Query 048159
Match_columns 840
No_of_seqs 290 out of 936
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 06:52:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048159.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048159hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07526 POX: Associated with 100.0 9.7E-41 2.1E-45 319.7 12.0 140 399-563 1-140 (140)
2 smart00574 POX domain associat 100.0 6.1E-40 1.3E-44 312.7 11.4 139 395-562 1-139 (140)
3 KOG0773 Transcription factor M 100.0 3E-33 6.5E-38 296.5 10.2 200 491-696 111-312 (342)
4 KOG0774 Transcription factor P 99.8 4.3E-19 9.3E-24 184.0 16.4 149 495-688 102-253 (334)
5 PF05920 Homeobox_KN: Homeobox 99.6 1.3E-15 2.8E-20 119.1 3.2 40 641-680 1-40 (40)
6 cd00086 homeodomain Homeodomai 99.3 2.5E-12 5.4E-17 103.3 5.8 57 625-684 2-58 (59)
7 smart00389 HOX Homeodomain. DN 99.3 6.2E-12 1.3E-16 100.7 6.0 55 625-682 2-56 (56)
8 PF00046 Homeobox: Homeobox do 99.2 6E-12 1.3E-16 101.9 4.8 57 624-683 1-57 (57)
9 KOG0775 Transcription factor S 99.1 3.2E-11 6.9E-16 126.9 4.3 50 630-682 183-232 (304)
10 KOG0487 Transcription factor A 98.7 7E-09 1.5E-13 111.6 3.7 63 622-687 234-296 (308)
11 KOG0842 Transcription factor t 98.7 1.5E-08 3.3E-13 108.9 4.2 66 621-689 150-216 (307)
12 KOG0489 Transcription factor z 98.6 2.7E-08 5.9E-13 104.5 2.9 63 622-687 158-220 (261)
13 KOG0843 Transcription factor E 98.6 1.1E-07 2.4E-12 95.9 6.8 64 622-688 101-164 (197)
14 KOG0493 Transcription factor E 98.6 4.8E-08 1E-12 102.9 4.3 61 621-684 244-304 (342)
15 TIGR01565 homeo_ZF_HD homeobox 98.5 1.8E-07 3.9E-12 79.1 5.7 53 623-678 1-57 (58)
16 KOG0488 Transcription factor B 98.5 1.1E-07 2.3E-12 102.8 5.0 61 624-687 173-233 (309)
17 KOG0483 Transcription factor H 98.5 1.2E-07 2.5E-12 97.0 4.6 66 623-691 50-115 (198)
18 KOG0850 Transcription factor D 98.5 1.3E-07 2.7E-12 98.3 4.3 61 623-686 122-182 (245)
19 KOG0485 Transcription factor N 98.4 1.7E-07 3.6E-12 96.9 3.4 66 621-689 102-167 (268)
20 KOG3802 Transcription factor O 98.3 6.6E-07 1.4E-11 98.9 4.5 60 623-685 294-353 (398)
21 KOG0484 Transcription factor P 98.3 1.5E-06 3.3E-11 81.6 6.1 65 624-691 18-82 (125)
22 KOG0492 Transcription factor M 98.2 1.7E-06 3.7E-11 89.1 4.6 65 622-689 143-207 (246)
23 KOG4577 Transcription factor L 98.1 1.2E-06 2.7E-11 93.5 3.4 73 615-690 159-231 (383)
24 KOG2251 Homeobox transcription 98.1 9.4E-06 2E-10 84.3 9.3 62 621-685 35-96 (228)
25 COG5576 Homeodomain-containing 98.1 2.4E-06 5.2E-11 84.7 4.6 62 621-685 49-110 (156)
26 KOG0848 Transcription factor C 98.1 1.4E-06 3E-11 92.4 2.7 56 630-688 206-261 (317)
27 KOG0486 Transcription factor P 98.0 5E-06 1.1E-10 89.8 3.7 55 630-687 119-173 (351)
28 KOG0494 Transcription factor C 97.9 7.8E-06 1.7E-10 86.6 4.3 55 628-685 146-200 (332)
29 KOG0491 Transcription factor B 97.8 8.4E-06 1.8E-10 81.7 1.2 57 626-685 103-159 (194)
30 KOG2252 CCAAT displacement pro 97.7 3.2E-05 6.9E-10 88.6 5.2 57 622-681 419-475 (558)
31 KOG0847 Transcription factor, 97.7 3.6E-05 7.8E-10 80.1 4.9 68 621-691 163-232 (288)
32 KOG0844 Transcription factor E 97.4 6.6E-05 1.4E-09 81.2 1.6 62 623-687 181-242 (408)
33 KOG0773 Transcription factor M 97.3 6.4E-05 1.4E-09 81.1 0.9 61 626-687 98-158 (342)
34 KOG0849 Transcription factor P 97.3 0.00019 4E-09 79.2 3.8 64 622-688 175-238 (354)
35 KOG0490 Transcription factor, 97.1 0.00021 4.6E-09 71.5 2.3 61 622-685 59-119 (235)
36 KOG1168 Transcription factor A 97.0 0.00029 6.2E-09 76.0 1.3 60 621-683 307-366 (385)
37 PF11569 Homez: Homeodomain le 95.6 0.0091 2E-07 50.9 2.7 43 635-680 10-52 (56)
38 KOG0490 Transcription factor, 93.5 0.056 1.2E-06 54.3 3.0 62 622-686 152-213 (235)
39 PF03792 PBC: PBC domain; Int 92.9 0.66 1.4E-05 48.3 9.6 78 491-572 102-182 (191)
40 KOG1146 Homeobox protein [Gene 85.0 0.63 1.4E-05 59.1 3.0 58 626-686 906-963 (1406)
41 PF04218 CENP-B_N: CENP-B N-te 76.3 3.9 8.5E-05 34.1 4.0 47 624-678 1-47 (53)
42 PF03791 KNOX2: KNOX2 domain ; 76.0 4.4 9.5E-05 34.5 4.2 29 541-569 17-51 (52)
43 PF11285 DUF3086: Protein of u 73.7 28 0.0006 38.4 10.4 60 496-571 7-66 (283)
44 KOG3623 Homeobox transcription 60.7 10 0.00022 46.6 4.4 44 635-681 568-611 (1007)
45 cd06171 Sigma70_r4 Sigma70, re 53.4 17 0.00036 27.4 3.2 46 629-682 10-55 (55)
46 cd00569 HTH_Hin_like Helix-tur 45.6 48 0.001 22.1 4.3 38 629-674 5-42 (42)
47 PF01527 HTH_Tnp_1: Transposas 44.1 30 0.00065 29.3 3.7 46 625-678 2-48 (76)
48 PRK09642 RNA polymerase sigma 37.9 29 0.00064 33.1 2.9 52 629-688 106-157 (160)
49 PF04545 Sigma70_r4: Sigma-70, 37.7 29 0.00063 27.7 2.5 47 629-683 4-50 (50)
50 PF13443 HTH_26: Cro/C1-type H 35.7 30 0.00065 28.5 2.3 34 655-688 12-45 (63)
51 TIGR02985 Sig70_bacteroi1 RNA 33.7 48 0.001 30.9 3.6 48 629-684 113-160 (161)
52 PRK06759 RNA polymerase factor 32.3 40 0.00086 31.8 2.8 47 629-683 106-152 (154)
53 TIGR02937 sigma70-ECF RNA poly 32.0 46 0.00099 30.0 3.1 48 629-684 110-157 (158)
54 PRK09644 RNA polymerase sigma 31.9 41 0.00089 32.4 2.9 52 628-687 107-158 (165)
55 PF08281 Sigma70_r4_2: Sigma-7 31.5 50 0.0011 26.5 2.9 45 629-681 10-54 (54)
56 cd00131 PAX Paired Box domain 29.1 1.7E+02 0.0037 28.5 6.5 48 627-677 73-127 (128)
57 PRK12512 RNA polymerase sigma 28.5 56 0.0012 32.0 3.2 51 629-687 131-181 (184)
58 PRK11924 RNA polymerase sigma 28.1 60 0.0013 30.9 3.3 51 629-687 125-175 (179)
59 PRK12514 RNA polymerase sigma 28.1 62 0.0013 31.6 3.4 48 629-684 129-176 (179)
60 PRK09646 RNA polymerase sigma 26.4 51 0.0011 32.9 2.6 49 629-685 142-190 (194)
61 COG4977 Transcriptional regula 25.7 3.2E+02 0.0069 31.1 8.7 96 535-677 164-260 (328)
62 PRK09652 RNA polymerase sigma 25.6 59 0.0013 31.0 2.8 50 629-686 128-177 (182)
