Query 029106
Match_columns 199
No_of_seqs 241 out of 1466
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 07:36:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029106.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029106hhsearch_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 6.3E-17 1.4E-21 143.6 4.8 54 146-199 153-207 (307)
2 KOG0489 Transcription factor z 99.6 2.2E-17 4.7E-22 143.9 0.9 59 141-199 154-213 (261)
3 KOG0487 Transcription factor A 99.6 5.4E-17 1.2E-21 144.0 3.2 56 144-199 233-289 (308)
4 KOG0488 Transcription factor B 99.6 1.7E-16 3.6E-21 141.6 3.3 56 144-199 170-226 (309)
5 KOG0850 Transcription factor D 99.6 3.5E-16 7.6E-21 133.3 3.5 58 142-199 118-176 (245)
6 KOG0484 Transcription factor P 99.6 1.2E-16 2.7E-21 121.8 -0.0 55 145-199 16-71 (125)
7 KOG0493 Transcription factor E 99.6 1.8E-15 3.8E-20 131.4 6.4 54 146-199 246-300 (342)
8 KOG0843 Transcription factor E 99.6 6.3E-16 1.4E-20 127.7 3.3 55 145-199 101-156 (197)
9 KOG0485 Transcription factor N 99.6 2E-15 4.3E-20 128.1 5.2 58 142-199 100-158 (268)
10 KOG0492 Transcription factor M 99.6 2.2E-15 4.7E-20 127.1 3.8 57 143-199 141-198 (246)
11 PF00046 Homeobox: Homeobox do 99.5 2.3E-15 5.1E-20 101.5 1.6 53 147-199 1-54 (57)
12 KOG2251 Homeobox transcription 99.5 1.5E-14 3.3E-19 122.7 4.3 56 144-199 35-91 (228)
13 KOG0494 Transcription factor C 99.5 1.8E-14 3.9E-19 125.0 3.4 52 148-199 143-195 (332)
14 TIGR01565 homeo_ZF_HD homeobox 99.5 7.3E-14 1.6E-18 96.4 5.5 52 146-197 1-57 (58)
15 smart00389 HOX Homeodomain. DN 99.5 3.8E-14 8.2E-19 94.7 3.1 53 147-199 1-54 (56)
16 KOG0848 Transcription factor C 99.4 2E-14 4.2E-19 125.1 0.7 53 147-199 200-253 (317)
17 KOG0483 Transcription factor H 99.4 5.3E-14 1.2E-18 118.4 3.0 54 146-199 50-104 (198)
18 cd00086 homeodomain Homeodomai 99.4 6.7E-14 1.5E-18 94.0 2.5 52 148-199 2-54 (59)
19 KOG0491 Transcription factor B 99.4 2.9E-14 6.2E-19 116.6 -1.8 54 146-199 100-154 (194)
20 COG5576 Homeodomain-containing 99.4 3.1E-13 6.8E-18 110.0 4.0 59 141-199 46-105 (156)
21 KOG0844 Transcription factor E 99.4 1.8E-13 4E-18 121.1 1.4 55 145-199 180-235 (408)
22 KOG3802 Transcription factor O 99.3 2.1E-12 4.5E-17 117.6 5.0 57 143-199 291-348 (398)
23 KOG0486 Transcription factor P 99.3 2.5E-12 5.5E-17 114.0 4.3 55 145-199 111-166 (351)
24 KOG4577 Transcription factor L 99.3 2.1E-12 4.7E-17 113.6 3.2 58 142-199 163-221 (383)
25 KOG0847 Transcription factor, 99.1 1.7E-11 3.6E-16 104.6 1.2 58 142-199 163-221 (288)
26 KOG0490 Transcription factor, 99.1 4.9E-11 1.1E-15 99.7 2.8 56 144-199 58-114 (235)
27 KOG0849 Transcription factor P 98.8 2E-09 4.3E-14 97.9 3.0 56 144-199 174-230 (354)
28 KOG1168 Transcription factor A 98.8 3.6E-09 7.8E-14 93.5 2.7 58 142-199 305-363 (385)
29 KOG0775 Transcription factor S 98.5 8.8E-08 1.9E-12 84.1 5.1 47 153-199 183-230 (304)
30 KOG0774 Transcription factor P 98.2 7.8E-07 1.7E-11 77.9 3.1 54 146-199 188-245 (334)
31 PF05920 Homeobox_KN: Homeobox 98.1 3E-07 6.5E-12 58.9 -1.7 33 167-199 7-40 (40)
32 KOG2252 CCAAT displacement pro 97.9 6.6E-06 1.4E-10 78.1 3.3 55 145-199 419-474 (558)
33 KOG0490 Transcription factor, 97.8 8.6E-06 1.9E-10 68.0 2.4 57 143-199 150-207 (235)
34 KOG1146 Homeobox protein [Gene 97.1 0.0002 4.3E-09 73.9 2.1 54 146-199 903-957 (1406)
35 PF11569 Homez: Homeodomain le 96.9 0.0003 6.4E-09 48.3 0.3 40 158-197 10-50 (56)
36 KOG0773 Transcription factor M 96.7 0.001 2.3E-08 59.6 2.9 54 146-199 239-296 (342)
37 KOG3623 Homeobox transcription 93.6 0.033 7.1E-07 55.3 1.6 42 158-199 568-610 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 91.9 0.18 3.9E-06 33.7 2.9 47 147-197 1-47 (53)
39 PF04618 HD-ZIP_N: HD-ZIP prot 89.9 1.7 3.7E-05 33.8 6.9 21 93-114 86-106 (111)
40 PF01527 HTH_Tnp_1: Transposas 62.9 3.9 8.4E-05 28.1 1.0 43 148-194 2-45 (76)
41 PF04967 HTH_10: HTH DNA bindi 60.3 10 0.00022 25.5 2.7 37 153-189 1-40 (53)
42 KOG3623 Homeobox transcription 56.7 12 0.00026 37.9 3.5 52 147-198 627-679 (1007)
43 cd06171 Sigma70_r4 Sigma70, re 53.9 5.7 0.00012 24.2 0.6 41 153-197 11-51 (55)
44 cd00569 HTH_Hin_like Helix-tur 53.7 20 0.00043 19.3 2.9 37 153-193 6-42 (42)
45 PF09607 BrkDBD: Brinker DNA-b 52.0 11 0.00023 26.1 1.7 45 150-195 3-48 (58)
46 PF10668 Phage_terminase: Phag 50.3 5.1 0.00011 27.8 -0.1 20 174-193 24-43 (60)
47 PF08281 Sigma70_r4_2: Sigma-7 46.7 5.5 0.00012 25.7 -0.3 41 153-197 11-51 (54)
48 PHA03308 transcriptional regul 44.7 19 0.0004 36.8 2.8 18 143-160 1291-1308(1463)
49 COG3413 Predicted DNA binding 43.9 26 0.00056 29.3 3.2 38 152-189 155-195 (215)
50 PRK10072 putative transcriptio 43.8 21 0.00045 26.8 2.4 41 152-198 32-72 (96)
51 PF04545 Sigma70_r4: Sigma-70, 41.1 20 0.00043 22.8 1.7 39 152-194 4-42 (50)
52 KOG1146 Homeobox protein [Gene 40.4 11 0.00025 40.1 0.6 52 146-197 444-496 (1406)
53 PRK09413 IS2 repressor TnpA; R 38.6 40 0.00087 25.7 3.3 42 149-194 9-51 (121)
54 cd04761 HTH_MerR-SF Helix-Turn 37.0 11 0.00023 23.5 -0.1 21 175-195 3-23 (49)
55 PRK03975 tfx putative transcri 35.8 18 0.00039 29.1 1.0 43 150-197 4-46 (141)
56 PF13518 HTH_28: Helix-turn-he 34.7 13 0.00029 23.3 0.1 21 175-195 15-35 (52)
57 PF11167 DUF2953: Protein of u 33.2 5.3 0.00012 26.3 -2.1 18 1-18 3-20 (53)
58 PF00196 GerE: Bacterial regul 32.3 12 0.00027 24.6 -0.4 39 152-195 3-41 (58)
59 COG4367 Uncharacterized protei 31.3 42 0.0009 25.3 2.2 37 153-189 3-40 (97)
60 TIGR03879 near_KaiC_dom probab 31.0 10 0.00023 27.2 -1.0 22 174-195 34-55 (73)
61 PF02796 HTH_7: Helix-turn-hel 29.7 35 0.00077 21.5 1.4 37 153-193 6-42 (45)
62 PF13936 HTH_38: Helix-turn-he 29.2 18 0.00039 22.9 -0.0 39 151-193 3-41 (44)
63 smart00421 HTH_LUXR helix_turn 29.1 30 0.00065 21.4 1.0 38 153-195 4-41 (58)
64 PF13443 HTH_26: Cro/C1-type H 28.3 18 0.00038 23.8 -0.2 22 175-196 13-34 (63)
65 COG2944 Predicted transcriptio 27.9 54 0.0012 25.2 2.4 40 153-198 44-83 (104)
66 cd02413 40S_S3_KH K homology R 26.7 51 0.0011 23.8 2.0 20 175-194 56-75 (81)
67 cd01392 HTH_LacI Helix-turn-he 25.1 19 0.00041 22.7 -0.5 21 177-197 2-22 (52)
68 PF13411 MerR_1: MerR HTH fami 25.1 24 0.00053 23.5 0.0 19 176-194 4-22 (69)
