Query 001086
Match_columns 1159
No_of_seqs 380 out of 1564
Neff 4.9
Searched_HMMs 46136
Date Thu Mar 28 15:26:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001086.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001086hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1473 Nucleosome remodeling 100.0 1.8E-34 4E-39 346.3 18.0 299 364-869 179-482 (1414)
2 PF02791 DDT: DDT domain; Int 99.6 4E-16 8.7E-21 136.5 5.4 59 375-433 2-61 (61)
3 smart00571 DDT domain in diffe 99.5 1.4E-14 3.1E-19 127.6 5.4 58 375-432 2-62 (63)
4 KOG0484 Transcription factor P 99.3 2.5E-13 5.4E-18 128.4 1.3 57 2-58 20-76 (125)
5 KOG0843 Transcription factor E 99.2 2E-12 4.2E-17 133.1 2.1 58 2-59 105-162 (197)
6 KOG0489 Transcription factor z 99.2 2.3E-12 5.1E-17 142.5 1.4 58 2-59 162-219 (261)
7 KOG0488 Transcription factor B 99.2 2.7E-12 5.8E-17 144.8 1.9 57 2-58 175-231 (309)
8 KOG2251 Homeobox transcription 99.2 9.2E-12 2E-16 132.0 5.4 59 1-59 39-97 (228)
9 KOG0850 Transcription factor D 99.2 5.9E-12 1.3E-16 133.9 1.8 57 3-59 126-182 (245)
10 KOG0842 Transcription factor t 99.2 3.5E-11 7.6E-16 134.4 7.4 56 3-58 157-212 (307)
11 KOG0487 Transcription factor A 99.1 3E-11 6.5E-16 135.0 2.7 56 3-58 239-294 (308)
12 KOG0492 Transcription factor M 99.1 3.2E-11 6.8E-16 126.4 2.3 57 3-59 148-204 (246)
13 KOG0494 Transcription factor C 99.1 4.6E-11 1E-15 128.3 3.3 57 2-58 144-200 (332)
14 KOG0485 Transcription factor N 99.1 3.4E-11 7.3E-16 126.8 0.8 57 2-58 107-163 (268)
15 PF00046 Homeobox: Homeobox do 99.1 2.9E-11 6.3E-16 103.4 0.3 55 2-56 3-57 (57)
16 KOG0848 Transcription factor C 99.0 5.2E-11 1.1E-15 128.6 0.4 57 3-59 203-259 (317)
17 KOG0493 Transcription factor E 98.9 2.7E-10 5.8E-15 122.6 2.2 57 3-59 250-306 (342)
18 PF15613 WHIM2: WSTF, HB1, Itc 98.9 8.5E-10 1.8E-14 88.2 4.2 35 787-821 1-35 (38)
19 KOG0844 Transcription factor E 98.9 4.5E-10 9.7E-15 123.0 2.7 63 3-65 185-247 (408)
20 smart00389 HOX Homeodomain. DN 98.9 7.5E-10 1.6E-14 93.8 2.5 54 2-55 3-56 (56)
21 KOG0491 Transcription factor B 98.9 2.8E-10 6E-15 115.8 -1.0 57 3-59 104-160 (194)
22 TIGR01565 homeo_ZF_HD homeobox 98.9 2.8E-09 6E-14 92.9 5.2 50 2-51 4-57 (58)
23 KOG0483 Transcription factor H 98.9 8.7E-10 1.9E-14 117.2 2.2 56 3-58 54-109 (198)
24 cd00086 homeodomain Homeodomai 98.8 1.1E-09 2.3E-14 93.5 2.0 56 2-57 3-58 (59)
25 KOG0486 Transcription factor P 98.8 1.4E-09 2.9E-14 120.3 2.5 57 2-58 115-171 (351)
26 PF15614 WHIM3: WSTF, HB1, Itc 98.8 3.4E-09 7.4E-14 87.7 4.2 36 827-862 1-37 (46)
27 COG5576 Homeodomain-containing 98.8 2.3E-09 5E-14 110.4 2.9 58 2-59 54-111 (156)
28 KOG0847 Transcription factor, 98.7 5.2E-09 1.1E-13 110.5 1.3 57 3-59 171-227 (288)
29 KOG4577 Transcription factor L 98.5 4.1E-08 8.8E-13 107.3 2.0 56 3-58 171-226 (383)
30 KOG0490 Transcription factor, 98.5 6.8E-08 1.5E-12 103.6 2.4 57 2-58 63-119 (235)
31 KOG3802 Transcription factor O 98.4 2E-07 4.4E-12 106.7 5.5 56 3-58 298-353 (398)
32 KOG1245 Chromatin remodeling c 98.4 1.2E-07 2.7E-12 124.0 2.0 75 776-857 812-936 (1404)
33 KOG0849 Transcription factor P 98.1 9.7E-07 2.1E-11 102.1 2.2 58 2-59 179-236 (354)
34 KOG0775 Transcription factor S 97.7 1.7E-05 3.8E-10 87.1 3.3 49 8-56 185-233 (304)
35 PF05066 HARE-HTH: HB1, ASXL, 97.6 2.4E-05 5.2E-10 70.6 1.7 67 515-583 1-71 (72)
36 PF15612 WHIM1: WSTF, HB1, Itc 97.5 9.3E-05 2E-09 62.4 3.3 41 656-696 3-43 (50)
37 KOG1168 Transcription factor A 97.4 5.9E-05 1.3E-09 83.3 2.0 56 3-58 313-368 (385)
38 KOG0774 Transcription factor P 97.0 0.001 2.3E-08 72.9 6.2 57 3-59 192-251 (334)
39 PF05920 Homeobox_KN: Homeobox 96.8 0.00019 4.1E-09 58.5 -1.4 34 20-53 7-40 (40)
40 KOG2252 CCAAT displacement pro 96.6 0.002 4.3E-08 77.2 4.3 52 3-54 424-475 (558)
41 KOG0490 Transcription factor, 96.1 0.0023 5.1E-08 68.8 1.4 56 3-58 157-212 (235)
42 KOG1146 Homeobox protein [Gene 93.2 0.1 2.2E-06 68.4 5.3 56 3-58 907-962 (1406)
43 PF11569 Homez: Homeodomain le 84.0 0.29 6.3E-06 43.1 -0.3 42 11-52 10-51 (56)
44 PF13913 zf-C2HC_2: zinc-finge 79.7 1.2 2.5E-05 33.1 1.6 23 985-1012 3-25 (25)
45 KOG0773 Transcription factor M 79.0 1.3 2.8E-05 51.4 2.6 54 5-58 245-301 (342)
46 KOG3623 Homeobox transcription 71.6 2.5 5.4E-05 53.0 2.4 48 11-58 568-615 (1007)
47 PF12172 DUF35_N: Rubredoxin-l 61.9 2.3 5E-05 34.0 -0.3 25 969-993 10-34 (37)
48 COG2995 PqiA Uncharacterized p 46.3 11 0.00025 44.8 1.8 45 945-994 200-245 (418)
49 PRK15103 paraquat-inducible me 32.6 28 0.00061 42.2 2.3 50 945-994 193-245 (419)
50 TIGR02098 MJ0042_CXXC MJ0042 f 31.7 11 0.00025 30.0 -0.8 25 971-995 3-36 (38)
51 PF08209 Sgf11: Sgf11 (transcr 31.3 22 0.00048 28.5 0.8 27 984-1015 4-30 (33)
52 COG5242 TFB4 RNA polymerase II 29.5 23 0.0005 39.5 0.8 32 964-995 254-285 (296)
53 KOG2891 Surface glycoprotein [ 29.2 49 0.0011 37.9 3.2 25 247-271 324-348 (445)
54 PF04218 CENP-B_N: CENP-B N-te 28.4 39 0.00084 29.3 1.9 44 2-50 3-46 (53)
55 PF09862 DUF2089: Protein of u 27.4 18 0.00038 36.5 -0.5 28 973-1000 1-28 (113)
56 PLN00180 NDF6 (NDH-dependent f 26.5 91 0.002 33.1 4.4 38 822-868 134-171 (180)