63 PRK12541 RNA polymerase sigma 24.9 56 0.0012 31.3 2.4 47 629-683 112-158 (161)
64 PRK12526 RNA polymerase sigma 24.1 61 0.0013 32.8 2.7 49 629-685 153-201 (206)
65 smart00421 HTH_LUXR helix_turn 23.9 1.5E+02 0.0032 22.8 4.2 51 629-688 3-53 (58)
66 PRK08583 RNA polymerase sigma 23.9 71 0.0015 33.5 3.2 49 629-685 205-253 (257)
67 PRK06811 RNA polymerase factor 23.5 62 0.0013 32.2 2.5 50 629-686 131-180 (189)
68 TIGR02948 SigW_bacill RNA poly 22.9 65 0.0014 31.3 2.5 49 629-685 136-184 (187)
69 PRK15369 two component system 22.9 1.4E+02 0.0031 27.8 4.7 54 628-690 148-201 (211)
70 PRK12547 RNA polymerase sigma 22.8 67 0.0015 31.1 2.6 49 629-685 112-160 (164)
71 PRK09648 RNA polymerase sigma 22.8 68 0.0015 31.6 2.7 49 629-685 139-187 (189)
72 PRK03975 tfx putative transcri 22.7 92 0.002 31.3 3.5 51 627-686 4-54 (141)
73 PRK12519 RNA polymerase sigma 22.6 61 0.0013 32.0 2.3 50 629-686 141-190 (194)
74 TIGR02939 RpoE_Sigma70 RNA pol 22.4 69 0.0015 31.2 2.6 49 629-685 138-186 (190)
75 PRK12530 RNA polymerase sigma 22.3 1.1E+02 0.0023 30.7 3.9 53 629-689 134-186 (189)
76 PRK12531 RNA polymerase sigma 22.1 73 0.0016 31.8 2.7 53 628-688 140-192 (194)
77 TIGR02999 Sig-70_X6 RNA polyme 22.0 71 0.0015 31.1 2.6 48 629-684 134-181 (183)
78 TIGR02941 Sigma_B RNA polymera 21.9 75 0.0016 33.3 2.9 49 629-685 205-253 (255)
79 TIGR02954 Sig70_famx3 RNA poly 21.4 68 0.0015 31.0 2.3 49 629-685 119-167 (169)
80 PRK04217 hypothetical protein; 21.4 97 0.0021 30.0 3.3 52 627-686 40-91 (110)
81 PRK12536 RNA polymerase sigma 20.7 70 0.0015 31.5 2.3 50 629-686 129-178 (181)
82 TIGR03001 Sig-70_gmx1 RNA poly 20.6 89 0.0019 33.2 3.1 53 629-689 161-213 (244)
83 TIGR02983 SigE-fam_strep RNA p 20.6 71 0.0015 30.5 2.2 49 629-685 110-158 (162)
84 PRK12532 RNA polymerase sigma 20.5 87 0.0019 31.1 2.9 52 629-688 136-187 (195)
85 TIGR02989 Sig-70_gvs1 RNA poly 20.3 1.1E+02 0.0025 28.8 3.6 48 628-683 110-157 (159)
86 PRK12520 RNA polymerase sigma 20.1 1.3E+02 0.0028 29.8 4.0 53 629-689 131-183 (191)
No 1
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=100.00 E-value=9.7e-41 Score=319.69 Aligned_cols=140 Identities=43% Similarity=0.659 Sum_probs=99.3
Q ss_pred hhhccCcccchHHHHHHHhhhccccccCCCCCcccccccccccccchhhhhhhcchhcccccCCCCCCCccCCCcccCCc
Q 048159 399 TILKNSRFLKPAQELLDEFCCVKKSKYGRRGNVSERFSGDRASASASAEADAADVADREVGAKGKNSTSRVSSPTFYSSN 478 (840)
Q Consensus 399 ~vL~~SRyLkpAQqLLdE~c~V~~~~~~~~~~~~~r~~~~~~~~s~~s~~d~~~~ad~e~G~~~~~~~s~~sss~~~~s~ 478 (840)
.+|++|||||||||||||||+|++........ ..... . +..+.... .+.....++
T Consensus 1 q~l~~SryLk~aQeLL~E~~~v~~~~~~~~~~-------~~~~~----~-~~~~~~~~-------------~~~~~~~~~ 55 (140)
T PF07526_consen 1 QVLLGSRYLKPAQELLDEFCSVGGANKKKSDD-------SSSGA----P-GGANSSGS-------------SSSSGGSSS 55 (140)
T ss_pred CccccchhHHHHHHHHHHHHcccchhhhcchh-------hcccc----c-cccccCCC-------------CCCCCCCCC
Confidence 47999999999999999999998741111000 00000 0 00000000 000000011
Q ss_pred ccccCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCchhHHHHHHHHHhhhhHHH
Q 048159 479 QISCEGGVGSSSGESHRPEYQEMRAKLLYLQEEVSKRYKLYHQQLQMVVSSFESVAGLSGATPYVSLAFKAISKNFRCLK 558 (840)
Q Consensus 479 ~~~~d~g~~ss~~~~~~~E~Q~kKaKLl~MLeEVdrRY~qY~~qmq~VvsSFe~vaG~gaA~pYt~lAlKamSRhFr~Lr 558 (840)
...+..+...+.+..+++|+|+||+|||.||||||+||+|||+|||+|+++||+|||+|+|+|||+||+|||||||||||
T Consensus 56 ~~~~~~~~~~~ls~~~~~e~q~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR~LR 135 (140)
T PF07526_consen 56 SSSSSDSSSPELSPAERQELQRKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFRCLR 135 (140)
T ss_pred CccccCCCCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHHHHH
Confidence 11111122334567889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q 048159 559 SAIMN 563 (840)
Q Consensus 559 naI~~ 563 (840)
++|.+
T Consensus 136 daI~~ 140 (140)
T PF07526_consen 136 DAISD 140 (140)
T ss_pred HHhcC
Confidence 99963
No 2
>smart00574 POX domain associated with HOX domains.
Probab=100.00 E-value=6.1e-40 Score=312.74 Aligned_cols=139 Identities=43% Similarity=0.656 Sum_probs=103.7
Q ss_pred chhhhhhccCcccchHHHHHHHhhhccccccCCCCCcccccccccccccchhhhhhhcchhcccccCCCCCCCccCCCcc
Q 048159 395 TGYATILKNSRFLKPAQELLDEFCCVKKSKYGRRGNVSERFSGDRASASASAEADAADVADREVGAKGKNSTSRVSSPTF 474 (840)
Q Consensus 395 tg~A~vL~~SRyLkpAQqLLdE~c~V~~~~~~~~~~~~~r~~~~~~~~s~~s~~d~~~~ad~e~G~~~~~~~s~~sss~~ 474 (840)
+||+++|++|||||||||||||||+|++....+... ++ .... ... + .+ +.++...+ +.+
T Consensus 1 ~g~~~~l~~SkyLk~aQeLLdEf~sv~~~~~~~~~~--~~---~~~~---~~~-~-~~----~~~~~~~~---g~s---- 59 (140)
T smart00574 1 TGGVFILRNSKYLKAAQELLDEFCNVGRGSSKKKKQ--SG---NDSP---VST-S-SN----EGGGENLS---GGS---- 59 (140)
T ss_pred CchhhhccCccccccHHHHHHHHhcccHHhhccccc--cc---cccc---ccc-c-cc----CCCcCCCC---CCC----
Confidence 689999999999999999999999998754322211 00 0000 000 0 00 00000000 000
Q ss_pred cCCcccccCCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCchhHHHHHHHHHhhh
Q 048159 475 YSSNQISCEGGVGSSSGESHRPEYQEMRAKLLYLQEEVSKRYKLYHQQLQMVVSSFESVAGLSGATPYVSLAFKAISKNF 554 (840)
Q Consensus 475 ~~s~~~~~d~g~~ss~~~~~~~E~Q~kKaKLl~MLeEVdrRY~qY~~qmq~VvsSFe~vaG~gaA~pYt~lAlKamSRhF 554 (840)
..+.....+.++++|+|+||+||+.||||||+||+|||+|||+|+++||+|||+|+|+|||+||+|+|||||
T Consensus 60 --------~~~~~~~ls~~~r~e~q~kk~kLl~mL~eVd~RY~qY~~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhF 131 (140)
T smart00574 60 --------SSSEVPPLSTAERQELQRKKAKLLSMLEEVDRRYKHYYEQMQTVVSSFDQAAGLGAAKPYTALALKTISRHF 131 (140)
T ss_pred --------CCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHH
Confidence 011123456788999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHH
Q 048159 555 RCLKSAIM 562 (840)
Q Consensus 555 r~LrnaI~ 562 (840)
||||++|.
