum_probs=39.4
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.+||++.+.++.-.|... -.-.++|+.+|++...|.+...-.|++.++-
T Consensus 130 ~~L~~~~r~i~~l~~~~g--------~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG--------EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred HhCCHHHHHHHHHHHHcc--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 368889999988655542 2235899999999999999999999998874
No 58
>PRK00118 putative DNA-binding protein; Validated
Probab=41.17 E-value=29 Score=30.27 Aligned_cols=47 Identities=6% Similarity=0.065 Sum_probs=38.4
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
.||..++.++..++... ..-..+|+.+|++..-|..|+...|++.++
T Consensus 17 ~L~ekqRevl~L~y~eg--------~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD--------YSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57888888987776652 334579999999999999999999988775
No 59
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=39.73 E-value=33 Score=31.52 Aligned_cols=48 Identities=10% Similarity=0.040 Sum_probs=38.4
Q ss_pred CCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 352 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 352 rgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
...|++.++.+|.. +.+. -.-.++|+.+|++...|..|....|++.++
T Consensus 4 ~~~Lt~rqreVL~l-r~~G--------lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERG--------LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHH-HHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999977 3331 234589999999999999999999988765
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=39.19 E-value=30 Score=30.37 Aligned_cols=48 Identities=8% Similarity=0.106 Sum_probs=37.1
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||+..+.+|...|...+ .-..+|+.+|++...|.+|....|++.++.
T Consensus 128 ~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEGL--------SYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 477888888866544321 234789999999999999999999998864
No 61
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=38.74 E-value=34 Score=29.32 Aligned_cols=48 Identities=15% Similarity=0.165 Sum_probs=36.9
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.+|...+... + .-.++|+.+|++...|.++..-.|++.++.
T Consensus 113 ~L~~~~r~il~l~~~~~----~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----K----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 47777888887754431 2 234689999999999999999999988763
No 62
>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=37.09 E-value=37 Score=30.35 Aligned_cols=48 Identities=6% Similarity=0.064 Sum_probs=39.2
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||+..+.++...+...+ .-.++|+.+|++..-|.+.+...|++.++.
T Consensus 134 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAGL--------TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 488888888887766522 345899999999999999999999998764
No 63
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=36.75 E-value=40 Score=29.31 Aligned_cols=48 Identities=19% Similarity=0.228 Sum_probs=37.4
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
..||...+.++..-|... -.-.++|+.+|++...|.++..-.|++.++
T Consensus 110 ~~L~~~~r~v~~l~~~~g--------~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG--------VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 357888888887744432 233579999999999999999999988775
No 64
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=36.55 E-value=27 Score=31.26 Aligned_cols=49 Identities=8% Similarity=0.014 Sum_probs=37.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||...+.++.--|.. ...-.++|+.+|++...|.++.-..|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~--------~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELE--------GLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3667777777654433 233458999999999999999999999988754
No 65
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.17 E-value=29 Score=26.02 Aligned_cols=23 Identities=13% Similarity=0.304 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChhhhhhhhhhh
Q 014533 380 DKARLVQETGLQLKQINNWFINQ 402 (423)
Q Consensus 380 eK~~LA~~TgLs~kQV~NWFiN~ 402 (423)
....||+.+|+++..|+.|+.+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 45689999999999999999976
No 66
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=35.99 E-value=14 Score=35.98 Aligned_cols=46 Identities=24% Similarity=0.328 Sum_probs=35.1
Q ss_pred CCCCcccccCCCcccchhhHHHHHHHhhCCChHHHHHHHHhhhhccCCCcc
Q 014533 155 KSEGVVVESGADGVVNWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQ 205 (423)
Q Consensus 155 ~~~~~~~~~~~~~~~~~e~e~lKAkI~sHPLYp~LL~AyIdClKVGAPpdv 205 (423)
+|..+|+.|=.+|. .--.+.||..|..+||+.+|+.||+ ||.+.-+
T Consensus 93 ~GRPfILaGHSQGs-~~l~~LL~e~~~~~pl~~rLVAAYl----iG~~v~~ 138 (207)
T PF11288_consen 93 NGRPFILAGHSQGS-MHLLRLLKEEIAGDPLRKRLVAAYL----IGYPVTV 138 (207)
T ss_pred CCCCEEEEEeChHH-HHHHHHHHHHhcCchHHhhhheeee----cCccccH
Confidence 56667777744333 2456789999999999999999998 8888543
No 67
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=35.30 E-value=86 Score=21.93 Aligned_cols=47 Identities=13% Similarity=0.143 Sum_probs=34.7
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.|+.....++..++.. ....++|+.+|++...|..|....+++..-.