69 PF13384 HTH_23: Homeodomain-l 24.9 21 0.00046 22.4 -0.3 22 174-195 19-40 (50)
70 PF06056 Terminase_5: Putative 23.7 30 0.00065 23.5 0.3 21 174-194 15-35 (58)
71 cd04762 HTH_MerR-trunc Helix-T 23.1 28 0.0006 20.9 -0.0 22 175-196 3-24 (49)
72 PF01381 HTH_3: Helix-turn-hel 22.9 29 0.00064 22.0 0.1 23 175-197 12-34 (55)
73 PF08280 HTH_Mga: M protein tr 22.8 67 0.0015 21.4 1.9 34 155-191 5-38 (59)
74 PHA02955 hypothetical protein; 22.7 1E+02 0.0022 26.6 3.4 41 155-195 60-102 (213)
75 TIGR03070 couple_hipB transcri 22.0 34 0.00074 21.5 0.3 23 175-197 18-40 (58)
76 cd06170 LuxR_C_like C-terminal 21.4 96 0.0021 19.1 2.4 36 154-194 2-37 (57)
77 PRK09646 RNA polymerase sigma 21.0 44 0.00095 27.0 0.8 41 153-197 143-183 (194)
No 1
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.66 E-value=6.3e-17 Score=143.60 Aligned_cols=54 Identities=35% Similarity=0.675 Sum_probs=49.5
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 146 NARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+||.|.-|+..|+.+||+.|+.++|++. +|++||..|.|++.||||||||||-|
T Consensus 153 kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK 207 (307)
T KOG0842|consen 153 KRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYK 207 (307)
T ss_pred ccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhh
Confidence 4444445999999999999999999999 99999999999999999999999976
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.65 E-value=2.2e-17 Score=143.92 Aligned_cols=59 Identities=34% Similarity=0.607 Sum_probs=55.3
Q ss_pred CcCCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 141 ~~~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
...++.||.|+.||..|+.+||+.|..++|+++ .|.+||..|.|+++||||||||||||
T Consensus 154 ~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK 213 (261)
T KOG0489|consen 154 ETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMK 213 (261)
T ss_pred cccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHH
Confidence 334557899999999999999999999999999 99999999999999999999999997
No 3
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.65 E-value=5.4e-17 Score=144.04 Aligned_cols=56 Identities=38% Similarity=0.589 Sum_probs=53.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 144 GVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 144 g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+..||||..+|+.|+.+||+.|..+.|++. .|.+|++.|+|++|||||||||||+|
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK 289 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMK 289 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhH
Confidence 457899999999999999999999999999 99999999999999999999999997
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.62 E-value=1.7e-16 Score=141.56 Aligned_cols=56 Identities=30% Similarity=0.498 Sum_probs=53.6
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 144 GVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 144 g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+++|+.|+.||..|+..||+.|++++|++. +|.+||..|||+..||++||||||+|
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 567788999999999999999999999999 99999999999999999999999997
No 5
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.60 E-value=3.5e-16 Score=133.31 Aligned_cols=58 Identities=29% Similarity=0.460 Sum_probs=54.1
Q ss_pred cCCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 142 ~~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+.+|.|+.||.|+.-||..|.++|++..|+-. +|.+||..|||+..||||||||||.|
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK 176 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSK 176 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHH
Confidence 34557788999999999999999999999999 99999999999999999999999986
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.59 E-value=1.2e-16 Score=121.76 Aligned_cols=55 Identities=31% Similarity=0.505 Sum_probs=52.7
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 145 VNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 145 ~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
++||-|+.|+..|+..||+.|...+||++ .|++||..+.|++.+|||||||||+|
T Consensus 16 KQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAK 71 (125)
T KOG0484|consen 16 KQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAK 71 (125)
T ss_pred HhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHH
Confidence 46788999999999999999999999999 99999999999999999999999986
No 7
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.59 E-value=1.8e-15 Score=131.40 Aligned_cols=54 Identities=35% Similarity=0.647 Sum_probs=51.5
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 146 NARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.||.|+.|+.+||..|+..|+.++|++. .|++||.+|+|.+.||||||||+|+|
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAK 300 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAK 300 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhh
Confidence 4677889999999999999999999999 99999999999999999999999987
No 8
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.58 E-value=6.3e-16 Score=127.69 Aligned_cols=55 Identities=36% Similarity=0.556 Sum_probs=52.8
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 145 VNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 145 ~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+.||.||.|+.+|+..||..|+.+.|..- +|++||..|+|++.||||||||||.|
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 57889999999999999999999999999 99999999999999999999999986
No 9
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.57 E-value=2e-15 Score=128.11 Aligned_cols=58 Identities=31% Similarity=0.556 Sum_probs=53.9
Q ss_pred cCCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 142 ~~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.++.+||.|++|+..|+..||..|+..+|++. +|..||++|.|++.||||||||||.|
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnK 158 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNK 158 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHH
