Query 013509
Match_columns 441
No_of_seqs 289 out of 1078
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:34:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013509.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013509hhsearch_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 2.1E-32 4.5E-37 265.6 17.9 209 171-424 26-249 (334)
2 KOG0773 Transcription factor M 99.9 2.2E-28 4.7E-33 243.4 0.3 253 170-430 46-306 (342)
3 PF03791 KNOX2: KNOX2 domain ; 99.9 3.5E-23 7.7E-28 158.4 7.2 50 231-284 3-52 (52)
4 PF03790 KNOX1: KNOX1 domain ; 99.8 4.4E-20 9.6E-25 137.5 3.4 44 174-217 1-44 (45)
5 PF05920 Homeobox_KN: Homeobox 99.6 6E-16 1.3E-20 112.6 4.3 40 381-420 1-40 (40)
6 PF03792 PBC: PBC domain; Int 99.5 6.2E-13 1.3E-17 125.3 13.0 150 171-362 24-190 (191)
7 cd00086 homeodomain Homeodomai 99.5 1.4E-13 3E-18 103.2 6.5 58 364-424 1-58 (59)
8 smart00389 HOX Homeodomain. DN 99.4 2.9E-13 6.4E-18 101.0 6.2 55 365-422 2-56 (56)
9 PF00046 Homeobox: Homeobox do 99.4 2.1E-13 4.6E-18 102.9 5.2 57 364-423 1-57 (57)
10 KOG0775 Transcription factor S 99.2 1.1E-11 2.5E-16 122.2 4.4 47 373-422 186-232 (304)
11 KOG0487 Transcription factor A 98.9 4.7E-10 1E-14 112.8 2.9 59 364-425 236-294 (308)
12 KOG0489 Transcription factor z 98.9 9.7E-10 2.1E-14 107.8 3.7 66 363-431 159-224 (261)
13 TIGR01565 homeo_ZF_HD homeobox 98.8 5.5E-09 1.2E-13 82.1 4.5 53 363-418 1-57 (58)
14 KOG0843 Transcription factor E 98.8 3.9E-09 8.3E-14 99.4 3.9 60 362-424 101-160 (197)
15 KOG0842 Transcription factor t 98.7 3.8E-09 8.2E-14 106.3 2.6 60 362-424 152-211 (307)
16 KOG0493 Transcription factor E 98.7 6.9E-09 1.5E-13 102.5 4.3 61 363-426 246-306 (342)
17 KOG0485 Transcription factor N 98.7 1.8E-08 4E-13 97.4 6.0 59 362-423 103-161 (268)
18 KOG3802 Transcription factor O 98.7 1.7E-08 3.7E-13 104.1 5.3 68 356-426 287-354 (398)
19 KOG0488 Transcription factor B 98.7 1.3E-08 2.9E-13 102.5 4.3 61 362-425 171-231 (309)
20 KOG0850 Transcription factor D 98.7 1.4E-08 3E-13 98.7 3.6 59 364-425 123-181 (245)
21 KOG0483 Transcription factor H 98.6 2.9E-08 6.2E-13 94.8 3.8 58 363-423 50-107 (198)
22 COG5576 Homeodomain-containing 98.5 5.7E-08 1.2E-12 89.6 4.1 62 362-426 50-111 (156)
23 KOG0491 Transcription factor B 98.5 5E-08 1.1E-12 91.1 3.4 61 360-423 97-157 (194)
24 KOG0484 Transcription factor P 98.5 7.9E-08 1.7E-12 84.1 3.0 65 356-423 10-74 (125)
25 KOG0492 Transcription factor M 98.4 1.2E-07 2.6E-12 91.3 2.8 66 355-423 136-201 (246)
26 KOG0494 Transcription factor C 98.3 3.4E-07 7.4E-12 90.6 3.9 55 367-424 145-199 (332)
27 KOG2251 Homeobox transcription 98.3 4.8E-07 1.1E-11 87.6 3.8 58 363-423 37-94 (228)
28 KOG0848 Transcription factor C 98.3 1.9E-07 4.1E-12 92.7 0.9 57 367-426 203-259 (317)
29 KOG0486 Transcription factor P 98.2 4.5E-07 9.7E-12 91.6 2.0 59 363-424 112-170 (351)
30 KOG4577 Transcription factor L 98.2 6.4E-07 1.4E-11 89.8 2.8 72 356-430 160-231 (383)
31 KOG2252 CCAAT displacement pro 97.8 1.8E-05 3.9E-10 84.9 5.2 56 363-421 420-475 (558)
32 KOG0847 Transcription factor, 97.8 8.2E-06 1.8E-10 79.5 2.3 62 362-426 166-227 (288)
33 KOG0490 Transcription factor, 97.8 1.1E-05 2.3E-10 75.3 2.3 63 360-425 57-119 (235)
34 KOG0849 Transcription factor P 97.7 2.6E-05 5.6E-10 80.2 4.0 61 363-426 176-236 (354)
35 KOG0844 Transcription factor E 97.7 1.1E-05 2.4E-10 81.6 1.1 54 367-423 185-238 (408)
36 KOG1168 Transcription factor A 97.6 1.5E-05 3.2E-10 80.3 0.8 67 359-428 305-371 (385)
37 KOG0773 Transcription factor M 97.4 9.4E-05 2E-09 74.5 2.8 65 363-428 95-159 (342)
38 PF11569 Homez: Homeodomain le 96.8 0.0012 2.5E-08 52.1 3.2 43 375-420 10-52 (56)
39 PF03789 ELK: ELK domain ; In 96.8 0.001 2.2E-08 43.4 2.2 22 341-362 1-22 (22)
40 KOG0490 Transcription factor, 95.3 0.014 3E-07 54.5 3.2 61 363-426 153-213 (235)
41 KOG1146 Homeobox protein [Gene 91.1 0.16 3.4E-06 60.2 3.1 60 362-424 902-961 (1406)
42 KOG3623 Homeobox transcription 83.0 2.1 4.5E-05 48.8 5.6 52 375-429 568-619 (1007)
43 PF04218 CENP-B_N: CENP-B N-te 80.7 2.7 5.8E-05 32.2 4.0 47 364-418 1-47 (53)
44 PF01527 HTH_Tnp_1: Transposas 65.7 7 0.00015 30.5 3.1 47 365-418 2-48 (76)
45 cd06171 Sigma70_r4 Sigma70, re 60.1 18 0.0004 24.9 4.1 46 369-422 10-55 (55)
46 cd00569 HTH_Hin_like Helix-tur 57.1 24 0.00053 21.6 4.0 40 367-414 3-42 (42)
47 PF08281 Sigma70_r4_2: Sigma-7 52.5 22 0.00047 26.2 3.6 44 369-420 10-53 (54)
48 PRK06759 RNA polymerase factor 49.0 20 0.00043 31.2 3.4 47 369-423 106-152 (154)
49 PF04545 Sigma70_r4: Sigma-70, 49.0 16 0.00034 26.8 2.4 47 369-423 4-50 (50)
50 KOG2070 Guanine nucleotide exc 43.9 66 0.0014 35.9 6.9 25 235-259 183-214 (661)
51 PRK09646 RNA polymerase sigma 43.7 23 0.0005 32.6 3.1 50 369-426 142-191 (194)
52 KOG4445 Uncharacterized conser 41.6 50 0.0011 34.6 5.4 47 237-285 134-180 (368)
53 PRK09644 RNA polymerase sigma 41.5 39 0.00084 30.1 4.1 48 368-423 107-154 (165)
54 PRK09642 RNA polymerase sigma 40.6 30 0.00066 30.4 3.3 48 369-424 106-153 (160)
55 PF12022 DUF3510: Domain of un 40.5 1.3E+02 0.0028 26.9 7.2 21 265-285 79-99 (125)
56 PF05190 MutS_IV: MutS family 38.5 52 0.0011 26.3 4.1 25 234-258 1-25 (92)
57 TIGR02937 sigma70-ECF RNA poly 38.0 34 0.00074 28.4 3.0 47 369-423 110-156 (158)
58 PRK11924 RNA polymerase sigma 36.7 34 0.00073 30.1 2.9 47 369-423 125-171 (179)
59 PF13443 HTH_26: Cro/C1-type H 36.3 28 0.0006 26.3 2.1 24 395-418 12-35 (63)
60 PRK09652 RNA polymerase sigma 35.6 38 0.00081 29.8 3.1 47 369-423 128-174 (182)
61 PF13097 CENP-U: CENP-A nucleo 35.5 97 0.0021 29.9 5.9 45 236-283 102-148 (175)
62 PF11288 DUF3089: Protein of u 35.4 14 0.0003 36.1 0.3 46 155-205 93-138 (207)
63 PRK12514 RNA polymerase sigma 34.6 39 0.00085 30.4 3.1 48 369-424 129-176 (179)
64 TIGR02983 SigE-fam_strep RNA p 34.1 42 0.00092 29.5 3.1 51 369-427 110-160 (162)
65 TIGR02939 RpoE_Sigma70 RNA pol 33.5 34 0.00073 30.8 2.5 49 369-425 138-186 (190)
66 KOG4511 Uncharacterized conser 33.3 3.1E+02 0.0068 28.6 9.4 28 178-205 49-78 (335)
67 PRK03975 tfx putative transcri 32.8 46 0.00099 30.8 3.2 48 367-423 4-51 (141)
68 PRK06811 RNA polymerase factor 32.5 47 0.001 30.4 3.3 50 368-425 130-179 (189)
69 PRK12541 RNA polymerase sigma 32.4 47 0.001 29.3 3.2 48 368-423 111-158 (161)
70 TIGR02999 Sig-70_X6 RNA polyme 31.9 51 0.0011 29.6 3.4 47 369-423 134-180 (183)
71 TIGR02989 Sig-70_gvs1 RNA poly 31.8 52 0.0011 28.7 3.3 48 368-423 110-157 (159)
72 PRK12547 RNA polymerase sigma 31.5 48 0.001 29.6 3.1 48 368-423 111-158 (164)
73 TIGR02985 Sig70_bacteroi1 RNA 31.4 56 0.0012 28.0 3.4 47 369-423 113-159 (161)
74 smart00421 HTH_LUXR helix_turn 31.4 93 0.002 21.9 4.1 47 369-424 3-49 (58)
75 PF13518 HTH_28: Helix-turn-he 30.0 56 0.0012 23.5 2.7 24 396-419 15-38 (52)
76 PRK12526 RNA polymerase sigma 29.1 54 0.0012 30.7 3.1 48 369-424 153-200 (206)
77 PRK00118 putative DNA-binding 28.2 84 0.0018 27.7 3.9 48 368-423 16-63 (104)
78 PRK13919 putative RNA polymera 26.8 83 0.0018 28.4 3.8 49 369-425 135-183 (186)
79 PRK12523 RNA polymerase sigma 26.8 70 0.0015 28.7 3.3 48 368-423 118-165 (172)
80 PF10668 Phage_terminase: Phag 26.8 50 0.0011 26.6 2.1 21 394-414 23-43 (60)
81 PRK09648 RNA polymerase sigma 26.6 69 0.0015 29.1 3.3 49 368-424 138-186 (189)