T Consensus 3 ~l~~~e~~i~~~~~~g---------~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLLAEG---------LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHHHcC---------CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4777777777554321 2346899999999999999999888777644
No 68
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=34.63 E-value=38 Score=31.54 Aligned_cols=49 Identities=16% Similarity=0.176 Sum_probs=38.7
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||...+.+|..-+... -.-.++|+.+|++...|.+++..+|++.++-.
T Consensus 153 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE--------LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 47888888887655442 23458999999999999999999999887644
No 69
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=33.22 E-value=44 Score=29.40 Aligned_cols=49 Identities=20% Similarity=0.125 Sum_probs=39.0
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
..||..++.++.-.+...+ .-.++|+.+|++...|..+....|++.++-
T Consensus 111 ~~L~~~~r~v~~l~~~~~~--------s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYGF--------SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHCCHHHHHHhhhHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4588888888877655422 235799999999999999999999998763
No 70
>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=33.17 E-value=48 Score=29.01 Aligned_cols=50 Identities=12% Similarity=0.203 Sum_probs=39.1
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
.||...+.++..-|...+ .-.++|+.+|++...|.++....|++.++...
T Consensus 110 ~L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 110 RLPARQRAVVVLRYYEDL--------SEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred hCCHHHHHHhhhHHHhcC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 578888888866554422 23478999999999999999999999887543
No 71
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=32.39 E-value=47 Score=30.12 Aligned_cols=48 Identities=10% Similarity=-0.031 Sum_probs=38.3
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++..-|... -.-.++|+.+|++..-|.++....|++.++.
T Consensus 139 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVVG--------LSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888887655442 2356899999999999999999999998864
No 72
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=32.26 E-value=41 Score=30.43 Aligned_cols=49 Identities=6% Similarity=0.076 Sum_probs=37.7
Q ss_pred CChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 355 LPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 355 lpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
||+..+.++..-|... ..-.++|+.+|++...|.++...+|++.++...
T Consensus 129 L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 129 LPERQREAIVLQYYQG--------LSNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CCHHHHHHhhHHHhcC--------CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 6777778876544432 223579999999999999999999999988544
No 73
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=31.92 E-value=47 Score=29.91 Aligned_cols=50 Identities=8% Similarity=-0.067 Sum_probs=40.4
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
.||+..+.++...+... -.-.++|+.+|++...|.+++...|++.++..-
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--------ASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 57888889988865542 234589999999999999999999999887543
No 74
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=31.27 E-value=57 Score=28.37 Aligned_cols=50 Identities=12% Similarity=0.064 Sum_probs=39.0
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.+||+..+.++.--+.+.+ .-.++|+.+|++...|.+...-.|++.++..
T Consensus 105 ~~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWEDM--------DVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4588888888877554422 2458999999999999999999999887643
No 75
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=30.99 E-value=44 Score=30.90 Aligned_cols=49 Identities=14% Similarity=0.054 Sum_probs=39.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||...+.++.-.+... -.-.++|+.+|++...|.+++.-.|++.++..
T Consensus 113 ~Lp~~~r~v~~L~~~~g--------~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGASG--------FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 57888989987765542 22357899999999999999999999988744
No 76
>PF13518 HTH_28: Helix-turn-helix domain
Probab=30.74 E-value=50 Score=23.59 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhhh
Q 014533 381 KARLVQETGLQLKQINNWFINQRK 404 (423)
Q Consensus 381 K~~LA~~TgLs~kQV~NWFiN~Rk 404 (423)
..++|+++|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456999999999999999987765
No 77
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=30.68 E-value=52 Score=29.59 Aligned_cols=48 Identities=15% Similarity=0.101 Sum_probs=38.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.+|...+...+ .-.++|+.+|++...|.++..-.|++.++.
T Consensus 135 ~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 135 ALSPEERRVIEVLYYQGY--------THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 388888888876655422 345899999999999999999999998764
No 78
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=30.55 E-value=50 Score=29.33 Aligned_cols=49 Identities=14% Similarity=0.001 Sum_probs=39.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||...+.++.-.+...+ .-.++|+.+|++...|.++..-.|++.++..
T Consensus 112 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 578888898877665533 2458999999999999999999999987643
No 79
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=30.39 E-value=53 Score=29.82 Aligned_cols=49 Identities=12% Similarity=0.141 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||+..+.+|..-+.. .-.-.++|+.+|++...|.+-+...|++.++..
