Query 015772
Match_columns 400
No_of_seqs 409 out of 1696
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 09:25:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015772hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 3.8E-23 8.3E-28 193.1 8.3 119 230-351 49-168 (198)
2 KOG0485 Transcription factor N 99.7 3.3E-17 7.1E-22 153.6 13.9 62 230-291 103-164 (268)
3 KOG0842 Transcription factor t 99.7 6.3E-18 1.4E-22 166.8 7.8 70 229-298 151-220 (307)
4 KOG0489 Transcription factor z 99.7 3.4E-18 7.4E-23 166.2 2.5 63 229-291 157-219 (261)
5 KOG0484 Transcription factor P 99.7 7.7E-18 1.7E-22 141.9 1.2 62 228-289 14-75 (125)
6 KOG0488 Transcription factor B 99.7 3.3E-17 7.1E-22 162.9 5.6 64 229-292 170-233 (309)
7 KOG0493 Transcription factor E 99.7 1.6E-16 3.5E-21 152.4 8.5 98 198-295 212-310 (342)
8 KOG0487 Transcription factor A 99.6 6.5E-17 1.4E-21 159.7 4.4 63 229-291 233-295 (308)
9 KOG0494 Transcription factor C 99.6 1.3E-16 2.9E-21 152.8 4.8 64 231-294 141-204 (332)
10 KOG0843 Transcription factor E 99.6 1.8E-16 4E-21 145.0 4.6 64 230-293 101-164 (197)
11 KOG2251 Homeobox transcription 99.6 3.1E-16 6.8E-21 147.5 4.9 66 228-293 34-99 (228)
12 KOG0850 Transcription factor D 99.6 7.1E-16 1.5E-20 145.8 4.8 60 230-289 121-180 (245)
13 PF00046 Homeobox: Homeobox do 99.6 1.3E-15 2.8E-20 114.3 3.4 57 232-288 1-57 (57)
14 KOG0848 Transcription factor C 99.6 5E-14 1.1E-18 135.8 14.3 59 233-291 201-259 (317)
15 KOG0492 Transcription factor M 99.5 7.2E-15 1.6E-19 137.2 5.8 59 231-289 144-202 (246)
16 smart00389 HOX Homeodomain. DN 99.4 6.6E-14 1.4E-18 104.1 3.5 56 232-287 1-56 (56)
17 cd00086 homeodomain Homeodomai 99.4 7.9E-14 1.7E-18 104.2 3.7 58 232-289 1-58 (59)
18 KOG0844 Transcription factor E 99.4 7.7E-14 1.7E-18 136.5 4.5 64 231-294 181-244 (408)
19 TIGR01565 homeo_ZF_HD homeobox 99.4 2.9E-13 6.3E-18 103.8 5.5 52 232-283 2-57 (58)
20 KOG0486 Transcription factor P 99.4 2.1E-13 4.6E-18 133.9 4.5 65 230-294 111-175 (351)
21 COG5576 Homeodomain-containing 99.4 4.9E-13 1.1E-17 121.3 5.3 66 229-294 49-114 (156)
22 KOG3802 Transcription factor O 99.3 6.2E-13 1.3E-17 134.4 5.2 59 230-288 293-351 (398)
23 KOG4577 Transcription factor L 99.3 2.5E-12 5.4E-17 125.2 8.7 70 229-298 165-234 (383)
24 KOG0491 Transcription factor B 99.3 1.4E-13 3.1E-18 124.5 -0.3 61 230-290 99-159 (194)
25 KOG0847 Transcription factor, 99.2 2.3E-12 4.9E-17 121.5 2.0 66 227-292 163-228 (288)
26 KOG0490 Transcription factor, 99.2 7.9E-12 1.7E-16 117.0 3.5 62 229-290 58-119 (235)
27 PF04618 HD-ZIP_N: HD-ZIP prot 99.1 1.3E-10 2.8E-15 99.9 6.2 81 65-173 23-103 (111)
28 KOG0849 Transcription factor P 99.0 4.3E-10 9.2E-15 114.2 4.0 62 229-290 174-235 (354)
29 KOG1168 Transcription factor A 98.9 1.3E-09 2.9E-14 106.5 3.5 62 228-289 306-367 (385)
30 KOG0775 Transcription factor S 98.7 1.2E-08 2.7E-13 99.2 3.8 50 238-287 183-232 (304)
31 KOG0774 Transcription factor P 98.6 1.4E-07 3E-12 91.4 8.7 58 231-288 188-248 (334)
32 smart00340 HALZ homeobox assoc 98.6 9.5E-08 2.1E-12 68.3 4.6 44 289-335 1-44 (44)
33 PF05920 Homeobox_KN: Homeobox 98.0 1.1E-06 2.3E-11 62.8 0.1 34 252-285 7-40 (40)
34 KOG0490 Transcription factor, 97.9 7.6E-06 1.6E-10 76.6 3.8 63 229-291 151-213 (235)
35 KOG2252 CCAAT displacement pro 97.9 8.5E-06 1.8E-10 86.0 3.9 59 229-287 418-476 (558)
36 KOG1146 Homeobox protein [Gene 97.4 0.00017 3.7E-09 82.6 4.8 62 230-291 902-963 (1406)
37 KOG0773 Transcription factor M 96.4 0.0021 4.5E-08 64.7 2.9 58 231-288 239-299 (342)
38 PF11569 Homez: Homeodomain le 95.6 0.0036 7.7E-08 48.0 0.1 42 243-284 10-51 (56)
39 PF02183 HALZ: Homeobox associ 92.6 0.27 5.9E-06 36.0 4.7 36 289-324 1-36 (45)
40 KOG3623 Homeobox transcription 92.2 0.087 1.9E-06 58.1 2.5 48 243-290 568-615 (1007)
41 PF04218 CENP-B_N: CENP-B N-te 91.8 0.17 3.6E-06 38.0 2.9 46 232-282 1-46 (53)
42 PRK09413 IS2 repressor TnpA; R 82.0 3.8 8.1E-05 35.4 5.9 44 234-281 9-52 (121)
43 KOG1924 RhoA GTPase effector D 62.6 75 0.0016 36.5 11.1 26 51-79 210-235 (1102)
44 KOG4196 bZIP transcription fac 58.2 33 0.00071 30.8 6.2 73 236-320 22-108 (135)
45 PF01527 HTH_Tnp_1: Transposas 56.6 2 4.4E-05 33.3 -1.5 44 233-280 2-45 (76)