T Consensus 132 r~LrdaI~ 139 (140)
T smart00574 132 RCLKDAIA 139 (140)
T ss_pred HHHHHHhc
Confidence 99999996
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=100.00 E-value=3e-33 Score=296.54 Aligned_cols=200 Identities=41% Similarity=0.593 Sum_probs=166.3
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCchhHHHHHHHHHhhhhHHHH--HHHHHHHHH
Q 048159 491 GESHRPEYQEMRAKLLYLQEEVSKRYKLYHQQLQMVVSSFESVAGLSGATPYVSLAFKAISKNFRCLKS--AIMNQLKHV 568 (840)
Q Consensus 491 ~~~~~~E~Q~kKaKLl~MLeEVdrRY~qY~~qmq~VvsSFe~vaG~gaA~pYt~lAlKamSRhFr~Lrn--aI~~QL~~~ 568 (840)
++.++.+++.+++|++.||.+|+.+|.+|+..|+.|.+.|+...+++.+.+|+..++..++++|+++++ +|..|+...
T Consensus 111 ~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~ 190 (342)
T KOG0773|consen 111 AWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSS 190 (342)
T ss_pred cchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccc
Confidence 467789999999999999999999999999999999999999999999999999999999999999999 899999988
Q ss_pred HHHhccccccCccccCCCCCCccccccccchhhhhhhhccCCCCCCCccCCcCCcCCCCCCCChHHHHHHHHHHHHccCC
Q 048159 569 AKALGEEMRSSATVTSSSRGHITNTSAKLNCLDQILQKHKSGGANVGFLEPQQHVWRPQRGLPERAVAILRAWLFEHFLH 648 (840)
Q Consensus 569 ~k~lgEd~~~~~~~~~~s~Gd~~~~s~Rlr~lDQ~lrk~~sg~~~lg~Le~~~~~kRkrR~Lpk~av~iLr~WL~eH~~n 648 (840)
+..+++....+... ..++ ....++.+..++.++.+.. ...+.......+||++++||+.++.+|++||++|+.|
T Consensus 191 ~~~~~~~~~~~~~~---~~~~-~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~ 264 (342)
T KOG0773|consen 191 EELLGESEQDDSED---ESGP-SGSEPPLRLAKQSLRQQRS--AYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLH 264 (342)
T ss_pred cccccccccccccc---ccCc-ccccCCccccccccccccc--ccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccC
Confidence 87776443211111 0111 1124555566666655543 1223333346789999999999999999999999999
Q ss_pred CCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHhhhhhccC
Q 048159 649 PYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEIHMLETQG 696 (840)
Q Consensus 649 PYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~~~~e~~~ 696 (840)
|||++.+|.+||++|||++.||+|||||+|+|+|+||+++++..+...
T Consensus 265 PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~~~~~~ 312 (342)
T KOG0773|consen 265 PYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEEMYLLEDKD 312 (342)
T ss_pred CCCcchhccccchhcCCCcccCCchhhhcccccCCchHHHHHHHhhcc
Confidence 999999999999999999999999999999999999999999887665
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=99.81 E-value=4.3e-19 Score=183.97 Aligned_cols=149 Identities=27% Similarity=0.411 Sum_probs=130.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh--hhccCCCCCchhHHHHHHHHHhhhhHHHHHHHHHHH-HHHHH
Q 048159 495 RPEYQEMRAKLLYLQEEVSKRYKLYHQQLQMVVSSF--ESVAGLSGATPYVSLAFKAISKNFRCLKSAIMNQLK-HVAKA 571 (840)
Q Consensus 495 ~~E~Q~kKaKLl~MLeEVdrRY~qY~~qmq~VvsSF--e~vaG~gaA~pYt~lAlKamSRhFr~LrnaI~~QL~-~~~k~ 571 (840)
..|+..|..++..++++--++|++-|.+....|... |......++.--++-.+..|+|.| +.|..||+ .+|.+
T Consensus 102 hsdYR~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~ke~e~m~~~i~~kF----~~iq~~lkqstce~ 177 (334)
T KOG0774|consen 102 HSDYRAKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMPKEIERMVQIISKKF----SHIQMQLKQSTCEA 177 (334)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHH----HHHHHHHHHHHHHH
Confidence 579999999999999999999999999998888876 666677777667899999999999 99999999 46654
Q ss_pred hccccccCccccCCCCCCccccccccchhhhhhhhccCCCCCCCccCCcCCcCCCCCCCChHHHHHHHHHHHHccCCCCC
Q 048159 572 LGEEMRSSATVTSSSRGHITNTSAKLNCLDQILQKHKSGGANVGFLEPQQHVWRPQRGLPERAVAILRAWLFEHFLHPYP 651 (840)
Q Consensus 572 lgEd~~~~~~~~~~s~Gd~~~~s~Rlr~lDQ~lrk~~sg~~~lg~Le~~~~~kRkrR~Lpk~av~iLr~WL~eH~~nPYP 651 (840)
+ ..-|.|++|+ +||||+|+|.++.||..||+.|+.||||
T Consensus 178 v--------------------miLr~r~lda---------------------rRKRRNFsK~aTeiLneyF~~h~~nPYP 216 (334)
T KOG0774|consen 178 V--------------------MILRSRFLDA---------------------RRKRRNFSKQATEILNEYFYSHLSNPYP 216 (334)
T ss_pred H--------------------HHHHHHHHHH---------------------HHhhcccchhHHHHHHHHHHHhcCCCCC
Confidence 3 2344455443 4789999999999999999999999999
Q ss_pred CHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 652 TDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 652 S~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
++++|.+||++++++..||+|||.|.|.|.+|.|...
T Consensus 217 See~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 217 SEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred cHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 9999999999999999999999999999999998764
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=99.56 E-value=1.3e-15 Score=119.13 Aligned_cols=40 Identities=65% Similarity=1.173 Sum_probs=36.6
Q ss_pred HHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhh
Q 048159 641 WLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVR 680 (840)
Q Consensus 641 WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrR 680 (840)
||.+|+.||||+++||.+||++|||+.+||+|||+|+|+|
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
>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=99.31 E-value=2.5e-12 Score=103.28 Aligned_cols=57 Identities=26% Similarity=0.515 Sum_probs=53.4
Q ss_pred CCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccch
Q 048159 625 RPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKP 684 (840)
Q Consensus 625 RkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKp 684 (840)
+++..++++++.+|++||.. +|||+.+++..||.+|||+..||.+||.|+|.|.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~---~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEK---NPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHh---CCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 46677999999999999999 9999999999999999999999999999999998764
No 7
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.27 E-value=6.2e-12 Score=100.69 Aligned_cols=55 Identities=29% Similarity=0.514 Sum_probs=50.9
Q ss_pred CCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhcc
Q 048159 625 RPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVW 682 (840)
Q Consensus 625 RkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlk 682 (840)
+++..|+++++.+|++||.. +|||+.+++..||..+||+..||.+||+|+|+|.+
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 44556999999999999999 89999999999999999999999999999999864
No 8
>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=99.25 E-value=6e-12 Score=101.90 Aligned_cols=57 Identities=32% Similarity=0.619 Sum_probs=54.0
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccc
Q 048159 624 WRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683 (840)
Q Consensus 624 kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkK 683 (840)
||+++.|+++++.+|+.+|.. +|||+.+++..||..+||+..||.+||.|+|.+.+|
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 577888999999999999998 999999999999999999999999999999999764
No 9
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=99.13 E-value=3.2e-11 Score=126.86 Aligned_cols=50 Identities=44% Similarity=0.821 Sum_probs=48.0
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhcc
Q 048159 630 LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVW 682 (840)
Q Consensus 630 Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlk 682 (840)
|.++.+.+||+||.. +|||+.++|.+||+.|||+..||.|||+|+|.|.+
T Consensus 183 FKekSR~~LrewY~~---~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQ---NPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhc---CCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 678899999999997 99999999999999999999999999999999987
No 10
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=98.71 E-value=7e-09 Score=111.56 Aligned_cols=63 Identities=21% Similarity=0.213 Sum_probs=54.6
Q ss_pred CcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 622 HVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 622 ~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
..||||-.++|.++..|++-|.- |-|.|++-|.+|++.++||..||+.||+|||+|+||-..|
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlf---N~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLF---NMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHH---HHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 33444445999999999888887 7899999999999999999999999999999998886544
No 11
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=98.66 E-value=1.5e-08 Score=108.93 Aligned_cols=66 Identities=21% Similarity=0.317 Sum_probs=59.4
Q ss_pred CCcCCCCCC-CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHh
Q 048159 621 QHVWRPQRG-LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEI 689 (840)
Q Consensus 621 ~~~kRkrR~-Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~ 689 (840)
..+|||+|. |++.+|-.|+.-|.+ ..|.+.-||+.||+..+||.+||+.||+|+|.|.|+.-+|..