Confidence 34457778889999999999999999999999 99999999999999999999999986
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.55 E-value=2.2e-15 Score=127.05 Aligned_cols=57 Identities=32% Similarity=0.564 Sum_probs=53.9
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 143 ~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.+..|+.|+.|+.+|+..||+.|+..+|+++ +|.+++..|.|++.||||||||||+|
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAK 198 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAK 198 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHH
Confidence 4457888999999999999999999999999 99999999999999999999999987
No 11
>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=99.53 E-value=2.3e-15 Score=101.51 Aligned_cols=53 Identities=45% Similarity=0.740 Sum_probs=50.6
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 147 ARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
||+|+.|+.+|+.+|+..|..++||+. +++.||..+||+..+|++||+|||+|
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 578889999999999999999999999 99999999999999999999999974
No 12
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.50 E-value=1.5e-14 Score=122.72 Aligned_cols=56 Identities=34% Similarity=0.568 Sum_probs=53.8
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 144 GVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 144 g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.+.||.||.|+-.|+.+||..|.+..||+. .|++||.+|+|.+.+|||||.|||+|
T Consensus 35 RkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK 91 (228)
T KOG2251|consen 35 RKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAK 91 (228)
T ss_pred hhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccch
Confidence 447899999999999999999999999999 99999999999999999999999997
No 13
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.48 E-value=1.8e-14 Score=125.03 Aligned_cols=52 Identities=33% Similarity=0.500 Sum_probs=49.9
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 148 RKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 148 R~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+-|+.||..|+..||+.|+..+||+. .|+.||..+.|.+.+|+|||||||+|
T Consensus 143 h~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAK 195 (332)
T KOG0494|consen 143 HFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAK 195 (332)
T ss_pred cccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHH
Confidence 34889999999999999999999999 99999999999999999999999997
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=99.47 E-value=7.3e-14 Score=96.38 Aligned_cols=52 Identities=13% Similarity=0.359 Sum_probs=49.8
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCC----CcH-HHHHHHHHhCCCCCcceecccccc
Q 029106 146 NARKKLRLTKEQSALLEESFKQHST----LNP-QKQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~----ps~-~r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
+||.|+.|+.+|+..|+..|...+| |+. ++++||..+||++++|||||||-+
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 3789999999999999999999999 999 999999999999999999999975
No 15
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.46 E-value=3.8e-14 Score=94.71 Aligned_cols=53 Identities=43% Similarity=0.685 Sum_probs=49.8
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 147 ARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
++.|+.|+.+|+.+|+..|..++||+. ++..||..+||+..||++||+|||++
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 356778999999999999999999999 99999999999999999999999975
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.43 E-value=2e-14 Score=125.13 Aligned_cols=53 Identities=38% Similarity=0.601 Sum_probs=49.8
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 147 ARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
-|.|.+++..|..+||+.|...+|+++ .+.+||..|+|++|||||||||||+|
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAK 253 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAK 253 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHH
Confidence 355677999999999999999999999 99999999999999999999999997
No 17
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.43 E-value=5.3e-14 Score=118.44 Aligned_cols=54 Identities=57% Similarity=0.903 Sum_probs=50.7
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 146 NARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
..+++.+|+.+|+..||..|+.+.++.+ ++..||++|||.+|||.|||||||||
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 4566677999999999999999999999 99999999999999999999999997
No 18
>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=99.42 E-value=6.7e-14 Score=94.00 Aligned_cols=52 Identities=44% Similarity=0.752 Sum_probs=49.3
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 148 RKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 148 R~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
++|..|+..|+.+|+..|..++||+. +++.||.++||+..||++||+|||++
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 56778999999999999999999999 99999999999999999999999974
No 19
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.38 E-value=2.9e-14 Score=116.57 Aligned_cols=54 Identities=33% Similarity=0.572 Sum_probs=51.6
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 146 NARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+++-|++|+..|+..|++.|+.++|++. +|.+||..|+|++.|||.||||||+|
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 5667899999999999999999999999 99999999999999999999999987
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.37 E-value=3.1e-13 Score=110.03 Aligned_cols=59 Identities=34% Similarity=0.568 Sum_probs=54.0
Q ss_pred CcCCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 141 DEDGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 141 ~~~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+.....+++|.+.+.+|+.+|++.|..++||+. .|..|+..++|+++-|||||||||++
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~ 105 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK 105 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHH
Confidence 334457788888999999999999999999999 99999999999999999999999975
No 21