57 KOG4364 Chromatin assembly fac 26.5 60 0.0013 41.2 3.6 9 836-844 719-727 (811)
58 PF00096 zf-C2H2: Zinc finger, 26.3 23 0.0005 24.8 0.1 21 986-1010 2-22 (23)
59 PRK13130 H/ACA RNA-protein com 25.7 35 0.00075 30.5 1.1 41 969-1011 4-48 (56)
60 KOG3926 F-box proteins [Amino 24.8 35 0.00076 39.1 1.2 37 949-986 270-307 (332)
61 COG2093 DNA-directed RNA polym 24.8 37 0.0008 30.9 1.1 23 972-994 6-29 (64)
62 COG3909 Cytochrome c556 [Energ 24.0 19 0.00041 37.3 -1.0 15 933-947 89-103 (147)
63 COG2956 Predicted N-acetylgluc 23.2 30 0.00066 40.7 0.3 28 667-694 98-126 (389)
64 KOG2412 Nuclear-export-signal 21.8 71 0.0015 39.8 3.0 71 261-331 216-292 (591)
65 TIGR00570 cdk7 CDK-activating 20.9 32 0.00068 40.2 -0.1 24 972-995 30-54 (309)
66 PF05071 NDUFA12: NADH ubiquin 20.6 82 0.0018 31.2 2.7 16 789-804 2-17 (105)
67 KOG1832 HIV-1 Vpr-binding prot 20.2 92 0.002 41.0 3.6 16 519-534 1339-1354(1516)
68 COG1245 Predicted ATPase, RNas 20.1 48 0.001 40.9 1.1 106 468-579 130-243 (591)
No 1
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=100.00 E-value=1.8e-34 Score=346.28 Aligned_cols=299 Identities=23% Similarity=0.262 Sum_probs=224.6
Q ss_pred CCCCCCCCCChhHHHhHHHHHHHHhhccccccccCCCHHHHHHHhc-cCCcchHHHHHHHHHHHHHhhhhhhhcCCCCCC
Q 001086 364 PFGTQPWDSSPETVKKLFKVFHFLCTYAGIVDICSFTLDEFAQAFH-DKDSMLLGKIHVALLKLLLSDVEMELGRGCPPH 442 (1159)
Q Consensus 364 p~~~~p~~~s~e~V~~LL~Vw~FL~~F~~vL~L~pFTlDDFv~Al~-d~ds~LL~EIH~aLLk~ii~d~Ed~~~~~~~~~ 442 (1159)
|-+.....++.++|.++|+||+|||+|+.+|.|+||+|+|||+||. ..+|.||+||||||||+|+++ ||..++.+++.
T Consensus 179 P~SSedi~IPne~Vm~alsIYevLRsF~~~LrisPF~feDFcaAL~~~~~ssLlaeVHvaLLrA~lr~-eD~~~Thfs~~ 257 (1414)
T KOG1473|consen 179 PESSEDIGIPNEHVMDALSIYEVLRSFSRQLRISPFRFEDFCAALISHEQSSLLAEVHVALLRALLRE-EDRLSTHFSPL 257 (1414)
T ss_pred CCcccccCCcHHHHHHHHHHHHHHHhhcceEEeCCccHHHHHHHHHhcCchhHHHHHHHHHHHHHhhh-hhhcccccCcc
Confidence 3333444455799999999999999999999999999999999998 899999999999999999999 78888888887
Q ss_pred CCcchhhhhhhhhhcchhhhhHhhhhcCCCCcHHHHHHHHHHHhcC--CCCccchhhhhhhHHHHHHHhhccccccchhh
Q 001086 443 LSVSCKFLALLHSVENQEFFVEFWNKSLNPLTWTEILRQVLVAAGF--GSKQGSSRKESLSKEMILMLKYGLRPGTLKGE 520 (1159)
Q Consensus 443 ~~~~~~~~~~~~~v~~~~~~i~~w~~~Ln~lTWpEiLrq~~~~aG~--gp~~~~~~~~~~~~~~~~m~~~~L~pgTvK~a 520 (1159)
..+++ |+.- -.++|.||||||||||+-|.|+ ||.|..++.
T Consensus 258 d~Kds--------vnI~-------l~liD~lTWPevLrqY~ea~~~ad~~v~~~~n~----------------------- 299 (1414)
T KOG1473|consen 258 DSKDS--------VNID-------LYLIDTLTWPEVLRQYFEADKHADGPVWDIFNP----------------------- 299 (1414)
T ss_pred ccccc--------eeee-------eehhccccHHHHHHHHHHhccccCcchhhhhcc-----------------------
Confidence 77776 3432 2458899999999999988766 555543220
Q ss_pred HHHHHHhhCCCCCchhHhhhhhhhhhhccccchHHHHHhhhhccccchhhhhhhccccceeccccCCCcCccCCcccccC
Q 001086 521 LFRILLEQGNNGSKVCQLARSSQIAELNLESTTEEVELLISSTLSSDITLFEKIASSTYRLRINTSKEADDFESDAEDIG 600 (1159)
Q Consensus 521 af~vLs~~g~~gl~v~e~a~~iQk~~lr~l~tsk~~ea~i~~~LsrD~~LFer~apsty~vr~~~~k~~~d~esd~ed~~ 600 (1159)
T Consensus 300 -------------------------------------------------------------------------------- 299 (1414)
T KOG1473|consen 300 -------------------------------------------------------------------------------- 299 (1414)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCCCCCCCCCCCCCCCCcccccccccccccccccccccccccccccccccccccccccccccccCCCCCCHHHHHHHHH
Q 001086 601 SVDDNSDDDDTCSNRDDSECNSENQRQRRPKYLNCCKSENNMLTVYMEIDESHRGDVWLSGLMEGEYSDLTIDEKLNALV 680 (1159)
Q Consensus 601 ~vded~d~~~~~~~~~~~e~~~~~~~~~~~~~~~~~K~~~~~~~~~~eIDEs~~ge~wl~~L~egeY~dLsiEERL~aLv 680 (1159)
=+.+.+|....|+.||++|.
T Consensus 300 ------------------------------------------------------------fv~~~eY~~~pv~~klkILQ 319 (1414)
T KOG1473|consen 300 ------------------------------------------------------------FVVEDEYPYRPVSNKLKILQ 319 (1414)
T ss_pred ------------------------------------------------------------ccccccccccchhhhHHHHH
Confidence 02345899999999999999
Q ss_pred HHHhhhccCCcccccchhhhhhhc--cccccccCccccccccCccccCCCCCCCCCCCCCCCccccccccCCCCCChhhh
Q 001086 681 GLIDLVSAGSSIRMEDPTKAIAES--VPSVRHYGSGAKIKRALPNQHSLPRPSWVHAGDFHGVRETNTSRELHPLDSFSL 758 (1159)
Q Consensus 681 aL~~l~l~g~sIR~~d~~r~~~E~--~~k~~~~~~~~~~K~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~p~e~~~~ 758 (1159)
+||++++..+++|.+...+-.-+. .=|.. + ......+. -+++.+.+.+|+.+ +.+.+....+
T Consensus 320 ~L~Dq~l~~~s~R~e~~se~~~~~ddhcrf~-~---------d~~~~lc~----Et~prvvhlEcv~h--P~~~~~s~~~ 383 (1414)
T KOG1473|consen 320 FLCDQFLTVNSLRDEIDSEGEIEYDDHCRFC-H---------DLGDLLCC----ETCPRVVHLECVFH--PRFAVPSAFW 383 (1414)
T ss_pred HHHHHHHHHHHHHHHHhcccceeeccccccc-C---------cccceeec----ccCCceEEeeecCC--ccccCCCccc
Confidence 999999999999993221100000 00000 0 00000000 11244445555544 4455666778
Q ss_pred hhhhcccccccchhhHhhhhhhhhcCCcccccCcccCCCCeeEEEeCCCCCCCCCCcceEEecCCCCcEEEecCHHHHHH
Q 001086 759 ISKSCGKEKSSSVKDAKATEVSTDLHPMQSIYLGSDRRYNRYWLFLGPCNEYDPGHKRVYFESSEDGHWEVIDTEEALRA 838 (1159)
Q Consensus 759 ~~~~~~~ek~~~~~krEe~~~a~e~~~~R~~pLG~DR~~nRYW~F~~~~~~~dp~~grifVE~~~~g~W~~ydt~eeld~ 838 (1159)
++.+|..+|..+..+.- ....+....+|..|+|.||+++.||+.. +||+||+.+...-+||+|.-++..