T Consensus 131 ~L~~~~r~vl~l~~~~--------~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYH--------EKSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4788888888665444 233458999999999999999999999988743
No 80
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=30.10 E-value=53 Score=28.83 Aligned_cols=47 Identities=13% Similarity=0.174 Sum_probs=37.4
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.+|.-.+ .. -.-.++|..+|++...|.++....|++.++-
T Consensus 112 ~L~~~~r~il~l~~-~g--------~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG--------YSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred cCCHHHHHHHHHHH-cC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47788888887665 42 2346899999999999999999999988763
No 81
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=30.06 E-value=41 Score=29.92 Aligned_cols=20 Identities=30% Similarity=0.459 Sum_probs=17.7
Q ss_pred HHHHHHHhhCCChHHHHHHH
Q 014533 174 ARYKAEILSHPLYEQLLSAH 193 (423)
Q Consensus 174 e~lKAkI~sHPLYp~LL~Ay 193 (423)
+..++.|..||++...|.+|
T Consensus 89 ~~~~~~a~~~P~V~avL~~F 108 (117)
T PF12362_consen 89 EARRAAARAHPLVKAVLAAF 108 (117)
T ss_pred HHHHHHHHhCcHHHHHHHHC
Confidence 46888999999999999876
No 82
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=29.92 E-value=40 Score=30.62 Aligned_cols=48 Identities=13% Similarity=0.161 Sum_probs=37.2
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||++.+.++..-+.. .-.-.++|+.+|++..-|.+|+..+|++.++.
T Consensus 141 ~L~~~~~~v~~l~~~~--------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 141 QLPESQRQVLELAYYE--------GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hCCHHHhhhhhhhhhc--------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5777788888655443 22345799999999999999999999988763
No 83
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=29.56 E-value=53 Score=30.08 Aligned_cols=48 Identities=13% Similarity=0.127 Sum_probs=38.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++.--+... -.-.++|+.+|+++.-|.++..-+|++.++.
T Consensus 134 ~Lp~~~R~v~~L~~~~g--------~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYLE--------LSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888887765542 2346899999999999999999999998763
No 84
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.68 E-value=55 Score=30.03 Aligned_cols=49 Identities=4% Similarity=0.026 Sum_probs=38.0
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||+..+.++.--+..- | .-.++|+.+|++..-|.+++.-+|++.++..
T Consensus 136 ~L~~~~r~i~~L~~~~g----~----s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIEG----L----SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 57888888876654431 2 2357999999999999999999999988743
No 85
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.58 E-value=59 Score=29.40 Aligned_cols=48 Identities=15% Similarity=0.210 Sum_probs=36.7
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++..-|.. ...-.++|+.+|++..-|.+|..-+|++.++.
T Consensus 133 ~L~~~~r~i~~l~~~~--------~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 133 QLEPARRNCILHAYVD--------GCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred hCCHHHHHHHHHHHHc--------CCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 4777787766554443 22345899999999999999999999988753
No 86
>PF13730 HTH_36: Helix-turn-helix domain
Probab=28.18 E-value=2.1e+02 Score=20.85 Aligned_cols=49 Identities=10% Similarity=0.162 Sum_probs=31.4
Q ss_pred CCChHHHHHHHHHHHh--cCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhh
Q 014533 354 KLPGDTTSVLKSWWQS--HSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 405 (423)
Q Consensus 354 klpKea~~iLk~Wf~~--H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR 405 (423)
.|+..++.++-.-+.. .....||+ ...||+.+|++.+.|..++..-+.+
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~~ 52 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELEEK 52 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3555555554322221 22347887 5579999999999999988765443
No 87
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=27.96 E-value=54 Score=29.27 Aligned_cols=48 Identities=10% Similarity=0.097 Sum_probs=36.9
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++..-|.. .-.-.++|+.+|++...|.+++...|++.++.
T Consensus 136 ~L~~~~r~v~~l~~~~--------g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME--------DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc--------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4788888887663333 12335799999999999999999999988764
No 88
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=27.68 E-value=67 Score=29.32 Aligned_cols=51 Identities=14% Similarity=0.005 Sum_probs=40.2
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
..||..++.++.-.+...+ .-.++|+.+|++..-|.++..-.|++.++-+.
T Consensus 129 ~~Lp~~~r~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~~ 179 (185)
T PRK09649 129 ADLTTDQREALLLTQLLGL--------SYADAAAVCGCPVGTIRSRVARARDALLADAE 179 (185)
T ss_pred HhCCHHHhHHhhhHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 3588888888876655422 24589999999999999999999999998443
No 89
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=27.54 E-value=64 Score=28.58 Aligned_cols=48 Identities=4% Similarity=0.006 Sum_probs=37.4
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++..-+... ..-.++|+.+|++...|.++..-.|++.++.
