Query 029009
Match_columns 200
No_of_seqs 244 out of 1338
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 06:02:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029009.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029009hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0842 Transcription factor t 99.7 1.6E-16 3.5E-21 141.3 8.0 58 143-200 150-207 (307)
2 KOG0850 Transcription factor D 99.6 2.2E-16 4.8E-21 134.8 5.0 58 143-200 119-176 (245)
3 KOG0489 Transcription factor z 99.6 1.3E-16 2.8E-21 139.3 1.2 58 143-200 156-213 (261)
4 KOG0484 Transcription factor P 99.6 1E-16 2.2E-21 122.5 0.3 58 143-200 14-71 (125)
5 KOG0488 Transcription factor B 99.6 4.9E-16 1.1E-20 138.8 4.0 57 144-200 170-226 (309)
6 KOG0487 Transcription factor A 99.6 4E-16 8.7E-21 138.8 3.1 57 144-200 233-289 (308)
7 KOG0485 Transcription factor N 99.6 7.4E-16 1.6E-20 131.0 4.4 60 141-200 99-158 (268)
8 KOG0843 Transcription factor E 99.6 1.4E-15 3.1E-20 125.9 3.5 56 145-200 101-156 (197)
9 PF00046 Homeobox: Homeobox do 99.5 1.3E-15 2.8E-20 102.9 1.7 54 147-200 1-54 (57)
10 KOG2251 Homeobox transcription 99.5 4E-15 8.6E-20 126.5 4.6 58 143-200 34-91 (228)
11 KOG0492 Transcription factor M 99.5 4.4E-15 9.6E-20 125.5 3.9 59 142-200 140-198 (246)
12 KOG0493 Transcription factor E 99.5 1.7E-14 3.8E-19 125.5 6.5 55 146-200 246-300 (342)
13 KOG0494 Transcription factor C 99.5 1.2E-14 2.6E-19 126.4 3.8 54 147-200 142-195 (332)
14 TIGR01565 homeo_ZF_HD homeobox 99.5 4.7E-14 1E-18 97.5 5.7 53 146-198 1-57 (58)
15 smart00389 HOX Homeodomain. DN 99.5 2.2E-14 4.8E-19 96.0 3.7 54 147-200 1-54 (56)
16 cd00086 homeodomain Homeodomai 99.5 3.8E-14 8.1E-19 95.4 3.0 53 148-200 2-54 (59)
17 KOG0483 Transcription factor H 99.4 9.6E-14 2.1E-18 117.1 3.4 55 146-200 50-104 (198)
18 KOG0848 Transcription factor C 99.4 5E-14 1.1E-18 122.9 0.6 53 148-200 201-253 (317)
19 KOG3802 Transcription factor O 99.4 2.6E-13 5.6E-18 123.7 4.9 57 144-200 292-348 (398)
20 COG5576 Homeodomain-containing 99.4 2.4E-13 5.3E-18 110.9 3.8 59 142-200 47-105 (156)
21 KOG0491 Transcription factor B 99.3 7.5E-14 1.6E-18 114.4 -1.2 55 146-200 100-154 (194)
22 KOG0486 Transcription factor P 99.3 9.3E-13 2E-17 117.0 4.0 56 145-200 111-166 (351)
23 KOG4577 Transcription factor L 99.3 1.7E-12 3.7E-17 114.5 3.4 60 141-200 162-221 (383)
24 KOG0844 Transcription factor E 99.3 1.9E-12 4.1E-17 115.0 2.2 59 142-200 177-235 (408)
25 KOG0490 Transcription factor, 99.1 3.6E-11 7.8E-16 100.6 2.6 57 144-200 58-114 (235)
26 KOG0847 Transcription factor, 99.1 3.1E-11 6.8E-16 103.2 1.5 60 141-200 162-221 (288)
27 KOG1168 Transcription factor A 98.9 6.4E-10 1.4E-14 98.4 2.1 58 143-200 306-363 (385)
28 KOG0849 Transcription factor P 98.9 1.3E-09 2.8E-14 99.2 3.4 59 142-200 172-230 (354)
29 KOG0775 Transcription factor S 98.7 1.4E-08 3.1E-13 89.1 3.7 48 153-200 183-230 (304)
30 PF05920 Homeobox_KN: Homeobox 98.3 7.4E-08 1.6E-12 61.8 -1.3 34 167-200 7-40 (40)
31 KOG2252 CCAAT displacement pro 98.2 9.8E-07 2.1E-11 83.8 4.2 61 140-200 414-474 (558)
32 KOG0774 Transcription factor P 98.2 1E-06 2.2E-11 77.4 3.5 55 146-200 188-245 (334)
33 KOG0490 Transcription factor, 97.9 6.4E-06 1.4E-10 68.9 2.5 59 142-200 149-207 (235)
34 KOG1146 Homeobox protein [Gene 97.3 0.00014 3.1E-09 75.0 2.9 55 146-200 903-957 (1406)
35 PF11569 Homez: Homeodomain le 97.1 0.00013 2.8E-09 50.2 0.4 41 158-198 10-50 (56)
36 KOG0773 Transcription factor M 97.0 0.00059 1.3E-08 61.3 3.9 55 146-200 239-296 (342)
37 KOG3623 Homeobox transcription 94.8 0.017 3.7E-07 57.4 2.2 43 158-200 568-610 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 92.0 0.2 4.4E-06 33.5 3.2 47 147-198 1-47 (53)
39 PF04618 HD-ZIP_N: HD-ZIP prot 79.1 8.8 0.00019 29.9 6.4 16 95-111 88-103 (111)
40 KOG3623 Homeobox transcription 65.2 6 0.00013 40.0 3.2 54 146-199 626-679 (1007)
41 PF04967 HTH_10: HTH DNA bindi 61.6 11 0.00023 25.5 3.0 38 153-190 1-40 (53)
42 cd00569 HTH_Hin_like Helix-tur 59.5 16 0.00035 19.7 3.2 38 152-194 5-42 (42)
43 PF01527 HTH_Tnp_1: Transposas 59.0 3.7 8.1E-05 28.2 0.4 43 148-195 2-45 (76)
44 PHA03308 transcriptional regul 52.6 10 0.00022 38.7 2.3 17 144-160 1292-1308(1463)
45 PF09607 BrkDBD: Brinker DNA-b 51.0 15 0.00032 25.5 2.3 44 150-195 3-47 (58)
46 PF10668 Phage_terminase: Phag 50.8 6.2 0.00013 27.4 0.4 19 176-194 25-43 (60)
47 cd06171 Sigma70_r4 Sigma70, re 50.2 8.2 0.00018 23.5 0.9 42 152-198 10-51 (55)
48 PRK09413 IS2 repressor TnpA; R 45.5 33 0.00072 26.2 3.8 44 148-195 8-51 (121)
49 PF08281 Sigma70_r4_2: Sigma-7 44.2 7.6 0.00017 25.0 0.0 41 153-198 11-51 (54)
50 COG3413 Predicted DNA binding 43.6 24 0.00052 29.5 3.0 39 152-190 155-195 (215)
51 PF04545 Sigma70_r4: Sigma-70, 42.3 20 0.00043 22.9 1.8 39 152-195 4-42 (50)
52 KOG1146 Homeobox protein [Gene 39.3 28 0.0006 37.5 3.2 55 146-200 705-759 (1406)
53 PF13518 HTH_28: Helix-turn-he 35.6 15 0.00031 23.2 0.4 21 176-196 15-35 (52)
54 cd04761 HTH_MerR-SF Helix-Turn 34.9 14 0.0003 22.9 0.2 21 176-196 3-23 (49)
55 PF11167 DUF2953: Protein of u 34.5 4.1 8.8E-05 26.9 -2.5 19 1-19 3-21 (53)
56 PRK10072 putative transcriptio 33.1 20 0.00043 27.0 0.8 41 152-199 32-72 (96)
57 PF13936 HTH_38: Helix-turn-he 30.3 21 0.00045 22.6 0.4 39 151-194 3-41 (44)
58 PF02796 HTH_7: Helix-turn-hel 30.0 45 0.00098 21.0 2.0 38 152-194 5-42 (45)
59 PF00196 GerE: Bacterial regul 29.9 35 0.00077 22.3 1.5 39 152-196 3-41 (58)
60 PF08280 HTH_Mga: M protein tr 29.8 41 0.00089 22.5 1.8 35 155-193 5-39 (59)
61 PF13411 MerR_1: MerR HTH fami 27.8 24 0.00052 23.6 0.4 20 176-195 3-22 (69)
62 PRK03975 tfx putative transcri 26.8 35 0.00075 27.5 1.2 43 150-198 4-46 (141)
63 PF06056 Terminase_5: Putative 24.8 34 0.00073 23.3 0.7 20 176-195 16-35 (58)
64 TIGR03879 near_KaiC_dom probab 24.5 16 0.00034 26.4 -1.1 22 175-196 34-55 (73)