T Consensus 384 e~evc~~hkvngvvd~v-l~~~K~~~~iR~~~iG~dr~gr~ywfi~----------rrl~Ie~~det~l~yysT~pqly~ 452 (1414)
T KOG1473|consen 384 ECEVCNIHKVNGVVDCV-LPPSKNVDSIRHTPIGRDRYGRKYWFIS----------RRLRIEGMDETLLWYYSTCPQLYH 452 (1414)
T ss_pred hhhhhhhhccCcccccc-cChhhcccceeccCCCcCccccchhcee----------eeeEEecCCCcEEEEecCcHHHHH
Confidence 88888777777655221 1112345558999999999999999998 899999988888889999999999
Q ss_pred HHHhhccCChhHHHHHHHHHHHHHHHHHHHh
Q 001086 839 LLSVLDDRGRQEALLIESLEKREAFLCQAMS 869 (1159)
Q Consensus 839 Ll~~Ld~rG~RE~~Lk~~L~~~~~~I~~~m~ 869 (1159)
||..|| |.+=|..|...|..+.+.|..+|.
T Consensus 453 ll~cLd-~~~~e~~L~d~i~~~~ee~~rqM~ 482 (1414)
T KOG1473|consen 453 LLRCLD-RTYVEMYLCDGIWERREEIIRQMG 482 (1414)
T ss_pred HHHHhc-hHHHHHhhccchhhhHHHHHHhcc
Confidence 999999 777799999999999999999995
No 2
>PF02791 DDT: DDT domain; InterPro: IPR004022 This domain is predicted to be a DNA binding domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors). It is found in foetal Alzheimer antigen and several hypothetical and uncharacterised proteins.
Probab=99.62 E-value=4e-16 Score=136.51 Aligned_cols=59 Identities=44% Similarity=0.672 Sum_probs=54.9
Q ss_pred hHHHhHHHHHHHHhhccccccccCCCHHHHHHHhc-cCCcchHHHHHHHHHHHHHhhhhh
Q 001086 375 ETVKKLFKVFHFLCTYAGIVDICSFTLDEFAQAFH-DKDSMLLGKIHVALLKLLLSDVEM 433 (1159)
Q Consensus 375 e~V~~LL~Vw~FL~~F~~vL~L~pFTlDDFv~Al~-d~ds~LL~EIH~aLLk~ii~d~Ed 433 (1159)
++++++||||+||++|+++|+|+|||||||++||. +.++.||+|||++||++|+++.||
T Consensus 2 ~~~~~~L~v~~Fl~~F~~~L~L~~ftlddf~~AL~~~~~~~ll~ei~~~LL~~l~~~~~d 61 (61)
T PF02791_consen 2 EAFGDLLMVWEFLNTFGEVLGLSPFTLDDFEQALLCNDPSGLLAEIHCALLKALLADEED 61 (61)
T ss_pred cHHHHHHHHHHHHHHHHHHHcCCcCCHHHHHHHHcCCCcchhHHHHHHHHHHHHHhccCC
Confidence 68999999999999999999999999999999998 555569999999999999999765
No 3
>smart00571 DDT domain in different transcription and chromosome remodeling factors.
Probab=99.51 E-value=1.4e-14 Score=127.64 Aligned_cols=58 Identities=29% Similarity=0.604 Sum_probs=54.0
Q ss_pred hHHHhHHHHHHHHhhccccccccCCC--HHHHHHHhc-cCCcchHHHHHHHHHHHHHhhhh
Q 001086 375 ETVKKLFKVFHFLCTYAGIVDICSFT--LDEFAQAFH-DKDSMLLGKIHVALLKLLLSDVE 432 (1159)
Q Consensus 375 e~V~~LL~Vw~FL~~F~~vL~L~pFT--lDDFv~Al~-d~ds~LL~EIH~aLLk~ii~d~E 432 (1159)
+.++++||||+||++|+++|+|+||| ||||++||+ ...+.||+|||++||++|++|.+
T Consensus 2 ~~~~d~l~V~eFl~~F~~~L~L~~f~~~l~~f~~Al~~~~~~~ll~ei~~~LL~~i~~d~~ 62 (63)
T smart00571 2 EAFGDLLMVYEFLRSFGKVLGLSPFRATLEDFIAALKCRDQNGLLTEVHVVLLRAILKDEG 62 (63)
T ss_pred cHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHhcCCcchHHHHHHHHHHHHHHhCCC
Confidence 68999999999999999999999999 999999998 55567999999999999999854
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.34 E-value=2.5e-13 Score=128.40 Aligned_cols=57 Identities=28% Similarity=0.437 Sum_probs=55.8
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
.||.||+.||..||+.|.+.+||++..|++||.++.|++.+|||||||||+|.|++.
T Consensus 20 IRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 20 IRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 589999999999999999999999999999999999999999999999999999987
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.24 E-value=2e-12 Score=133.09 Aligned_cols=58 Identities=28% Similarity=0.376 Sum_probs=56.1
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
.||.||++|+..||..|..++|....+|++||+.|+|++.||+|||||||.|.||.+.
T Consensus 105 ~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~ 162 (197)
T KOG0843|consen 105 IRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQ 162 (197)
T ss_pred cccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHH
Confidence 5899999999999999999999999999999999999999999999999999999873
No 6
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.22 E-value=2.3e-12 Score=142.46 Aligned_cols=58 Identities=33% Similarity=0.390 Sum_probs=56.2
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
.||.||..|+..||+.|..|+|.++..|.+||..|.|+++||+|||||||+||||...
T Consensus 162 ~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 162 RRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 5899999999999999999999999999999999999999999999999999999874
No 7
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.22 E-value=2.7e-12 Score=144.79 Aligned_cols=57 Identities=32% Similarity=0.382 Sum_probs=55.7
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
=||.||..|+..||+.|++++|.+..+|.+||+.|||+..||++||||||+||||+.
T Consensus 175 sRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred chhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 389999999999999999999999999999999999999999999999999999988
No 8
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.21 E-value=9.2e-12 Score=131.97 Aligned_cols=59 Identities=25% Similarity=0.385 Sum_probs=57.1
Q ss_pred CccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 1 MEVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 1 ~e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
.|||.||..|+.+||..|.+.+||+..+|++||.+++|++.+|+|||+|||+|+|+++.
T Consensus 39 RERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 39 RERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred cccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 48999999999999999999999999999999999999999999999999999999874
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.18 E-value=5.9e-12 Score=133.90 Aligned_cols=57 Identities=32% Similarity=0.409 Sum_probs=55.6
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
||.|+..||..|.+.|++++|.-..+|.+||+.|||+..||+|||||||.|.||.+.
T Consensus 126 RTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 126 RTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 899999999999999999999999999999999999999999999999999999874
No 10
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.17 E-value=3.5e-11 Score=134.40 Aligned_cols=56 Identities=29% Similarity=0.422 Sum_probs=54.1
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
|-.||..|+.+||+.|+.++|.+..+|+.||..|+||++||||||||||-|.||+.
T Consensus 157 RVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 157 RVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred ccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 45699999999999999999999999999999999999999999999999999987
No 11
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.10 E-value=3e-11 Score=135.00 Aligned_cols=56 Identities=32% Similarity=0.357 Sum_probs=54.2
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
|.-||..|+.+||+.|--|.|++...|.+|++.|+|+++||+|||||||+|.||..
T Consensus 239 RcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 239 RCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 56799999999999999999999999999999999999999999999999999987
No 12
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.09 E-value=3.2e-11 Score=126.38 Aligned_cols=57 Identities=28% Similarity=0.394 Sum_probs=55.4
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
||.||.+||..||+.|+..+|.++.+|.+++..|.|++.||+|||||||+|.||.+.