46 PF12824 MRP-L20: Mitochondria 55.8 42 0.00091 31.1 6.8 78 234-315 82-162 (164)
47 cd06171 Sigma70_r4 Sigma70, re 52.2 5.9 0.00013 27.3 0.5 43 237-284 10-52 (55)
48 PF04545 Sigma70_r4: Sigma-70, 50.9 9.1 0.0002 27.6 1.3 39 237-280 4-42 (50)
49 PF13443 HTH_26: Cro/C1-type H 50.1 7.4 0.00016 29.0 0.8 39 260-298 12-50 (63)
50 cd00569 HTH_Hin_like Helix-tur 50.0 19 0.00041 21.9 2.7 38 237-279 5-42 (42)
51 PF02183 HALZ: Homeobox associ 49.1 41 0.00089 24.6 4.5 33 290-322 9-41 (45)
52 PF04967 HTH_10: HTH DNA bindi 48.3 20 0.00043 27.2 2.8 38 238-275 1-40 (53)
53 PRK00888 ftsB cell division pr 45.8 33 0.00072 29.3 4.2 46 274-320 16-61 (105)
54 KOG1146 Homeobox protein [Gene 45.4 13 0.00028 44.3 2.1 56 233-288 446-501 (1406)
55 KOG3119 Basic region leucine z 42.7 43 0.00093 33.2 5.1 30 295-324 224-253 (269)
56 KOG4005 Transcription factor X 41.5 1.6E+02 0.0035 29.3 8.5 21 295-315 113-133 (292)
57 PRK03975 tfx putative transcri 39.7 27 0.00059 31.5 2.9 48 235-288 4-51 (141)
58 PF09607 BrkDBD: Brinker DNA-b 38.4 23 0.0005 27.5 1.9 44 235-280 3-47 (58)
59 PF07716 bZIP_2: Basic region 37.8 88 0.0019 23.2 5.0 27 294-320 26-52 (54)
60 KOG4571 Activating transcripti 34.3 81 0.0017 32.0 5.4 22 295-316 250-271 (294)
61 KOG3755 SATB1 matrix attachmen 33.8 9.8 0.00021 41.9 -1.1 60 231-290 691-758 (769)
62 PF10668 Phage_terminase: Phag 32.5 14 0.00031 28.7 -0.1 19 260-278 24-42 (60)
63 PF15234 LAT: Linker for activ 30.2 1.1E+02 0.0024 29.3 5.3 10 68-77 70-79 (230)
64 COG3413 Predicted DNA binding 28.9 48 0.0011 31.2 2.8 38 237-274 155-194 (215)
65 PF00424 REV: REV protein (ant 28.4 79 0.0017 26.8 3.6 37 243-293 14-50 (91)
66 COG4367 Uncharacterized protei 28.4 42 0.00091 28.4 2.0 40 237-276 2-41 (97)
67 PF06156 DUF972: Protein of un 27.9 1.4E+02 0.003 25.8 5.2 36 289-324 18-53 (107)
68 PHA02955 hypothetical protein; 27.5 72 0.0016 30.9 3.7 43 240-282 60-103 (213)
69 PF08281 Sigma70_r4_2: Sigma-7 27.4 45 0.00098 24.0 1.9 41 238-283 11-51 (54)
70 PF00196 GerE: Bacterial regul 24.8 43 0.00093 24.8 1.3 45 237-287 3-47 (58)
71 TIGR03879 near_KaiC_dom probab 23.6 15 0.00032 29.7 -1.4 36 247-282 21-56 (73)
72 COG2963 Transposase and inacti 23.2 3.2E+02 0.007 22.8 6.6 42 235-280 5-47 (116)
73 KOG4403 Cell surface glycoprot 23.2 1.2E+02 0.0026 32.6 4.6 26 276-301 229-257 (575)
74 PRK10072 putative transcriptio 22.4 59 0.0013 27.5 1.8 42 237-285 32-73 (96)
75 smart00421 HTH_LUXR helix_turn 22.3 61 0.0013 22.5 1.7 40 237-282 3-42 (58)
76 PF00170 bZIP_1: bZIP transcri 22.3 2.9E+02 0.0062 21.0 5.6 23 298-320 31-53 (64)
77 PRK09646 RNA polymerase sigma 21.9 58 0.0013 29.6 1.9 46 237-287 142-187 (194)
78 PF13936 HTH_38: Helix-turn-he 21.6 34 0.00073 24.4 0.2 40 235-279 2-41 (44)
79 PF08280 HTH_Mga: M protein tr 21.6 69 0.0015 24.1 1.9 33 241-277 6-38 (59)
80 PRK04217 hypothetical protein; 21.5 68 0.0015 27.8 2.1 45 236-285 41-85 (110)
81 TIGR02937 sigma70-ECF RNA poly 20.9 67 0.0015 26.5 2.0 46 237-287 110-155 (158)
82 PRK06759 RNA polymerase factor 20.9 73 0.0016 27.4 2.2 46 237-287 106-151 (154)
83 PRK13169 DNA replication intia 20.4 2.4E+02 0.0052 24.6 5.2 36 289-324 18-53 (110)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.88 E-value=3.8e-23 Score=193.13 Aligned_cols=119 Identities=53% Similarity=0.689 Sum_probs=109.1
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhhhHHHHHHhhhhhHHHH
Q 015772 230 CSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEEN 309 (400)
Q Consensus 230 ~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~~e~l~~~~e~L~~En 309 (400)
...+++.||+.+|+..||+.|+.+.|+.+.+|..||++|||.++||+|||||||||||.++++.++++|+++++.|..++
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~ 128 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEN 128 (198)
T ss_pred ccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhh
Confidence 34566778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCccCC-CCCCCcCCCCCCCCCC
Q 015772 310 RRLQKELQELRALKSTAGNNPFYMQL-PATTLTMCPSCERVAT 351 (400)
Q Consensus 310 ~~l~~e~~~l~al~~a~~~~p~~~~l-p~~~~~~c~sc~~~~~ 351 (400)
++|++++.+|++++. ....+++. +..++.+|+.|+....