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrq---QRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQ---QRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHh---hhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 345666776 899999999999998 899999999999999999999999999999999998877764
No 12
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=98.56 E-value=2.7e-08 Score=104.55 Aligned_cols=63 Identities=19% Similarity=0.230 Sum_probs=57.1
Q ss_pred CcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 622 HVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 622 ~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
+.||.|+.|+..++..|+.-|.- |.|.++..|++||..+.|++.||++||+|||+|+||...+
T Consensus 158 ~~kR~RtayT~~QllELEkEFhf---N~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHF---NKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhcc---ccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 45777888999999999999988 8999999999999999999999999999999998875433
No 13
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=98.56 E-value=1.1e-07 Score=95.92 Aligned_cols=64 Identities=22% Similarity=0.287 Sum_probs=58.0
Q ss_pred CcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 622 HVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 622 ~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
..||.|+.|+.+++..|+..|.. +-|-.-.||..||+.++|+..||+.||+|+|.|.||.-.++
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~---~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEG---NQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhc---CCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 34667777999999999999998 89999999999999999999999999999999998876554
No 14
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.56 E-value=4.8e-08 Score=102.87 Aligned_cols=61 Identities=28% Similarity=0.485 Sum_probs=57.6
Q ss_pred CCcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccch
Q 048159 621 QHVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKP 684 (840)
Q Consensus 621 ~~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKp 684 (840)
.+-||+|+.|+.++.+.|+.-|.+ +.|.|+..|..||.++||.+.||+.||+|+|.++||.
T Consensus 244 ~eeKRPRTAFtaeQL~RLK~EF~e---nRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 244 KEEKRPRTAFTAEQLQRLKAEFQE---NRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred chhcCccccccHHHHHHHHHHHhh---hhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 456888999999999999999999 8999999999999999999999999999999999874
No 15
>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=98.50 E-value=1.8e-07 Score=79.13 Aligned_cols=53 Identities=11% Similarity=0.243 Sum_probs=49.8
Q ss_pred cCCCCCCCChHHHHHHHHHHHHccCCCC----CCHHHHHHHHHHhCCChhhHhhccchhh
Q 048159 623 VWRPQRGLPERAVAILRAWLFEHFLHPY----PTDTDKHMLATQTGLSRNQVSNWFINAR 678 (840)
Q Consensus 623 ~kRkrR~Lpk~av~iLr~WL~eH~~nPY----PS~eEK~~LA~qTGLS~kQVsNWFiNaR 678 (840)
++|+|+.|+.+++..|+..|.. .+| |+..++..||..+||++.+|+.||+|.+
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 3678888999999999999999 899 9999999999999999999999999965
No 16
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=98.49 E-value=1.1e-07 Score=102.76 Aligned_cols=61 Identities=23% Similarity=0.380 Sum_probs=53.7
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 624 WRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 624 kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
+|.|+.|+..++..|+.-|.. --|.+..||.+||...|||..||++||+|||.|+|+...+
T Consensus 173 RksRTaFT~~Ql~~LEkrF~~---QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 173 RKSRTAFSDHQLFELEKRFEK---QKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred ccchhhhhHHHHHHHHHHHHH---hhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 334445999999999999887 6899999999999999999999999999999997776655
No 17
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.47 E-value=1.2e-07 Score=97.00 Aligned_cols=66 Identities=26% Similarity=0.234 Sum_probs=59.5
Q ss_pred cCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHhhh
Q 048159 623 VWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEIHM 691 (840)
Q Consensus 623 ~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~~~ 691 (840)
.+++|++|+.+++..|+.-|.. +-|-.+++|..||++.||...||..||+|+|.|+|.+-.|.-|.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~---~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~ 115 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFES---EKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYE 115 (198)
T ss_pred cccccccccHHHHHHhHHhhcc---ccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHH
Confidence 5678999999999999999998 67788899999999999999999999999999998887776553
No 18
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=98.46 E-value=1.3e-07 Score=98.34 Aligned_cols=61 Identities=25% Similarity=0.341 Sum_probs=55.6
Q ss_pred cCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 623 VWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 623 ~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
.||+|+.++.-+...|++-|.+ ..|..--||.+||..+|||..||+.||+|+|-|+||.|.
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQk---TQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQ---TQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhh---cchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3455666899999999999998 899999999999999999999999999999999998775
No 19
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=98.39 E-value=1.7e-07 Score=96.86 Aligned_cols=66 Identities=18% Similarity=0.248 Sum_probs=60.1
Q ss_pred CCcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHh
Q 048159 621 QHVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEI 689 (840)
Q Consensus 621 ~~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~ 689 (840)
-+|||+|+.|+..++..|+.-|.. ..|.+..||.-||+++.||+.||+.||+|+|.|+|+....++
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~---krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFEL---KRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHH---HhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 356777888999999999999998 789999999999999999999999999999999998876654
No 20
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.26 E-value=6.6e-07 Score=98.85 Aligned_cols=60 Identities=18% Similarity=0.320 Sum_probs=53.9
Q ss_pred cCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 623 VWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 623 ~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
+||||+.+...++..|+..|.+ +|-|+.+|.-.||.+++|.+..|++||+|||.|.|+..
T Consensus 294 kRKKRTSie~~vr~aLE~~F~~---npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 294 KRKKRTSIEVNVRGALEKHFLK---NPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccceeHHHHHHHHHHHHh---CCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 3444445999999999999999 99999999999999999999999999999999988753
No 21
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=98.26 E-value=1.5e-06 Score=81.56 Aligned_cols=65 Identities=22% Similarity=0.296 Sum_probs=57.5
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHhhh
Q 048159 624 WRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEIHM 691 (840)
Q Consensus 624 kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~~~ 691 (840)
+|-|+.|+..+.+.|+..|.+ .-||..-.|++||.+..||+..|+.||+|+|.+.+|...-..+.
T Consensus 18 RRIRTTFTS~QLkELErvF~E---THYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~ 82 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFAE---THYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAK 82 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHHh---hcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 444556999999999999999 78999999999999999999999999999999999876665543
No 22
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=98.16 E-value=1.7e-06 Score=89.15 Aligned_cols=65 Identities=18% Similarity=0.313 Sum_probs=58.3
Q ss_pred CcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHh
Q 048159 622 HVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEI 689 (840)
Q Consensus 622 ~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~ 689 (840)
..+++|+.|+..+...|++-|.+ ..|-+.+|+.+++..+.||..||+.||+|+|.|-|+-..+|+
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfre---kqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFRE---KQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhH---hhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence 34677888999999999999999 899999999999999999999999999999999887655554
No 23
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.15 E-value=1.2e-06 Score=93.46 Aligned_cols=73 Identities=22% Similarity=0.318 Sum_probs=65.9
Q ss_pred CccCCcCCcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHhh
Q 048159 615 GFLEPQQHVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEIH 690 (840)
Q Consensus 615 g~Le~~~~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~~ 690 (840)
..|+.+...||||++++.++...|+.-|.. .|-|.+--|++|+.+|||....|+.||+|+|.+.|+-..+.-.
T Consensus 159 ~~l~gd~~nKRPRTTItAKqLETLK~AYn~---SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 159 NELEGDASNKRPRTTITAKQLETLKQAYNT---SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred cccccccccCCCcceeeHHHHHHHHHHhcC---CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 356777889999999999999999999988 8999999999999999999999999999999998877666543
No 24
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=98.13 E-value=9.4e-06 Score=84.27 Aligned_cols=62 Identities=21% Similarity=0.389 Sum_probs=56.4
Q ss_pred CCcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 621 QHVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 621 ~~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
+..+|.|+.|+..+..+|++-|.+ .-||....+++||.+.+|.+.+|++||+|+|.+.++.-
T Consensus 35 RkqRRERTtFtr~QlevLe~LF~k---TqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 35 RKQRRERTTFTRKQLEVLEALFAK---TQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred hhcccccceecHHHHHHHHHHHHh---hcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 445667778999999999999999 89999999999999999999999999999999987653
No 25
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.12 E-value=2.4e-06 Score=84.68 Aligned_cols=62 Identities=19% Similarity=0.296 Sum_probs=57.1
Q ss_pred CCcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 621 QHVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 621 ~~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
...+++|++.+..++.+|+.-|.. +|||+..+|..|+..++++.+-|+.||+|+|.+.++.-
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i---~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEI---NPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred CcCcccceechHHHHHHHHHHhcc---CCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 356778888999999999999999 99999999999999999999999999999999988654
No 26
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=98.10 E-value=1.4e-06 Score=92.41 Aligned_cols=56 Identities=29% Similarity=0.312 Sum_probs=52.1
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 630 LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 630 Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
++..++-.|++-|.- .+|.|...|.+||..+||++.||+.||+|||.|.+|...+.