65 PHA02955 hypothetical protein; 24.5 1E+02 0.0022 26.7 3.7 42 155-196 60-102 (213)
66 COG4367 Uncharacterized protei 23.4 72 0.0016 24.1 2.3 39 153-191 3-41 (97)
67 PF01381 HTH_3: Helix-turn-hel 23.3 35 0.00075 21.7 0.5 23 176-198 12-34 (55)
68 cd01392 HTH_LacI Helix-turn-he 23.3 25 0.00055 22.1 -0.2 21 178-198 2-22 (52)
69 cd02413 40S_S3_KH K homology R 22.4 78 0.0017 22.8 2.3 21 175-195 55-75 (81)
70 COG2963 Transposase and inacti 21.6 1.2E+02 0.0026 22.5 3.3 42 150-195 5-47 (116)
71 PF13384 HTH_23: Homeodomain-l 21.5 33 0.00072 21.5 0.1 22 175-196 19-40 (50)
72 cd04762 HTH_MerR-trunc Helix-T 21.5 37 0.00079 20.4 0.3 22 176-197 3-24 (49)
73 smart00027 EH Eps15 homology d 21.0 1.1E+02 0.0023 22.0 2.8 43 153-195 4-51 (96)
74 cd04764 HTH_MlrA-like_sg1 Heli 20.1 42 0.00092 22.5 0.5 21 176-196 3-23 (67)
No 1
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.66 E-value=1.6e-16 Score=141.28 Aligned_cols=58 Identities=33% Similarity=0.613 Sum_probs=53.6
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 143 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
..++||.|.-|+..|+.+||+.|++++|++..+|+.||..|+|++.||||||||||-|
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK 207 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYK 207 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhh
Confidence 3456666777999999999999999999999999999999999999999999999976
No 2
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.63 E-value=2.2e-16 Score=134.79 Aligned_cols=58 Identities=29% Similarity=0.449 Sum_probs=54.6
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 143 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.+|.||.||.|+.-||..|.+.|++++|+-..+|.+||..|||+..||||||||||.|
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK 176 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSK 176 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHH
Confidence 3556778999999999999999999999999999999999999999999999999976
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.61 E-value=1.3e-16 Score=139.29 Aligned_cols=58 Identities=34% Similarity=0.603 Sum_probs=55.4
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 143 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.++.||.|+.||..|+.+||+.|..++|+++..|.+||..|.|+++||||||||||+|
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK 213 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMK 213 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHH
Confidence 4557899999999999999999999999999999999999999999999999999986
No 4
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.60 E-value=1e-16 Score=122.49 Aligned_cols=58 Identities=29% Similarity=0.464 Sum_probs=55.2
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 143 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
..++||-|+.|+..|+..||+.|...+||++..|++||.++.|++.+|||||||||||
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAK 71 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAK 71 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHH
Confidence 4567888999999999999999999999999999999999999999999999999986
No 5
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.60 E-value=4.9e-16 Score=138.80 Aligned_cols=57 Identities=30% Similarity=0.487 Sum_probs=54.8
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 144 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+|+|+.|+.||..|+..||+.|++.+|++..+|++||..|||+..||++||||||+|
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtK 226 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTK 226 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHH
Confidence 667788999999999999999999999999999999999999999999999999987
No 6
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.59 E-value=4e-16 Score=138.78 Aligned_cols=57 Identities=37% Similarity=0.586 Sum_probs=54.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 144 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+..||||..+|+.|+.+||+.|..|.|++.+.|.+|++.|+|++|||+|||||||+|
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK 289 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMK 289 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhH
Confidence 556888999999999999999999999999999999999999999999999999987
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.59 E-value=7.4e-16 Score=130.97 Aligned_cols=60 Identities=30% Similarity=0.514 Sum_probs=56.2
Q ss_pred CccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 141 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
-.+.++||.|++|+..|+..||..|+..+|++..+|..||++|.|++.||+|||||||.|
T Consensus 99 ~g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnK 158 (268)
T KOG0485|consen 99 LGDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNK 158 (268)
T ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHH
Confidence 345567888999999999999999999999999999999999999999999999999986
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.56 E-value=1.4e-15 Score=125.85 Aligned_cols=56 Identities=36% Similarity=0.544 Sum_probs=53.7
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 145 VNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 145 k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+.||.||.|+.+|+..||..|+.++|..-.+|+.||+.|+|++.||+|||||||.|
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk 156 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTK 156 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHH
Confidence 56788999999999999999999999999999999999999999999999999975
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.55 E-value=1.3e-15 Score=102.90 Aligned_cols=54 Identities=44% Similarity=0.734 Sum_probs=51.8
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 147 rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