T Consensus 148 RtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 148 RTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 899999999999999999999999999999999999999999999999999999883
No 13
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.08 E-value=4.6e-11 Score=128.31 Aligned_cols=57 Identities=25% Similarity=0.340 Sum_probs=55.4
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
-||.||..|+..||+.|++.+||+...|+-||..+.|++.+|+|||||||+||||..
T Consensus 144 ~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~E 200 (332)
T KOG0494|consen 144 FRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTE 200 (332)
T ss_pred ccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhh
Confidence 389999999999999999999999999999999999999999999999999999987
No 14
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.06 E-value=3.4e-11 Score=126.77 Aligned_cols=57 Identities=30% Similarity=0.397 Sum_probs=55.4
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
-||.|+..|+..||..|....|.+..+|..||++|.|++.||+|||||||.||||+-
T Consensus 107 tRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 107 TRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred chhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 389999999999999999999999999999999999999999999999999999987
No 15
>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=99.05 E-value=2.9e-11 Score=103.38 Aligned_cols=55 Identities=42% Similarity=0.679 Sum_probs=53.0
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeecccccccccc
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKG 56 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR 56 (1159)
-|+.||.+|+..|+..|..++||+...+..||..+||+..+|++||+|||+++|+
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 4789999999999999999999999999999999999999999999999999875
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.02 E-value=5.2e-11 Score=128.63 Aligned_cols=57 Identities=32% Similarity=0.426 Sum_probs=54.2
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
|-+||..|.-+||+.|..++|+++..+.+||..|||+++||+|||||||+|+||.+.
T Consensus 203 RvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred eEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 457999999999999999999999999999999999999999999999999999873
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=98.94 E-value=2.7e-10 Score=122.56 Aligned_cols=57 Identities=30% Similarity=0.422 Sum_probs=55.3
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
||.||.+||..|...|+.+.|.+...|.+||.+|||.+.||+|||||+|+|.||..+
T Consensus 250 RTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 250 RTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred cccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 899999999999999999999999999999999999999999999999999999774
No 18
>PF15613 WHIM2: WSTF, HB1, Itc1p, MBD9 motif 2
Probab=98.93 E-value=8.5e-10 Score=88.21 Aligned_cols=35 Identities=29% Similarity=0.419 Sum_probs=30.9
Q ss_pred ccccCcccCCCCeeEEEeCCCCCCCCCCcceEEec
Q 001086 787 QSIYLGSDRRYNRYWLFLGPCNEYDPGHKRVYFES 821 (1159)
Q Consensus 787 R~~pLG~DR~~nRYW~F~~~~~~~dp~~grifVE~ 821 (1159)
|.+|||+||++||||||..+.+...+..+++|||.
T Consensus 1 R~~pLG~DR~~NrYwwf~~s~~~~~~~~~~~~v~~ 35 (38)
T PF15613_consen 1 RLKPLGKDRYGNRYWWFSSSSSNSQYYNGGRFVEQ 35 (38)
T ss_pred CcccccccCCCceEEEEecccccCCCCCceEEEEe
Confidence 78999999999999999766666778889999986
No 19
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=98.91 E-value=4.5e-10 Score=122.97 Aligned_cols=63 Identities=27% Similarity=0.319 Sum_probs=58.6
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCCCCCCCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNGIVIPSS 65 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~~~~~~~ 65 (1159)
||.||.+|+..||+.|-+..|.+...|.+||..|||++..|+|||||||+|+||+...+..|-
T Consensus 185 RTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPh 247 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPH 247 (408)
T ss_pred HhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCC
Confidence 789999999999999999999999999999999999999999999999999999996554443
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.88 E-value=7.5e-10 Score=93.84 Aligned_cols=54 Identities=37% Similarity=0.569 Sum_probs=51.3
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccc
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDK 55 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~K 55 (1159)
-+++|+..|+..|+..|..++||+...+..||..+||+..+|+.||+|||++.+
T Consensus 3 ~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 3 KRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 367899999999999999999999999999999999999999999999999864
No 21
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.86 E-value=2.8e-10 Score=115.76 Aligned_cols=57 Identities=30% Similarity=0.433 Sum_probs=55.4
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
||+|+..|+..|++.|+.+.|.+..+|.+||..|+|+++||+.||||||+|.||...
T Consensus 104 Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 104 RTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred cccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 899999999999999999999999999999999999999999999999999999873
No 22
>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=98.86 E-value=2.8e-09 Score=92.90 Aligned_cols=50 Identities=14% Similarity=0.307 Sum_probs=48.1
Q ss_pred ccccCCHHHHHHHHHhHhhCCC----CCHHHHHHHHHHcCCCCCceeeeccccc
Q 001086 2 EVKRKTPLQAKALLKFYSEEKY----PTKSEMEGLAAALDLTYKQVRTWFIEKR 51 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~Y----Ps~~~R~eLA~~LgLse~qVqVWFQNRR 51 (1159)
-||.||++|+..|+..|..++| |+...+.+||..+||++.+|+|||||-+
T Consensus 4 ~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 4 RRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4899999999999999999999 9999999999999999999999999964
No 23
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=98.85 E-value=8.7e-10 Score=117.25 Aligned_cols=56 Identities=34% Similarity=0.385 Sum_probs=54.1
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
..|||.+|+..||..|....|..+..+..||..|||.++||.|||||||||||.++
T Consensus 54 k~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 54 KRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 36899999999999999999999999999999999999999999999999999988
No 24
>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=98.84 E-value=1.1e-09 Score=93.49 Aligned_cols=56 Identities=38% Similarity=0.570 Sum_probs=53.2
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGD 57 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~ 57 (1159)
.++.|+..|+..|+..|..++||+...+..||..+||+..+|+.||+|||++.++.
T Consensus 3 ~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 3 KRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 46889999999999999999999999999999999999999999999999998764
No 25
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=98.82 E-value=1.4e-09 Score=120.28 Aligned_cols=57 Identities=26% Similarity=0.402 Sum_probs=56.0
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
+||.||.+|++.||..|+++.||+...|++||.-++|++.+|+|||.|||+|||+.+
T Consensus 115 QrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 115 QRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 799999999999999999999999999999999999999999999999999999987
No 26
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=98.82 E-value=3.4e-09 Score=87.75 Aligned_cols=36 Identities=36% Similarity=0.637 Sum_probs=34.8
Q ss_pred EEEecCHHHHHHHHHhh-ccCChhHHHHHHHHHHHHH
Q 001086 827 WEVIDTEEALRALLSVL-DDRGRQEALLIESLEKREA 862 (1159)
Q Consensus 827 W~~ydt~eeld~Ll~~L-d~rG~RE~~Lk~~L~~~~~ 862 (1159)
|+||+++++||+|+.|| ||||+||++|++.|.+.+.
T Consensus 1 W~~~~~~e~ld~L~~aL~~prG~RE~~L~~~L~~~~k 37 (46)
T PF15614_consen 1 WGYYDDPEELDELLKALENPRGKRESKLKKELDKHRK 37 (46)
T ss_pred CccccCHHHHHHHHHHHcCcccHhHHHHHHHHHHHhc
Confidence 99999999999999999 9999999999999999883
No 27
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.79 E-value=2.3e-09 Score=110.43 Aligned_cols=58 Identities=26% Similarity=0.409 Sum_probs=55.5
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
.|+|.|..|+.+|+..|..++||+...|..|+..+||+++.|||||||||++.|+...
T Consensus 54 ~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 54 KRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred cceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 4789999999999999999999999999999999999999999999999999999873
No 28
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=98.68 E-value=5.2e-09 Score=110.55 Aligned_cols=57 Identities=25% Similarity=0.363 Sum_probs=54.4
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
|..|+..|+..|+..|...+|+-...|.++|..+|+++.||+|||||||+||||+..