T Consensus 206 YTDhQRLELEKEfh~---SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHT---SRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecchhhhhhhhhhcc---ccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 899999999999988 89999999999999999999999999999999988766555
No 27
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=97.96 E-value=5e-06 Score=89.79 Aligned_cols=55 Identities=24% Similarity=0.360 Sum_probs=51.5
Q ss_pred CChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 630 LPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 630 Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
|+..+.+.|+.||.. +.||+.+.|++||--|+||+..|.+||+|+|.+++|....
T Consensus 119 FtSqqlqele~tF~r---NrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 119 FTSQQLQELEATFQR---NRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred hHHHHHHHHHHHHhh---ccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence 999999999999999 9999999999999999999999999999999998775443
No 28
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=97.93 E-value=7.8e-06 Score=86.57 Aligned_cols=55 Identities=25% Similarity=0.362 Sum_probs=51.0
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 628 RGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 628 R~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
+.|+..+...|++-|.+ --||..-.|++||.+|+|.+..|..||+|+|.+++|..
T Consensus 146 TiFT~~Qle~LEkaFke---aHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 146 TIFTSYQLEELEKAFKE---AHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred chhhHHHHHHHHHHHhh---ccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 34999999999999999 78999999999999999999999999999999987753
No 29
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=97.76 E-value=8.4e-06 Score=81.71 Aligned_cols=57 Identities=23% Similarity=0.359 Sum_probs=50.6
Q ss_pred CCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 626 PQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 626 krR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.|+.|...+...|++-|.. -.|.+-.|+.+||..++|+++||+.||+|+|++.||-.
T Consensus 103 ~Rtvfs~~ql~~l~~rFe~---QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 103 ARTVFSDPQLSGLEKRFER---QRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hcccccCccccccHHHHhh---hhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 3445899999999999886 57999999999999999999999999999999988754
No 30
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.72 E-value=3.2e-05 Score=88.58 Aligned_cols=57 Identities=25% Similarity=0.336 Sum_probs=54.0
Q ss_pred CcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhc
Q 048159 622 HVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRV 681 (840)
Q Consensus 622 ~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRl 681 (840)
..||+|-.|+..+++.|++.|.+ ++||+.+.-+.|+.+++|.+.-|.|||-|+|+|-
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke---~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKE---NKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhc---CCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 45778888999999999999999 9999999999999999999999999999999996
No 31
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=97.71 E-value=3.6e-05 Score=80.14 Aligned_cols=68 Identities=21% Similarity=0.283 Sum_probs=57.6
Q ss_pred CCcCCC--CCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHhhh
Q 048159 621 QHVWRP--QRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEIHM 691 (840)
Q Consensus 621 ~~~kRk--rR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~~~ 691 (840)
...+|+ +-+|.-.++..|+.-|.+ ..||--.++.+||...|+++.||..||+|+|.+++|+-.-|+-.
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feq---tkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQ---TKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhh---hhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence 444444 334899999999999998 78999999999999999999999999999999998877666543
No 32
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=97.38 E-value=6.6e-05 Score=81.16 Aligned_cols=62 Identities=18% Similarity=0.336 Sum_probs=54.5
Q ss_pred cCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 623 VWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 623 ~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
.+|=|+.|+.+++..|++-|+. .-|-++-.|.+||..++|.+.-|+.||+|+|+|.|+..+.
T Consensus 181 mRRYRTAFTReQIaRLEKEFyr---ENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYR---ENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHH---hccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3556677999999999888876 5799999999999999999999999999999999886554
No 33
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.33 E-value=6.4e-05 Score=81.14 Aligned_cols=61 Identities=43% Similarity=0.658 Sum_probs=55.0
Q ss_pred CCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 626 PQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 626 krR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
++..++.+. .+|+.|+.+|..+|||++.++..|+-.++++..||++||+|+|+|+++.+..
T Consensus 98 ~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 98 RRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred ccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 445678888 8999999999999999999999999999999999999999999998875543
No 34
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=97.28 E-value=0.00019 Score=79.21 Aligned_cols=64 Identities=23% Similarity=0.393 Sum_probs=56.8
Q ss_pred CcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 622 HVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 622 ~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
..+|.|+.|+..+...|++||.. .|||....++.||++++|+...|..||.|+|.|.+|.....
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~r---t~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~~ 238 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQR---TPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRDC 238 (354)
T ss_pred cccccccccccchHHHHHHHhcC---CCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccccc
Confidence 34455667999999999999998 78999999999999999999999999999999998876443
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.15 E-value=0.00021 Score=71.50 Aligned_cols=61 Identities=16% Similarity=0.072 Sum_probs=55.0
Q ss_pred CcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 622 HVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 622 ~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.++|.|.+|+..+...|+.-|.. .+||....++.||..+++++..|.+||+|+|.++++..
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~---~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEK---VHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcC---CCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 44666777999999999999998 59999999999999999999999999999999987654
No 36
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=96.96 E-value=0.00029 Score=75.97 Aligned_cols=60 Identities=22% Similarity=0.349 Sum_probs=54.7
Q ss_pred CCcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccc
Q 048159 621 QHVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683 (840)
Q Consensus 621 ~~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkK 683 (840)
.++||||+.+-..-++-|+++|.. -|-|+.+....+|.++.|.+..|..||+|.|.+.|+
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFav---QPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAV---QPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred cccccccccccCcccccHHHHhcc---CCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 467888888877778899999998 899999999999999999999999999999999877
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.61 E-value=0.0091 Score=50.95 Aligned_cols=43 Identities=21% Similarity=0.413 Sum_probs=31.2
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhh
Q 048159 635 VAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVR 680 (840)
Q Consensus 635 v~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrR 680 (840)
.+.|++.|.. |.++.+.+...|+.+++|+..||.+||.-++.+
T Consensus 10 ~~pL~~Yy~~---h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLK---HKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHH---T----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHH---cCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 3459999999 799999999999999999999999999876543
No 38
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=93.48 E-value=0.056 Score=54.32 Aligned_cols=62 Identities=29% Similarity=0.503 Sum_probs=54.0
Q ss_pred CcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 622 HVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 622 ~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
..++.+..+...+..+|..-|.. .+||....+..|+..+|++...|.+||.|.|.+.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~---~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRA---TPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccC---CCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34556677888899888888877 899999999999999999999999999999999877544
No 39
>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=92.92 E-value=0.66 Score=48.28 Aligned_cols=78 Identities=15% Similarity=0.186 Sum_probs=66.5
Q ss_pred CCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh--hhccCCCCCchhHHHHHHHHHhhhhHHHHHHHHHHH-H
Q 048159 491 GESHRPEYQEMRAKLLYLQEEVSKRYKLYHQQLQMVVSSF--ESVAGLSGATPYVSLAFKAISKNFRCLKSAIMNQLK-H 567 (840)
Q Consensus 491 ~~~~~~E~Q~kKaKLl~MLeEVdrRY~qY~~qmq~VvsSF--e~vaG~gaA~pYt~lAlKamSRhFr~LrnaI~~QL~-~ 567 (840)
...+..|++.|.+++-.++++--++|.+-|.+.-..|... |...-.+++.--+..++..|++.| ++|..||+ .
T Consensus 102 ~~~d~~dYr~kL~~ir~~y~~el~kye~ac~eF~~hV~~lLreQs~~RPIs~keiE~m~~~i~~Kf----~~iq~qLKQs 177 (191)
T PF03792_consen 102 NSIDHSDYRAKLSQIRQIYHSELEKYEQACNEFTEHVMNLLREQSEFRPISPKEIERMVNIIHRKF----SKIQMQLKQS 177 (191)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHH----HHHHHHHHHH
Confidence 3456789999999999999999999999999988877776 666677777778899999999999 99999999 5
Q ss_pred HHHHh
Q 048159 568 VAKAL 572 (840)
Q Consensus 568 ~~k~l 572 (840)
||.++
T Consensus 178 tCEaV 182 (191)
T PF03792_consen 178 TCEAV 182 (191)
T ss_pred HHHHH
Confidence 88764
No 40
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=85.01 E-value=0.63 Score=59.14 Aligned_cols=58 Identities=22% Similarity=0.346 Sum_probs=52.5
Q ss_pred CCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 626 PQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 626 krR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
.|..+...++++|+..|.+ --||++++.+.|-+..+|....|..||+|+|.+-+|+..