T Consensus 119 ~L~~~~r~i~~l~~~~g--------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD--------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47777888886655442 2345799999999999999999999988763
No 90
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=27.28 E-value=1.5e+02 Score=25.36 Aligned_cols=48 Identities=10% Similarity=0.126 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.|+...+++|+-+ .+++ . ..++|+..+++.+-|.++..+.|+|..-.+
T Consensus 149 ~lt~~e~~vl~l~-~~g~----~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~ 196 (211)
T PRK15369 149 LLTPRERQILKLI-TEGY----T----NRDIAEQLSISIKTVETHRLNMMRKLDVHK 196 (211)
T ss_pred CCCHHHHHHHHHH-HCCC----C----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 5888889998874 4322 2 468899999999999999999999987554
No 91
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=27.04 E-value=65 Score=30.29 Aligned_cols=47 Identities=11% Similarity=0.238 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
.||+..+.++...|.. .-.-.++|+.+|++...|..|..-.+++.++
T Consensus 178 ~L~~~~r~vl~l~y~~--------~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE--------DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5888888888876654 2245689999999999999999999988875
No 92
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=26.85 E-value=67 Score=28.83 Aligned_cols=49 Identities=14% Similarity=0.147 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
+||+..+.+|.-.+...+ .-.++|+.+|++...|.++..-.|++.++-.
T Consensus 100 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL--------SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888877655422 3458999999999999999999999887743
No 93
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=26.71 E-value=68 Score=28.98 Aligned_cols=48 Identities=17% Similarity=-0.009 Sum_probs=37.3
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||+..+.++...+...+ .-.++|+.+|++...|.+.+...|++.++.
T Consensus 129 ~L~~~~r~v~~l~~~~g~--------s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEGL--------SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467777777765554422 345899999999999999999999998874
No 94
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.67 E-value=65 Score=29.39 Aligned_cols=49 Identities=14% Similarity=0.094 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||...+.++.-.+...+ .-.++|+.+|++..-|.++...+|++.++..
T Consensus 136 ~L~~~~r~i~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEILGF--------SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888876544422 2458999999999999999999999988743
No 95
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=26.09 E-value=65 Score=29.62 Aligned_cols=50 Identities=16% Similarity=0.075 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
.||...+.++.-.+...+ .-.++|+.+|++..-|.++....|++.++...
T Consensus 116 ~Lp~~~r~i~~L~~~~g~--------s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGASGF--------AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888876555422 23479999999999999999999999987544
No 96
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=25.97 E-value=73 Score=28.95 Aligned_cols=48 Identities=17% Similarity=0.101 Sum_probs=37.7
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++.-.+...+ .-.++|+.+|++..-|.+.....|++.++-
T Consensus 131 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 131 RLPPRTGRVFMMREWLEL--------ETEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888876655422 235899999999999999999999988763
No 97
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=25.88 E-value=77 Score=28.31 Aligned_cols=49 Identities=10% Similarity=0.254 Sum_probs=38.0
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
..||.+.+.++.-.+...+ .-.++|+.+|++..-|.++...+|++.+..
T Consensus 118 ~~Lp~~~r~v~~L~~~~g~--------s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDGM--------GHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3578888888876655422 234799999999999999999999987653
No 98
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=25.87 E-value=71 Score=27.99 Aligned_cols=49 Identities=14% Similarity=0.195 Sum_probs=37.6
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
..||+..+.++..-|... -.-.++|+.+|++...|.....-.|++.++.
T Consensus 108 ~~L~~~~r~v~~l~~~~~--------~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 108 SELPARTRYAFEMYRLHG--------ETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred HhCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357888888886654442 2245799999999999999998888887763
No 99
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=25.10 E-value=71 Score=28.53 Aligned_cols=48 Identities=10% Similarity=0.129 Sum_probs=35.9
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.+|..-+.. ...-.++|+.+|++...|.+.....|++.++.
T Consensus 136 ~L~~~~r~il~l~~~~--------~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 136 QLPEKYRTVIVLKYIE--------DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHHHHhhhHHhh--------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3677777777443322 23345899999999999999999999998764
No 100
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.00 E-value=66 Score=29.46 Aligned_cols=51 Identities=14% Similarity=0.199 Sum_probs=39.7
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 411 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~ 411 (423)
..||+..+.++..-+...+ .-.++|+.+|++...|.+-+...|++.++...