82 PRK12546 RNA polymerase sigma 26.5 60 0.0013 30.1 2.9 47 369-423 113-159 (188)
83 PRK05602 RNA polymerase sigma 26.2 63 0.0014 29.3 2.9 48 370-425 129-176 (186)
84 PRK09649 RNA polymerase sigma 25.8 75 0.0016 29.1 3.4 49 368-424 129-177 (185)
85 PRK12512 RNA polymerase sigma 25.7 69 0.0015 28.9 3.1 49 369-425 131-179 (184)
86 PRK09047 RNA polymerase factor 25.3 79 0.0017 27.6 3.3 48 368-423 105-152 (161)
87 PF10281 Ish1: Putative stress 24.6 1.7E+02 0.0036 20.8 4.3 28 372-400 3-31 (38)
88 PRK12532 RNA polymerase sigma 24.6 72 0.0016 29.2 3.0 47 369-423 136-182 (195)
89 PF04859 DUF641: Plant protein 24.3 3.3E+02 0.0071 25.1 7.1 27 233-259 78-105 (131)
90 PRK12516 RNA polymerase sigma 23.8 77 0.0017 29.3 3.1 49 369-425 116-164 (187)
91 TIGR02954 Sig70_famx3 RNA poly 23.7 81 0.0018 28.0 3.1 47 369-423 119-165 (169)
92 PRK15369 two component system 23.7 1.5E+02 0.0033 25.4 4.8 48 369-425 149-196 (211)
93 PRK12519 RNA polymerase sigma 23.6 62 0.0013 29.5 2.4 47 369-423 141-187 (194)
94 PRK12531 RNA polymerase sigma 23.5 72 0.0016 29.3 2.8 50 368-425 140-189 (194)
95 PRK12520 RNA polymerase sigma 23.3 85 0.0018 28.6 3.2 47 369-423 131-177 (191)
96 PRK12536 RNA polymerase sigma 23.1 1.1E+02 0.0024 27.7 3.9 48 369-424 129-176 (181)
97 PRK09413 IS2 repressor TnpA; R 23.0 1.2E+02 0.0027 26.5 4.0 48 365-419 8-55 (121)
98 PRK12524 RNA polymerase sigma 23.0 81 0.0018 29.0 3.1 48 369-424 136-183 (196)
99 PRK09639 RNA polymerase sigma 23.0 1.1E+02 0.0023 27.0 3.7 46 369-423 112-157 (166)
100 PRK08241 RNA polymerase factor 22.7 1E+02 0.0023 30.9 4.0 50 369-426 153-202 (339)
101 PRK09636 RNA polymerase sigma 22.7 1.2E+02 0.0026 30.0 4.4 51 369-427 115-165 (293)
102 PRK12530 RNA polymerase sigma 22.6 84 0.0018 28.9 3.1 47 369-423 134-180 (189)
103 TIGR02959 SigZ RNA polymerase 22.3 93 0.002 28.0 3.3 47 369-423 100-146 (170)
104 KOG4040 NADH:ubiquinone oxidor 22.1 62 0.0013 31.1 2.1 38 372-409 23-61 (186)
105 PF13730 HTH_36: Helix-turn-he 22.1 2.6E+02 0.0057 20.5 5.1 29 388-419 23-51 (55)
106 PRK12542 RNA polymerase sigma 22.1 90 0.0019 28.3 3.1 47 369-423 122-168 (185)
107 PF01381 HTH_3: Helix-turn-hel 22.0 63 0.0014 23.5 1.8 21 396-416 12-32 (55)
108 PF13865 FoP_duplication: C-te 22.0 80 0.0017 25.9 2.5 7 237-243 47-53 (74)
109 PF00196 GerE: Bacterial regul 21.5 1.1E+02 0.0025 23.0 3.1 48 369-425 3-50 (58)
110 PF13551 HTH_29: Winged helix- 21.4 4E+02 0.0087 21.6 6.6 46 370-415 58-109 (112)
111 PF06729 CENP-R: Kinetochore c 21.4 6.9E+02 0.015 23.5 9.5 31 237-276 56-86 (139)
112 PRK12533 RNA polymerase sigma 21.3 85 0.0018 30.1 2.9 49 369-425 134-182 (216)
113 PF07425 Pardaxin: Pardaxin; 20.9 61 0.0013 22.9 1.3 22 176-197 5-26 (33)
114 PRK12537 RNA polymerase sigma 20.7 1E+02 0.0022 28.0 3.1 47 369-423 133-179 (182)
115 PRK08583 RNA polymerase sigma 20.7 1.2E+02 0.0025 29.5 3.7 47 369-423 205-251 (257)
116 PRK12515 RNA polymerase sigma 20.3 1.1E+02 0.0023 27.9 3.3 48 369-424 131-178 (189)
117 PF12878 SICA_beta: SICA extra 20.1 1E+02 0.0022 29.2 3.2 24 234-259 95-118 (169)
118 TIGR02948 SigW_bacill RNA poly 20.1 1.2E+02 0.0025 27.2 3.4 47 369-423 136-182 (187)
No 1
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=100.00 E-value=2.1e-32 Score=265.64 Aligned_cols=209 Identities=23% Similarity=0.377 Sum_probs=183.3
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHh-----hhhccCCCcchhhHHHHHHHHHHHHhhhhccCCCCCC-------CCCChH
Q 013509 171 WQNARYKAEILSHPLYEQLLSAHVA-----CLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQGL-------VTDDKE 238 (441)
Q Consensus 171 ~e~e~lKAkI~sHPlYp~LL~Ayid-----ClKVGAPpevv~rLd~~l~~~~~~~~k~~~~~~~~~~-------~g~DPE 238 (441)
+|+++.|..|.+||+||.|++++|+ .+.|....|.-|. |.++.++++|+..+++.||..+. -|+..+
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 5666999999999999999999999 5566666665444 77888899999999998886421 234488
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCCCCcccccccCccccCCCCCCCCC
Q 013509 239 LDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSLEGPD 318 (441)
Q Consensus 239 LDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~~s~~~~~g~~~S~ded~~~~s~~~~~~~~~~~~d 318 (441)
+.+-+. +|...|++||++ +..+|+++.+.+.+|.. +
T Consensus 105 YR~kL~---qiR~iy~~Elek--------yeqaCneftthV~nlL~---------------------------------e 140 (334)
T KOG0774|consen 105 YRAKLL---QIRQIYHNELEK--------YEQACNEFTTHVMNLLR---------------------------------E 140 (334)
T ss_pred HHHHHH---HHHHHHHHHHHH--------HHHHHHHHHHHHHHHHH---------------------------------H
Confidence 888777 999999999987 55679999999999995 3
Q ss_pred CCCCCCCCCchhhhHh--HHHHHHHHHHHHHhhhhhHHHhHHHHHhh-ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHH
Q 013509 319 TMGFGPLIPTESERSL--MERVRQELKHELKQGYKEKIVDIREEILR-KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEED 395 (441)
Q Consensus 319 ~~~f~Pi~p~~~e~~l--m~r~~~ELK~~Lkrky~~~i~~lree~~k-kRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeE 395 (441)
++.||||.+.++|+++ |.+.|.-++..|++..|..+..||.++.. +|||++|+|.++.+|.+||..|..||||++++
T Consensus 141 Qsr~RPi~~ke~e~m~~~i~~kF~~iq~~lkqstce~vmiLr~r~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~ 220 (334)
T KOG0774|consen 141 QSRTRPIMPKEIERMVQIISKKFSHIQMQLKQSTCEAVMILRSRFLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEA 220 (334)
T ss_pred hcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHH
Confidence 3469999999999975 89999999999999999999999999996 66788999999999999999999999999999
Q ss_pred HHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 396 KARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 396 K~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
|++||++||++..||+|||.|+|.|.||.
T Consensus 221 K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 221 KEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHHHHcCceehhhccccccceeehhhh
Confidence 99999999999999999999999999983
No 2
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=99.94 E-value=2.2e-28 Score=243.42 Aligned_cols=253 Identities=21% Similarity=0.261 Sum_probs=181.2
Q ss_pred hhhhHHHHHHHhhCCChHHHHHHHHhhhhccCCCcchhhHHHHHHHHHHHHhhhhccCCCC---CCCCCChHHHHHHHHH
Q 013509 170 NWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQ---GLVTDDKELDQFMTHY 246 (441)
Q Consensus 170 ~~e~e~lKAkI~sHPlYp~LL~AyidClKVGAPpevv~rLd~~l~~~~~~~~k~~~~~~~~---~~~g~DPELDQFMeaY 246 (441)
.....-+|..+.+||+|..++.||++|++++++.+.+.+++............++.++... ..-+.+.+|+.||..|
T Consensus 46 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k~ 125 (342)
T KOG0773|consen 46 MVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSKL 125 (342)
T ss_pred ccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchHH
Confidence 4555667999999999999999999999999999998887654433322222222221110 1235779999999999
Q ss_pred HHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCCCCccccccc---CccccCCCCCCCCCCCCCC
Q 013509 247 VLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVD---SDANLFDGSLEGPDTMGFG 323 (441)
Q Consensus 247 C~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~~s~~~~~g~~~S~ded~~~~---s~~~~~~~~~~~~d~~~f~ 323 (441)
+.+|..++..|+..+. -++|+.++++|+..+..++..++....+.+...+.++... ++.... .+.+++.