T Consensus 906 ~~~~~~d~qlk~i~~~~~~---q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 906 YRTQESDLQLKIIKACYEA---QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hccchhHHHHHHHHHHHhh---ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4445888999999999998 889999999999999999999999999999999888764
No 41
>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=76.29 E-value=3.9 Score=34.05 Aligned_cols=47 Identities=26% Similarity=0.220 Sum_probs=31.3
Q ss_pred CCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhh
Q 048159 624 WRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINAR 678 (840)
Q Consensus 624 kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaR 678 (840)
||+|+.|+-+.+-.+-.-+.. .+ -+..||+++|++..+|.+|..|+.
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 467778887775444444444 33 588999999999999999999854
No 42
>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=75.99 E-value=4.4 Score=34.54 Aligned_cols=29 Identities=21% Similarity=0.372 Sum_probs=25.8
Q ss_pred hhHHHHHHH---HHhhhh---HHHHHHHHHHHHHH
Q 048159 541 PYVSLAFKA---ISKNFR---CLKSAIMNQLKHVA 569 (840)
Q Consensus 541 pYt~lAlKa---mSRhFr---~LrnaI~~QL~~~~ 569 (840)
.||.++.|+ ++|||+ .|.+.|+.||..+|
T Consensus 17 aYc~~L~kykeeL~~p~~EA~~f~~~ie~qL~~Lt 51 (52)
T PF03791_consen 17 AYCDMLVKYKEELQRPFQEAMEFCREIEQQLSSLT 51 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 399999999 899999 78888999999876
No 43
>PF11285 DUF3086: Protein of unknown function (DUF3086); InterPro: IPR021437 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=73.71 E-value=28 Score=38.37 Aligned_cols=60 Identities=18% Similarity=0.328 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhccCCCCCchhHHHHHHHHHhhhhHHHHHHHHHHHHHHHH
Q 048159 496 PEYQEMRAKLLYLQEEVSKRYKLYHQQLQMVVSSFESVAGLSGATPYVSLAFKAISKNFRCLKSAIMNQLKHVAKA 571 (840)
Q Consensus 496 ~E~Q~kKaKLl~MLeEVdrRY~qY~~qmq~VvsSFe~vaG~gaA~pYt~lAlKamSRhFr~LrnaI~~QL~~~~k~ 571 (840)
.|++.+|..|..-++++++|-++-..+| .++| ||- .+.|.+.-+-||+-+..-|+.+..+
T Consensus 7 ~eL~qrk~~Lq~eIe~LerR~~ri~~Em---rtsF---aG~----------Sq~lA~RVqGFkdYLvGsLQDLa~s 66 (283)
T PF11285_consen 7 KELEQRKQALQIEIEQLERRRERIEKEM---RTSF---AGQ----------SQDLAIRVQGFKDYLVGSLQDLAQS 66 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH---Hccc---ccc----------hHHHHHHHhhhHHHHHHHHHHHHHH
Confidence 5899999999999999999999999998 4565 232 2334445567788888888766554
No 44
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=60.73 E-value=10 Score=46.59 Aligned_cols=44 Identities=23% Similarity=0.449 Sum_probs=40.8
Q ss_pred HHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhc
Q 048159 635 VAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRV 681 (840)
Q Consensus 635 v~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRl 681 (840)
+.+|++.|.. ++.|+.+|...+|.+.||...-|+.||.+.+...
T Consensus 568 ~sllkayyal---n~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYAL---NGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 7788999888 9999999999999999999999999999988754
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=53.35 E-value=17 Score=27.42 Aligned_cols=46 Identities=24% Similarity=0.256 Sum_probs=35.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhcc
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVW 682 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlk 682 (840)
.||+....++...+.+. -.-.++|..+|++...|..|....+.+++
T Consensus 10 ~l~~~~~~~~~~~~~~~--------~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGEG--------LSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 36777778887776542 24577899999999999999988887764
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=45.65 E-value=48 Score=22.13 Aligned_cols=38 Identities=18% Similarity=0.233 Sum_probs=26.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhcc
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWF 674 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWF 674 (840)
.++.+....+..++.+ .+ ....+|+.+|++...|.+|.
T Consensus 5 ~~~~~~~~~i~~~~~~----~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA----GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHhC
Confidence 4666665555555433 33 45688999999999999984
No 47
>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=44.10 E-value=30 Score=29.34 Aligned_cols=46 Identities=22% Similarity=0.308 Sum_probs=30.1
Q ss_pred CCCCCCChHHHH-HHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhh
Q 048159 625 RPQRGLPERAVA-ILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINAR 678 (840)
Q Consensus 625 RkrR~Lpk~av~-iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaR 678 (840)
++++.|+++.+. +++..+.. ......+|++.|++..+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~--------g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES--------GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH--------HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC--------CCceEeeecccccccccccHHHHHHh
Confidence 356778887754 44444333 36889999999999999999987766
No 48
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=37.95 E-value=29 Score=33.10 Aligned_cols=52 Identities=25% Similarity=0.228 Sum_probs=41.3
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
.||+....++.--+++. .+ -.++|..+|++...|.+.+.-+|.++++.+.++
T Consensus 106 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 157 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE--KS------YQEIALQEKIEVKTVEMKLYRARKWIKKHWKEE 157 (160)
T ss_pred hCCHHHHHHHHHHHHhC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhhh
Confidence 48999888887665552 22 258999999999999999999999998776543
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=37.73 E-value=29 Score=27.74 Aligned_cols=47 Identities=28% Similarity=0.391 Sum_probs=36.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccc
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkK 683 (840)
.||++...+|..-|++ ++ .-.++|...|++...|+.+...+..++++
T Consensus 4 ~L~~~er~vi~~~y~~----~~----t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----GL----TLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T-----SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----CC----CHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 4788888888877644 33 35789999999999999999999888763
No 50
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=35.68 E-value=30 Score=28.45 Aligned_cols=34 Identities=24% Similarity=0.244 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 655 DKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 655 EK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
....||+.+|+++..|+.|+.+...++.-..++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ 45 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEK 45 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHH
Confidence 5678999999999999999998754444444443
No 51
>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=33.65 E-value=48 Score=30.88 Aligned_cols=48 Identities=25% Similarity=0.234 Sum_probs=37.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccch
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKP 684 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKp 684 (840)
.||++...+|.-.+.+ .+| -.++|+.+|++...|.++...+|+++++.
T Consensus 113 ~L~~~~r~il~l~~~~----~~~----~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 113 KLPEQCRKIFILSRFE----GKS----YKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred HCCHHHHHHHHHHHHc----CCC----HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5788888888765544 343 35699999999999999999999988764
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=32.27 E-value=40 Score=31.82 Aligned_cols=47 Identities=19% Similarity=0.125 Sum_probs=38.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccc
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkK 683 (840)
.||+....++..-+++. + .-.++|..+|++...|.+|...+|.++++
T Consensus 106 ~L~~~~r~ii~l~~~~~----~----s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG----K----TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 58888888886555542 2 35789999999999999999999999875
No 53
>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=32.03 E-value=46 Score=29.97 Aligned_cols=48 Identities=25% Similarity=0.291 Sum_probs=36.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccch
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKP 684 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKp 684 (840)
.||+....++..-+.. .+ ...++|+.+|+++..|.+|...++.++++.
T Consensus 110 ~L~~~~~~ii~~~~~~----g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 110 KLPEREREVLVLRYLE----GL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred hCCHHHHHHHhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5677777776433333 34 446899999999999999999999888753
No 54
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=31.89 E-value=41 Score=32.44 Aligned_cols=52 Identities=15% Similarity=0.093 Sum_probs=42.2
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 628 RGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 628 R~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
..||+....++.-.+.++ + .-.++|..+|++...|.+|..-+|+++++-+.+
T Consensus 107 ~~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE----L----TYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred HhCCHHHHHHHHhHHHhc----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 458999999998777664 2 346899999999999999999999998775533
No 55
>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=31.48 E-value=50 Score=26.53 Aligned_cols=45 Identities=27% Similarity=0.351 Sum_probs=32.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhc
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRV 681 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRl 681 (840)
.||+....++.--+.+. + .-.++|..+|++..-|.+|...+|+++
T Consensus 10 ~L~~~~r~i~~l~~~~g----~----s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG----M----SYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHHTS-----------HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC----c----CHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 47888877776655442 3 457899999999999999999998874
No 56
>cd00131 PAX Paired Box domain
Probab=29.06 E-value=1.7e+02 Score=28.45 Aligned_cols=48 Identities=17% Similarity=0.100 Sum_probs=33.3
Q ss_pred CCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCC-------ChhhHhhccchh
Q 048159 627 QRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGL-------SRNQVSNWFINA 677 (840)
Q Consensus 627 rR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGL-------S~kQVsNWFiNa 677 (840)
++.+..+....+..+..+ +|.-|..|...+-...|+ +...|+.||.++
T Consensus 73 pr~~~~~~~~~i~~~v~~---~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 73 PRVATPEVVKKIEIYKQE---NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCcCCHHHHHHHHHHHHH---CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 334555565666667677 898888777666345677 899999987653
No 57
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.47 E-value=56 Score=32.03 Aligned_cols=51 Identities=14% Similarity=0.097 Sum_probs=41.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
.||++...++.--+++. . .-.++|..+|++...|.+++..+|.++++.+..