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.35 E-value=1.8e-13 Score=121.08 Aligned_cols=55 Identities=36% Similarity=0.558 Sum_probs=52.9
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 145 VNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 145 ~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
..||.|+.|+.+|+..||+.|-+..|.++ .|.+||..|+|++..|||||||||+|
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMK 235 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMK 235 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhh
Confidence 36899999999999999999999999999 99999999999999999999999997
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.30 E-value=2.1e-12 Score=117.62 Aligned_cols=57 Identities=25% Similarity=0.440 Sum_probs=53.6
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 143 ~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.+++|||||.|.......||++|..|+.|+. ++-.||.+|+|.+..|+|||||||.|
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQk 348 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQK 348 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccc
Confidence 3467888999999999999999999999999 99999999999999999999999976
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.28 E-value=2.5e-12 Score=114.03 Aligned_cols=55 Identities=31% Similarity=0.522 Sum_probs=52.5
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 145 VNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 145 ~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
++||.|+.|+.+|+..||..|++++||+. .|++||...+|++.+|+|||.|||+|
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrak 166 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 166 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhh
Confidence 46778889999999999999999999999 99999999999999999999999997
No 24
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.27 E-value=2.1e-12 Score=113.64 Aligned_cols=58 Identities=31% Similarity=0.528 Sum_probs=54.8
Q ss_pred cCCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 142 ~~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.++..||.|+.+++.|++.|+..|+..+.|-+ .|++|+.++||..|.|||||||||||
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAK 221 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAK 221 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHH
Confidence 44558999999999999999999999999999 99999999999999999999999997
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.11 E-value=1.7e-11 Score=104.59 Aligned_cols=58 Identities=36% Similarity=0.574 Sum_probs=53.9
Q ss_pred cCCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 142 ~~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.+|+++..|..|+-.|+..|++.|+..+|+.- +|.+||..+|+++.||+|||||||.|
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTK 221 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTK 221 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhh
Confidence 56667777888999999999999999999999 99999999999999999999999986
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.08 E-value=4.9e-11 Score=99.74 Aligned_cols=56 Identities=30% Similarity=0.336 Sum_probs=52.9
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 144 GVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 144 g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.+.|+.|+.|+..|+.+|++.|...+||+. .|+.||..+++++..|+|||||||+|
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 347889999999999999999999999999 99999999999999999999999986
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.82 E-value=2e-09 Score=97.85 Aligned_cols=56 Identities=32% Similarity=0.532 Sum_probs=52.5
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 144 GVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 144 g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.+.+|.|+.|+..|+..|++.|+.++||+. .|+.||.++++++.+|+|||+|||+|
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~ 230 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAK 230 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhh
Confidence 346777899999999999999999999999 99999999999999999999999985
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.76 E-value=3.6e-09 Score=93.53 Aligned_cols=58 Identities=28% Similarity=0.477 Sum_probs=54.0
Q ss_pred cCCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 142 EDGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 142 ~~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
..+.+||||+.+...+.+.||.+|..++.|+. .+..+|.+|.|.+..|+|||+|+|.|
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK 363 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 363 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence 45668999999999999999999999999999 88999999999999999999999975
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.55 E-value=8.8e-08 Score=84.08 Aligned_cols=47 Identities=36% Similarity=0.593 Sum_probs=44.3
Q ss_pred CCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 153 LTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
|...-..+|+.+|..++||++ ++.+||+.+||+..||-.||.|||.|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR 230 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQR 230 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence 677778999999999999999 99999999999999999999999975
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.22 E-value=7.8e-07 Score=77.92 Aligned_cols=54 Identities=33% Similarity=0.548 Sum_probs=49.6
Q ss_pred CCCCCCcCCHHHHHHHHHHH---hhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 146 NARKKLRLTKEQSALLEESF---KQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F---~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.||||..|++....+|..+| ..++||+. .+++||++++++..||-.||.|+|-+
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIr 245 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIR 245 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceee
Confidence 57888899999999999999 56789999 99999999999999999999999853
No 31