T Consensus 129 ~~Lq~e~~eL~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~ 168 (198)
T KOG0483|consen 129 DRLQSEVQELVAELS---SLKREMQKSPENTLTMCPNSESSSS 168 (198)
T ss_pred hHHHHHHHHHHHHHh---hhhhhhccCcccccccCccccccCC
Confidence 999999999998877 55667777 7788899999995543
No 2
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.73 E-value=3.3e-17 Score=153.62 Aligned_cols=62 Identities=31% Similarity=0.474 Sum_probs=58.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhh
Q 015772 230 CSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 291 (400)
Q Consensus 230 ~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~ 291 (400)
++||.||+|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+..
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 56777999999999999999999999999999999999999999999999999999997543
No 3
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.72 E-value=6.3e-18 Score=166.80 Aligned_cols=70 Identities=34% Similarity=0.533 Sum_probs=63.4
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhhhHHHH
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYL 298 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~~e~l 298 (400)
.++||+|..|+..|+.+||+.|++.+|++..+|++||..|+|++.||||||||||.|.||+++.+..+.+
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 3556667789999999999999999999999999999999999999999999999999998887775543
No 4
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.70 E-value=3.4e-18 Score=166.24 Aligned_cols=63 Identities=35% Similarity=0.579 Sum_probs=59.4
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhh
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 291 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~ 291 (400)
++.||.|+.||..|+.+||+.|..|+|+++.+|.+||..|.|+|+||||||||||+||||..+
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 457899999999999999999999999999999999999999999999999999999997543
No 5
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.68 E-value=7.7e-18 Score=141.91 Aligned_cols=62 Identities=27% Similarity=0.391 Sum_probs=58.7
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhh
Q 015772 228 NGCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 289 (400)
Q Consensus 228 ~~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krk 289 (400)
+.++||-|+.||..||.+||++|.+.+||++..|++||.++.|++.+|||||||||+|.||+
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 34678889999999999999999999999999999999999999999999999999999964
No 6
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.67 E-value=3.3e-17 Score=162.89 Aligned_cols=64 Identities=31% Similarity=0.473 Sum_probs=59.9
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhh
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 292 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~ 292 (400)
+|+||.||.||..|+..||+.|++.+|++..+|.+||+.|||+..|||+||||||+|||++..+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 5677789999999999999999999999999999999999999999999999999999976544
No 7
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.66 E-value=1.6e-16 Score=152.35 Aligned_cols=98 Identities=21% Similarity=0.306 Sum_probs=82.7
Q ss_pred CCCCCCCcccccCCCCCCCCCCCCCcccc-CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccee
Q 015772 198 NIRKSCGDIFRASNDNNNEVVDGCSELED-ENGCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVE 276 (400)
Q Consensus 198 ~~~~s~~~~~~~ss~~~~~~~~g~~~~~~-~~~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVq 276 (400)
..|..|.++.+++++.+....-....... ..+..||.||.||.+||+.|+..|+.++|++...|++||.+|+|.+.|||
T Consensus 212 ~mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK 291 (342)
T KOG0493|consen 212 SMWPAWVYCTRYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK 291 (342)
T ss_pred cccceeeeeecccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence 67889999999999997776544333222 33456889999999999999999999999999999999999999999999
Q ss_pred ecccchhhhhhhhhhhhhH
Q 015772 277 VWFQNRRARTKLKQTEVDC 295 (400)
Q Consensus 277 vWFQNRRaK~Krkq~~~~~ 295 (400)
|||||+|+|.||..--+..
T Consensus 292 IWFQNKRAKiKKsTgskn~ 310 (342)
T KOG0493|consen 292 IWFQNKRAKIKKSTGSKNR 310 (342)
T ss_pred HHhhhhhhhhhhccCCCCc
Confidence 9999999999986554443
No 8
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.65 E-value=6.5e-17 Score=159.70 Aligned_cols=63 Identities=35% Similarity=0.550 Sum_probs=58.9
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhh
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 291 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~ 291 (400)
+..||||.-+|+.|+.+||+.|..|.|++.+.|.+|++.|+|+++||||||||||+|.||...