T Consensus 171 rPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 171 RPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred CCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 456999999999999999999999999999999999999999999999999999874
No 29
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=98.50 E-value=4.1e-08 Score=107.30 Aligned_cols=56 Identities=23% Similarity=0.376 Sum_probs=54.7
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
||..|..||+.|...|+..+.|-...|++|+..+||..+.|||||||||+|.||.+
T Consensus 171 RTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 171 RTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred cceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 78999999999999999999999999999999999999999999999999999987
No 30
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.45 E-value=6.8e-08 Score=103.60 Aligned_cols=57 Identities=23% Similarity=0.274 Sum_probs=55.1
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
.||.|+..|+..|++.|+.++||+...|+.+|..+++++..|+|||||||+||++..
T Consensus 63 ~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 63 ARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 478999999999999999999999999999999999999999999999999999977
No 31
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.43 E-value=2e-07 Score=106.74 Aligned_cols=56 Identities=27% Similarity=0.399 Sum_probs=54.4
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
||.+......+||..|.+|+.|+..+...||.+|+|....|+|||||||.|.||..
T Consensus 298 RTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 298 RTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 78899999999999999999999999999999999999999999999999999987
No 32
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=98.36 E-value=1.2e-07 Score=124.00 Aligned_cols=75 Identities=28% Similarity=0.534 Sum_probs=59.7
Q ss_pred hhhhhhhcCCcccccCcccCCCCeeEEEeCCCCCCCCCCcceEEec----------------------------------
Q 001086 776 ATEVSTDLHPMQSIYLGSDRRYNRYWLFLGPCNEYDPGHKRVYFES---------------------------------- 821 (1159)
Q Consensus 776 e~~~a~e~~~~R~~pLG~DR~~nRYW~F~~~~~~~dp~~grifVE~---------------------------------- 821 (1159)
.+.+.....++|..|||+||+|||||||.... +++|+|.
T Consensus 812 ~eki~~~~~~~r~~~lG~DR~~rRYwvl~~~~-------~~~~ie~i~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ 884 (1404)
T KOG1245|consen 812 AEKILKASLVLRLNPLGKDRNYRRYWVLPDLV-------SGLFIEEIAKKEEIDYKCNGNEDDEKASEDREYSLEASNTT 884 (1404)
T ss_pred HHHHHHHHHHhhccccccchhhceeeeeeccC-------cccchhHHhhhccccccchhhhhhcccchhhcccccccchh
Confidence 34455667899999999999999999998322 3344431
Q ss_pred ----------------CCCCcEEEecCHHHHHHHHHhhccCChhHHHHHHHH
Q 001086 822 ----------------SEDGHWEVIDTEEALRALLSVLDDRGRQEALLIESL 857 (1159)
Q Consensus 822 ----------------~~~g~W~~ydt~eeld~Ll~~Ld~rG~RE~~Lk~~L 857 (1159)
.....|.++++.+++++|+..++++|+||..|...|
T Consensus 885 ~~~~~~~~gt~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~g~~e~~lse~l 936 (1404)
T KOG1245|consen 885 NAAMNLQNGTDQKTPKTKQTRWFLVSIQEQEKELLYTLNPRGILESILSEGL 936 (1404)
T ss_pred hhhhcccccccccCCcchhhhHHHHHhhHHHHhhhhhcCccchHHHHHhhhh
Confidence 011259999999999999999999999999999976
No 33
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.12 E-value=9.7e-07 Score=102.11 Aligned_cols=58 Identities=24% Similarity=0.379 Sum_probs=55.9
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
.||.|+..|+..|+..|.+++||+...|++||.++++++..|+|||+|||++++|...
T Consensus 179 ~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 179 NRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 4789999999999999999999999999999999999999999999999999999884
No 34
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=97.74 E-value=1.7e-05 Score=87.12 Aligned_cols=49 Identities=35% Similarity=0.609 Sum_probs=45.1
Q ss_pred HHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeecccccccccc
Q 001086 8 PLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKG 56 (1159)
Q Consensus 8 ~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR 56 (1159)
..-...|...|..++||++.++.+||+.+||+..||-.||+|||.|+|-
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 3345789999999999999999999999999999999999999999993
No 35
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=97.61 E-value=2.4e-05 Score=70.65 Aligned_cols=67 Identities=25% Similarity=0.286 Sum_probs=54.3
Q ss_pred ccchhhHHHHHHhhCCCCCchhHhhhhhhhhhhccccchHHHHHhhhhccccchh----hhhhhccccceecc
Q 001086 515 GTLKGELFRILLEQGNNGSKVCQLARSSQIAELNLESTTEEVELLISSTLSSDIT----LFEKIASSTYRLRI 583 (1159)
Q Consensus 515 gTvK~aaf~vLs~~g~~gl~v~e~a~~iQk~~lr~l~tsk~~ea~i~~~LsrD~~----LFer~apsty~vr~ 583 (1159)
+|++-+|++||...| ..|+..|+.++|+..++-... .++|++.|++.|.+|++ .|.++.|++|.||.
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~~~~~~~-~k~p~~~i~a~ly~~~~~~d~~F~~vg~~~~~L~~ 71 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQERGLYKKS-GKTPEATIAAQLYTDIKNEDSRFVKVGPGRWGLRS 71 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHHHHTS----GGGGGHHHH-HHHHHHH-T-SS-EESSSSEEE-GG
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHhCCCCcc-cCCHHHHHHHHHHHHcccCCCCEEEeCCCcEEeee
Confidence 477889999999999 999999999999999887765 78899999999999998 99999999999984
No 36
>PF15612 WHIM1: WSTF, HB1, Itc1p, MBD9 motif 1; PDB: 2Y9Z_B 2Y9Y_B.
Probab=97.47 E-value=9.3e-05 Score=62.45 Aligned_cols=41 Identities=37% Similarity=0.405 Sum_probs=35.3
Q ss_pred ccccccccccCCCCCCHHHHHHHHHHHHhhhccCCcccccc
Q 001086 656 DVWLSGLMEGEYSDLTIDEKLNALVGLIDLVSAGSSIRMED 696 (1159)
Q Consensus 656 e~wl~~L~egeY~dLsiEERL~aLvaL~~l~l~g~sIR~~d 696 (1159)
+.|+..|.+++|.+|++++|+.+|.+|||.++++.+||.+.
T Consensus 3 ~~~~~~l~~~~y~~L~~~~kl~iL~~L~~~~l~s~~vr~~i 43 (50)
T PF15612_consen 3 PGLAPPLETGEYYELSPEEKLEILRALCDQLLSSSSVRNEI 43 (50)
T ss_dssp GGG-CCCCCSTCCCS-HHHHHHHHHHHHHHHCC-CCHHHHH
T ss_pred hhhhHHHHcCCcccCCHHHHHHHHHHHHHHHcCcHHHHHHH
Confidence 56889999999999999999999999999999999999943
No 37
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.42 E-value=5.9e-05 Score=83.25 Aligned_cols=56 Identities=21% Similarity=0.457 Sum_probs=50.7
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
||....-..+.||.+|..++.|+......||.+|.|....|+|||+|.|.|.||..
T Consensus 313 RTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 313 RTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 45555566789999999999999999999999999999999999999999999966
No 38
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.02 E-value=0.001 Score=72.89 Aligned_cols=57 Identities=28% Similarity=0.464 Sum_probs=53.0
Q ss_pred cccCCHHHHHHHHHhH---hhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCCC
Q 001086 3 VKRKTPLQAKALLKFY---SEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDNG 59 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~F---q~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~~ 59 (1159)
|+-|+..-..+|...| -.++||+...+++||.+.|++..||..||.|+|-+.||..+
T Consensus 192 RRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 192 RRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred hcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 6779999999999999 46899999999999999999999999999999999999874
No 39
>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=96.77 E-value=0.00019 Score=58.52 Aligned_cols=34 Identities=47% Similarity=0.817 Sum_probs=28.9
Q ss_pred hCCCCCHHHHHHHHHHcCCCCCceeeeccccccc
Q 001086 20 EEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRR 53 (1159)
Q Consensus 20 ~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK 53 (1159)
.+|||+..++..||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4799999999999999999999999999998864
No 40
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=96.55 E-value=0.002 Score=77.24 Aligned_cols=52 Identities=27% Similarity=0.448 Sum_probs=50.1
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeecccccccc
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRD 54 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~ 54 (1159)
|.+||..|.+.|..+|+.+++|+..+.+.|+.+|||....|..||-|-|.|.