T Consensus 140 ~~Lp~~~r~v~~l~~~eg~--------s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEEL--------PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 4588888899876544422 23479999999999999999999999887543
No 101
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=24.14 E-value=77 Score=28.65 Aligned_cols=48 Identities=17% Similarity=0.120 Sum_probs=37.4
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||+..+.++...+... -.-.++|+.+|++..-|.+...-.|++.++.
T Consensus 122 ~L~~~~r~i~~l~~~~g--------~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN--------LTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888887644432 2235799999999999999999999988763
No 102
>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=23.95 E-value=61 Score=25.88 Aligned_cols=22 Identities=14% Similarity=0.299 Sum_probs=18.3
Q ss_pred HHHHHHHHHhCCChhhhhhhhh
Q 014533 379 EDKARLVQETGLQLKQINNWFI 400 (423)
Q Consensus 379 ~eK~~LA~~TgLs~kQV~NWFi 400 (423)
-.-..||+++|++..+|..|=.
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHhh
Confidence 3456899999999999999943
No 103
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=23.91 E-value=76 Score=29.87 Aligned_cols=48 Identities=13% Similarity=0.134 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.+|...|...+ .-.++|+.+|++...|..+...++++.++.
T Consensus 175 ~L~~~~r~il~l~y~~~~--------s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEEL--------NLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred hCCHHHHHHHHHHHhCCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 488888899988765422 346899999999999999999999988753
No 104
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.81 E-value=68 Score=30.54 Aligned_cols=48 Identities=17% Similarity=0.193 Sum_probs=38.2
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++..-|... -.-.++|+.+|++..-|.++...+|++.++.
T Consensus 184 ~L~~~~r~vl~l~~~~g--------~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE--------LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhccC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47888888887655432 2356899999999999999999999998764
No 105
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=23.74 E-value=68 Score=31.93 Aligned_cols=39 Identities=5% Similarity=-0.004 Sum_probs=31.8
Q ss_pred CcccchhhHHHHHHHhhCCChHH----HHHHHHhhhhccCCCc
Q 014533 166 DGVVNWQNARYKAEILSHPLYEQ----LLSAHVACLRIATPVD 204 (423)
Q Consensus 166 ~~~~~~e~e~lKAkI~sHPLYp~----LL~AyIdClKVGAPpd 204 (423)
|+......+.+++++..|-+.+. ...-|++++|-|+||-
T Consensus 196 G~~r~~d~~~l~~~~~~~~~~~~~~~~~~~~yl~a~~~G~pp~ 238 (269)
T cd00669 196 GSSRLHDPDIQAEVFQEQGINKEAGMEYFEFYLKALEYGLPPH 238 (269)
T ss_pred CchhcCCHHHHHHHHHHhCcChhhccccHHHHHHHHHcCCCCC
Confidence 44556667788899998888887 7888999999999985
No 106
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=23.46 E-value=82 Score=30.06 Aligned_cols=49 Identities=14% Similarity=0.070 Sum_probs=39.9
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||...+.++...|...+ .-.++|+.+|++..-|.++....|++.++..
T Consensus 134 ~Lp~~~R~v~~L~y~eg~--------s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELEDM--------SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 588888899988766533 2347899999999999999999999998844
No 107
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.46 E-value=77 Score=28.96 Aligned_cols=48 Identities=15% Similarity=0.116 Sum_probs=37.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++..-+.+ .-.-.++|..+|++..-|.+.+.-.|++.++.
T Consensus 106 ~L~~~~r~i~~l~~~~--------g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 106 ALPEKYAEALRLTELE--------GLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred hCCHHHHHHHHHHHhc--------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5788888888665443 22345799999999999999999999988763
No 108
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=23.35 E-value=64 Score=31.08 Aligned_cols=49 Identities=6% Similarity=0.122 Sum_probs=37.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||...+.++.-.|... -.-.++|+.+|++..-|.+.+...|++.++..
T Consensus 171 ~Lp~~~R~v~~L~~~eg--------~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN--------MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46777888765554432 22357999999999999999999999988743
No 109
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=23.11 E-value=80 Score=30.44 Aligned_cols=47 Identities=13% Similarity=0.104 Sum_probs=38.1
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
.||...+.++...|.. .-.-.++|..+|++...|.+++...|++.++
T Consensus 201 ~L~~~~r~vl~l~~~~--------~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYKE--------ELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHhc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4788888888776554 2235689999999999999999999998875
No 110
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=23.02 E-value=81 Score=30.42 Aligned_cols=48 Identities=8% Similarity=0.108 Sum_probs=38.8
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.+|...|...+ .-.++|+.+|++...|..|....|++.++.