>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=98.08 E-value=3e-07 Score=58.88 Aligned_cols=33 Identities=33% Similarity=0.577 Sum_probs=27.7
Q ss_pred hCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 167 QHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 167 ~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.++||+. +++.||.++||+..||..||-|.|.|
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 4789999 99999999999999999999999864
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.92 E-value=6.6e-06 Score=78.10 Aligned_cols=55 Identities=27% Similarity=0.388 Sum_probs=51.4
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 145 VNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 145 ~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
..||.|.+|+..|...|..+|+.+++|+. ..+.|+.+|+|....|..||-|-|.|
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 36778999999999999999999999999 88999999999999999999998865
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.84 E-value=8.6e-06 Score=68.02 Aligned_cols=57 Identities=32% Similarity=0.575 Sum_probs=52.2
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 143 DGVNARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 143 ~g~~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
..+.++.|+.+...|+..+...|....+|.. .++.|+..++++.+.|++||||+|++
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~ 207 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAK 207 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHH
Confidence 3446788889999999999999999999999 99999999999999999999999864
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.14 E-value=0.0002 Score=73.89 Aligned_cols=54 Identities=22% Similarity=0.419 Sum_probs=50.9
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 146 NARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+|++|++++..|+.+|...|....||.. +.+.|-..+++..+.|++||||-|.|
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 6778999999999999999999999999 88999999999999999999999975
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.86 E-value=0.0003 Score=48.29 Aligned_cols=40 Identities=25% Similarity=0.434 Sum_probs=30.1
Q ss_pred HHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceecccccc
Q 029106 158 SALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 158 l~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
+..|+++|..++++.. ....|..+.+|+..||+.||--|+
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 4569999999999999 999999999999999999996654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.74 E-value=0.001 Score=59.63 Aligned_cols=54 Identities=33% Similarity=0.405 Sum_probs=44.7
Q ss_pred CCCCCCcCCHHHHHHHHHHHh---hCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 146 NARKKLRLTKEQSALLEESFK---QHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~---~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
.+|.+..+......+|+.+.. ..+||+. ++..||.++||+..||..||-|.|-|
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 344455699999999998743 2468998 88899999999999999999999865
No 37
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.65 E-value=0.033 Score=55.34 Aligned_cols=42 Identities=21% Similarity=0.422 Sum_probs=39.4
Q ss_pred HHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccCC
Q 029106 158 SALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRAR 199 (199)
Q Consensus 158 l~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRaK 199 (199)
+.+|..+|..+..|+. +...+|.+.||+.+.|+.||++++++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~ 610 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAE 610 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhh
Confidence 7889999999999999 99999999999999999999999863
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=91.91 E-value=0.18 Score=33.75 Aligned_cols=47 Identities=21% Similarity=0.350 Sum_probs=33.5
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecccccc
Q 029106 147 ARKKLRLTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
||+|..+|-++...+-..++... ....||.++|+...+|..|..|+.
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 57788899888776666676554 466899999999999999998863
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=89.89 E-value=1.7 Score=33.77 Aligned_cols=21 Identities=33% Similarity=0.344 Sum_probs=14.7
Q ss_pred hhccCCCCCCCCCCCCcccCCC
Q 029106 93 YQILNRQASPHSAVSNSFSSGR 114 (199)
Q Consensus 93 ~~~l~~~sSp~S~~S~S~S~~~ 114 (199)
-.|...-+||+|.+| |+|..+
T Consensus 86 ~eEe~gvSSPNStiS-S~sgkr 106 (111)
T PF04618_consen 86 CEEEAGVSSPNSTIS-SVSGKR 106 (111)
T ss_pred ccccccccCCCccce-eccccc
Confidence 344566789999998 766544
No 40
>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=62.88 E-value=3.9 Score=28.07 Aligned_cols=43 Identities=19% Similarity=0.299 Sum_probs=26.5
Q ss_pred CCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccc
Q 029106 148 RKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQ 194 (199)
Q Consensus 148 R~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQ 194 (199)
++|..|+.++...+-..+. ... ....+|.++|+++.++..|-+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHH
Confidence 4566788888665555441 113 677899999999999999963
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=60.25 E-value=10 Score=25.50 Aligned_cols=37 Identities=22% Similarity=0.299 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhhCCC--CcH-HHHHHHHHhCCCCCcc
Q 029106 153 LTKEQSALLEESFKQHST--LNP-QKQALARQLNLRPRQV 189 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~--ps~-~r~~LA~~LgLs~rQV 189 (199)
+|..|..+|...|..--| |-. ...+||.+||++..-|
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 578899999999986554 434 6789999999987644
No 42
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=56.75 E-value=12 Score=37.94 Aligned_cols=52 Identities=19% Similarity=0.385 Sum_probs=38.9
Q ss_pred CCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceeccccccC
Q 029106 147 ARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRRA 198 (199)
Q Consensus 147 rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRRa 198 (199)
-|-++....++...|...|..+..+.. +....+.+|-..+..|++||++|+.