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 456888999999999999999999999999999999999999999999999999999997543
No 9
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.64 E-value=1.3e-16 Score=152.78 Aligned_cols=64 Identities=27% Similarity=0.351 Sum_probs=58.2
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhhh
Q 015772 231 STRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVD 294 (400)
Q Consensus 231 ~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~ 294 (400)
+|+-||.||..|+.+||+.|++.+||+.+.|+.||.++.|.+.+|+|||||||+||||+...-.
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 3334899999999999999999999999999999999999999999999999999998655444
No 10
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.63 E-value=1.8e-16 Score=144.98 Aligned_cols=64 Identities=33% Similarity=0.470 Sum_probs=60.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhh
Q 015772 230 CSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 293 (400)
Q Consensus 230 ~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~ 293 (400)
+.||.||.|+.+|+..||..|+.++|..-.+|++||+.|+|++.||||||||||.|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 6788999999999999999999999999999999999999999999999999999999877664
No 11
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.62 E-value=3.1e-16 Score=147.47 Aligned_cols=66 Identities=29% Similarity=0.429 Sum_probs=61.7
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhh
Q 015772 228 NGCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 293 (400)
Q Consensus 228 ~~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~ 293 (400)
.++.||.||+|+..|+++||..|.+..||++..|++||.+|+|.+.+|||||+|||+|+|+++...
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 357889999999999999999999999999999999999999999999999999999999866654
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.59 E-value=7.1e-16 Score=145.78 Aligned_cols=60 Identities=30% Similarity=0.423 Sum_probs=56.1
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhh
Q 015772 230 CSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 289 (400)
Q Consensus 230 ~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krk 289 (400)
|-||.||.|+..||..|.+.|+++.|+-..+|.+||..|||+..||||||||||.|.||.
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 345559999999999999999999999999999999999999999999999999999964
No 13
>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=99.57 E-value=1.3e-15 Score=114.33 Aligned_cols=57 Identities=44% Similarity=0.667 Sum_probs=55.1
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhh
Q 015772 232 TRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 288 (400)
Q Consensus 232 rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Kr 288 (400)
||+|+.|+.+|+.+|+.+|..++||+..+++.||.+|||+..+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999985
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.56 E-value=5e-14 Score=135.75 Aligned_cols=59 Identities=34% Similarity=0.558 Sum_probs=55.0
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhh
Q 015772 233 RKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 291 (400)
Q Consensus 233 RkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~ 291 (400)
|-|.++|..|..+||+.|..++|.++.++.+||..|+|+||||||||||||+|+||..+
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 34778999999999999999999999999999999999999999999999999997543
No 15
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.53 E-value=7.2e-15 Score=137.17 Aligned_cols=59 Identities=32% Similarity=0.543 Sum_probs=56.0
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhh
Q 015772 231 STRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 289 (400)
Q Consensus 231 ~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krk 289 (400)
.|+.|+-||.+||..||+.|++.+|+++.+|.+++..|.|++.||||||||||+|.||-
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 46669999999999999999999999999999999999999999999999999999964
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.44 E-value=6.6e-14 Score=104.08 Aligned_cols=56 Identities=39% Similarity=0.607 Sum_probs=52.6
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhh
Q 015772 232 TRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTK 287 (400)
Q Consensus 232 rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~K 287 (400)
++.|+.|+.+|+.+|+.+|..++||+..++..||.++||+..||++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35677899999999999999999999999999999999999999999999998864
No 17
>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=99.43 E-value=7.9e-14 Score=104.23 Aligned_cols=58 Identities=40% Similarity=0.633 Sum_probs=54.4
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhh
Q 015772 232 TRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 289 (400)
Q Consensus 232 rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krk 289 (400)
+++|..|+..|+.+|+.+|..++||+..++..||.++||++.+|++||+|||.+.|+.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3567899999999999999999999999999999999999999999999999998853
No 18
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.43 E-value=7.7e-14 Score=136.46 Aligned_cols=64 Identities=30% Similarity=0.493 Sum_probs=60.4
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhhh
Q 015772 231 STRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVD 294 (400)
Q Consensus 231 ~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~ 294 (400)
-||-||.||.+||..||+.|-+..|-+...|.+||..|||.+..|||||||||+|+||+.+.+-
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlama 244 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMA 244 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhcc
Confidence 4788999999999999999999999999999999999999999999999999999999877654
No 19
>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=99.41 E-value=2.9e-13 Score=103.79 Aligned_cols=52 Identities=10% Similarity=0.305 Sum_probs=50.3
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCCccceeecccchh
Q 015772 232 TRKKLRLSKQQSAFLEESFKEHTT----LTPKQKLALAKQLNLRPRQVEVWFQNRR 283 (400)
Q Consensus 232 rRkRtrfT~~Ql~~LE~~F~~~~y----Ps~~~R~eLA~~LgLserQVqvWFQNRR 283 (400)
||.||.||.+|+..||..|+.++| |+...|.+||.+|||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 788999999999999999999999 9999999999999999999999999964
No 20
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.39 E-value=2.1e-13 Score=133.92 Aligned_cols=65 Identities=26% Similarity=0.401 Sum_probs=60.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhhh
Q 015772 230 CSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVD 294 (400)
Q Consensus 230 ~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~ 294 (400)
|+||.|+.|+.+|+.+||.+|++++||+...|++||..++|++.+|+|||.|||+||||+..-..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 67788999999999999999999999999999999999999999999999999999997655444
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.37 E-value=4.9e-13 Score=121.29 Aligned_cols=66 Identities=29% Similarity=0.485 Sum_probs=60.0
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhhh
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVD 294 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~ 294 (400)
...+++|++.+.+|+.+|++.|+.++||+...|..|+..|+|+++-||+||||||++.|++...+.