||+|+.|+.+|+.+|+..|..++||+..+++.||..+||+..+|++||+|||++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHH
Confidence 578999999999999999999999999999999999999999999999999964
No 10
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.54 E-value=4e-15 Score=126.46 Aligned_cols=58 Identities=33% Similarity=0.525 Sum_probs=55.7
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 143 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.++.||.||.|+..|+++||..|.+.+||++..|++||.+|+|.+.+|||||.|||+|
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK 91 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAK 91 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccch
Confidence 3568899999999999999999999999999999999999999999999999999997
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.53 E-value=4.4e-15 Score=125.46 Aligned_cols=59 Identities=31% Similarity=0.550 Sum_probs=55.5
Q ss_pred ccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 142 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+.+..|+.|+.|+..|+..||+.|+..+|+++++|.+++..|.|++.||+|||||||+|
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAK 198 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAK 198 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHH
Confidence 34556888999999999999999999999999999999999999999999999999997
No 12
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.52 E-value=1.7e-14 Score=125.50 Aligned_cols=55 Identities=35% Similarity=0.645 Sum_probs=52.6
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
-||.|+.|+.+|+..|+..|+.++|++...|+.||.+|+|.+.||+|||||+|+|
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAK 300 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAK 300 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhh
Confidence 3577899999999999999999999999999999999999999999999999987
No 13
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.50 E-value=1.2e-14 Score=126.42 Aligned_cols=54 Identities=31% Similarity=0.465 Sum_probs=51.4
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 147 rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
|+-||.||..|+..||+.|+..+||+...|+.||.++.|.+.+|+|||||||||
T Consensus 142 Rh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAK 195 (332)
T KOG0494|consen 142 RHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAK 195 (332)
T ss_pred ccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHH
Confidence 333899999999999999999999999999999999999999999999999997
No 14
>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=99.49 E-value=4.7e-14 Score=97.53 Aligned_cols=53 Identities=13% Similarity=0.360 Sum_probs=51.0
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCcccccccccccc
Q 029009 146 NARKKLRLTKEQSALLEESFKQHST----LNPKQKQALARQLNLRPRQVEVWFQNRR 198 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~~~~~----Ps~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (200)
+||.||.|+.+|+..|+..|..++| |+..++++||..+||++++|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999976
No 15
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.49 E-value=2.2e-14 Score=95.99 Aligned_cols=54 Identities=43% Similarity=0.680 Sum_probs=51.0
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 147 rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
++.|++|+..|+..|+..|..++||+..++..||..+||+..||+.||+|||++
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 356778999999999999999999999999999999999999999999999975
No 16
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.45 E-value=3.8e-14 Score=95.36 Aligned_cols=53 Identities=43% Similarity=0.745 Sum_probs=50.5
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 148 r~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+.|..|+..|+.+|+.+|..++||+..+++.||.++||+..||++||+|||++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAK 54 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 56778999999999999999999999999999999999999999999999974
No 17
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.41 E-value=9.6e-14 Score=117.11 Aligned_cols=55 Identities=56% Similarity=0.894 Sum_probs=51.9
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
..+++.+|+.+|...||..|+.+.++.+.++..||++|||.+|||.|||||||||
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRAR 104 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRAR 104 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhcccc
Confidence 4556678999999999999999999999999999999999999999999999997
No 18
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.40 E-value=5e-14 Score=122.86 Aligned_cols=53 Identities=38% Similarity=0.619 Sum_probs=50.8
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 148 r~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
|.|.+++..|+-+||+.|..++|.++..+.+||..|+|++|||||||||||||
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAK 253 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAK 253 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHH
Confidence 45778999999999999999999999999999999999999999999999997
No 19
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.39 E-value=2.6e-13 Score=123.67 Aligned_cols=57 Identities=25% Similarity=0.444 Sum_probs=54.8
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 144 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+++|||||.|.......||++|.+|+.|+..++..||.+|+|.+.+|+|||||||.|
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQk 348 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQK 348 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccc
Confidence 368899999999999999999999999999999999999999999999999999986
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.38 E-value=2.4e-13 Score=110.87 Aligned_cols=59 Identities=32% Similarity=0.530 Sum_probs=54.9