T Consensus 627 ~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrss 679 (1007)
T KOG3623|consen 627 VKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSS 679 (1007)
T ss_pred ccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCC
Confidence 344566666777778888887777776 6555566677888889999999986
No 43
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=53.89 E-value=5.7 Score=24.22 Aligned_cols=41 Identities=12% Similarity=0.172 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecccccc
Q 029106 153 LTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
++..+..++...|.... ...++|..+|++...|..|....+
T Consensus 11 l~~~~~~~~~~~~~~~~----~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred CCHHHHHHHHHHHhcCC----CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56677777776663221 356789999999999999986544
No 44
>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=53.75 E-value=20 Score=19.25 Aligned_cols=37 Identities=19% Similarity=0.210 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecc
Q 029106 153 LTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWF 193 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWF 193 (199)
++..+...+...|.... ....+|..++++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcCC----CHHHHHHHHCCCHHHHHHhC
Confidence 55666666666664321 34577889999988887774
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=51.97 E-value=11 Score=26.08 Aligned_cols=45 Identities=29% Similarity=0.380 Sum_probs=23.3
Q ss_pred CCcCCHHH-HHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecccc
Q 029106 150 KLRLTKEQ-SALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQN 195 (199)
Q Consensus 150 Rt~ft~~Q-l~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQN 195 (199)
|..|+... +.+++.++.....-.-+|.. |.++|+.+++|+-|-+-
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAa-arkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAA-ARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHH-HHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHH-HHHhCccHHHHHHHHHH
Confidence 34466554 45555444333221114444 99999999999999753
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=50.26 E-value=5.1 Score=27.79 Aligned_cols=20 Identities=15% Similarity=0.429 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCCCcceecc
Q 029106 174 QKQALARQLNLRPRQVEVWF 193 (199)
Q Consensus 174 ~r~~LA~~LgLs~rQVqvWF 193 (199)
...+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45678999999999999994
No 47
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=46.66 E-value=5.5 Score=25.67 Aligned_cols=41 Identities=17% Similarity=0.211 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecccccc
Q 029106 153 LTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
+++.+..++...|-... ...++|..+|++...|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~~g~----s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQGM----SYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS-------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHCc----CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 55666666666543221 567899999999999999987544
No 48
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=44.69 E-value=19 Score=36.79 Aligned_cols=18 Identities=22% Similarity=0.302 Sum_probs=13.0
Q ss_pred CCCCCCCCCcCCHHHHHH
Q 029106 143 DGVNARKKLRLTKEQSAL 160 (199)
Q Consensus 143 ~g~~rR~Rt~ft~~Ql~~ 160 (199)
.+.+||-|.++..+|..+
T Consensus 1291 g~~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1291 GGGKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred CCccccCCCCCChHHhhh
Confidence 344677788888888766
No 49
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=43.89 E-value=26 Score=29.28 Aligned_cols=38 Identities=21% Similarity=0.258 Sum_probs=30.6
Q ss_pred cCCHHHHHHHHHHHhhCCC--CcH-HHHHHHHHhCCCCCcc
Q 029106 152 RLTKEQSALLEESFKQHST--LNP-QKQALARQLNLRPRQV 189 (199)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~--ps~-~r~~LA~~LgLs~rQV 189 (199)
.+|..|+.+|..+|..--| |-. ...+||+++|+++.-+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 5999999999999986544 444 6789999999987543
No 50
>PRK10072 putative transcriptional regulator; Provisional
Probab=43.82 E-value=21 Score=26.81 Aligned_cols=41 Identities=17% Similarity=0.173 Sum_probs=29.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceeccccccC
Q 029106 152 RLTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQNRRA 198 (199)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQNRRa 198 (199)
+.+...+..|...... ...+||..+|++...|..|.+.+|.
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 3456666666443221 3568999999999999999998874
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=41.07 E-value=20 Score=22.78 Aligned_cols=39 Identities=10% Similarity=0.215 Sum_probs=28.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceeccc
Q 029106 152 RLTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQ 194 (199)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQ 194 (199)
.+++.+..+|...|.... .-.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~~~----t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL----TLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTST-----SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC----CHHHHHHHHCCcHHHHHHHHH
Confidence 367888899999883221 456889999999998887653
No 52
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=40.40 E-value=11 Score=40.13 Aligned_cols=52 Identities=19% Similarity=0.078 Sum_probs=42.8
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcceecccccc
Q 029106 146 NARKKLRLTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 146 ~rR~Rt~ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
.+-.++++..-|...|...|+...+|.- +...++..|++..|.+-.|||+++
T Consensus 444 ~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~ 496 (1406)
T KOG1146|consen 444 PLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAY 496 (1406)
T ss_pred hhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhH
Confidence 4455677888899999999988889988 999999999999999666666543
No 53
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=38.59 E-value=40 Score=25.70 Aligned_cols=42 Identities=24% Similarity=0.423 Sum_probs=27.8
Q ss_pred CCCcCCHHHHH-HHHHHHhhCCCCcHHHHHHHHHhCCCCCcceeccc
Q 029106 149 KKLRLTKEQSA-LLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQ 194 (199)
Q Consensus 149 ~Rt~ft~~Ql~-~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQ 194 (199)
+|.+|+.++.. ++...+.. .. ...++|.++|+++.+|..|.+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~-g~---sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEP-GM---TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcC-CC---CHHHHHHHHCcCHHHHHHHHH
Confidence 34557777644 44444432 21 345789999999999999964
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=36.97 E-value=11 Score=23.48 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCCCcceecccc
Q 029106 175 KQALARQLNLRPRQVEVWFQN 195 (199)
Q Consensus 175 r~~LA~~LgLs~rQVqvWFQN 195 (199)
..++|+.+|+++..|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999654
No 55
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=35.79 E-value=18 Score=29.07 Aligned_cols=43 Identities=21% Similarity=0.127 Sum_probs=32.3
Q ss_pred CCcCCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecccccc
Q 029106 150 KLRLTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 150 Rt~ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
...+++.|..+|...++.. ...++|..||++...|+.|-++.+
T Consensus 4 ~~~Lt~rqreVL~lr~~Gl-----Tq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 4 ESFLTERQIEVLRLRERGL-----TQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred ccCCCHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3468899999997743211 356899999999999999886544
No 56
>PF13518 HTH_28: Helix-turn-helix domain
Probab=34.72 E-value=13 Score=23.31 Aligned_cols=21 Identities=19% Similarity=0.493 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCCCcceecccc
Q 029106 175 KQALARQLNLRPRQVEVWFQN 195 (199)
Q Consensus 175 r~~LA~~LgLs~rQVqvWFQN 195 (199)
..++|.++|++..+|..|.+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHH
Confidence 456899999999999999864
No 57
>PF11167 DUF2953: Protein of unknown function (DUF2953); InterPro: IPR021338 This family of proteins has no known function.