T Consensus 126 ~~~ll~~~~~~~~~~~--~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~------~~~~~~~ 197 (342)
T KOG0773|consen 126 EKILLAVITKLTLTQV--STWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSS------EELLGES 197 (342)
T ss_pred HHHHHHHHHHhhhhhH--HHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccc------ccccccc
Confidence 9999999999999863 3899999999999999998876655444333222211100 000000 0111222
Q ss_pred CCCCchhhhHhH--HHHHHHHHHHHHhhhhhHHHhHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHH
Q 013509 324 PLIPTESERSLM--ERVRQELKHELKQGYKEKIVDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQ 401 (441)
Q Consensus 324 Pi~p~~~e~~lm--~r~~~ELK~~Lkrky~~~i~~lree~~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~ 401 (441)
+....+.+...+ .+....++..+.+.+..++.....+..++|+.+.||+.++.+|+.||.+|..||||++.+|..||.
T Consensus 198 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~ 277 (342)
T KOG0773|consen 198 EQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAK 277 (342)
T ss_pred cccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccch
Confidence 221111111111 234556667777777666677767777888899999999999999999999999999999999999
Q ss_pred HhCCChhhhhhhhhhHHhhcccCCCCCCh
Q 013509 402 ETGLQLKQINNWFINQRKRNWHSNPSTST 430 (441)
Q Consensus 402 ~TGLs~kQV~NWF~NrRrR~KK~n~s~st 430 (441)
+|||+..||+|||||+|+|.|++......
T Consensus 278 ~TGLs~~Qv~NWFINaR~R~w~p~~~~~~ 306 (342)
T KOG0773|consen 278 QTGLSRPQVSNWFINARVRLWKPMIEEMY 306 (342)
T ss_pred hcCCCcccCCchhhhcccccCCchHHHHH
Confidence 99999999999999999999998775443
No 3
>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=99.88 E-value=3.5e-23 Score=158.37 Aligned_cols=50 Identities=50% Similarity=0.712 Sum_probs=47.7
Q ss_pred CCCCCChHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhC
Q 013509 231 GLVTDDKELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTG 284 (441)
Q Consensus 231 ~~~g~DPELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~ 284 (441)
+++|+||||||||++||.||+||||||+||| .||++|||+||+||++||+
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~----~EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPF----QEAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhC
Confidence 4689999999999999999999999999998 5999999999999999995
No 4
>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=99.79 E-value=4.4e-20 Score=137.47 Aligned_cols=44 Identities=43% Similarity=0.744 Sum_probs=40.8
Q ss_pred HHHHHHHhhCCChHHHHHHHHhhhhccCCCcchhhHHHHHHHHH
Q 013509 174 ARYKAEILSHPLYEQLLSAHVACLRIATPVDQLPRIDAQLAQSQ 217 (441)
Q Consensus 174 e~lKAkI~sHPlYp~LL~AyidClKVGAPpevv~rLd~~l~~~~ 217 (441)
+.|||+|++||+||+||+|||+|+|||||||++++||++..+++
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 46999999999999999999999999999999999999886653
No 5
>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=99.60 E-value=6e-16 Score=112.62 Aligned_cols=40 Identities=53% Similarity=1.020 Sum_probs=36.5
Q ss_pred HHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 013509 381 WWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (441)
Q Consensus 381 Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR 420 (441)
||.+|..+|||+++||..||.+|||+.+||++||+|+|+|
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 6
>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=99.46 E-value=6.2e-13 Score=125.25 Aligned_cols=150 Identities=21% Similarity=0.300 Sum_probs=118.1
Q ss_pred hhhHHHHHHHhhCCChHHHHHHHHh-----hhhccCCCcchhhHHHHHHHHHHHHhhhhccCCCCCC------CCC--C-
Q 013509 171 WQNARYKAEILSHPLYEQLLSAHVA-----CLRIATPVDQLPRIDAQLAQSQHVVSKYSALGAGQGL------VTD--D- 236 (441)
Q Consensus 171 ~e~e~lKAkI~sHPlYp~LL~Ayid-----ClKVGAPpevv~rLd~~l~~~~~~~~k~~~~~~~~~~------~g~--D- 236 (441)
+|+..+|..|.+||+||.|.+++|+ .+++..+.+..+. |+++.++++|+...++.||+.+. .|. |
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 4779999999999999999999999 4555665544343 77888899999999998886311 111 1
Q ss_pred -hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhCCCCCCCCCCCCCCcccccccCccccCCCCCC
Q 013509 237 -KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGVSPGEGTGATMSDDDEDQVDSDANLFDGSLE 315 (441)
Q Consensus 237 -PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~~s~~~~~g~~~S~ded~~~~s~~~~~~~~~~ 315 (441)
-|-+.|-...-.+...|++||++ +..+|+++...+.+|..
T Consensus 103 ~~d~~dYr~kL~~ir~~y~~el~k--------ye~ac~eF~~hV~~lLr------------------------------- 143 (191)
T PF03792_consen 103 SIDHSDYRAKLSQIRQIYHSELEK--------YEQACNEFTEHVMNLLR------------------------------- 143 (191)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHH--------HHHHhhhhHHHHHHHHH-------------------------------
Confidence 12334444455888899999987 44579999999999985
Q ss_pred CCCCCCCCCCCCchhhhHh--HHHHHHHHHHHHHhhhhhHHHhHHHHHh
Q 013509 316 GPDTMGFGPLIPTESERSL--MERVRQELKHELKQGYKEKIVDIREEIL 362 (441)
Q Consensus 316 ~~d~~~f~Pi~p~~~e~~l--m~r~~~ELK~~Lkrky~~~i~~lree~~ 362 (441)
+++.||||+|.++|+++ |.+.|+-+..+||++.|+.+..||.+|+
T Consensus 144 --eQs~~RPIs~keiE~m~~~i~~Kf~~iq~qLKQstCEaVm~LRsRfl 190 (191)
T PF03792_consen 144 --EQSEFRPISPKEIERMVNIIHRKFSKIQMQLKQSTCEAVMILRSRFL 190 (191)
T ss_pred --HhcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 23469999999999964 8999999999999999999999998875
No 7
>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=99.45 E-value=1.4e-13 Score=103.16 Aligned_cols=58 Identities=28% Similarity=0.567 Sum_probs=54.2
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 364 kRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
++++..|++++..+|+.||.. +|||+.+++..||..+||+..||.+||.|+|.|.++.
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 8899999999999999999999999999999998764
No 8
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.42 E-value=2.9e-13 Score=101.03 Aligned_cols=55 Identities=27% Similarity=0.531 Sum_probs=51.3
Q ss_pred cCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcc
Q 013509 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (441)
Q Consensus 365 RkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~K 422 (441)
+.|..|+++++.+|+.||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
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 77999999999999999999999999999999864
No 9
>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=99.42 E-value=2.1e-13 Score=102.91 Aligned_cols=57 Identities=33% Similarity=0.740 Sum_probs=54.1
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 364 kRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
||+|..|+.+++.+|+.+|.. +|||+.+++..||..+||+..||.+||+|+|.+.|+
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 577899999999999999998 899999999999999999999999999999999874
No 10
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.19 E-value=1.1e-11 Score=122.20 Aligned_cols=47 Identities=38% Similarity=0.881 Sum_probs=45.4
Q ss_pred chHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcc
Q 013509 373 DTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (441)
Q Consensus 373 ea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~K 422 (441)
..+.+|++||.. +|||+.++|++||+.|||+..||.|||.|+|.|.+
T Consensus 186 kSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 186 KSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 589999999997 99999999999999999999999999999999998
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.92 E-value=4.7e-10 Score=112.82 Aligned_cols=59 Identities=22% Similarity=0.342 Sum_probs=54.8
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 364 kRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
+|||..++|.|+..|+.-|.-|. |.|++-|.+|++.++|+..||+.||||||+|.||-+
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 56678999999999999999855 999999999999999999999999999999999865
No 12
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.88 E-value=9.7e-10 Score=107.83 Aligned_cols=66 Identities=23% Similarity=0.282 Sum_probs=59.5
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCCChh
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTSTV 431 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~s~st~ 431 (441)
.||.|+.|+..++..|+.-|.- |.|.|+..|.+||..+.|++.||++||+|||+|.||.+...+..