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence 356778889999999999999999999999999999999999999999999999999997655433
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.35 E-value=6.2e-13 Score=134.43 Aligned_cols=59 Identities=27% Similarity=0.428 Sum_probs=57.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhh
Q 015772 230 CSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 288 (400)
Q Consensus 230 ~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Kr 288 (400)
++|||||.|....+..||+.|.+|++|+..++..||.+|+|.+.+|+|||||||.|.||
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR 351 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKR 351 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeecccccccc
Confidence 67889999999999999999999999999999999999999999999999999999996
No 23
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.34 E-value=2.5e-12 Score=125.23 Aligned_cols=70 Identities=23% Similarity=0.384 Sum_probs=63.3
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhhhHHHH
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYL 298 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~~e~l 298 (400)
...||.||.+|..||+.|+..|...++|-...|++|+.++||..+.|||||||||+|+||-++......+
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RW 234 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRW 234 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHH
Confidence 3568899999999999999999999999999999999999999999999999999999987666555444
No 24
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.33 E-value=1.4e-13 Score=124.53 Aligned_cols=61 Identities=33% Similarity=0.496 Sum_probs=56.7
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhh
Q 015772 230 CSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 290 (400)
Q Consensus 230 ~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq 290 (400)
+++|-|++|+..|+..||+.|+..+|++..+|.+||..|+|++.|||.||||||+|.||.+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 3455699999999999999999999999999999999999999999999999999999743
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.24 E-value=2.3e-12 Score=121.48 Aligned_cols=66 Identities=32% Similarity=0.505 Sum_probs=59.4
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhh
Q 015772 227 ENGCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 292 (400)
Q Consensus 227 ~~~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~ 292 (400)
.+++++..|..|+..|+..||+.|++.+|+--.+|.+||..+|+++.||+|||||||.||||+...
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 345566678889999999999999999999999999999999999999999999999999976543
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.20 E-value=7.9e-12 Score=116.96 Aligned_cols=62 Identities=26% Similarity=0.295 Sum_probs=58.7
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhh
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 290 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq 290 (400)
.++||.|+.|+..|+++||+.|++.+||+...|+.||..+++++..|+|||||||+||+++.
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 46788899999999999999999999999999999999999999999999999999999754
No 27
>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=99.10 E-value=1.3e-10 Score=99.89 Aligned_cols=81 Identities=28% Similarity=0.275 Sum_probs=56.3
Q ss_pred ccCcccccccCCCCCCCCCCCCCCCCCCccccccCCCCCCCCCccccCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCC
Q 015772 65 TANIIQQLDLLPNTPVVVPLPRNPTPSSILASFPAANWTSAGSSEAAGSGQMARDANKLPMAIPAPLDLLVPHHNDDEDP 144 (400)
Q Consensus 65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~rg~d~n~~p~~~~~~~~~~~~~~~d~~~s 144 (400)
...+++||+|+|+.+ |.+.++.+.++...|.......+......+.|+||||||++|+++.
T Consensus 23 ~~~~plql~L~P~s~---p~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~flRgiDVNr~p~~~~---------------- 83 (111)
T PF04618_consen 23 SQQPPLQLNLLPSSS---PSNSHPLFSSHNQPFWSDDRMMASCDSETRSFLRGIDVNRLPSTVE---------------- 83 (111)
T ss_pred ccCCCcccccCCccc---cccccCccccccccCCccccccccccccccccccceeccCCCcccc----------------
Confidence 457799999999987 4455555555555555554443332222366999999999999885
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 015772 145 SSPEAEDGDGSHGAGALSSSSLNTTSSAQ 173 (400)
Q Consensus 145 ~see~ede~~~~~~~a~~SSp~Ss~ss~s 173 (400)
+|+||| +++|||||++|+.+
T Consensus 84 --~d~eEe-------~gvSSPNStiSS~s 103 (111)
T PF04618_consen 84 --ADCEEE-------AGVSSPNSTISSVS 103 (111)
T ss_pred --cccccc-------ccccCCCccceecc
Confidence 145555 66899999999973
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.95 E-value=4.3e-10 Score=114.18 Aligned_cols=62 Identities=32% Similarity=0.437 Sum_probs=58.4
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhh
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 290 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq 290 (400)
.+.+|+|+.|+..|+..||+.|+.++||+...|++||++++|++.+|+|||+|||+|++|..
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 45677899999999999999999999999999999999999999999999999999999754
No 29
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.86 E-value=1.3e-09 Score=106.50 Aligned_cols=62 Identities=27% Similarity=0.447 Sum_probs=58.1
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhh
Q 015772 228 NGCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 289 (400)
Q Consensus 228 ~~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krk 289 (400)
.+.+|||||.+-......||.+|...+.|+.+.+..||.+|.|.+..|+|||+|.|.|.||.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 34678999999999999999999999999999999999999999999999999999998863
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.68 E-value=1.2e-08 Score=99.16 Aligned_cols=50 Identities=30% Similarity=0.558 Sum_probs=47.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhh
Q 015772 238 LSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTK 287 (400)
Q Consensus 238 fT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~K 287 (400)
|...-...|..+|.+++||++.++.+||+.+||+..||-.||+|||+|+|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 66666889999999999999999999999999999999999999999998
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.61 E-value=1.4e-07 Score=91.43 Aligned_cols=58 Identities=38% Similarity=0.501 Sum_probs=54.7
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhh
Q 015772 231 STRKKLRLSKQQSAFLEESFK---EHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 288 (400)
Q Consensus 231 ~rRkRtrfT~~Ql~~LE~~F~---~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Kr 288 (400)
.+|||..|++.-.++|..+|. .++||+...+++||++.|++..||-.||.|+|-++||
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhh
Confidence 478889999999999999996 6899999999999999999999999999999999985
No 32
>smart00340 HALZ homeobox associated leucin zipper.