Probab=33.18 E-value=5.3 Score=26.26 Aligned_cols=18 Identities=39% Similarity=0.833 Sum_probs=14.6
Q ss_pred CCCCCCCcccceeccccc
Q 029106 1 MGFDDGCNTGLVLGLGFA 18 (199)
Q Consensus 1 ~~~~~~~~~~l~l~~g~~ 18 (199)
+|++|.+.||++.|+--+
T Consensus 3 ~G~~Daa~Tgi~~G~l~~ 20 (53)
T PF11167_consen 3 IGLGDAADTGILYGLLWA 20 (53)
T ss_pred eeccCHHHHHHHHHHHHH
Confidence 589999999998887544
No 58
>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=32.29 E-value=12 Score=24.57 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=29.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecccc
Q 029106 152 RLTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQN 195 (199)
Q Consensus 152 ~ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQN 195 (199)
.||+.++.+|....... ...++|..+++++..|+.+..+
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 47888888888776543 4678899999999998887654
No 59
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.26 E-value=42 Score=25.31 Aligned_cols=37 Identities=22% Similarity=0.326 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhCCCCcH-HHHHHHHHhCCCCCcc
Q 029106 153 LTKEQSALLEESFKQHSTLNP-QKQALARQLNLRPRQV 189 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~-~r~~LA~~LgLs~rQV 189 (199)
+.++|...-...|+.+.-++. ..+++|..|++++-.|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 567888888888888877888 8889999999887544
No 60
>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=31.02 E-value=10 Score=27.22 Aligned_cols=22 Identities=14% Similarity=0.226 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCCCCcceecccc
Q 029106 174 QKQALARQLNLRPRQVEVWFQN 195 (199)
Q Consensus 174 ~r~~LA~~LgLs~rQVqvWFQN 195 (199)
...++|..+|++...|+.|+.+
T Consensus 34 S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 34 TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CHHHHHHHHCcCHHHHHHHHhc
Confidence 5678999999999999999865
No 61
>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=29.67 E-value=35 Score=21.48 Aligned_cols=37 Identities=22% Similarity=0.323 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecc
Q 029106 153 LTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWF 193 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWF 193 (199)
++.++...+...+.... ...++|+.+|++...|..|+
T Consensus 6 ~~~~~~~~i~~l~~~G~----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEGM----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCCC----CHHHHHHHHCcCHHHHHHHH
Confidence 66666666666665441 46689999999998887765
No 62
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=29.23 E-value=18 Score=22.88 Aligned_cols=39 Identities=21% Similarity=0.209 Sum_probs=18.9
Q ss_pred CcCCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecc
Q 029106 151 LRLTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWF 193 (199)
Q Consensus 151 t~ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWF 193 (199)
..++..+...++..+.... ...++|..+|.+...|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~----s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM----SIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS-------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC----CHHHHHHHHCcCcHHHHHHH
Confidence 4578888888888765331 34568999999988776664
No 63
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=29.14 E-value=30 Score=21.35 Aligned_cols=38 Identities=18% Similarity=0.295 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecccc
Q 029106 153 LTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQN 195 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQN 195 (199)
++..+..++...+... ...++|..++++...|+.|.+.