T Consensus 159 ~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 6788899999999999999887 66999999999999999999999999999999999876654443
No 13
>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=98.80 E-value=5.5e-09 Score=82.08 Aligned_cols=53 Identities=19% Similarity=0.437 Sum_probs=50.0
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCC----CCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPY----PTEEDKARLVQETGLQLKQINNWFINQR 418 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPY----PSeeEK~~LA~~TGLs~kQV~NWF~NrR 418 (441)
+||.|+.|+.+++..|+..|.. .+| |+..++.+||..+||+..+|.+||+|-+
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 4788999999999999999999 789 9999999999999999999999999954
No 14
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.79 E-value=3.9e-09 Score=99.40 Aligned_cols=60 Identities=20% Similarity=0.304 Sum_probs=55.8
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 362 ~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
..||.|+.|+.+++..|+..|.. +-|-.-.||..||+.++|++.||++||+|+|.|+|+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~ 160 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRM 160 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHH
Confidence 45778899999999999999999 5599999999999999999999999999999999873
No 15
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.74 E-value=3.8e-09 Score=106.34 Aligned_cols=60 Identities=17% Similarity=0.333 Sum_probs=54.8
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 362 ~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
+|||+|--|++.|+-.|++-|.+.+ |.|..||+.||..++||..||+.||||+|-|.|+.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQR---YLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~ 211 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQR---YLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQ 211 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhh---ccccHhHHHHHHhcCCCchheeeeeecchhhhhhh
Confidence 4566667899999999999999966 99999999999999999999999999999998863
No 16
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.74 E-value=6.9e-09 Score=102.46 Aligned_cols=61 Identities=33% Similarity=0.462 Sum_probs=56.5
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
.||.|+-|+.++.+.|+.-|.+++ |.|+..|.+||.++||.+.||..||+|+|.+.||..-
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enR---YlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENR---YLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhh---hHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 467789999999999999999966 9999999999999999999999999999999998543
No 17
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.71 E-value=1.8e-08 Score=97.36 Aligned_cols=59 Identities=20% Similarity=0.308 Sum_probs=55.2
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 362 ~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.|||.|+.|+..++..|+.-|...+ |.+..||.-||.++.|++.||+.||||+|.|.|+
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~kr---YLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKR 161 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKR---YLSSAERAGLAASLQLTETQVKIWFQNRRNKWKR 161 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHh---hhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHH
Confidence 4677889999999999999999966 9999999999999999999999999999999886
No 18
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.69 E-value=1.7e-08 Score=104.15 Aligned_cols=68 Identities=16% Similarity=0.393 Sum_probs=62.0
Q ss_pred hHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 356 DIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 356 ~lree~~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
.+-...+|||||+.+...++..|+..|.. ||.|+.+|.-.||++++|....|++||+|||.|.|+.++
T Consensus 287 ~i~a~~RkRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 287 KIGAQSRKRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HhhccccccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 34444467788889999999999999998 999999999999999999999999999999999999888
No 19
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.68 E-value=1.3e-08 Score=102.46 Aligned_cols=61 Identities=20% Similarity=0.370 Sum_probs=54.9
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 362 ~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
+++|.|+.|+..++..|+.-|..-. |.+..||.+||+.+||+-.||..||+|||+|.|+..
T Consensus 171 K~RksRTaFT~~Ql~~LEkrF~~QK---YLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 171 KRRKSRTAFSDHQLFELEKRFEKQK---YLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred ccccchhhhhHHHHHHHHHHHHHhh---cccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 4456678999999999999999855 999999999999999999999999999999988743
No 20
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.66 E-value=1.4e-08 Score=98.67 Aligned_cols=59 Identities=20% Similarity=0.306 Sum_probs=53.9
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 364 kRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
+|.|+.++.-+.+.|.+-|++ .-|.--.||.+||..+||+..||+.||+|||-|.||..
T Consensus 123 RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 456778999999999999998 66999999999999999999999999999999998743
No 21
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.60 E-value=2.9e-08 Score=94.76 Aligned_cols=58 Identities=29% Similarity=0.447 Sum_probs=53.4
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.++++.+|+.+++..|+.-|..|. |..+++|..||+++||.+.||.+||+|||+|.|.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~---~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~ 107 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEK---KLEPERKKKLAKELGLQPRQVAVWFQNRRARWKT 107 (198)
T ss_pred cccccccccHHHHHHhHHhhcccc---ccChHHHHHHHHhhCCChhHHHHHHhhccccccc
Confidence 456667899999999999999966 8999999999999999999999999999999875
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.54 E-value=5.7e-08 Score=89.59 Aligned_cols=62 Identities=19% Similarity=0.356 Sum_probs=56.7
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 362 ~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
..+++|.+.+..++.+|+..|.. +|||+..+|..|+..++|+++-|..||+|+|.+.|+...
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred cCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 45677788999999999999998 999999999999999999999999999999999987544
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.54 E-value=5e-08 Score=91.08 Aligned_cols=61 Identities=18% Similarity=0.361 Sum_probs=54.9
Q ss_pred HHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 360 EILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 360 e~~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
...++|.|+.|+..+...|+.-|.... |.+-.|+.+||..++|+++||..||+|+|+++||
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 344566678999999999999999755 9999999999999999999999999999999986
No 24
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.48 E-value=7.9e-08 Score=84.08 Aligned_cols=65 Identities=15% Similarity=0.283 Sum_probs=58.3
Q ss_pred hHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 356 DIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 356 ~lree~~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.+.+..+.+|-|+.|+..+...|+..|.+ .-||..-.|++||.+..|++..|.+||+|+|.+++|
T Consensus 10 ~l~ekrKQRRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK 74 (125)
T KOG0484|consen 10 GLTEKRKQRRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK 74 (125)
T ss_pred ChhHHHHhhhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence 44555666777899999999999999999 559999999999999999999999999999999986
No 25
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.42 E-value=1.2e-07 Score=91.28 Aligned_cols=66 Identities=15% Similarity=0.275 Sum_probs=60.2
Q ss_pred HhHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 355 VDIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 355 ~~lree~~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
..||+....++.|+.|+..+...|++-|.+ ..|.+.+||.+++..+.|+..||+.||+|+|.|-|+
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 456777777888999999999999999999 459999999999999999999999999999999885
No 26
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=98.34 E-value=3.4e-07 Score=90.61 Aligned_cols=55 Identities=20% Similarity=0.319 Sum_probs=51.4
Q ss_pred CCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 367 R~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
|+.|+..+...|+.-|.+-. ||+.-.|+.||.+|+|.+..|.+||+|+|.+.+|.
T Consensus 145 RTiFT~~Qle~LEkaFkeaH---YPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAH---YPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred cchhhHHHHHHHHHHHhhcc---CccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 77899999999999999944 99999999999999999999999999999998764
No 27
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.29 E-value=4.8e-07 Score=87.55 Aligned_cols=58 Identities=19% Similarity=0.359 Sum_probs=53.2
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.+|-|+.|+..+..+|+.-|.+ .-||+...+++||.+++|.+.+|.+||.|+|++.++
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 3456789999999999999999 559999999999999999999999999999998875
No 28
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.29 E-value=1.9e-07 Score=92.68 Aligned_cols=57 Identities=23% Similarity=0.328 Sum_probs=51.1
Q ss_pred CCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 367 R~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
|-.++..++-.|+.-|-- .+|.|...|.+||..+||++.||+.||+|||.|.+|-++
T Consensus 203 RvVYTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred eEEecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 456888999999988765 789999999999999999999999999999999987543
No 29
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.23 E-value=4.5e-07 Score=91.62 Aligned_cols=59 Identities=19% Similarity=0.377 Sum_probs=53.5
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
++|.|..|+..+.+.|+.||..+. ||+.+.|++||--++|++..|++||.|+|.+.+|.
T Consensus 112 qrrQrthFtSqqlqele~tF~rNr---ypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 112 QRRQRTHFTSQQLQELEATFQRNR---YPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhcc---CCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 345567899999999999999955 99999999999999999999999999999998764
No 30
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.22 E-value=6.4e-07 Score=89.83 Aligned_cols=72 Identities=21% Similarity=0.424 Sum_probs=64.1
Q ss_pred hHHHHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCCCh
Q 013509 356 DIREEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTST 430 (441)
Q Consensus 356 ~lree~~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~s~st 430 (441)
.|.-+-..||.|+.++..+...|+.-|.. .|.|.+-.|++|+.+|||+...|++||+|+|.+.|+-.+..+.
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 34456778999999999999999999887 8999999999999999999999999999999999886666554
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.83 E-value=1.8e-05 Score=84.85 Aligned_cols=56 Identities=21% Similarity=0.363 Sum_probs=52.8
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhc
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRN 421 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~ 421 (441)
.||.|-.|+..+++.|...|.+ +|||+.++-+.|+.++||...-|.|||-|+|+|.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 4667789999999999999999 8899999999999999999999999999999994
No 32
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.83 E-value=8.2e-06 Score=79.49 Aligned_cols=62 Identities=24% Similarity=0.395 Sum_probs=54.6
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 362 ~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
+||..|.+|+..+...|+.-|.+ .-||--.++.+||...|+++.||.+||+|+|.+.+|+..
T Consensus 166 ~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 45566678999999999999999 459999999999999999999999999999999876543
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.79 E-value=1.1e-05 Score=75.31 Aligned_cols=63 Identities=13% Similarity=0.145 Sum_probs=56.9
Q ss_pred HHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 360 EILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 360 e~~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
.++++|.|..|+..+...|+.-|.. .+||+...++.||..+++++..|.+||+|+|++.++..
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 4556778889999999999999998 58999999999999999999999999999999988644
No 34
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.72 E-value=2.6e-05 Score=80.18 Aligned_cols=61 Identities=25% Similarity=0.453 Sum_probs=55.2
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
.+|.|+.|+..+...|+.+|.. +|||....|+.||.++||+...|..||.|+|.|.+|-..
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3445689999999999999998 789999999999999999999999999999998887653
No 35
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.71 E-value=1.1e-05 Score=81.61 Aligned_cols=54 Identities=17% Similarity=0.308 Sum_probs=48.6
Q ss_pred CCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 367 R~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
|+-|+.+++..|+.-|+.. -|-++..|.+||..++|.+.-|++||||+|+|.|+
T Consensus 185 RTAFTReQIaRLEKEFyrE---NYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKR 238 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYRE---NYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKR 238 (408)
T ss_pred HhhhhHHHHHHHHHHHHHh---ccccCchhhhHHHhhCCCcceeehhhhhchhhhhh
Confidence 4679999999998877773 38999999999999999999999999999999986
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.63 E-value=1.5e-05 Score=80.26 Aligned_cols=67 Identities=21% Similarity=0.379 Sum_probs=58.1
Q ss_pred HHHhhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCC
Q 013509 359 EEILRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPST 428 (441)
Q Consensus 359 ee~~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~s~ 428 (441)
..--|||||+.+-..-++.|+.+|.. -|-|+.+-...||+++.|....|++||+|+|.+.|+..-+.