Probab=98.56 E-value=9.5e-08 Score=68.34 Aligned_cols=44 Identities=82% Similarity=1.229 Sum_probs=40.3
Q ss_pred hhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhhcCCCCCccCC
Q 015772 289 KQTEVDCEYLKRCCETLTEENRRLQKELQELRALKSTAGNNPFYMQL 335 (400)
Q Consensus 289 kq~~~~~e~l~~~~e~L~~En~~l~~e~~~l~al~~a~~~~p~~~~l 335 (400)
+|++.+|++|+++++.|.+||++|++|+++|++|+. ..|+||++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLralk~---~~~~~m~~ 44 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRALKL---SPPLYMQH 44 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc---CCcccccC
Confidence 478999999999999999999999999999999988 77888763
No 33
>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=98.03 E-value=1.1e-06 Score=62.80 Aligned_cols=34 Identities=35% Similarity=0.528 Sum_probs=29.1
Q ss_pred hcCCCCHHHHHHHHHHcCCCccceeecccchhhh
Q 015772 252 EHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRAR 285 (400)
Q Consensus 252 ~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK 285 (400)
.++||+..+++.||+++||+..||..||-|.|.|
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 4799999999999999999999999999999865
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.93 E-value=7.6e-06 Score=76.62 Aligned_cols=63 Identities=27% Similarity=0.474 Sum_probs=58.1
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhh
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 291 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~ 291 (400)
.+.++.|+.|...|+..|+..|..+++|+...++.|+..+|+.++.|++||||+|++.++.+.
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 466778999999999999999999999999999999999999999999999999999986533
No 35
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.89 E-value=8.5e-06 Score=86.02 Aligned_cols=59 Identities=25% Similarity=0.327 Sum_probs=54.8
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhh
Q 015772 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTK 287 (400)
Q Consensus 229 ~~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~K 287 (400)
-..||.|.+||..|+..|..+|+++++|+.+..+.|+.+|||...-|.+||-|-|.|.+
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 35677899999999999999999999999999999999999999999999999988753
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.36 E-value=0.00017 Score=82.59 Aligned_cols=62 Identities=24% Similarity=0.367 Sum_probs=58.4
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhh
Q 015772 230 CSTRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 291 (400)
Q Consensus 230 ~~rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~ 291 (400)
.+|++|++++..||.+|..+|....||...+.+.|-..++|..+.|+|||||-|+|.|+..+
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 46778999999999999999999999999999999999999999999999999999998655
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.40 E-value=0.0021 Score=64.75 Aligned_cols=58 Identities=33% Similarity=0.347 Sum_probs=49.5
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhh
Q 015772 231 STRKKLRLSKQQSAFLEESFK---EHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 288 (400)
Q Consensus 231 ~rRkRtrfT~~Ql~~LE~~F~---~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Kr 288 (400)
.+|.+..|......+|+.+.. ..+||+..++..||+++||+..||.+||-|.|-|..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 445566799999999998843 3579999999999999999999999999999887664
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.56 E-value=0.0036 Score=47.99 Aligned_cols=42 Identities=24% Similarity=0.370 Sum_probs=31.4
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhh
Q 015772 243 SAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRA 284 (400)
Q Consensus 243 l~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRa 284 (400)
+..|++.|..++++.......|..+.+|+..||+.||-.|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999976543
No 39
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=92.60 E-value=0.27 Score=36.05 Aligned_cols=36 Identities=39% Similarity=0.428 Sum_probs=32.2
Q ss_pred hhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHh
Q 015772 289 KQTEVDCEYLKRCCETLTEENRRLQKELQELRALKS 324 (400)
Q Consensus 289 kq~~~~~e~l~~~~e~L~~En~~l~~e~~~l~al~~ 324 (400)
+|++.+++.|+.+++.|..++++|.+|+..|++.+.