T Consensus 424 RlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 424 RLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred eeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 7789999999999999999999999999999999999999999999988875
No 41
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=96.07 E-value=0.0023 Score=68.83 Aligned_cols=56 Identities=20% Similarity=0.320 Sum_probs=53.5
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
++.|+..|+..+...|..++||+...+..|+..+|++...+++||||+|++.++..
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 157 RTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 57889999999999999999999999999999999999999999999999999876
No 42
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=93.22 E-value=0.1 Score=68.37 Aligned_cols=56 Identities=25% Similarity=0.454 Sum_probs=53.8
Q ss_pred cccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 3 VKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 3 ~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
||+++..|+..+...|....||.....+.+...++++.+.|++||||-|.|.|+..
T Consensus 907 ~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~ 962 (1406)
T KOG1146|consen 907 RTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAK 962 (1406)
T ss_pred ccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhh
Confidence 78999999999999999999999999999999999999999999999999999876
No 43
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=83.97 E-value=0.29 Score=43.10 Aligned_cols=42 Identities=26% Similarity=0.599 Sum_probs=31.0
Q ss_pred HHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeecccccc
Q 001086 11 AKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRR 52 (1159)
Q Consensus 11 l~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRa 52 (1159)
.+.|+..|...+++....-..|..+.+|+..||+.||-.|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 467999999999999999999999999999999999965543
No 44
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=79.73 E-value=1.2 Score=33.06 Aligned_cols=23 Identities=30% Similarity=0.762 Sum_probs=19.5
Q ss_pred CcccccccccccCcchhhHhhhhhhhhc
Q 001086 985 KHCKICHTTFELDFDLEERYAVHAATCR 1012 (1159)
Q Consensus 985 ~hC~~CH~tf~~~~~~e~~~~~h~~~c~ 1012 (1159)
..|++|+++|.. +.+.+|...|+
T Consensus 3 ~~C~~CgR~F~~-----~~l~~H~~~C~ 25 (25)
T PF13913_consen 3 VPCPICGRKFNP-----DRLEKHEKICK 25 (25)
T ss_pred CcCCCCCCEECH-----HHHHHHHHhcC
Confidence 579999999964 67899999984
No 45
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=78.96 E-value=1.3 Score=51.41 Aligned_cols=54 Identities=26% Similarity=0.276 Sum_probs=43.9
Q ss_pred cCCHHHHHHHHHhH-h--hCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 5 RKTPLQAKALLKFY-S--EEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 5 rfT~~Ql~~LE~~F-q--~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
.+......+|+... + ..+||+...+..||.++||+..||..||.|.|.+.-+..
T Consensus 245 ~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 245 GLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 45566666776553 2 258999999999999999999999999999999877766
No 46
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=71.62 E-value=2.5 Score=53.04 Aligned_cols=48 Identities=19% Similarity=0.494 Sum_probs=45.1
Q ss_pred HHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeeccccccccccCC
Q 001086 11 AKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEKRRRDKGDN 58 (1159)
Q Consensus 11 l~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNRRaK~KR~~ 58 (1159)
+..|...|..|..|+...-..+|.+.||+...|+.||++++++.....
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 678889999999999999999999999999999999999999988876
No 47
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=61.91 E-value=2.3 Score=33.95 Aligned_cols=25 Identities=20% Similarity=0.541 Sum_probs=16.5
Q ss_pred hhhhhccccccccCCCCcccccccc
Q 001086 969 ALARCERCHDLYWRDEKHCKICHTT 993 (1159)
Q Consensus 969 ~l~~C~~C~~~y~~~~~hC~~CH~t 993 (1159)
++.+|..|..++|+-...|+.||.+
T Consensus 10 ~~~rC~~Cg~~~~pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 10 LGQRCRDCGRVQFPPRPVCPHCGSD 34 (37)
T ss_dssp EEEE-TTT--EEES--SEETTTT--
T ss_pred EEEEcCCCCCEecCCCcCCCCcCcc
Confidence 4678999999999999999999843
No 48
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=46.31 E-value=11 Score=44.84 Aligned_cols=45 Identities=24% Similarity=0.640 Sum_probs=36.2
Q ss_pred HHHHHHhhhhhhhhhhcCCcchhhhhhhhccccccccC-CCCccccccccc
Q 001086 945 DAWIWNSFYLNLNAVKHGKRSYLDALARCERCHDLYWR-DEKHCKICHTTF 994 (1159)
Q Consensus 945 ~kw~w~~~~~~l~a~K~gkk~~~~~l~~C~~C~~~y~~-~~~hC~~CH~tf 994 (1159)
.+|+|.+||-- .+.-.+.|-+..|..||.+.-. ++-+|+-||..-
T Consensus 200 ~~~lwe~~~pq-----~~~~~~~~~~~~C~~C~~~~~~~~~~~CpRC~~~L 245 (418)
T COG2995 200 RRWLWERFYPQ-----TLATGAREGLRSCLCCHYILPHDAEPRCPRCGSKL 245 (418)
T ss_pred HHHHHHhhccc-----cCCCCCcccceecccccccCCHhhCCCCCCCCChh
Confidence 36999999851 1124678899999999998888 899999999876
No 49
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=32.63 E-value=28 Score=42.20 Aligned_cols=50 Identities=24% Similarity=0.549 Sum_probs=32.4
Q ss_pred HHHHHHhhhhh---hhhhhcCCcchhhhhhhhccccccccCCCCccccccccc
Q 001086 945 DAWIWNSFYLN---LNAVKHGKRSYLDALARCERCHDLYWRDEKHCKICHTTF 994 (1159)
Q Consensus 945 ~kw~w~~~~~~---l~a~K~gkk~~~~~l~~C~~C~~~y~~~~~hC~~CH~tf 994 (1159)
.+|+|...... -....-|...-.+-+..|..|+-++=.+..||+-||.+-
T Consensus 193 ~~~lW~~~~~~~~~~~~~~~~~~~~~~~l~~C~~Cd~l~~~~~a~CpRC~~~L 245 (419)
T PRK15103 193 RRWLWDDIAPMPALPQPLKPGVTGLRQGLRSCSCCTAILPADQPVCPRCHTKG 245 (419)
T ss_pred HHHHHHhhccccccCccccccCCccccCCCcCCCCCCCCCCCCCCCCCCCCcC
Confidence 35788755311 111122333334567789999999877777999999987
No 50
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=31.72 E-value=11 Score=29.98 Aligned_cols=25 Identities=16% Similarity=0.550 Sum_probs=17.7
Q ss_pred hhhccccccccCCC---------Ccccccccccc
Q 001086 971 ARCERCHDLYWRDE---------KHCKICHTTFE 995 (1159)
Q Consensus 971 ~~C~~C~~~y~~~~---------~hC~~CH~tf~ 995 (1159)
..|..|...|..++ ..|+.||.+|.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 46778888776552 37888888875
No 51
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=31.26 E-value=22 Score=28.48 Aligned_cols=27 Identities=30% Similarity=0.669 Sum_probs=21.1
Q ss_pred CCcccccccccccCcchhhHhhhhhhhhcCCC
Q 001086 984 EKHCKICHTTFELDFDLEERYAVHAATCRGKG 1015 (1159)
Q Consensus 984 ~~hC~~CH~tf~~~~~~e~~~~~h~~~c~~k~ 1015 (1159)
.-+|+.|++.+.. .+|+-|.-.|-+..
T Consensus 4 ~~~C~nC~R~v~a-----~RfA~HLekCmg~g 30 (33)
T PF08209_consen 4 YVECPNCGRPVAA-----SRFAPHLEKCMGRG 30 (33)
T ss_dssp EEE-TTTSSEEEG-----GGHHHHHHHHTCH-
T ss_pred eEECCCCcCCcch-----hhhHHHHHHHHccC
Confidence 3479999999986 69999999997643
No 52
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=29.54 E-value=23 Score=39.45 Aligned_cols=32 Identities=22% Similarity=0.476 Sum_probs=27.2
Q ss_pred cchhhhhhhhccccccccCCCCcccccccccc
Q 001086 964 RSYLDALARCERCHDLYWRDEKHCKICHTTFE 995 (1159)
Q Consensus 964 k~~~~~l~~C~~C~~~y~~~~~hC~~CH~tf~ 995 (1159)
+|-..+--+|-.|+-.+-+-..||+-||.-|.