T Consensus 4 l~~~e~~i~~~~~~g~-----s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 4 LTPREREVLRLLAEGL-----TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHH
Confidence 5677777775543211 3567899999999999888654
No 64
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.26 E-value=18 Score=23.84 Aligned_cols=22 Identities=14% Similarity=0.303 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCCCcceeccccc
Q 029106 175 KQALARQLNLRPRQVEVWFQNR 196 (199)
Q Consensus 175 r~~LA~~LgLs~rQVqvWFQNR 196 (199)
...||+.+|++..+|..|+.++
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT
T ss_pred HHHHHHHHCcCHHHHHHHHhcc
Confidence 5678999999999999999877
No 65
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=27.92 E-value=54 Score=25.20 Aligned_cols=40 Identities=23% Similarity=0.371 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceeccccccC
Q 029106 153 LTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQNRRA 198 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQNRRa 198 (199)
++..++..+.+.+... ....|..||++...|+-|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lS------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLS------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCC------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 8888888888876543 567899999999999999999874
No 66
>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=26.75 E-value=51 Score=23.78 Aligned_cols=20 Identities=15% Similarity=0.381 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCCcceeccc
Q 029106 175 KQALARQLNLRPRQVEVWFQ 194 (199)
Q Consensus 175 r~~LA~~LgLs~rQVqvWFQ 194 (199)
++.|...++|..-||++|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 56788899999999999985
No 67
>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=25.07 E-value=19 Score=22.70 Aligned_cols=21 Identities=14% Similarity=0.188 Sum_probs=18.2
Q ss_pred HHHHHhCCCCCcceecccccc
Q 029106 177 ALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 177 ~LA~~LgLs~rQVqvWFQNRR 197 (199)
+||..+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 588999999999999998874
No 68
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.06 E-value=24 Score=23.54 Aligned_cols=19 Identities=16% Similarity=0.405 Sum_probs=16.5
Q ss_pred HHHHHHhCCCCCcceeccc
Q 029106 176 QALARQLNLRPRQVEVWFQ 194 (199)
Q Consensus 176 ~~LA~~LgLs~rQVqvWFQ 194 (199)
.++|+.+|++...|+.|=+
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999953
No 69
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.90 E-value=21 Score=22.41 Aligned_cols=22 Identities=18% Similarity=0.450 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCCCcceecccc
Q 029106 174 QKQALARQLNLRPRQVEVWFQN 195 (199)
Q Consensus 174 ~r~~LA~~LgLs~rQVqvWFQN 195 (199)
...++|..+|++...|..|.+.
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 4568899999999999999764
No 70
>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=23.72 E-value=30 Score=23.48 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCCCcceeccc
Q 029106 174 QKQALARQLNLRPRQVEVWFQ 194 (199)
Q Consensus 174 ~r~~LA~~LgLs~rQVqvWFQ 194 (199)
...++|..||++.+.|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 356899999999999999964
No 71
>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=23.06 E-value=28 Score=20.94 Aligned_cols=22 Identities=18% Similarity=0.469 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCCCcceeccccc
Q 029106 175 KQALARQLNLRPRQVEVWFQNR 196 (199)
Q Consensus 175 r~~LA~~LgLs~rQVqvWFQNR 196 (199)
..++|..+|++.+.|..|.++.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3578888999999999887543
No 72
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.89 E-value=29 Score=22.00 Aligned_cols=23 Identities=17% Similarity=0.310 Sum_probs=19.2
Q ss_pred HHHHHHHhCCCCCcceecccccc
Q 029106 175 KQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 175 r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
..+||..+|+++..|..|..++|
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 46799999999999999998865
No 73
>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=22.80 E-value=67 Score=21.36 Aligned_cols=34 Identities=32% Similarity=0.428 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCccee
Q 029106 155 KEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEV 191 (199)
Q Consensus 155 ~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqv 191 (199)
..|+.+|+-.|. +...+ ..+||..++++++.|+.
T Consensus 5 ~rq~~Ll~~L~~-~~~~~--~~ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWIT--LKELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHHH-HTSBB--HHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHHc-CCCCc--HHHHHHHHCCCHHHHHH
Confidence 356778888887 55444 44899999999988764
No 74
>PHA02955 hypothetical protein; Provisional
Probab=22.70 E-value=1e+02 Score=26.59 Aligned_cols=41 Identities=10% Similarity=0.182 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhhC-CCCcH-HHHHHHHHhCCCCCcceecccc
Q 029106 155 KEQSALLEESFKQH-STLNP-QKQALARQLNLRPRQVEVWFQN 195 (199)
Q Consensus 155 ~~Ql~~Le~~F~~~-~~ps~-~r~~LA~~LgLs~rQVqvWFQN 195 (199)
..|+..|-+.|... ..+.. +|..++++||+....|..||.+
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 45667777777544 45667 9999999999999878999976
No 75
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=22.02 E-value=34 Score=21.48 Aligned_cols=23 Identities=13% Similarity=0.036 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCCcceecccccc
Q 029106 175 KQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 175 r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46799999999999999997765
No 76
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=21.45 E-value=96 Score=19.07 Aligned_cols=36 Identities=14% Similarity=0.232 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceeccc
Q 029106 154 TKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQ 194 (199)
Q Consensus 154 t~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQ 194 (199)
+..+..++...+.. + ...++|..++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~~~--~---s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAEG--K---TNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHcC--C---CHHHHHHHHCCCHHHHHHHHH
Confidence 34455555443321 1 456789999999999998864
No 77
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=21.03 E-value=44 Score=26.97 Aligned_cols=41 Identities=15% Similarity=0.146 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhCCCCcHHHHHHHHHhCCCCCcceecccccc
Q 029106 153 LTKEQSALLEESFKQHSTLNPQKQALARQLNLRPRQVEVWFQNRR 197 (199)
Q Consensus 153 ft~~Ql~~Le~~F~~~~~ps~~r~~LA~~LgLs~rQVqvWFQNRR 197 (199)
++..+..+|...|-... .-.++|..||++...|++|...-|
T Consensus 143 L~~~~r~vl~l~~~~~~----s~~EIA~~Lgis~~tVk~~l~ra~ 183 (194)
T PRK09646 143 LTDTQRESVTLAYYGGL----TYREVAERLAVPLGTVKTRMRDGL 183 (194)
T ss_pred CCHHHHHHHHHHHHcCC----CHHHHHHHhCCChHhHHHHHHHHH
Confidence 77777777766543221 456899999999999999875443
Done!