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred CccccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 33447888888888888999999998 89999999999999999999999999999999998754443
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.38 E-value=9.4e-05 Score=74.51 Aligned_cols=65 Identities=32% Similarity=0.564 Sum_probs=59.4
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCC
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPST 428 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~s~ 428 (441)
..+++++++.+. ..|+.|...|..+|||++.++..|+..++++..||.+||+|.|+|.++.+..+
T Consensus 95 ~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~ 159 (342)
T KOG0773|consen 95 KGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMT 159 (342)
T ss_pred cccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCC
Confidence 345678899999 99999999999999999999999999999999999999999999999866653
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.81 E-value=0.0012 Score=52.12 Aligned_cols=43 Identities=21% Similarity=0.502 Sum_probs=31.4
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 013509 375 TSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (441)
Q Consensus 375 ~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR 420 (441)
.+.|+++|..|. ++.+.+...|+.++||+..||..||.-++.+
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 456999999965 9999999999999999999999999877543
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=96.76 E-value=0.001 Score=43.42 Aligned_cols=22 Identities=41% Similarity=0.622 Sum_probs=20.5
Q ss_pred HHHHHHHhhhhhHHHhHHHHHh
Q 013509 341 ELKHELKQGYKEKIVDIREEIL 362 (441)
Q Consensus 341 ELK~~Lkrky~~~i~~lree~~ 362 (441)
|||.+|+++|+++|++||+||+
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=95.29 E-value=0.014 Score=54.49 Aligned_cols=61 Identities=26% Similarity=0.505 Sum_probs=52.5
Q ss_pred hccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 363 RKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 363 kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
.++.+..+...+...|..-|.. .|||....+..|+..+|++...|.+||+|+|.+.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4455677888888888888777 889999999999999999999999999999999986533
No 41
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=91.08 E-value=0.16 Score=60.19 Aligned_cols=60 Identities=20% Similarity=0.332 Sum_probs=53.9
Q ss_pred hhccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 362 LRKRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 362 ~kkRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
-+++.|..+...++.+|+..|..-. ||+.++-+.|....+|....|..||+|.|.+.+|.
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~---~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQR---TPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhcc---CChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence 3556677888899999999999855 99999999999999999999999999999999874
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=83.01 E-value=2.1 Score=48.80 Aligned_cols=52 Identities=27% Similarity=0.537 Sum_probs=46.3
Q ss_pred HHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCCCC
Q 013509 375 TSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPSTS 429 (441)
Q Consensus 375 ~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~s~s 429 (441)
+.+|+.+|.. |+.|++++...+|.+.||...-|..||.+.+........+++
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 6888999988 889999999999999999999999999999998876654444
No 43
>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=80.71 E-value=2.7 Score=32.21 Aligned_cols=47 Identities=15% Similarity=0.186 Sum_probs=31.6
Q ss_pred ccCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 013509 364 KRRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQR 418 (441)
Q Consensus 364 kRkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrR 418 (441)
||+|..|+-+..-.+-.-+.. .+ -+..||+++|++..+|..|..|+.
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 466778887775555555554 22 578999999999999999999964
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=65.71 E-value=7 Score=30.55 Aligned_cols=47 Identities=15% Similarity=0.246 Sum_probs=30.7
Q ss_pred cCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHH
Q 013509 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQR 418 (441)
Q Consensus 365 RkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrR 418 (441)
++++.||.+.+..+-.-+.. .......+|+..|+++.+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~-------~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE-------SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH-------HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH-------CCCceEeeecccccccccccHHHHHHh
Confidence 45678888876555444322 346788999999999999999988777
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=60.06 E-value=18 Score=24.95 Aligned_cols=46 Identities=13% Similarity=0.159 Sum_probs=34.8
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNW 422 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~K 422 (441)
.++...+.++...+.... .-.++|..+|++...|..|....+.+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~~--------~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEGL--------SYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 467777788877764422 3457899999999999999988887754
No 46
>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=57.10 E-value=24 Score=21.60 Aligned_cols=40 Identities=10% Similarity=0.174 Sum_probs=27.3
Q ss_pred CCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 013509 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWF 414 (441)
Q Consensus 367 R~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF 414 (441)
+..++.+....+...+.. .+ ....+|+.+|++...|.+|.
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 344666666666555543 22 34578899999999999984
No 47
>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=52.54 E-value=22 Score=26.23 Aligned_cols=44 Identities=14% Similarity=0.238 Sum_probs=32.2
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhh
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKR 420 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR 420 (441)
.||...+.++...|... -.-.++|+.+|++...|.+|....|++
T Consensus 10 ~L~~~~r~i~~l~~~~g--------~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG--------MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC--------cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 47888888887655542 344689999999999999999998876
No 48
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=49.05 E-value=20 Score=31.18 Aligned_cols=47 Identities=9% Similarity=0.067 Sum_probs=37.5
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.++...|.... .-.++|+.+|++...|.+|....|++.++
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 24589999999999999999999998875
No 49
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=48.95 E-value=16 Score=26.85 Aligned_cols=47 Identities=11% Similarity=0.179 Sum_probs=36.1
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.+|...|... -.-.++|+.+|++...|..+.....++.|+
T Consensus 4 ~L~~~er~vi~~~y~~~--------~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG--------LTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTST---------SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC--------CCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 57888888888777432 224589999999999999999998888763
No 50
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=43.91 E-value=66 Score=35.87 Aligned_cols=25 Identities=12% Similarity=0.290 Sum_probs=15.2
Q ss_pred CChHHHHHHHHHH-------HHHHHHHHHHhH
Q 013509 235 DDKELDQFMTHYV-------LLLCSFKEQLQQ 259 (441)
Q Consensus 235 ~DPELDQFMeaYC-------~mL~kYkEEL~k 259 (441)
.-|++....-+|| .||.||++||++
T Consensus 183 ~ap~mkt~~~aYcanHP~AV~VL~k~~dELek 214 (661)
T KOG2070|consen 183 LAPQMKTLYLAYCANHPSAVNVLTKHSDELEK 214 (661)
T ss_pred hhHHHHHHHHHHHhcCchhhhHHHHhHHHHHH
Confidence 3466666666666 466666666655
No 51
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=43.72 E-value=23 Score=32.59 Aligned_cols=50 Identities=6% Similarity=-0.007 Sum_probs=39.7
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
.||...+.+|...|.... .-.++|+.+|++...|.+++...|++.++...
T Consensus 142 ~L~~~~r~vl~l~~~~~~--------s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGL--------TYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 488888888876555432 23589999999999999999999999987543
No 52
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=41.58 E-value=50 Score=34.62 Aligned_cols=47 Identities=13% Similarity=0.217 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHHHHHHHhhCC
Q 013509 237 KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIEQSLQSLTGV 285 (441)
Q Consensus 237 PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IEsQL~sL~~~ 285 (441)
-+-|.||.-||. .+|-.+|.+=+|-++++|..-+..+-.|+..||.+
T Consensus 134 T~C~Hy~H~~Cl--aRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcpV 180 (368)
T KOG4445|consen 134 TACDHYMHFACL--ARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCPV 180 (368)
T ss_pred ehhHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhhH
Confidence 478999999994 56666666666666778888888999999999864
No 53
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=41.48 E-value=39 Score=30.05 Aligned_cols=48 Identities=15% Similarity=0.040 Sum_probs=39.4
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
..||...+.++.-++..+. .-.++|..+|++...|.+|..-.|++.++
T Consensus 107 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHEL--------TYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred HhCCHHHHHHHHhHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4578888889887665533 23589999999999999999999999986
No 54
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=40.55 E-value=30 Score=30.41 Aligned_cols=48 Identities=13% Similarity=0.204 Sum_probs=38.0
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
.||+..+.++.-.+.+.. + -.++|+.+|++...|.+.+.-.|++.++.
T Consensus 106 ~Lp~~~r~v~~l~~~~g~--s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEK--S------YQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHhCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 488888888866555422 2 24899999999999999999999998763
No 55
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=40.51 E-value=1.3e+02 Score=26.89 Aligned_cols=21 Identities=29% Similarity=0.316 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHhhCC
Q 013509 265 AMEAVMACWEIEQSLQSLTGV 285 (441)
Q Consensus 265 ~~EA~~fc~~IEsQL~sL~~~ 285 (441)
+.|...-.+++|..|+-|-..
T Consensus 79 ~~evL~sv~KtEeSL~rlkk~ 99 (125)
T PF12022_consen 79 ASEVLTSVRKTEESLKRLKKR 99 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 356667788999999999653
No 56
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=38.51 E-value=52 Score=26.26 Aligned_cols=25 Identities=28% Similarity=0.349 Sum_probs=20.3
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHh
Q 013509 234 TDDKELDQFMTHYVLLLCSFKEQLQ 258 (441)
Q Consensus 234 g~DPELDQFMeaYC~mL~kYkEEL~ 258 (441)
|-|+|||...+.|..+.....+.+.
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~~ 25 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELLE 25 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999988777666554
No 57
>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=38.01 E-value=34 Score=28.37 Aligned_cols=47 Identities=17% Similarity=0.251 Sum_probs=35.3
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.++...+... | .-.++|+.+|+++..|.+|....+++.++
T Consensus 110 ~L~~~~~~ii~~~~~~g----~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG----L----SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 36667777775543331 2 33489999999999999999999998875
No 58
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=36.72 E-value=34 Score=30.05 Aligned_cols=47 Identities=11% Similarity=0.128 Sum_probs=36.6
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.++...+.... .-.++|+.+|++...|.+|..-.|++.++
T Consensus 125 ~L~~~~r~i~~l~~~~~~--------~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 125 ALPVKQREVFLLRYVEGL--------SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred hCCHHHHHHhhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 377777778766544422 23689999999999999999999999875
No 59
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=36.30 E-value=28 Score=26.29 Aligned_cols=24 Identities=13% Similarity=0.279 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCChhhhhhhhhhHH
Q 013509 395 DKARLVQETGLQLKQINNWFINQR 418 (441)
Q Consensus 395 EK~~LA~~TGLs~kQV~NWF~NrR 418 (441)
....||+.+|++..+|+.|+.+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 456899999999999999999763
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=35.57 E-value=38 Score=29.83 Aligned_cols=47 Identities=9% Similarity=0.107 Sum_probs=36.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.+|...|.... + -.++|+.+|++...|.+|....|++.++
T Consensus 128 ~L~~~~r~vl~l~~~~~~--s------~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREIEGL--S------YEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHHcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 477788888866544322 2 2479999999999999999999999876
No 61
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=35.49 E-value=97 Score=29.92 Aligned_cols=45 Identities=16% Similarity=0.258 Sum_probs=36.7
Q ss_pred C-hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHH-HHHHHHHHHHHHHhh
Q 013509 236 D-KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEA-VMACWEIEQSLQSLT 283 (441)
Q Consensus 236 D-PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA-~~fc~~IEsQL~sL~ 283 (441)
| -|||-.+.++-.++..|++.++-.+= .+| ..||..|..||-.+.