T Consensus 131 ~L~~~~r~v~~l~~~~g--~------s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG--A------SIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred hCCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 58899999988766552 2 347899999999999999999999999876543
No 58
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=28.14 E-value=60 Score=30.89 Aligned_cols=51 Identities=16% Similarity=0.161 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhH
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVE 687 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmie 687 (840)
.||+..+.++..-+.+ -+ .-.++|...|++...|.+|..-+|.++++.+..
T Consensus 125 ~L~~~~r~i~~l~~~~----~~----~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 125 ALPVKQREVFLLRYVE----GL----SYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred hCCHHHHHHhhHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4788888887655444 23 347899999999999999999999999876544
No 59
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=28.05 E-value=62 Score=31.59 Aligned_cols=48 Identities=17% Similarity=0.259 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccch
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKP 684 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKp 684 (840)
.||++...++...+++ .+ .-.++|..+|++...|.+++..+|+++++-
T Consensus 129 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLE----GL----SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 4888999888888776 23 246899999999999999999999998764
No 60
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=26.38 E-value=51 Score=32.87 Aligned_cols=49 Identities=8% Similarity=0.103 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||+..+.+|.--+++. + .-.++|+.+|++...|.+++..+|+++++-+
T Consensus 142 ~L~~~~r~vl~l~~~~~----~----s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG----L----TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 58999998887665553 2 3468999999999999999999999987654
No 61
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=25.65 E-value=3.2e+02 Score=31.10 Aligned_cols=96 Identities=23% Similarity=0.288 Sum_probs=60.1
Q ss_pred CCCCCchhHHHHHHHHHhhhh-HHHHHHHHHHHHHHHHhccccccCccccCCCCCCccccccccchhhhhhhhccCCCCC
Q 048159 535 GLSGATPYVSLAFKAISKNFR-CLKSAIMNQLKHVAKALGEEMRSSATVTSSSRGHITNTSAKLNCLDQILQKHKSGGAN 613 (840)
Q Consensus 535 G~gaA~pYt~lAlKamSRhFr-~LrnaI~~QL~~~~k~lgEd~~~~~~~~~~s~Gd~~~~s~Rlr~lDQ~lrk~~sg~~~ 613 (840)
.+++.++-++|+|..|.|+|. .+-+.+.+++-.-. .+.+++
T Consensus 164 T~aG~~a~iDl~L~lI~~~~G~~~a~~va~~lv~~~-------------------------------------~R~~~~- 205 (328)
T COG4977 164 TCAGGTAAIDLMLALIRRDFGAALANRVARQLVVDP-------------------------------------IRSGGD- 205 (328)
T ss_pred EcCCchHHHHHHHHHHHHHhCHHHHHHHHHHhhhcc-------------------------------------ccCCCc-
Confidence 455566678999999999998 77777777773200 000000
Q ss_pred CCccCCcCCcCCCCCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchh
Q 048159 614 VGFLEPQQHVWRPQRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINA 677 (840)
Q Consensus 614 lg~Le~~~~~kRkrR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNa 677 (840)
. +......+.+-....+..+-.|+..|...|. ..+.||+..||+..|+.-=|...
T Consensus 206 ~-----Q~~~~~~~~~~~~~~l~~~i~~me~nle~pl----sl~~LA~~~~~S~R~leRlF~~~ 260 (328)
T COG4977 206 R-----QRLPLLGRLGHRDPRLLRAIELMEANLEEPL----SLEELADRAGLSRRQLERLFRAE 260 (328)
T ss_pred c-----ccccccccCCCCCHHHHHHHHHHHHhhcCCc----CHHHHHHHhCCCHHHHHHHHHHH
Confidence 0 0111222333223334444579999999997 45779999999999987665543
No 62
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=25.64 E-value=59 Score=31.02 Aligned_cols=50 Identities=18% Similarity=0.171 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
.||+....+|..-+++ -+ .-.++|+.+|++...|.+|...+|+++++-+.
T Consensus 128 ~L~~~~r~vl~l~~~~----~~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 128 SLPEELRTAITLREIE----GL----SYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4788888888654443 13 23579999999999999999999999987653
No 63
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=24.90 E-value=56 Score=31.34 Aligned_cols=47 Identities=21% Similarity=0.167 Sum_probs=38.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccc
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkK 683 (840)
.||+.+..++.-.+.+. + .-.++|..+|++...|..+...+|.++++
T Consensus 112 ~L~~~~r~v~~l~~~~~----~----s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG----F----SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 58998988887765553 3 23679999999999999999999999875
No 64
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=24.05 E-value=61 Score=32.85 Aligned_cols=49 Identities=20% Similarity=0.274 Sum_probs=39.7
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||++...+|..-+++. + .-.++|..+|++...|.+++..+|+++++-+
T Consensus 153 ~L~~~~r~vl~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE----L----SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48899988887655552 2 3468999999999999999999999987655
No 65
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=23.89 E-value=1.5e+02 Score=22.81 Aligned_cols=51 Identities=20% Similarity=0.215 Sum_probs=36.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
.|++....++..+ .. .+ ...++|+.+|++...|..|....+.++.-....+
T Consensus 3 ~l~~~e~~i~~~~-~~----g~----s~~eia~~l~is~~tv~~~~~~~~~kl~~~~~~~ 53 (58)
T smart00421 3 SLTPREREVLRLL-AE----GL----TNKEIAERLGISEKTVKTHLSNIMRKLGVRSRTQ 53 (58)
T ss_pred CCCHHHHHHHHHH-Hc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHH
Confidence 4777777777543 32 22 4578999999999999999998888776544433
No 66
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=23.88 E-value=71 Score=33.53 Aligned_cols=49 Identities=18% Similarity=0.246 Sum_probs=40.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||+..+.+|.-.|++. + .-.++|..+|++...|.+|...+|+++++.+
T Consensus 205 ~L~~~~r~vl~l~~~~g----~----s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN----L----SQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 58999999988776652 2 2378999999999999999999999987644
No 67
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.52 E-value=62 Score=32.17 Aligned_cols=50 Identities=18% Similarity=0.221 Sum_probs=40.2
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
.||++.+.++.-.+.+. .+ -.++|..+|++...|.+...-+|.++++..+
T Consensus 131 ~L~~~~r~i~~l~~~~g--~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG--EK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred hCCHHHHHHHHHHHHcc--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 58999999998665552 22 3689999999999999999999999877543
No 68
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.90 E-value=65 Score=31.31 Aligned_cols=49 Identities=14% Similarity=0.164 Sum_probs=38.1
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||+..+.++..-+++ .+ .-.++|..+|++...|.+++..+|+++++-+
T Consensus 136 ~L~~~~r~v~~l~~~~----g~----s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME----DL----SLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred hCCHHHhHHhhhHHhc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5888888888664443 13 3478999999999999999999999887643
No 69
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=22.88 E-value=1.4e+02 Score=27.81 Aligned_cols=54 Identities=24% Similarity=0.190 Sum_probs=42.2
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHhh
Q 048159 628 RGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEIH 690 (840)
Q Consensus 628 R~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~~ 690 (840)
..|++...++|+-+ .++ |. ..++|+..+++.+-|.++..+.|+++.-.-..++.