T Consensus 205 ~L~~~~r~vl~l~~~~g~--------s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL--------SQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 488888899887665422 236899999999999999999999988764
No 111
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.70 E-value=66 Score=23.31 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=18.4
Q ss_pred HHHHHHhCCChhhhhhhhhhh
Q 014533 382 ARLVQETGLQLKQINNWFINQ 402 (423)
Q Consensus 382 ~~LA~~TgLs~kQV~NWFiN~ 402 (423)
.+||+.+|+++..|..|..+.
T Consensus 13 ~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHhCCCcchhHHHhcCC
Confidence 689999999999999999883
No 112
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=22.55 E-value=1.2e+02 Score=22.56 Aligned_cols=48 Identities=19% Similarity=0.147 Sum_probs=35.4
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.|++....+|..+..- ....++|+..|++++-|..+..+.++|..-.+
T Consensus 3 ~LT~~E~~vl~~l~~G---------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG---------MSNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHHTT---------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHHhc---------CCcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 4667777777665543 33458999999999999999999999876543
No 113
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=22.44 E-value=1.5e+02 Score=25.70 Aligned_cols=48 Identities=6% Similarity=0.060 Sum_probs=32.5
Q ss_pred cCCCCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhh
Q 014533 350 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 404 (423)
Q Consensus 350 RKrgklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~Rk 404 (423)
+++++++.+-+...-.....+ ......+|+.+|++..+|.+|..-.|.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~-------g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEP-------GMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcC-------CCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 455678888755443333331 223457899999999999999776654
No 114
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.34 E-value=90 Score=27.83 Aligned_cols=48 Identities=8% Similarity=0.104 Sum_probs=36.2
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++...|.. .-.-.++|+.+|++...|.......|++.++.
T Consensus 119 ~L~~~~r~i~~l~~~~--------~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 119 LLNEKYKTVLVLYYYE--------QYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred hCCHHHHHHHHHHHHc--------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4677777777554433 22335799999999999999999999988763
No 115
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=22.32 E-value=75 Score=30.35 Aligned_cols=24 Identities=33% Similarity=0.585 Sum_probs=20.1
Q ss_pred CCCCC-CHHHHHHHHHHhCCChhhh
Q 014533 372 KWPYP-TEEDKARLVQETGLQLKQI 395 (423)
Q Consensus 372 ~~PYP-Se~eK~~LA~~TgLs~kQV 395 (423)
=-||| |++||...|++.||.+..-
T Consensus 33 PgpyP~t~eer~aaAkKY~l~pedY 57 (179)
T PF05821_consen 33 PGPYPKTPEERAAAAKKYGLRPEDY 57 (179)
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHc
Confidence 35898 7899999999999987653
No 116
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.93 E-value=94 Score=28.49 Aligned_cols=48 Identities=15% Similarity=0.080 Sum_probs=38.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++..-|... -.-.++|+.+|++..-|.+...-.|++.++.
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG--------FESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHHhC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888887765542 2346899999999999999999999998763
No 117
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.55 E-value=96 Score=27.52 Aligned_cols=49 Identities=10% Similarity=0.098 Sum_probs=39.1
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||+..+.+|.--+...+ .-.++|+.+|++..-|.....-.|++.++..
T Consensus 118 ~L~~~~r~vl~L~~~~g~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGW--------STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 488888888877555422 2357999999999999999999999988754
No 118
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=21.39 E-value=81 Score=28.48 Aligned_cols=47 Identities=11% Similarity=0.159 Sum_probs=37.5
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
+||+..+.++..-+...+ .-.++|+.+|++...|.++..-.|++.++
T Consensus 127 ~L~~~~r~v~~l~~~~g~--------s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYEEL--------SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 588888888766554422 23589999999999999999999998876
No 119
>PRK04217 hypothetical protein; Provisional
Probab=21.36 E-value=1.1e+02 Score=27.04 Aligned_cols=49 Identities=8% Similarity=-0.062 Sum_probs=39.1
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
..|+.+.+.++..++...+ .-.++|+.+|++..-|.+.+...|++.+..