Q ss_pred ccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 142 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.....+++|++.+..|+.+|++.|+.++||+...|..|+..++|+++-|||||||||++
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~ 105 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK 105 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHH
Confidence 34457888899999999999999999999999999999999999999999999999975
No 21
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.35 E-value=7.5e-14 Score=114.40 Aligned_cols=55 Identities=33% Similarity=0.558 Sum_probs=52.8
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+++-|++|+..|+..|++.|+.++|++..+|.+||..|+|++.||+.||||||+|
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK 154 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMK 154 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 5667999999999999999999999999999999999999999999999999986
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.32 E-value=9.3e-13 Score=117.04 Aligned_cols=56 Identities=30% Similarity=0.513 Sum_probs=53.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 145 VNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 145 k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
|+||.|+.|+..|+..||.+|+++.||+...|++||..++|++.+|+|||.|||+|
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrak 166 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 166 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhh
Confidence 56788999999999999999999999999999999999999999999999999997
No 23
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.28 E-value=1.7e-12 Score=114.50 Aligned_cols=60 Identities=30% Similarity=0.529 Sum_probs=56.7
Q ss_pred CccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 141 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+.++..||.|+.++..|++.|+..|+..+.|-++.|+.|+.++||..|.|||||||||||
T Consensus 162 ~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAK 221 (383)
T KOG4577|consen 162 EGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAK 221 (383)
T ss_pred ccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHH
Confidence 355668999999999999999999999999999999999999999999999999999997
No 24
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.25 E-value=1.9e-12 Score=114.96 Aligned_cols=59 Identities=36% Similarity=0.544 Sum_probs=55.5
Q ss_pred ccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 142 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.+.+.||.||.|+.+|+..||+.|-+..|-++..|.+||..|+|.+..|||||||||+|
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMK 235 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMK 235 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhh
Confidence 34567899999999999999999999999999999999999999999999999999987
No 25
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.10 E-value=3.6e-11 Score=100.65 Aligned_cols=57 Identities=30% Similarity=0.328 Sum_probs=54.4
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 144 GVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 144 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.++|+.|+.|+..|+++|++.|+..+||+...|+.||..+++++..|+|||||||+|
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak 114 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAK 114 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHh
Confidence 457888999999999999999999999999999999999999999999999999985
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.08 E-value=3.1e-11 Score=103.16 Aligned_cols=60 Identities=35% Similarity=0.565 Sum_probs=56.5
Q ss_pred CccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 141 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+++++++..|..|+-.|+..|+..|+..+|+--.+|.+||..+|+++.||+|||||||.|
T Consensus 162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTK 221 (288)
T KOG0847|consen 162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTK 221 (288)
T ss_pred CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhh
Confidence 467778888999999999999999999999999999999999999999999999999975
No 27
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.88 E-value=6.4e-10 Score=98.42 Aligned_cols=58 Identities=28% Similarity=0.487 Sum_probs=54.6
Q ss_pred cCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 143 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.+.+||+|+.+-....+.||.+|..+++|+.+.+..||++|+|-+..|+|||||+|+|
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK 363 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 363 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence 4557899999999999999999999999999999999999999999999999999976
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.86 E-value=1.3e-09 Score=99.20 Aligned_cols=59 Identities=31% Similarity=0.485 Sum_probs=54.7
Q ss_pred ccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 142 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.+++.+|.|+.|+..|+..|++.|++++||....|+.||.++++++.+|+|||+|||+|
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~ 230 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAK 230 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhh
Confidence 34456777899999999999999999999999999999999999999999999999985
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.67 E-value=1.4e-08 Score=89.12 Aligned_cols=48 Identities=35% Similarity=0.599 Sum_probs=45.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
|...-..+|..+|..++||++.++.+||+.+||+..||-.||.|||+|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR 230 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQR 230 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence 556668899999999999999999999999999999999999999986
No 30
>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=98.29 E-value=7.4e-08 Score=61.82 Aligned_cols=34 Identities=32% Similarity=0.572 Sum_probs=28.9