T Consensus 254 ~rvv~~GfvCsVCLsvfc~p~~~C~~C~skF~ 285 (296)
T COG5242 254 NRVVLLGFVCSVCLSVFCRPVPVCKKCKSKFS 285 (296)
T ss_pred ccEEEEeeehhhhheeecCCcCcCcccccccc
Confidence 34445567899999999999999999999985
No 53
>KOG2891 consensus Surface glycoprotein [General function prediction only]
Probab=29.18 E-value=49 Score=37.87 Aligned_cols=25 Identities=16% Similarity=0.092 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHhhhhhhccCcc
Q 001086 247 RAQQIVSLLKQRRLANNLQSKRKPV 271 (1159)
Q Consensus 247 ~~~~~~~~~k~~~~~~~~~~k~~~~ 271 (1159)
++||+++-.||...++++++|++..
T Consensus 324 kkrqlerqekqeleqmaeeekkr~e 348 (445)
T KOG2891|consen 324 KKRQLERQEKQELEQMAEEEKKREE 348 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555556666666666665443
No 54
>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=28.40 E-value=39 Score=29.32 Aligned_cols=44 Identities=18% Similarity=0.169 Sum_probs=32.4
Q ss_pred ccccCCHHHHHHHHHhHhhCCCCCHHHHHHHHHHcCCCCCceeeecccc
Q 001086 2 EVKRKTPLQAKALLKFYSEEKYPTKSEMEGLAAALDLTYKQVRTWFIEK 50 (1159)
Q Consensus 2 e~TrfT~~Ql~~LE~~Fq~~~YPs~~~R~eLA~~LgLse~qVqVWFQNR 50 (1159)
-|+.+|..|...+-..+.... ....+|..+|++..+|..|..|+
T Consensus 3 kR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 3 KRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 367788888888878787665 46789999999999999999885
No 55
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=27.43 E-value=18 Score=36.51 Aligned_cols=28 Identities=29% Similarity=0.583 Sum_probs=25.5
Q ss_pred hccccccccCCCCcccccccccccCcch
Q 001086 973 CERCHDLYWRDEKHCKICHTTFELDFDL 1000 (1159)
Q Consensus 973 C~~C~~~y~~~~~hC~~CH~tf~~~~~~ 1000 (1159)
|..|.+..-..+-||++|+.+++..|.+
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i~G~F~l 28 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEIEGEFEL 28 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEEEeeecc
Confidence 8889999999999999999999987765
No 56
>PLN00180 NDF6 (NDH-dependent flow 6); Provisional
Probab=26.54 E-value=91 Score=33.09 Aligned_cols=38 Identities=21% Similarity=0.385 Sum_probs=25.8
Q ss_pred CCCCcEEEecCHHHHHHHHHhhccCChhHHHHHHHHHHHHHHHHHHH
Q 001086 822 SEDGHWEVIDTEEALRALLSVLDDRGRQEALLIESLEKREAFLCQAM 868 (1159)
Q Consensus 822 ~~~g~W~~ydt~eeld~Ll~~Ld~rG~RE~~Lk~~L~~~~~~I~~~m 868 (1159)
++.|+| ||+.+|+|++ -.||--+|++|......-..++
T Consensus 134 DGT~hW-~Yd~QEd~E~--------sAReeL~REELiEEIEQkVGGL 171 (180)
T PLN00180 134 DGTGHW-VYERQEDIEE--------SARAELWREELIEEIEQKVGGL 171 (180)
T ss_pred CCceee-EeehHHHHHH--------HHHHHHHHHHHHHHHHHHhhhH
Confidence 455678 8999999986 3577777777755544444443
No 57
>KOG4364 consensus Chromatin assembly factor-I [Chromatin structure and dynamics]
Probab=26.45 E-value=60 Score=41.19 Aligned_cols=9 Identities=11% Similarity=0.416 Sum_probs=4.0
Q ss_pred HHHHHHhhc
Q 001086 836 LRALLSVLD 844 (1159)
Q Consensus 836 ld~Ll~~Ld 844 (1159)
+...+..|+
T Consensus 719 ~~~~~~t~~ 727 (811)
T KOG4364|consen 719 INRVVETLQ 727 (811)
T ss_pred HHHHHHhhh
Confidence 344444444
No 58
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=26.27 E-value=23 Score=24.83 Aligned_cols=21 Identities=24% Similarity=0.545 Sum_probs=15.2
Q ss_pred cccccccccccCcchhhHhhhhhhh
Q 001086 986 HCKICHTTFELDFDLEERYAVHAAT 1010 (1159)
Q Consensus 986 hC~~CH~tf~~~~~~e~~~~~h~~~ 1010 (1159)
-|+.|.++|....+ +..|+..
T Consensus 2 ~C~~C~~~f~~~~~----l~~H~~~ 22 (23)
T PF00096_consen 2 KCPICGKSFSSKSN----LKRHMRR 22 (23)
T ss_dssp EETTTTEEESSHHH----HHHHHHH
T ss_pred CCCCCCCccCCHHH----HHHHHhH
Confidence 49999999997644 4666653
No 59
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=25.72 E-value=35 Score=30.45 Aligned_cols=41 Identities=17% Similarity=0.475 Sum_probs=31.9
Q ss_pred hhhhhccccccccCCCCccccccccccc----CcchhhHhhhhhhhh
Q 001086 969 ALARCERCHDLYWRDEKHCKICHTTFEL----DFDLEERYAVHAATC 1011 (1159)
Q Consensus 969 ~l~~C~~C~~~y~~~~~hC~~CH~tf~~----~~~~e~~~~~h~~~c 1011 (1159)
.+..|..|.--.+ ...|+.|+....+ .|+.+.+|++|-...
T Consensus 4 ~mr~C~~CgvYTL--k~~CP~CG~~t~~~~P~rfSp~D~y~~yR~~~ 48 (56)
T PRK13130 4 KIRKCPKCGVYTL--KEICPVCGGKTKNPHPPRFSPEDKYGKYRRAL 48 (56)
T ss_pred cceECCCCCCEEc--cccCcCCCCCCCCCCCCCCCCCCccHHHHHHH
Confidence 4678999988888 8899999987744 567788888876543
No 60
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=24.83 E-value=35 Score=39.13 Aligned_cols=37 Identities=32% Similarity=0.924 Sum_probs=26.9
Q ss_pred HHhhhhhhhhhhcCCcc-hhhhhhhhccccccccCCCCc
Q 001086 949 WNSFYLNLNAVKHGKRS-YLDALARCERCHDLYWRDEKH 986 (1159)
Q Consensus 949 w~~~~~~l~a~K~gkk~-~~~~l~~C~~C~~~y~~~~~h 986 (1159)
||-.|-.|.- =||-|- |.+.|+.|..|+-++|.+.-|
T Consensus 270 Wkqmyf~L~r-~yg~keqyad~lhlCrhC~~LfWks~gH 307 (332)
T KOG3926|consen 270 WKQMYFQLRR-TYGVKEQYADTLHLCRHCCILFWKSDGH 307 (332)
T ss_pred HHHHHHHHHH-hcChHHHHHHHHHHHhhceEeeecCCCC
Confidence 5555544331 245443 899999999999999999887
No 61
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=24.79 E-value=37 Score=30.94 Aligned_cols=23 Identities=30% Similarity=0.803 Sum_probs=18.7
Q ss_pred hhccccccccCCCCcccccccc-c
Q 001086 972 RCERCHDLYWRDEKHCKICHTT-F 994 (1159)
Q Consensus 972 ~C~~C~~~y~~~~~hC~~CH~t-f 994 (1159)
-|..|+-+-=.+...||.||.+ |
T Consensus 6 AC~~Ck~l~~~d~e~CP~Cgs~~~ 29 (64)
T COG2093 6 ACKNCKRLTPEDTEICPVCGSTDL 29 (64)
T ss_pred HHhhccccCCCCCccCCCCCCccc
Confidence 4777887777777789999998 5
No 62
>COG3909 Cytochrome c556 [Energy production and conversion]
Probab=23.99 E-value=19 Score=37.35 Aligned_cols=15 Identities=20% Similarity=0.556 Sum_probs=11.4
Q ss_pred HHHHHHHhhhhHHHH
Q 001086 933 EQHRMWSRLQEFDAW 947 (1159)
Q Consensus 933 e~~~~~~r~~~f~kw 947 (1159)
=+=.+|.+.++|..=
T Consensus 89 A~p~IWe~~~~FKA~ 103 (147)
T COG3909 89 ALPAIWEDMADFKAK 103 (147)
T ss_pred ccHHHHHhHHHHHHH
Confidence 345789999999754
No 63
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=23.18 E-value=30 Score=40.70 Aligned_cols=28 Identities=32% Similarity=0.280 Sum_probs=20.8
Q ss_pred CCCCCHHHHHHHHHHHHhhhccCCcc-cc
Q 001086 667 YSDLTIDEKLNALVGLIDLVSAGSSI-RM 694 (1159)
Q Consensus 667 Y~dLsiEERL~aLvaL~~l~l~g~sI-R~ 694 (1159)
-+||+.++|+-||..|---.+....+ |.