T Consensus 41 ~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4688888888877765522 456799999999999999999999887653
No 120
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.33 E-value=1.1e+02 Score=27.66 Aligned_cols=47 Identities=13% Similarity=0.145 Sum_probs=37.2
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
.||...+.++..-+...+ .-.++|+.+|++..-|.+.....|++.++
T Consensus 117 ~Lp~~~r~i~~l~~~e~~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 117 KLPYKLRQVIILRYLHDY--------SQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred hCCHHHHHHHHHHHHccC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888876544422 34579999999999999999999998876
No 121
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=20.94 E-value=94 Score=28.36 Aligned_cols=46 Identities=15% Similarity=0.197 Sum_probs=35.4
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
.||...+.+|..+|.. -.-.++|..+|++...|.+.+...|++.++
T Consensus 155 ~L~~~~r~vl~l~~e~---------~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 155 LLSELEKEVLELYLDG---------KSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred hCCHHHHHHHHHHHcc---------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3677777888763332 233579999999999999999999998876
No 122
>PHA03397 vlf-1 very late expression factor 1; Provisional
Probab=20.93 E-value=94 Score=32.75 Aligned_cols=31 Identities=23% Similarity=0.426 Sum_probs=26.6
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhhccCCCcc
Q 014533 174 ARYKAEILSHPLYEQLLSAHVACLRIATPVDQ 205 (423)
Q Consensus 174 e~lKAkI~sHPLYp~LL~AyIdClKVGAPpdv 205 (423)
..-|-+|..||+|+..+.+=++-|| +.|.++
T Consensus 13 ~~w~~~i~~~~~f~~~~~~~~~rq~-~~~~~~ 43 (363)
T PHA03397 13 NIWKLVIQNHPRFEEVFDLAIDRQK-CTPDEV 43 (363)
T ss_pred HHHHHHHhccchHHHHHHHHHHhhc-CCCccc
Confidence 5679999999999999999999998 555543
No 123
>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=20.84 E-value=48 Score=30.20 Aligned_cols=48 Identities=10% Similarity=0.028 Sum_probs=36.4
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++.-.+.. .-.-.++|+.+|++...|.++..-.|++.++.
T Consensus 131 ~Lp~~~r~i~~L~~~~--------g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 178 (193)
T TIGR02947 131 GLPEEFRQAVYLADVE--------GFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQ 178 (193)
T ss_pred hCCHHHhhheeehhhc--------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4677777777544433 22345899999999999999999999988864
No 124
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=20.74 E-value=92 Score=30.40 Aligned_cols=48 Identities=13% Similarity=0.127 Sum_probs=38.6
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||+..+.+|...|... -.-.++|..+|++...|.......+++.++.
T Consensus 212 ~L~~~~r~vl~l~~~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYYED--------LTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHHcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 57888888887766542 2356899999999999999999999888763
No 125
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.65 E-value=1.1e+02 Score=27.78 Aligned_cols=49 Identities=10% Similarity=-0.013 Sum_probs=39.1
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||+..+.++.-.+... -.-.++|+.+|++..-|.++.--.|++.++..
T Consensus 131 ~L~~~~r~v~~l~~~~g--------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG--------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC--------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 48888988987655442 23458999999999999999999999988743
No 126
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=20.60 E-value=42 Score=29.00 Aligned_cols=46 Identities=20% Similarity=0.163 Sum_probs=34.6
Q ss_pred CChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhccc
Q 014533 355 LPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 408 (423)
Q Consensus 355 lpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK 408 (423)
||+..+.++...+.. .-.-.++|+.+|++...|.++..-.|++.++
T Consensus 106 L~~~~r~i~~l~~~~--------g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREFK--------EFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhhc--------cCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 666666666543332 2345689999999999999999999998875
No 127
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=20.45 E-value=1.2e+02 Score=29.98 Aligned_cols=51 Identities=10% Similarity=-0.041 Sum_probs=39.3
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCCCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 412 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n~s 412 (423)
+||+..+.++.--+... . .-.++|+.+|++..-|.+.+..+|++.++..+.
T Consensus 115 ~L~~~~R~v~~L~~~~g--~------s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~ 165 (293)
T PRK09636 115 RLSPLERAAFLLHDVFG--V------PFDEIASTLGRSPAACRQLASRARKHVRAARPR 165 (293)
T ss_pred hCCHHHHHHHHHHHHhC--C------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 37777877775543331 2 235799999999999999999999999997764
No 128
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=20.45 E-value=51 Score=23.02 Aligned_cols=22 Identities=41% Similarity=0.591 Sum_probs=17.5
Q ss_pred HHHHHhhCCChHHHHHHHHhhh
Q 014533 176 YKAEILSHPLYEQLLSAHVACL 197 (423)
Q Consensus 176 lKAkI~sHPLYp~LL~AyIdCl 197 (423)
+-.||++-|||.-||+|--..+
T Consensus 5 lipkiissplfktllsavgsal 26 (33)
T PF07425_consen 5 LIPKIISSPLFKTLLSAVGSAL 26 (33)
T ss_dssp CHHHHCCTTTCHHHHHHHHHHC
T ss_pred hhhHHHccHHHHHHHHHHHHHH
Confidence 3468999999999998865543
No 129
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=20.40 E-value=60 Score=30.91 Aligned_cols=36 Identities=28% Similarity=0.667 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhcCCCCCCC-HHHHHHHHHHhCCChhh
Q 014533 359 TTSVLKSWWQSHSKWPYPT-EEDKARLVQETGLQLKQ 394 (423)
Q Consensus 359 a~~iLk~Wf~~H~~~PYPS-e~eK~~LA~~TgLs~kQ 394 (423)
..+..-.|...|.--|||+ ++||..-|++.||-+..