Q ss_pred hCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 167 QHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 167 ~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.++||+.++++.||.++||+..||..||-|.|.|
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 4799999999999999999999999999999864
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.23 E-value=9.8e-07 Score=83.76 Aligned_cols=61 Identities=26% Similarity=0.364 Sum_probs=56.0
Q ss_pred CCccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 140 EDEDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 140 ~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.+...+.||.|.+|+..|.+.|..+|+.+++|+.++.+.|+.+|+|...-|..||-|-|.|
T Consensus 414 ~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 414 DDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred ccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 4455567888999999999999999999999999999999999999999999999998865
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.21 E-value=1e-06 Score=77.39 Aligned_cols=55 Identities=33% Similarity=0.545 Sum_probs=51.0
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 146 NARKKLRLTKEQSALLEESFK---QHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~---~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.||+|..|++...++|..+|- .++||+.+.+++||++++++..||-.||.|.|-|
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIr 245 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIR 245 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceee
Confidence 578889999999999999996 5899999999999999999999999999999853
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.90 E-value=6.4e-06 Score=68.85 Aligned_cols=59 Identities=31% Similarity=0.559 Sum_probs=54.1
Q ss_pred ccCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 142 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
...+.++.|+.+...|+..+...|....+|+...++.|+..++++.+.|++||||+|++
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~ 207 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAK 207 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHH
Confidence 34557788999999999999999999999999999999999999999999999999864
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.29 E-value=0.00014 Score=74.99 Aligned_cols=55 Identities=22% Similarity=0.421 Sum_probs=52.6
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+|++|++++..|+..|...|....||...+.+.|...+++..+.|+|||||-|+|
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~ 957 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAK 957 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhh
Confidence 6788999999999999999999999999999999999999999999999999975
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.13 E-value=0.00013 Score=50.19 Aligned_cols=41 Identities=24% Similarity=0.434 Sum_probs=31.2
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccc
Q 029009 158 SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (200)
Q Consensus 158 l~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (200)
+..|+++|..++++...+...|+.+.+|+..||+.||--|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 45699999999999999999999999999999999996654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=97.03 E-value=0.00059 Score=61.29 Aligned_cols=55 Identities=33% Similarity=0.420 Sum_probs=47.2
Q ss_pred CCCCCccCCHHHHHHHHHHHhh---CCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 146 NARKKLRLTKEQSALLEESFKQ---HSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~~---~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+.|.+..+.+....+|+.++.. ++||+..++..||.++||+..||-.||.|.|.|
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R 296 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVR 296 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccc
Confidence 4455557999999999988443 679999999999999999999999999999965
No 37
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.75 E-value=0.017 Score=57.35 Aligned_cols=43 Identities=21% Similarity=0.421 Sum_probs=40.7
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 158 SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 158 l~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
+.+|+.+|..+..|+..+...+|.+.||+.+.|+.||++++++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~ 610 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAE 610 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhh
Confidence 7889999999999999999999999999999999999998863
No 38
>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=92.03 E-value=0.2 Score=33.53 Aligned_cols=47 Identities=21% Similarity=0.350 Sum_probs=34.3
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccc
Q 029009 147 ARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (200)
Q Consensus 147 rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (200)
+|+|..++-++...+-..++... ....||.++|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 56788899988777777777665 467899999999999999998863
No 39
>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=79.11 E-value=8.8 Score=29.87 Aligned_cols=16 Identities=38% Similarity=0.343 Sum_probs=10.4
Q ss_pred hccCCCCCCCCCCCCCC
Q 029009 95 ILNRQASPHSAVSNSFS 111 (200)
Q Consensus 95 ~l~~~sSp~s~~S~S~S 111 (200)
+....+||.|..| |.|
T Consensus 88 Ee~gvSSPNStiS-S~s 103 (111)
T PF04618_consen 88 EEAGVSSPNSTIS-SVS 103 (111)
T ss_pred ccccccCCCccce-ecc
Confidence 3355778888887 433
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=65.23 E-value=6 Score=40.04 Aligned_cols=54 Identities=19% Similarity=0.369 Sum_probs=42.3
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccC
Q 029009 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRa 199 (200)
.-|.++....++...|..+|..+-.++-.+-..++.++...+..|+|||++|+.