T Consensus 98 spdlT~~qr~lAl~qL~~Dym~aGl~DRA 126 (389)
T COG2956 98 SPDLTFEQRLLALQQLGRDYMAAGLLDRA 126 (389)
T ss_pred CCCCchHHHHHHHHHHHHHHHHhhhhhHH
Confidence 37899999999998887666655554 44
No 64
>KOG2412 consensus Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification]
Probab=21.82 E-value=71 Score=39.77 Aligned_cols=71 Identities=10% Similarity=0.100 Sum_probs=36.0
Q ss_pred hhhhhhccCccchhhhh-----hhhhhhhhcCCchhhhcccCchhhhHHh-HhhhhccCchHHHHHHhhhhCCCCCc
Q 001086 261 ANNLQSKRKPVAKGKQV-----KLDKGERLRQPNKEKCELAPDSVISQER-LDQIAMLVDDEELELRELEVGPNPPT 331 (1159)
Q Consensus 261 ~~~~~~k~~~~~~~r~~-----e~~~~e~~~~~~~e~~~la~~~~~~~~~-~~~~~~l~ddE~LeL~e~~~~~~~l~ 331 (1159)
.+++++|+++.+++|++ -+++++..+++..|+++++.|+...+++ +.+.-+...-..-+..+..+..++..
T Consensus 216 ~~~~e~kr~Eaerk~~~~qEe~Rqk~d~~~~~~eqekiR~~eekqeee~ke~e~~~~k~~q~~~~~eek~a~qk~~~ 292 (591)
T KOG2412|consen 216 KERSEEKREEAERKRRAHQEELRQKEDEEAELQEQEKIRAEEEKQEEERKEAEEQAEKEVQDPKAHEEKLAEQKAVI 292 (591)
T ss_pred HHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCchhcccccccccccc
Confidence 34455555555544432 2345555566678888888877444433 22233333333334455555555543
No 65
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.91 E-value=32 Score=40.19 Aligned_cols=24 Identities=33% Similarity=0.766 Sum_probs=19.8
Q ss_pred hhccccccccCCC-Ccccccccccc
Q 001086 972 RCERCHDLYWRDE-KHCKICHTTFE 995 (1159)
Q Consensus 972 ~C~~C~~~y~~~~-~hC~~CH~tf~ 995 (1159)
.|.+|.+.+|... .+||.|++++.
T Consensus 30 ~C~sCv~~l~~~~~~~CP~C~~~lr 54 (309)
T TIGR00570 30 LCESCVDLLFVRGSGSCPECDTPLR 54 (309)
T ss_pred ccHHHHHHHhcCCCCCCCCCCCccc
Confidence 5888999999664 58999999873
No 66
>PF05071 NDUFA12: NADH ubiquinone oxidoreductase subunit NDUFA12; InterPro: IPR007763 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. this entry represents the 17.2kDa subunit from NADH:ubiquinone oxidoreductase and its homologues []. This subunit is believed to be one of the 36 structural complex I proteins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0009055 electron carrier activity, 0016020 membrane
Probab=20.60 E-value=82 Score=31.16 Aligned_cols=16 Identities=25% Similarity=0.364 Sum_probs=14.5
Q ss_pred ccCcccCCCCeeEEEe
Q 001086 789 IYLGSDRRYNRYWLFL 804 (1159)
Q Consensus 789 ~pLG~DR~~nRYW~F~ 804 (1159)
...|.|-++|+||-+.
T Consensus 2 ~lVG~D~~GN~YyE~~ 17 (105)
T PF05071_consen 2 TLVGTDEFGNKYYENP 17 (105)
T ss_pred CEeeEeCCCCEEEeec
Confidence 3689999999999998
No 67
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=20.23 E-value=92 Score=40.95 Aligned_cols=16 Identities=13% Similarity=-0.047 Sum_probs=7.7
Q ss_pred hhHHHHHHhhCCCCCc
Q 001086 519 GELFRILLEQGNNGSK 534 (1159)
Q Consensus 519 ~aaf~vLs~~g~~gl~ 534 (1159)
|++|+-+--..+..++
T Consensus 1339 fSSFRTf~a~dYs~ia 1354 (1516)
T KOG1832|consen 1339 FSSFRTFDAIDYSDIA 1354 (1516)
T ss_pred hhhhccccccccccce
Confidence 3555555444444443
No 68
>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]
Probab=20.08 E-value=48 Score=40.86 Aligned_cols=106 Identities=20% Similarity=0.287 Sum_probs=68.9
Q ss_pred hcCCCCcHHHHHHHHHHHhcCCCCccchhhhhhhHHHHHHHh-hc--cccccchhhHHHHHHhhCCCCCchhHhhhhhhh
Q 001086 468 KSLNPLTWTEILRQVLVAAGFGSKQGSSRKESLSKEMILMLK-YG--LRPGTLKGELFRILLEQGNNGSKVCQLARSSQI 544 (1159)
Q Consensus 468 ~~Ln~lTWpEiLrq~~~~aG~gp~~~~~~~~~~~~~~~~m~~-~~--L~pgTvK~aaf~vLs~~g~~gl~v~e~a~~iQk 544 (1159)
++=++-.|.||+++|. |..+..+-+...+.++...++ .+ +-|--||+..=.+|-....+| ...|+.+++..
T Consensus 130 ~~~~pp~wdeVi~~Fr-----GtELq~YF~~l~~g~~r~v~K~QYVd~iPk~~KG~v~elLk~~de~g-~~devve~l~L 203 (591)
T COG1245 130 RYEDPPSWDEVIKRFR-----GTELQNYFKKLYEGELRAVHKPQYVDLIPKVVKGKVGELLKKVDERG-KFDEVVERLGL 203 (591)
T ss_pred CCCCCCCHHHHHHHhh-----hhHHHHHHHHHHcCCcceecchHHHHHHHHHhcchHHHHHHhhhhcC-cHHHHHHHhcc
Confidence 3445778999999994 555655555544444432222 11 567777776667777777777 45666666655
Q ss_pred h-----hhccccchHHHHHhhhhccccchhhhhhhccccc
Q 001086 545 A-----ELNLESTTEEVELLISSTLSSDITLFEKIASSTY 579 (1159)
Q Consensus 545 ~-----~lr~l~tsk~~ea~i~~~LsrD~~LFer~apsty 579 (1159)
. .+..|.--+-..-+|+++|.||...+-=.-||+|
T Consensus 204 ~nvl~r~v~~LSGGELQr~aIaa~l~rdADvY~FDEpsSy 243 (591)
T COG1245 204 ENVLDRDVSELSGGELQRVAIAAALLRDADVYFFDEPSSY 243 (591)
T ss_pred hhhhhhhhhhcCchHHHHHHHHHHHhccCCEEEEcCCccc
Confidence 3 4555666666789999999999855555556666
Done!