T Consensus 102 DItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~i 148 (175)
T PF13097_consen 102 DITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEMI 148 (175)
T ss_pred cchHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHHH
Confidence 5 89999999999999999999977652 233 358899999997776
No 62
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=35.44 E-value=14 Score=36.12 Aligned_cols=46 Identities=24% Similarity=0.328 Sum_probs=34.7
Q ss_pred CCCCcccccCCCCcchhhhHHHHHHHhhCCChHHHHHHHHhhhhccCCCcc
Q 013509 155 KSEGVVVESGADGVVNWQNARYKAEILSHPLYEQLLSAHVACLRIATPVDQ 205 (441)
Q Consensus 155 ~~~~~~~~~~~~~~~~~e~e~lKAkI~sHPlYp~LL~AyidClKVGAPpev 205 (441)
+|-.+|..|-.+|- .-=...||.+|..+|++.+||.||+ ||.|.-+
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 46667776744443 2345689999999999999999998 8888543
No 63
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=34.62 E-value=39 Score=30.35 Aligned_cols=48 Identities=10% Similarity=0.227 Sum_probs=38.1
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
.||+..+.++...|.+.. .-.++|+.+|++...|.+++.-.|++.++.
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 477788888877765522 135899999999999999999999998763
No 64
>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=34.08 E-value=42 Score=29.48 Aligned_cols=51 Identities=12% Similarity=0.200 Sum_probs=39.3
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 427 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~s 427 (441)
.||...+.++...|.... .-.++|..+|++...|.++....|++.++....
T Consensus 110 ~L~~~~r~i~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 160 (162)
T TIGR02983 110 RLPARQRAVVVLRYYEDL--------SEAQVAEALGISVGTVKSRLSRALARLRELLEE 160 (162)
T ss_pred hCCHHHHHHhhhHHHhcC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 478888888866554422 234789999999999999999999999875443
No 65
>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=33.48 E-value=34 Score=30.76 Aligned_cols=49 Identities=8% Similarity=0.015 Sum_probs=37.2
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
.||+..+.++.-.|.... .-.++|+.+|++...|.++.-..|++.++..
T Consensus 138 ~L~~~~r~v~~l~~~~~~--------s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEGL--------SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 367777777765443322 3458999999999999999999999988644
No 66
>KOG4511 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.33 E-value=3.1e+02 Score=28.62 Aligned_cols=28 Identities=25% Similarity=0.437 Sum_probs=23.2
Q ss_pred HHHhhCCChHHHHHHHHh--hhhccCCCcc
Q 013509 178 AEILSHPLYEQLLSAHVA--CLRIATPVDQ 205 (441)
Q Consensus 178 AkI~sHPlYp~LL~Ayid--ClKVGAPpev 205 (441)
.=|+.|-=|..|+.-.++ |--||.-|++
T Consensus 49 ~y~~IH~EYk~LVd~lle~f~eevgi~p~q 78 (335)
T KOG4511|consen 49 VYIMIHKEYKQLVDTLLECFCEEVGITPTQ 78 (335)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhCCCHHH
Confidence 347889999999999999 5678888764
No 67
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=32.79 E-value=46 Score=30.80 Aligned_cols=48 Identities=10% Similarity=0.045 Sum_probs=37.9
Q ss_pred CCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 367 AGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 367 R~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
...|++.++.+|.. +.+.+ .-.++|+.+|++...|..|....|++.++
T Consensus 4 ~~~Lt~rqreVL~l-r~~Gl--------Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERGL--------TQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHH-HHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36788889999877 33311 24589999999999999999999988765
No 68
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=32.51 E-value=47 Score=30.42 Aligned_cols=50 Identities=14% Similarity=0.140 Sum_probs=39.6
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
..||+..+.++.-.|.+. .+ -.++|+.+|++...|.+...-.|++.++..
T Consensus 130 ~~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred HhCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 368889999987655542 22 358999999999999999999999988743
No 69
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=32.43 E-value=47 Score=29.32 Aligned_cols=48 Identities=21% Similarity=0.140 Sum_probs=38.5
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
..||..++.++.-.|.... + -.++|..+|++...|..+..-.|++.++
T Consensus 111 ~~L~~~~r~v~~l~~~~~~--s------~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 111 SSLPLERRNVLLLRDYYGF--S------YKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HHCCHHHHHHhhhHHhcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4588888888877655433 2 2479999999999999999999999875
No 70
>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=31.94 E-value=51 Score=29.57 Aligned_cols=47 Identities=6% Similarity=0.063 Sum_probs=38.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.++.-.+.+.. .-.++|+.+|+++..|.+.+...|++.++
T Consensus 134 ~Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAGL--------TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred cCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 488888888877765533 23589999999999999999999998875
No 71
>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=31.81 E-value=52 Score=28.66 Aligned_cols=48 Identities=19% Similarity=0.234 Sum_probs=37.3
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
..||...+.++...|.... .-.++|+.+|++...|.++..-.|++.++
T Consensus 110 ~~L~~~~r~v~~l~~~~g~--------~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRGV--------SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3578888888877444422 23479999999999999999999988765
No 72
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=31.51 E-value=48 Score=29.57 Aligned_cols=48 Identities=15% Similarity=0.039 Sum_probs=38.7
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
..||...+.++.-.+.+.. .-.++|+.+|++...|.++..-.|++.++
T Consensus 111 ~~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 111 NLLSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3588888898877665533 23489999999999999999999999875
No 73
>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=31.41 E-value=56 Score=28.03 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=36.2
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||...+.+|.-.+... ++ -.++|..+|++...|.++..-.|++.++
T Consensus 113 ~L~~~~r~il~l~~~~~----~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG----KS----YKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC----CC----HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46777888887654431 22 3469999999999999999999998875
No 74
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=31.36 E-value=93 Score=21.86 Aligned_cols=47 Identities=13% Similarity=0.176 Sum_probs=34.1
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
.|+.....++..+ .. . + ...++|+.+|++...|..|....+.+..-.
T Consensus 3 ~l~~~e~~i~~~~-~~-g---~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLL-AE-G---L----TNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHH-Hc-C---C----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4677777777543 22 1 1 346899999999999999999888777643
No 75
>PF13518 HTH_28: Helix-turn-helix domain
Probab=29.96 E-value=56 Score=23.48 Aligned_cols=24 Identities=17% Similarity=0.432 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChhhhhhhhhhHHh
Q 013509 396 KARLVQETGLQLKQINNWFINQRK 419 (441)
Q Consensus 396 K~~LA~~TGLs~kQV~NWF~NrRr 419 (441)
..++|.++|++..+|..|....+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456999999999999999987765
No 76
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=29.07 E-value=54 Score=30.66 Aligned_cols=48 Identities=17% Similarity=0.199 Sum_probs=37.8
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
.||...+.+|...+.... .-.++|+.+|++...|.+++...|++.++-
T Consensus 153 ~L~~~~r~vl~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQEL--------SQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 478888888876554422 235899999999999999999999988753
No 77
>PRK00118 putative DNA-binding protein; Validated
Probab=28.15 E-value=84 Score=27.67 Aligned_cols=48 Identities=6% Similarity=0.072 Sum_probs=38.3
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
..||..++.++..++.... .-.++|+.+|++..-|..|+...|++.++
T Consensus 16 ~~L~ekqRevl~L~y~eg~--------S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 16 SLLTEKQRNYMELYYLDDY--------SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred ccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3478888888877766533 23469999999999999999999988875
No 78
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=26.82 E-value=83 Score=28.36 Aligned_cols=49 Identities=14% Similarity=0.079 Sum_probs=38.7
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
.||...+.+|.-.+.... .-.++|+.+|++...|.++..-.|++.++..
T Consensus 135 ~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l 183 (186)
T PRK13919 135 ALSPEERRVIEVLYYQGY--------THREAAQLLGLPLGTLKTRARRALSRLKEVL 183 (186)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 388888888876555432 2358999999999999999999999987643
No 79
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=26.78 E-value=70 Score=28.69 Aligned_cols=48 Identities=10% Similarity=0.240 Sum_probs=37.5
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
..||+..+.++.-.+.+.. + -.++|+.+|++..-|.++....|+|.+.
T Consensus 118 ~~Lp~~~r~v~~L~~~~g~--s------~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDGM--G------HAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HhCCHHHHHHHHHHHHcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3478888888876554422 2 2489999999999999999999998864
No 80
>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=26.77 E-value=50 Score=26.57 Aligned_cols=21 Identities=14% Similarity=0.341 Sum_probs=18.0
Q ss_pred HHHHHHHHHhCCChhhhhhhh
Q 013509 394 EDKARLVQETGLQLKQINNWF 414 (441)
Q Consensus 394 eEK~~LA~~TGLs~kQV~NWF 414 (441)
-.-..||+++|++..+|..|=
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHh
Confidence 345689999999999999994
No 81
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.58 E-value=69 Score=29.11 Aligned_cols=49 Identities=10% Similarity=-0.025 Sum_probs=38.3
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
..||+..+.++..-|.... .-.++|+.+|++...|..+....|++.++.