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrss 679 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSS 679 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCC
Confidence 344456677777888899998877777666666677788888999999999985
No 41
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=61.59 E-value=11 Score=25.46 Aligned_cols=38 Identities=21% Similarity=0.273 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCCcccc
Q 029009 153 LTKEQSALLEESFKQHST--LNPKQKQALARQLNLRPRQV 190 (200)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~--Ps~~~r~~LA~~lgLs~rqV 190 (200)
+|..|.++|...|..--| |-.....+||.++|+++.-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 478899999999987554 65566789999999988654
No 42
>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=59.45 E-value=16 Score=19.69 Aligned_cols=38 Identities=18% Similarity=0.225 Sum_probs=25.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q 029009 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWF 194 (200)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWF 194 (200)
.++..+...+...|... + ....+|..++++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 35566666666666532 2 35578899999988888774
No 43
>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=58.98 E-value=3.7 Score=28.20 Aligned_cols=43 Identities=19% Similarity=0.352 Sum_probs=27.6
Q ss_pred CCCccCCHHHHHHHHHHH-hhCCCCCHHHHHHHHHHhCCCccccccccc
Q 029009 148 RKKLRLTKEQSALLEESF-KQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (200)
Q Consensus 148 r~Rt~ft~~Ql~~Le~~F-~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQ 195 (200)
++|.+|+.++...+-..+ ... .....+|.++|+++.+|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence 456789999877666555 322 3567899999999999999963
No 44
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=52.55 E-value=10 Score=38.69 Aligned_cols=17 Identities=24% Similarity=0.317 Sum_probs=12.6
Q ss_pred CCCCCCCccCCHHHHHH
Q 029009 144 GVNARKKLRLTKEQSAL 160 (200)
Q Consensus 144 ~k~rr~Rt~ft~~Ql~~ 160 (200)
+.+||-|.++.++|...
T Consensus 1292 ~~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1292 GGKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred CccccCCCCCChHHhhh
Confidence 34677788899988766
No 45
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=50.99 E-value=15 Score=25.50 Aligned_cols=44 Identities=27% Similarity=0.376 Sum_probs=22.7
Q ss_pred CccCCHHH-HHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccc
Q 029009 150 KLRLTKEQ-SALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (200)
Q Consensus 150 Rt~ft~~Q-l~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQ 195 (200)
|..|+... +.+++..++.+.. -..+|. .|.++|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc-~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNC-KGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTT-TT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccch-hhhHHH-HHHHhCccHHHHHHHHH
Confidence 34555555 4455554443321 112333 49999999999999975
No 46
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=50.75 E-value=6.2 Score=27.45 Aligned_cols=19 Identities=16% Similarity=0.426 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCcccccccc
Q 029009 176 KQALARQLNLRPRQVEVWF 194 (200)
Q Consensus 176 r~~LA~~lgLs~rqVqvWF 194 (200)
...||.+||+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 4578999999999999994
No 47
>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=50.21 E-value=8.2 Score=23.49 Aligned_cols=42 Identities=12% Similarity=0.189 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccc
Q 029009 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (200)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (200)
.++..+..++...|.... ....+|..+|++...|..|....+
T Consensus 10 ~l~~~~~~~~~~~~~~~~-----~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEGL-----SYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcCC-----CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356777788877774221 345679999999999999976543
No 48
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=45.54 E-value=33 Score=26.23 Aligned_cols=44 Identities=18% Similarity=0.240 Sum_probs=29.0
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccc
Q 029009 148 RKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (200)
Q Consensus 148 r~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQ 195 (200)
++|.+|+.++....-..+....+ ....+|.++|+++.+|..|.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 34556888875543333333332 245679999999999999964
No 49
>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=44.18 E-value=7.6 Score=25.03 Aligned_cols=41 Identities=17% Similarity=0.211 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccc
Q 029009 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (200)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (200)
+++.+..++...|-.. ....++|..+|++...|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5566667776665433 2466889999999999999986533
No 50
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=43.64 E-value=24 Score=29.53 Aligned_cols=39 Identities=21% Similarity=0.237 Sum_probs=32.3
Q ss_pred cCCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCCcccc
Q 029009 152 RLTKEQSALLEESFKQHST--LNPKQKQALARQLNLRPRQV 190 (200)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~--Ps~~~r~~LA~~lgLs~rqV 190 (200)
.+|..|+++|...|..--| |-......||+++|+++.-+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 6999999999999986544 66667789999999998654
No 51
>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=42.26 E-value=20 Score=22.85 Aligned_cols=39 Identities=10% Similarity=0.215 Sum_probs=28.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccc
Q 029009 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (200)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQ 195 (200)
.+++.+..+|...|... ..-.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHH
Confidence 46788899999998332 2356789999999999887653
No 52
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=39.28 E-value=28 Score=37.48 Aligned_cols=55 Identities=20% Similarity=0.352 Sum_probs=49.3
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccCC
Q 029009 146 NARKKLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRAR 200 (200)
Q Consensus 146 ~rr~Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRaK 200 (200)
.++-|...-.++...|-++|-.+.-|+.+.+..|......+.+++++||+|-|.|
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~r 759 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRER 759 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhh
Confidence 4556777778999999999999999999999999999999999999999998764
No 53
>PF13518 HTH_28: Helix-turn-helix domain
Probab=35.64 E-value=15 Score=23.18 Aligned_cols=21 Identities=19% Similarity=0.493 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCcccccccccc
Q 029009 176 KQALARQLNLRPRQVEVWFQN 196 (200)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQN 196 (200)
...+|.++|++..+|..|.+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHH
Confidence 446899999999999999864
No 54
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.87 E-value=14 Score=22.94 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCcccccccccc
Q 029009 176 KQALARQLNLRPRQVEVWFQN 196 (200)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQN 196 (200)
..++|+.+|++...|+.|.+.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999654
No 55
>PF11167 DUF2953: Protein of unknown function (DUF2953); InterPro: IPR021338 This family of proteins has no known function.
Probab=34.52 E-value=4.1 Score=26.88 Aligned_cols=19 Identities=37% Similarity=0.758 Sum_probs=15.5
Q ss_pred CCCCCCCCCcceeeccccc
Q 029009 1 MGFDDGCNTGLVLGLGFAS 19 (200)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~ 19 (200)
+|++|.+.||++.|+--+.
T Consensus 3 ~G~~Daa~Tgi~~G~l~~~ 21 (53)
T PF11167_consen 3 IGLGDAADTGILYGLLWAI 21 (53)
T ss_pred eeccCHHHHHHHHHHHHHH
Confidence 5899999999988876554
No 56
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.14 E-value=20 Score=26.98 Aligned_cols=41 Identities=17% Similarity=0.173 Sum_probs=29.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccccccccC
Q 029009 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRRA 199 (200)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRRa 199 (200)
+.+...+..|...... ...+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3456556666443222 2568899999999999999988774
No 57
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=30.29 E-value=21 Score=22.65 Aligned_cols=39 Identities=21% Similarity=0.209 Sum_probs=19.5
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q 029009 151 LRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWF 194 (200)
Q Consensus 151 t~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWF 194 (200)
..++.++...++..++.. .-..+||..+|.+..-|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 467888888888887643 234568999999988877665
No 58
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=30.00 E-value=45 Score=21.02 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=26.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccc
Q 029009 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWF 194 (200)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWF 194 (200)
.++.++.+.+...+... + -...||+.+|++...|..|+
T Consensus 5 ~~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHH
Confidence 46666777777777655 2 36689999999998887765
No 59
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=29.89 E-value=35 Score=22.35 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=29.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccc
Q 029009 152 RLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQN 196 (200)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQN 196 (200)
.+|+.++.+|.....-. ...++|..+++++..|+.+..+
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~ 41 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRR 41 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHH
Confidence 57888888887776543 3668899999999998887654
No 60
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=29.79 E-value=41 Score=22.49 Aligned_cols=35 Identities=34% Similarity=0.380 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccccc
Q 029009 155 KEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVW 193 (200)
Q Consensus 155 ~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvW 193 (200)
..|+..|+-.+. +...+.. +||..+|++.+.|+.-
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 357788888888 6666554 8999999999988653
No 61
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=27.83 E-value=24 Score=23.61 Aligned_cols=20 Identities=15% Similarity=0.350 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCccccccccc
Q 029009 176 KQALARQLNLRPRQVEVWFQ 195 (200)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQ 195 (200)
..++|+.+|++...|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999953
No 62
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=26.83 E-value=35 Score=27.50 Aligned_cols=43 Identities=23% Similarity=0.169 Sum_probs=32.0
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCcccccccccccc
Q 029009 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVEVWFQNRR 198 (200)
Q Consensus 150 Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVqvWFQNRR 198 (200)