T Consensus 148 ~~lt~~e~~vl~l~-~~g----~~----~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~l~ 201 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG----YT----NRDIAEQLSISIKTVETHRLNMMRKLDVHKVAELL 201 (211)
T ss_pred cCCCHHHHHHHHHH-HCC----CC----HHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHH
Confidence 34899999999875 342 32 47899999999999999999999998755555543
No 70
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.80 E-value=67 Score=31.09 Aligned_cols=49 Identities=12% Similarity=0.020 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||+..+.++.-.+.+. + .-.++|..+|++...|.++..-+|+++++-+
T Consensus 112 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 112 LLSADQREAIILIGASG----F----SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58999998887776663 2 2468999999999999999999999987543
No 71
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=22.79 E-value=68 Score=31.65 Aligned_cols=49 Identities=20% Similarity=0.140 Sum_probs=40.1
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||+..+.++..-+++. + .-.++|..+|++..-|.++...+|.++++.+
T Consensus 139 ~L~~~~r~i~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVVG----L----SAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 58999988887766552 2 3578999999999999999999999988654
No 72
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=22.74 E-value=92 Score=31.34 Aligned_cols=51 Identities=27% Similarity=0.220 Sum_probs=40.2
Q ss_pred CCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 627 QRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 627 rR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
...|++.++.+|+. +.+ .+ .-.++|..+|++...|++|...+|.++++-..
T Consensus 4 ~~~Lt~rqreVL~l-r~~----Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRL-RER----GL----TQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHH-HHc----CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34689999999976 333 33 45689999999999999999999988776543
No 73
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=22.55 E-value=61 Score=32.03 Aligned_cols=50 Identities=16% Similarity=0.240 Sum_probs=39.5
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
.||++...++.--+++. + .-.++|..+|++..-|.+|+..+|+++++-+.
T Consensus 141 ~L~~~~~~v~~l~~~~g----~----s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 141 QLPESQRQVLELAYYEG----L----SQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred hCCHHHhhhhhhhhhcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 57888888886555442 2 34689999999999999999999999987654
No 74
>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=22.42 E-value=69 Score=31.23 Aligned_cols=49 Identities=16% Similarity=0.122 Sum_probs=38.9
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||++.+.++.--++++ + .-.++|..+|++...|.++.-.+|+++++-+
T Consensus 138 ~L~~~~r~v~~l~~~~~----~----s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLRELEG----L----SYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhhcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 57888888886554442 2 3478999999999999999999999988765
No 75
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.26 E-value=1.1e+02 Score=30.67 Aligned_cols=53 Identities=9% Similarity=0.199 Sum_probs=42.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEI 689 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~ 689 (840)
.||+..+.++.--+++. + .-.++|..+|++..-|.++..-+|+++++-+.+..
T Consensus 134 ~Lp~~~R~v~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~ 186 (189)
T PRK12530 134 HLPAQQARVFMMREYLE----L----SSEQICQECDISTSNLHVLLYRARLQLQACLSKNW 186 (189)
T ss_pred hCCHHHHHHHhHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58888888887665552 2 34789999999999999999999999998776544
No 76
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=22.12 E-value=73 Score=31.81 Aligned_cols=53 Identities=21% Similarity=0.244 Sum_probs=41.5
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 628 RGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 628 R~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
..||++...++.--+++. .+ -.++|..+|++...|.+.+..+|+++++-+-+|
T Consensus 140 ~~Lp~~~r~v~~l~~~eg--~s------~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~~~ 192 (194)
T PRK12531 140 DRLPKAQRDVLQAVYLEE--LP------HQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAE 192 (194)
T ss_pred HhCCHHHHHHHHHHHHcC--CC------HHHHHHHhCcCHHHHHHHHHHHHHHHHHHhhhc
Confidence 458999999987655552 23 368999999999999999999999988765544
No 77
>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=22.00 E-value=71 Score=31.10 Aligned_cols=48 Identities=17% Similarity=0.160 Sum_probs=39.6
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccch
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKP 684 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKp 684 (840)
.||++...++.-.+++. + .-.++|..+|++..-|.+.+..+|.++++-
T Consensus 134 ~Lp~~~r~v~~l~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAG----L----TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred cCCHHHHHHHHHHHHcC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 38999999988777663 2 236899999999999999999999998764
No 78
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=21.90 E-value=75 Score=33.31 Aligned_cols=49 Identities=20% Similarity=0.197 Sum_probs=40.2
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||+..+.++...|++. + .-.++|..+|++...|+.+...++.++++-|
T Consensus 205 ~L~~~~r~ii~l~~~~g----~----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN----L----SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred cCCHHHHHHHHHHHcCC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 58999988887776653 2 2368999999999999999999999988654
No 79
>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=21.43 E-value=68 Score=31.00 Aligned_cols=49 Identities=10% Similarity=0.130 Sum_probs=39.2
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||++...++..-+++. + .-..+|..+|++...|.++..-+|.++++-+
T Consensus 119 ~L~~~~r~i~~l~~~~g----~----s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD----L----TIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred hCCHHHhHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 47888888887666652 2 2367999999999999999999999988754
No 80
>PRK04217 hypothetical protein; Provisional
Probab=21.39 E-value=97 Score=29.97 Aligned_cols=52 Identities=21% Similarity=0.197 Sum_probs=41.5
Q ss_pred CCCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 627 QRGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 627 rR~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
-..|+++.+.++..++++.+ .-.++|+.+|++..-|.+.+..+|.+++.-+.
T Consensus 40 ~~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 33588888988888876632 45679999999999999999999888866543
No 81
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.70 E-value=70 Score=31.50 Aligned_cols=50 Identities=20% Similarity=0.092 Sum_probs=39.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMV 686 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmi 686 (840)
.||+....++.--+.+. + .-.++|+.+|++...|.+.+..+|+++++.+.
T Consensus 129 ~L~~~~r~v~~l~~~~g----~----s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~ 178 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG----L----SVAETAQLTGLSESAVKVGIHRGLKALAAKIR 178 (181)
T ss_pred HCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 47888887766554442 2 34789999999999999999999999987553
No 82
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=20.63 E-value=89 Score=33.22 Aligned_cols=53 Identities=23% Similarity=0.383 Sum_probs=43.7
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEI 689 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~ 689 (840)
.||+..+.++.-.+++. + .-.++|..+|++..-|.++...+|+++++.+..+.
T Consensus 161 ~Lp~~~R~v~~L~~~eg----~----S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~ 213 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG----L----SMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRL 213 (244)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58999888887776663 2 23689999999999999999999999998876654
No 83
>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=20.62 E-value=71 Score=30.47 Aligned_cols=49 Identities=22% Similarity=0.317 Sum_probs=38.7
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPM 685 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpm 685 (840)
.||+..+.++..-+++ .+ .-.++|..+|++...|.++...+|.++++-+
T Consensus 110 ~L~~~~r~i~~l~~~~----g~----s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE----DL----SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred hCCHHHHHHhhhHHHh----cC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 5788888888665554 23 2367899999999999999999999988654
No 84
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=20.46 E-value=87 Score=31.14 Aligned_cols=52 Identities=13% Similarity=0.187 Sum_probs=41.0
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHH
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEE 688 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee 688 (840)
.||+..+.++.-.+++. + .-.++|..+|++..-|.++...+|+++++-+...
T Consensus 136 ~L~~~~r~i~~L~~~~g----~----s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 187 (195)
T PRK12532 136 NLPENTARVFTLKEILG----F----SSDEIQQMCGISTSNYHTIMHRARESLRQCLQIK 187 (195)
T ss_pred hCCHHHHHHhhhHHHhC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 57888888887554442 2 3468999999999999999999999998876433
No 85
>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=20.33 E-value=1.1e+02 Score=28.82 Aligned_cols=48 Identities=29% Similarity=0.291 Sum_probs=37.9
Q ss_pred CCCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccc
Q 048159 628 RGLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWK 683 (840)
Q Consensus 628 R~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkK 683 (840)
..||++...++..-+++ .+ .-.++|..+|++...|.++..-+|+++++
T Consensus 110 ~~L~~~~r~v~~l~~~~----g~----~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQR----GV----SLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHhc----CC----CHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 35888888888774444 23 34679999999999999999999988875
No 86
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=20.12 E-value=1.3e+02 Score=29.83 Aligned_cols=53 Identities=11% Similarity=0.113 Sum_probs=42.4
Q ss_pred CCChHHHHHHHHHHHHccCCCCCCHHHHHHHHHHhCCChhhHhhccchhhhhccchhhHHh
Q 048159 629 GLPERAVAILRAWLFEHFLHPYPTDTDKHMLATQTGLSRNQVSNWFINARVRVWKPMVEEI 689 (840)
Q Consensus 629 ~Lpk~av~iLr~WL~eH~~nPYPS~eEK~~LA~qTGLS~kQVsNWFiNaRrRlkKpmiee~ 689 (840)
.||++.+.++.-.+++. .+ -.++|..+|++..-|.+....+|+++++-+..+-
T Consensus 131 ~Lp~~~r~v~~l~~~~g--~s------~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE--LE------TEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred hCCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 48888888887766652 22 3689999999999999999999999987665543
Done!