T Consensus 138 ~~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 138 DTLPEKQREILILRVVVGL--------SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HhCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3578888888876554422 246899999999999999999999988763
No 82
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=26.47 E-value=60 Score=30.12 Aligned_cols=47 Identities=15% Similarity=0.099 Sum_probs=38.2
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||...+.++.-.+.... + -.++|..+|++...|.+++.-.|++.++
T Consensus 113 ~Lp~~~r~v~~L~~~~g~--s------~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 113 QLPDEQREALILVGASGF--S------YEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred hCCHHHhHHhhhHHhcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 588889899877655422 2 3478999999999999999999999986
No 83
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.20 E-value=63 Score=29.30 Aligned_cols=48 Identities=6% Similarity=0.081 Sum_probs=36.7
Q ss_pred CCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 370 LPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 370 lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
||+..+.++..-|.... .-.++|+.+|++...|.++....|++.++..
T Consensus 129 L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYYQGL--------SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHhcCC--------CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 67778788755444322 2347999999999999999999999988743
No 84
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=25.76 E-value=75 Score=29.12 Aligned_cols=49 Identities=14% Similarity=0.011 Sum_probs=39.0
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
..||..++.++.-.+.+.. .-.++|+.+|+++..|.++..-.|++.++.
T Consensus 129 ~~Lp~~~r~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 177 (185)
T PRK09649 129 ADLTTDQREALLLTQLLGL--------SYADAAAVCGCPVGTIRSRVARARDALLAD 177 (185)
T ss_pred HhCCHHHhHHhhhHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3588888888866555433 235899999999999999999999999873
No 85
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=25.67 E-value=69 Score=28.91 Aligned_cols=49 Identities=8% Similarity=-0.054 Sum_probs=39.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
.||+..+.++...|.... .-.++|..+|++...|.+++...|++.++..
T Consensus 131 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA--------SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 578888899887655422 2458999999999999999999999987643
No 86
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=25.33 E-value=79 Score=27.58 Aligned_cols=48 Identities=10% Similarity=0.043 Sum_probs=38.0
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
..||+..+.++.-.+.+.+ + -.++|+.+|++...|.+...-.|++.++
T Consensus 105 ~~Lp~~~r~v~~l~~~~g~--s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 105 QKLPARQREAFLLRYWEDM--D------VAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred HhCCHHHHHHHHHHHHhcC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3588888888876554422 2 3589999999999999999999999875
No 87
>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=24.63 E-value=1.7e+02 Score=20.84 Aligned_cols=28 Identities=36% Similarity=0.580 Sum_probs=19.0
Q ss_pred cchHHHHHHHHHhcCCCCCCCHH-HHHHHH
Q 013509 372 GDTTSVLKSWWQSHSKWPYPTEE-DKARLV 400 (441)
Q Consensus 372 kea~~iLk~Wf~~H~~nPYPSee-EK~~LA 400 (441)
.-....|+.|+..|. -|+|... .|.+|.
T Consensus 3 tWs~~~L~~wL~~~g-i~~~~~~~~rd~Ll 31 (38)
T PF10281_consen 3 TWSDSDLKSWLKSHG-IPVPKSAKTRDELL 31 (38)
T ss_pred CCCHHHHHHHHHHcC-CCCCCCCCCHHHHH
Confidence 345678999999987 7777444 454443
No 88
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=24.57 E-value=72 Score=29.20 Aligned_cols=47 Identities=15% Similarity=0.119 Sum_probs=37.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||...+.++.-.+.+.+ .-.++|+.+|++...|.++....|++.++
T Consensus 136 ~L~~~~r~i~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 136 NLPENTARVFTLKEILGF--------SSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred hCCHHHHHHhhhHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888875444422 23589999999999999999999999886
No 89
>PF04859 DUF641: Plant protein of unknown function (DUF641); InterPro: IPR006943 This conserved region is found in a number of plant proteins of unknown function.
Probab=24.34 E-value=3.3e+02 Score=25.09 Aligned_cols=27 Identities=11% Similarity=0.415 Sum_probs=23.2
Q ss_pred CCCC-hHHHHHHHHHHHHHHHHHHHHhH
Q 013509 233 VTDD-KELDQFMTHYVLLLCSFKEQLQQ 259 (441)
Q Consensus 233 ~g~D-PELDQFMeaYC~mL~kYkEEL~k 259 (441)
+++. .|+..-|.+|--++.+++.|+..
T Consensus 78 l~a~~~e~qsli~~yE~~~~kLe~e~~~ 105 (131)
T PF04859_consen 78 LAAEIQEQQSLIKTYEIVVKKLEAELRA 105 (131)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444 89999999999999999999976
No 90
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=23.84 E-value=77 Score=29.29 Aligned_cols=49 Identities=18% Similarity=0.149 Sum_probs=38.1
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
.||...+.++.-.+.+.+ +| .++|+.+|++...|.++....|++.++..
T Consensus 116 ~Lp~~~r~i~~L~~~~g~--s~------~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGASGF--AY------EEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHHcCC--CH------HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 478888888876555422 22 47999999999999999999999997633
No 91
>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=23.72 E-value=81 Score=28.03 Aligned_cols=47 Identities=4% Similarity=0.013 Sum_probs=36.8
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||...+.++..-|.... .-.++|+.+|++...|.++..-.|++.++
T Consensus 119 ~L~~~~r~i~~l~~~~g~--------s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDL--------TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred hCCHHHhHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 477778888866554422 23479999999999999999999998875
No 92
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=23.67 E-value=1.5e+02 Score=25.40 Aligned_cols=48 Identities=10% Similarity=0.126 Sum_probs=38.3
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
.|++..+++|+-+ .++. . ..++|+..+++.+-|.++..+.|++..-.+
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 4888888888774 4422 2 468899999999999999999999987554
No 93
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.63 E-value=62 Score=29.45 Aligned_cols=47 Identities=13% Similarity=0.180 Sum_probs=36.5
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.++.--+.... .-.++|+.+|++...|.+|+.-.|++.++
T Consensus 141 ~L~~~~~~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 141 QLPESQRQVLELAYYEGL--------SQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hCCHHHhhhhhhhhhcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 477788888865544322 23589999999999999999999998875
No 94
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=23.47 E-value=72 Score=29.31 Aligned_cols=50 Identities=16% Similarity=0.262 Sum_probs=38.9
Q ss_pred CCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 368 GKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 368 ~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
..||+..+.++.-.+.+.. + -.++|+.+|++...|.+-+...|++.++..
T Consensus 140 ~~Lp~~~r~v~~l~~~eg~--s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEEL--P------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred HhCCHHHHHHHHHHHHcCC--C------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 4588888888876544422 2 247999999999999999999999887643
No 95
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=23.30 E-value=85 Score=28.64 Aligned_cols=47 Identities=17% Similarity=0.080 Sum_probs=37.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||..++.++.-.+.+.+ + -.++|+.+|++..-|.+.....|++.++
T Consensus 131 ~Lp~~~r~v~~l~~~~g~--s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (191)
T PRK12520 131 RLPPRTGRVFMMREWLEL--E------TEEICQELQITATNAWVLLYRARMRLRE 177 (191)
T ss_pred hCCHHHHHHHHHHHHcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888876655422 2 3589999999999999999999999875
No 96
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=23.10 E-value=1.1e+02 Score=27.74 Aligned_cols=48 Identities=17% Similarity=-0.009 Sum_probs=37.0
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
.||+..+.++.-.+.+.. .-.++|+.+|++...|.+.+...|++.++.
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 367777777665554433 235899999999999999999999998763
No 97
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=23.01 E-value=1.2e+02 Score=26.45 Aligned_cols=48 Identities=6% Similarity=0.068 Sum_probs=32.2
Q ss_pred cCCCCCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHh
Q 013509 365 RRAGKLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRK 419 (441)
Q Consensus 365 RkR~~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRr 419 (441)
+++++++.+-+...-.....+. ....++|++.|++..+|.+|..-.|.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g-------~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPG-------MTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCC-------CCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 4556788777554433333321 23457899999999999999776654
No 98
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=23.00 E-value=81 Score=29.02 Aligned_cols=48 Identities=4% Similarity=0.046 Sum_probs=37.2
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
.||+..+.++.-.+..- |+ -.++|+.+|++...|.+++.-.|++.++.
T Consensus 136 ~L~~~~r~i~~L~~~~g----~s----~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 136 ALPERQRQAVVLRHIEG----LS----NPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred hCCHHHHHHHHHHHHcC----CC----HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 47888887776644431 22 35799999999999999999999999863
No 99
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=22.97 E-value=1.1e+02 Score=26.96 Aligned_cols=46 Identities=13% Similarity=0.196 Sum_probs=36.8
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||...+.+|.-.+ ... .-.++|..+|++...|.++....|++.++
T Consensus 112 ~L~~~~r~il~l~~-~g~--------s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGY--------SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred cCCHHHHHHHHHHH-cCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47777888887665 322 34589999999999999999999998875
No 100
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=22.71 E-value=1e+02 Score=30.85 Aligned_cols=50 Identities=16% Similarity=0.082 Sum_probs=38.9
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNP 426 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~ 426 (441)
.||...+.++.-.+.+.+ .-.++|+.+|++..-|.+...-.|++.++..+
T Consensus 153 ~Lp~~~R~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~ 202 (339)
T PRK08241 153 HLPPRQRAVLILRDVLGW--------SAAEVAELLDTSVAAVNSALQRARATLAERGP 202 (339)
T ss_pred hCCHHHhhhhhhHHhhCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence 477778788765544422 23479999999999999999999999998544
No 101
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=22.68 E-value=1.2e+02 Score=29.97 Aligned_cols=51 Identities=12% Similarity=0.013 Sum_probs=39.1
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCCCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSNPS 427 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n~s 427 (441)
.||+.++.++.--+... .+ -.++|+.+|++..-|.+.+...|++.++..+.