...+++.|..+|...++ . . ...++|..+|++...|..|-++.+
T Consensus 4 ~~~Lt~rqreVL~lr~~-G--l---Tq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 4 ESFLTERQIEVLRLRER-G--L---TQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred ccCCCHHHHHHHHHHHc-C--C---CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45688999999987432 1 2 345889999999999999876543
No 63
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=24.77 E-value=34 Score=23.28 Aligned_cols=20 Identities=20% Similarity=0.375 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCccccccccc
Q 029009 176 KQALARQLNLRPRQVEVWFQ 195 (200)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQ 195 (200)
..+||..||++.+.|..|-+
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 45789999999999999964
No 64
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=24.54 E-value=16 Score=26.40 Aligned_cols=22 Identities=14% Similarity=0.226 Sum_probs=19.2
Q ss_pred HHHHHHHHhCCCcccccccccc
Q 029009 175 QKQALARQLNLRPRQVEVWFQN 196 (200)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQN 196 (200)
...+||..+|++...|+.|+.+
T Consensus 34 S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 34 TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CHHHHHHHHCcCHHHHHHHHhc
Confidence 4568999999999999999864
No 65
>PHA02955 hypothetical protein; Provisional
Probab=24.48 E-value=1e+02 Score=26.69 Aligned_cols=42 Identities=12% Similarity=0.203 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHhhC-CCCCHHHHHHHHHHhCCCcccccccccc
Q 029009 155 KEQSALLEESFKQH-STLNPKQKQALARQLNLRPRQVEVWFQN 196 (200)
Q Consensus 155 ~~Ql~~Le~~F~~~-~~Ps~~~r~~LA~~lgLs~rqVqvWFQN 196 (200)
..++..|-+.|... ..+..++|..+++++|+....|..||.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 44566666666654 5688899999999999999888999975
No 66
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.38 E-value=72 Score=24.13 Aligned_cols=39 Identities=23% Similarity=0.322 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCccccc
Q 029009 153 LTKEQSALLEESFKQHSTLNPKQKQALARQLNLRPRQVE 191 (200)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgLs~rqVq 191 (200)
++++|...-...|+.+--.+.-..+++|..|++++--|+
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 567777776667776666666677889999998875543
No 67
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=23.32 E-value=35 Score=21.69 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCcccccccccccc
Q 029009 176 KQALARQLNLRPRQVEVWFQNRR 198 (200)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNRR 198 (200)
..+||..+|++...|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 36789999999999999998865
No 68
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=23.26 E-value=25 Score=22.14 Aligned_cols=21 Identities=14% Similarity=0.188 Sum_probs=18.2
Q ss_pred HHHHHhCCCcccccccccccc
Q 029009 178 ALARQLNLRPRQVEVWFQNRR 198 (200)
Q Consensus 178 ~LA~~lgLs~rqVqvWFQNRR 198 (200)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 579999999999999998864
No 69
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=22.39 E-value=78 Score=22.85 Aligned_cols=21 Identities=14% Similarity=0.338 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCCccccccccc
Q 029009 175 QKQALARQLNLRPRQVEVWFQ 195 (200)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQ 195 (200)
-+..|...++|..-||++|+.
T Consensus 55 L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 55 LTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHhCCCCCeEEEEEE
Confidence 356788889999999999985
No 70
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.58 E-value=1.2e+02 Score=22.54 Aligned_cols=42 Identities=12% Similarity=0.184 Sum_probs=32.2
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-Cccccccccc
Q 029009 150 KLRLTKEQSALLEESFKQHSTLNPKQKQALARQLNL-RPRQVEVWFQ 195 (200)
Q Consensus 150 Rt~ft~~Ql~~Le~~F~~~~~Ps~~~r~~LA~~lgL-s~rqVqvWFQ 195 (200)
|.+|+.+....+-..+....+ -...+|+++|+ ...++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 678999987776666655544 46689999996 9999998864
No 71
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=21.53 E-value=33 Score=21.55 Aligned_cols=22 Identities=18% Similarity=0.450 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCcccccccccc
Q 029009 175 QKQALARQLNLRPRQVEVWFQN 196 (200)
Q Consensus 175 ~r~~LA~~lgLs~rqVqvWFQN 196 (200)
-..++|+.+|++...|..|.+.
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4567899999999999999764
No 72
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=21.49 E-value=37 Score=20.40 Aligned_cols=22 Identities=18% Similarity=0.469 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCccccccccccc
Q 029009 176 KQALARQLNLRPRQVEVWFQNR 197 (200)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQNR 197 (200)
..++|+.+|++...|..|.++.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3578889999999999997543
No 73
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.03 E-value=1.1e+02 Score=22.05 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCCccccccccc
Q 029009 153 LTKEQSALLEESFKQ-----HSTLNPKQKQALARQLNLRPRQVEVWFQ 195 (200)
Q Consensus 153 ft~~Ql~~Le~~F~~-----~~~Ps~~~r~~LA~~lgLs~rqVqvWFQ 195 (200)
++.+|+..+...|.. ..+.+..+...+...++++..+|+.+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 567778888888764 3457777777766667887777776653
No 74
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=20.13 E-value=42 Score=22.48 Aligned_cols=21 Identities=5% Similarity=0.325 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCcccccccccc
Q 029009 176 KQALARQLNLRPRQVEVWFQN 196 (200)
Q Consensus 176 r~~LA~~lgLs~rqVqvWFQN 196 (200)
..++|+.+|++.+.|+.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999653
Done!