T Consensus 25 g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 25 GPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 4455667888898899995 78889999999987654
No 130
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=20.39 E-value=1.9e+02 Score=20.39 Aligned_cols=27 Identities=37% Similarity=0.615 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHhcCCCCCCCHH-HHHHHH
Q 014533 358 DTTSVLKSWWQSHSKWPYPTEE-DKARLV 385 (423)
Q Consensus 358 ea~~iLk~Wf~~H~~~PYPSe~-eK~~LA 385 (423)
.....|+.|+..|. -|+|... .|.+|.
T Consensus 4 Ws~~~L~~wL~~~g-i~~~~~~~~rd~Ll 31 (38)
T PF10281_consen 4 WSDSDLKSWLKSHG-IPVPKSAKTRDELL 31 (38)
T ss_pred CCHHHHHHHHHHcC-CCCCCCCCCHHHHH
Confidence 34578999999976 6677444 444443
No 131
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.33 E-value=4.4e+02 Score=21.29 Aligned_cols=46 Identities=20% Similarity=0.128 Sum_probs=28.7
Q ss_pred CChHHHHHHHHHHHhcCCCC--CCCHHHHHH-H-HHHhC--CChhhhhhhhh
Q 014533 355 LPGDTTSVLKSWWQSHSKWP--YPTEEDKAR-L-VQETG--LQLKQINNWFI 400 (423)
Q Consensus 355 lpKea~~iLk~Wf~~H~~~P--YPSe~eK~~-L-A~~Tg--Ls~kQV~NWFi 400 (423)
++.+....|.+++.++...- ..+...-.. | .+.+| ++...|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999999843211 223333333 4 33333 77777777764
No 132
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=20.27 E-value=45 Score=30.33 Aligned_cols=49 Identities=10% Similarity=0.119 Sum_probs=36.3
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccCC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 410 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~n 410 (423)
.||+..+.++...+.. .-.-.++|+.+|++..-|.++...+|++.++..
T Consensus 139 ~L~~~~r~i~~l~~~~--------g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 139 TLPDEQREVFLLREHG--------DLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hCCHhHhhheeeehcc--------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4666677777654332 122357899999999999999999999988743
No 133
>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=20.19 E-value=2.4e+02 Score=21.83 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=36.3
Q ss_pred CChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 014533 355 LPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQ 402 (423)
Q Consensus 355 lpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~ 402 (423)
|+..++.+|+.-+..=| .=+|-+..-..||++.|++..-|..-+.+.
T Consensus 1 LT~~Q~e~L~~A~~~GY-fd~PR~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 1 LTDRQREILKAAYELGY-FDVPRRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CCHHHHHHHHHHHHcCC-CCCCCcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 56778888888777644 557888999999999999998877654443
No 134
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.06 E-value=1.2e+02 Score=26.71 Aligned_cols=47 Identities=13% Similarity=0.161 Sum_probs=36.0
Q ss_pred CCCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcc
Q 014533 353 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 407 (423)
Q Consensus 353 gklpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~k 407 (423)
..||+..+.++...+...+ .-.++|+.+|++...|.++....+++..
T Consensus 112 ~~L~~~~r~v~~L~~~~g~--------s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVDGL--------GYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HHCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3578888888866655422 2357999999999999999998887654
No 135
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=20.01 E-value=94 Score=29.91 Aligned_cols=48 Identities=6% Similarity=0.083 Sum_probs=38.7
Q ss_pred CCChHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhhhhhcccC
Q 014533 354 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 409 (423)
Q Consensus 354 klpKea~~iLk~Wf~~H~~~PYPSe~eK~~LA~~TgLs~kQV~NWFiN~RkR~kK~ 409 (423)
.||...+.++...|...+ .-.++|+.+|++...|..+...++++.++.
T Consensus 205 ~L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 588888888877765432 236899999999999999999999988763
Done!