T Consensus 115 ~L~~~~R~v~~L~~~~g--~s------~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~ 165 (293)
T PRK09636 115 RLSPLERAAFLLHDVFG--VP------FDEIASTLGRSPAACRQLASRARKHVRAARPR 165 (293)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 37888877775543332 22 35799999999999999999999999887664
No 102
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.60 E-value=84 Score=28.89 Aligned_cols=47 Identities=13% Similarity=0.134 Sum_probs=37.9
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||...+.++.-.+.... .-.++|..+|+++..|.++..-.|++.++
T Consensus 134 ~Lp~~~R~v~~L~~~~g~--------s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMREYLEL--------SSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578888888876655422 23589999999999999999999999885
No 103
>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=22.30 E-value=93 Score=28.03 Aligned_cols=47 Identities=15% Similarity=0.189 Sum_probs=37.6
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.+|.-.|.+.+ .-.++|+.+|++...|.++..-.|++.++
T Consensus 100 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL--------SQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578888888877655433 23589999999999999999999998876
No 104
>KOG4040 consensus NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion]
Probab=22.10 E-value=62 Score=31.11 Aligned_cols=38 Identities=26% Similarity=0.615 Sum_probs=29.9
Q ss_pred cchHHHHHHHHHhcCCCCCCC-HHHHHHHHHHhCCChhh
Q 013509 372 GDTTSVLKSWWQSHSKWPYPT-EEDKARLVQETGLQLKQ 409 (441)
Q Consensus 372 kea~~iLk~Wf~~H~~nPYPS-eeEK~~LA~~TGLs~kQ 409 (441)
.......-.|...|.-.|||+ ++||..-|++.||-+..
T Consensus 23 ~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 23 PRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 445566778999999999995 67888889999986654
No 105
>PF13730 HTH_36: Helix-turn-helix domain
Probab=22.08 E-value=2.6e+02 Score=20.47 Aligned_cols=29 Identities=10% Similarity=0.287 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHHHHhCCChhhhhhhhhhHHh
Q 013509 388 WPYPTEEDKARLVQETGLQLKQINNWFINQRK 419 (441)
Q Consensus 388 nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRr 419 (441)
..||+ ...||+.+|++...|..++..-+.
T Consensus 23 ~~~pS---~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 23 GCFPS---QETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCCcC---HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 48887 557999999999999998765544
No 106
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.07 E-value=90 Score=28.33 Aligned_cols=47 Identities=17% Similarity=0.137 Sum_probs=36.8
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.++.-.+.... .-.++|+.+|++..-|.+...-.|++.++
T Consensus 122 ~L~~~~r~i~~l~~~~g~--------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 122 ELNESNRQVFKYKVFYNL--------TYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 488888888876444322 23479999999999999999999998876
No 107
>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=22.00 E-value=63 Score=23.55 Aligned_cols=21 Identities=14% Similarity=0.189 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 013509 396 KARLVQETGLQLKQINNWFIN 416 (441)
Q Consensus 396 K~~LA~~TGLs~kQV~NWF~N 416 (441)
..+||+.+|++...|..|..+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHhCCCcchhHHHhcC
Confidence 368999999999999999988
No 108
>PF13865 FoP_duplication: C-terminal duplication domain of Friend of PRMT1
Probab=21.96 E-value=80 Score=25.95 Aligned_cols=7 Identities=57% Similarity=1.004 Sum_probs=2.9
Q ss_pred hHHHHHH
Q 013509 237 KELDQFM 243 (441)
Q Consensus 237 PELDQFM 243 (441)
.|||+||
T Consensus 47 aELD~Ym 53 (74)
T PF13865_consen 47 AELDAYM 53 (74)
T ss_pred HHHHHHH
Confidence 3444444
No 109
>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=21.54 E-value=1.1e+02 Score=22.95 Aligned_cols=48 Identities=19% Similarity=0.147 Sum_probs=34.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
.|++....+|.-+..- ..-.++|...|++++-|..+..+.++|..-.+
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 3666667777555433 23458999999999999999999999986543
No 110
>PF13551 HTH_29: Winged helix-turn helix
Probab=21.39 E-value=4e+02 Score=21.64 Aligned_cols=46 Identities=17% Similarity=0.081 Sum_probs=28.2
Q ss_pred CCcchHHHHHHHHHhcCCCC--CCCHHHHHH-H-HHHh--CCChhhhhhhhh
Q 013509 370 LPGDTTSVLKSWWQSHSKWP--YPTEEDKAR-L-VQET--GLQLKQINNWFI 415 (441)
Q Consensus 370 lpkea~~iLk~Wf~~H~~nP--YPSeeEK~~-L-A~~T--GLs~kQV~NWF~ 415 (441)
++.+....|.+++.++...- ..+...-.. | .+.+ .++...|..|+.
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 233333333 4 3333 367777777763
No 111
>PF06729 CENP-R: Kinetochore component, CENP-R; InterPro: IPR009601 This family consists of mammalian nuclear receptor co-activator NRIF3 proteins. NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. NRIF3 as a coregulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of coregulators may play dual roles in mediating both positive and negative regulatory effects on gene expression [].
Probab=21.36 E-value=6.9e+02 Score=23.47 Aligned_cols=31 Identities=29% Similarity=0.416 Sum_probs=20.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhHHHhhhHHHHHHHHHHHH
Q 013509 237 KELDQFMTHYVLLLCSFKEQLQQHVRVHAMEAVMACWEIE 276 (441)
Q Consensus 237 PELDQFMeaYC~mL~kYkEEL~kP~~~~~~EA~~fc~~IE 276 (441)
.+.|.||. +|-+-+.-|.+ |||++.-|..|-
T Consensus 56 t~dD~fm~----L~SkvekS~ee-----ime~~qnL~slQ 86 (139)
T PF06729_consen 56 TEDDEFMV----LLSKVEKSLEE-----IMEIRQNLSSLQ 86 (139)
T ss_pred cchhHHHH----HHHHHHHHHHH-----HHHHHHHHHHHH
Confidence 45599996 56666666654 577776665543
No 112
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.33 E-value=85 Score=30.07 Aligned_cols=49 Identities=14% Similarity=0.069 Sum_probs=39.7
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccCC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHSN 425 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~n 425 (441)
.||...+.++.-.|.+++ + -.++|+.+|++..-|.++....|++.++..
T Consensus 134 ~Lp~~~R~v~~L~y~eg~--s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELEDM--S------YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 588888899988766533 2 247899999999999999999999998743
No 113
>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=20.89 E-value=61 Score=22.93 Aligned_cols=22 Identities=41% Similarity=0.591 Sum_probs=17.4
Q ss_pred HHHHHhhCCChHHHHHHHHhhh
Q 013509 176 YKAEILSHPLYEQLLSAHVACL 197 (441)
Q Consensus 176 lKAkI~sHPlYp~LL~AyidCl 197 (441)
+-.+|++-|||.-||+|--..+
T Consensus 5 lipkiissplfktllsavgsal 26 (33)
T PF07425_consen 5 LIPKIISSPLFKTLLSAVGSAL 26 (33)
T ss_dssp CHHHHCCTTTCHHHHHHHHHHC
T ss_pred hhhHHHccHHHHHHHHHHHHHH
Confidence 3468999999999999865443
No 114
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=20.70 E-value=1e+02 Score=28.00 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=36.1
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.++..-|.... .-.++|+.+|++...|.+|..-.|++.++
T Consensus 133 ~L~~~~r~i~~l~~~~~~--------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHAYVDGC--------SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 477788886655444322 23589999999999999999999998875
No 115
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.68 E-value=1.2e+02 Score=29.45 Aligned_cols=47 Identities=9% Similarity=0.102 Sum_probs=38.1
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||+..+.+|...|.... + -.++|+.+|++...|..|....|++.++
T Consensus 205 ~L~~~~r~vl~l~~~~g~--s------~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 205 VLSDREKSIIQCTFIENL--S------QKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred hCCHHHHHHHHHHHhCCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 488888888877665422 2 3689999999999999999999998875
No 116
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=20.30 E-value=1.1e+02 Score=27.92 Aligned_cols=48 Identities=10% Similarity=0.135 Sum_probs=37.4
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhcccC
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWHS 424 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK~ 424 (441)
.||+..+.+|.--+.+.. .-.++|+.+|++...|.+-+...|++.++.
T Consensus 131 ~L~~~~r~vl~l~~~~~~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEK--------SVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 478888888865444322 235799999999999999999999988763
No 117
>PF12878 SICA_beta: SICA extracellular beta domain; InterPro: IPR024285 The schizont-infected cell agglutination (SICA) proteins of Plasmodium knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. SICA proteins comprise multiple domains, with the extracellular cysteine-rich domains (CRDs) occurring at different frequencies. They contain a five-cysteine CRD (SICA-alpha) at the N terminus, which occurs once or twice, then between 1 and 10 SICA-beta CRDs with 7-10 cysteine residues, a transmembrane domain, and a conserved C-terminal domain []. This entry represents the extracellular SICA-beta domain.
Probab=20.15 E-value=1e+02 Score=29.23 Aligned_cols=24 Identities=21% Similarity=0.492 Sum_probs=21.8
Q ss_pred CCChHHHHHHHHHHHHHHHHHHHHhH
Q 013509 234 TDDKELDQFMTHYVLLLCSFKEQLQQ 259 (441)
Q Consensus 234 g~DPELDQFMeaYC~mL~kYkEEL~k 259 (441)
..+|.++|.|- |.+|..|...|..
T Consensus 95 ~~~~~f~qtm~--C~lLnaYAkkmke 118 (169)
T PF12878_consen 95 DDNPSFKQTMG--CFLLNAYAKKMKE 118 (169)
T ss_pred cCCccHHHHHH--HHHHHHHHHHHHH
Confidence 46799999999 9999999999976
No 118
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=20.10 E-value=1.2e+02 Score=27.21 Aligned_cols=47 Identities=11% Similarity=0.101 Sum_probs=36.3
Q ss_pred CCCcchHHHHHHHHHhcCCCCCCCHHHHHHHHHHhCCChhhhhhhhhhHHhhccc
Q 013509 369 KLPGDTTSVLKSWWQSHSKWPYPTEEDKARLVQETGLQLKQINNWFINQRKRNWH 423 (441)
Q Consensus 369 ~lpkea~~iLk~Wf~~H~~nPYPSeeEK~~LA~~TGLs~kQV~NWF~NrRrR~KK 423 (441)
.||...+.++...|... + .-.++|+.+|++...|.+++...|++.++
T Consensus 136 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMED----L----SLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47888888876633331 2 23579999999999999999999998875
Done!