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~ 36 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQ 36 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478899999999999999999999999999987654
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=92.24 E-value=0.087 Score=58.15 Aligned_cols=48 Identities=17% Similarity=0.308 Sum_probs=44.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhh
Q 015772 243 SAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 290 (400)
Q Consensus 243 l~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq 290 (400)
+..|...|..|..|+..+...+|.++||..+.|++||++++++....+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999886533
No 41
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=91.82 E-value=0.17 Score=38.00 Aligned_cols=46 Identities=17% Similarity=0.304 Sum_probs=35.1
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccch
Q 015772 232 TRKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNR 282 (400)
Q Consensus 232 rRkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNR 282 (400)
||+|..+|-++...+-..++... ....||+++|+...+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 57888999998888777787665 57889999999999999999885
No 42
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=82.02 E-value=3.8 Score=35.44 Aligned_cols=44 Identities=18% Similarity=0.198 Sum_probs=28.8
Q ss_pred CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccc
Q 015772 234 KKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQN 281 (400)
Q Consensus 234 kRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQN 281 (400)
+|.+|+.++....-..+..+. ....++|+++|+++.+|..|.+-
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 345677776543333332232 23567899999999999999543
No 43
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=62.58 E-value=75 Score=36.47 Aligned_cols=26 Identities=23% Similarity=0.172 Sum_probs=15.0
Q ss_pred hhhhccCCCcccccccCcccccccCCCCC
Q 015772 51 AEIRRCSTPTATAETANIIQQLDLLPNTP 79 (400)
Q Consensus 51 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 79 (400)
.||.|| +..+-++.-.+++-|-+..+
T Consensus 210 ~eiIrC---lka~mNn~~Gl~~vL~~e~~ 235 (1102)
T KOG1924|consen 210 QEIIRC---LKAFMNNKFGLVLVLRRERS 235 (1102)
T ss_pred HHHHHH---HHHHhccccceeeeecCCcc
Confidence 466677 45566666666655555443
No 44
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=58.16 E-value=33 Score=30.85 Aligned_cols=73 Identities=27% Similarity=0.270 Sum_probs=48.4
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhh----------hhh----hhhhhhHHHHHHh
Q 015772 236 LRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRAR----------TKL----KQTEVDCEYLKRC 301 (400)
Q Consensus 236 trfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK----------~Kr----kq~~~~~e~l~~~ 301 (400)
.+|+.++|..|- .|+.--+.-|++...|-.|=|.||+- .|+ ..++.+...|+..
T Consensus 22 d~lsDd~LvsmS------------VReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qq 89 (135)
T KOG4196|consen 22 DRLSDDELVSMS------------VRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQ 89 (135)
T ss_pred CCcCHHHHHHhh------------HHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578888876652 22222233478888888888877753 333 3344445568888
Q ss_pred hhhhHHHHHHHHHHHHHHH
Q 015772 302 CETLTEENRRLQKELQELR 320 (400)
Q Consensus 302 ~e~L~~En~~l~~e~~~l~ 320 (400)
.+.|.+||.+++.|+..++
T Consensus 90 v~~L~~e~s~~~~E~da~k 108 (135)
T KOG4196|consen 90 VEKLKEENSRLRRELDAYK 108 (135)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 8899999999988876665
No 45
>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=56.62 E-value=2 Score=33.27 Aligned_cols=44 Identities=18% Similarity=0.305 Sum_probs=28.7
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeeccc
Q 015772 233 RKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQ 280 (400)
Q Consensus 233 RkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQ 280 (400)
++|.+|+.++...+-..+.. ......+||+++||++.+|..|-+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHH
Confidence 56778999887777666522 225688899999999999999954
No 46
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=55.84 E-value=42 Score=31.08 Aligned_cols=78 Identities=22% Similarity=0.191 Sum_probs=48.7
Q ss_pred CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhhhHH---HHHHhhhhhHHHHH
Q 015772 234 KKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCE---YLKRCCETLTEENR 310 (400)
Q Consensus 234 kRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~~e---~l~~~~e~L~~En~ 310 (400)
++..++.+++.++.+.-.+ -|....+..||+++|++..-|.+=..--..+.+ ..+...+ .-|.....+..|.+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~--DP~~wTr~~LAkkF~~S~~fV~~v~~~~~e~~~--~~~~~le~~k~rWg~~r~~ARedR 157 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAE--DPEKWTRKKLAKKFNCSPLFVSMVAPAPKEKKK--EMEARLEAIKSRWGPRRRIAREDR 157 (164)
T ss_pred ccccCCHHHHHHHHHHHHc--CchHhhHHHHHHHhCCCHHHHHHhcCCCHHHHH--HHHHHHHHHHHhccHHHHHHHHHH
Confidence 3467999999999887654 467788999999999998877765544333222 2222222 23333444445555
Q ss_pred HHHHH
Q 015772 311 RLQKE 315 (400)
Q Consensus 311 ~l~~e 315 (400)
+.++|
T Consensus 158 ~kRke 162 (164)
T PF12824_consen 158 QKRKE 162 (164)
T ss_pred HHHHH
Confidence 55544
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=52.20 E-value=5.9 Score=27.30 Aligned_cols=43 Identities=14% Similarity=0.166 Sum_probs=31.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhh
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRA 284 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRa 284 (400)
.++..+..++...|... ....++|..+|++...|..|....+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36777777887776422 34677899999999999988765443
No 48
>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=50.87 E-value=9.1 Score=27.57 Aligned_cols=39 Identities=10% Similarity=0.164 Sum_probs=29.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeeccc
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQ 280 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQ 280 (400)
.++..+..+|...|- ....-.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHH
Confidence 467888899998882 223467899999999988877654
No 49
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=50.08 E-value=7.4 Score=29.03 Aligned_cols=39 Identities=13% Similarity=0.171 Sum_probs=23.4
Q ss_pred HHHHHHHHcCCCccceeecccchhhhhhhhhhhhhHHHH
Q 015772 260 QKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYL 298 (400)
Q Consensus 260 ~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~~~e~l 298 (400)
...+||+.+|++...|..||.++..+........-+..+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKAL 50 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHc
Confidence 467899999999999999999876666554444444443
No 50
>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=50.02 E-value=19 Score=21.93 Aligned_cols=38 Identities=11% Similarity=0.166 Sum_probs=25.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecc
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWF 279 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWF 279 (400)
.++..+...+...|... + ...++|+.++++...|..|.
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 35666666666666532 2 46678899999888877763
No 51
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=49.10 E-value=41 Score=24.64 Aligned_cols=33 Identities=30% Similarity=0.457 Sum_probs=28.0
Q ss_pred hhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 015772 290 QTEVDCEYLKRCCETLTEENRRLQKELQELRAL 322 (400)
Q Consensus 290 q~~~~~e~l~~~~e~L~~En~~l~~e~~~l~al 322 (400)
..+..++.|+..+..|..||..|+.++..|...
T Consensus 9 ~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~k 41 (45)
T PF02183_consen 9 ALKASYDSLKAEYDSLKKENEKLRAEVQELKEK 41 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345677899999999999999999999888754
No 52
>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=48.28 E-value=20 Score=27.19 Aligned_cols=38 Identities=18% Similarity=0.211 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCccce
Q 015772 238 LSKQQSAFLEESFKEHTT--LTPKQKLALAKQLNLRPRQV 275 (400)
Q Consensus 238 fT~~Ql~~LE~~F~~~~y--Ps~~~R~eLA~~LgLserQV 275 (400)
+|..|..+|...|+..-| |-...-.+||++||++..-|
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 578999999999986544 66677889999999987554
No 53
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=45.84 E-value=33 Score=29.31 Aligned_cols=46 Identities=17% Similarity=0.316 Sum_probs=28.6
Q ss_pred ceeecccchhhhhhhhhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHH
Q 015772 274 QVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELR 320 (400)
Q Consensus 274 QVqvWFQNRRaK~Krkq~~~~~e~l~~~~e~L~~En~~l~~e~~~l~ 320 (400)
++..||++.-- .+-.+.+.+.+.++..+..+..+|..|+.++..|+
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 55678865411 12233444555667777777888888887777665
No 54
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=45.41 E-value=13 Score=44.28 Aligned_cols=56 Identities=18% Similarity=0.086 Sum_probs=50.6
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhh
Q 015772 233 RKKLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 288 (400)
Q Consensus 233 RkRtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Kr 288 (400)
-.+++++.-|...|..+|+...||.-.+...++..|++..+.+-.||+++++++.+
T Consensus 446 ~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq 501 (1406)
T KOG1146|consen 446 LESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQ 501 (1406)
T ss_pred hhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcc
Confidence 34778889999999999999999999999999999999999999999998888865
No 55
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=42.74 E-value=43 Score=33.19 Aligned_cols=30 Identities=33% Similarity=0.361 Sum_probs=19.2
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHh
Q 015772 295 CEYLKRCCETLTEENRRLQKELQELRALKS 324 (400)
Q Consensus 295 ~e~l~~~~e~L~~En~~l~~e~~~l~al~~ 324 (400)
...|.+.++.|..+..+|++|+..++.++.
T Consensus 224 ~~~leken~~lr~~v~~l~~el~~~~~~~~ 253 (269)
T KOG3119|consen 224 VAELEKENEALRTQVEQLKKELATLRRLFL 253 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666677777777777766544
No 56
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=41.50 E-value=1.6e+02 Score=29.27 Aligned_cols=21 Identities=29% Similarity=0.392 Sum_probs=9.2
Q ss_pred HHHHHHhhhhhHHHHHHHHHH
Q 015772 295 CEYLKRCCETLTEENRRLQKE 315 (400)
Q Consensus 295 ~e~l~~~~e~L~~En~~l~~e 315 (400)
++.|+..++.|..+|..+..+
T Consensus 113 n~~Lr~~n~~L~~~n~el~~~ 133 (292)
T KOG4005|consen 113 NDSLRAINESLLAKNHELDSE 133 (292)
T ss_pred HHHHHHHHHHHHhhhHHHHHH
Confidence 344444444444444444433
No 57
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=39.74 E-value=27 Score=31.55 Aligned_cols=48 Identities=15% Similarity=0.054 Sum_probs=36.4
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhh
Q 015772 235 KLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 288 (400)
Q Consensus 235 RtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Kr 288 (400)
...++..|..+|...+ .. ....+||..||++...|+.|.++.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4578999999997732 11 346689999999999999998866655553
No 58
>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=38.41 E-value=23 Score=27.53 Aligned_cols=44 Identities=20% Similarity=0.305 Sum_probs=21.6
Q ss_pred CccCCHHH-HHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeeccc
Q 015772 235 KLRLSKQQ-SAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQ 280 (400)
Q Consensus 235 RtrfT~~Q-l~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQ 280 (400)
|..|+... |.+++..+ ....--..+| .-|+++|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~-~~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAE-KDNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHH-H-TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHH-HccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 34455544 44444443 3332222333 349999999999999954
No 59
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=37.82 E-value=88 Score=23.19 Aligned_cols=27 Identities=33% Similarity=0.482 Sum_probs=18.5
Q ss_pred hHHHHHHhhhhhHHHHHHHHHHHHHHH
Q 015772 294 DCEYLKRCCETLTEENRRLQKELQELR 320 (400)
Q Consensus 294 ~~e~l~~~~e~L~~En~~l~~e~~~l~ 320 (400)
..+.+......|..+|..|+.++..|.
T Consensus 26 ~~~~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 26 REEELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334456667778888888887776654
No 60
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=34.27 E-value=81 Score=31.96 Aligned_cols=22 Identities=27% Similarity=0.215 Sum_probs=10.7
Q ss_pred HHHHHHhhhhhHHHHHHHHHHH
Q 015772 295 CEYLKRCCETLTEENRRLQKEL 316 (400)
Q Consensus 295 ~e~l~~~~e~L~~En~~l~~e~ 316 (400)
.|.+-.+++.|..+|++|+.++
T Consensus 250 ~E~l~ge~~~Le~rN~~LK~qa 271 (294)
T KOG4571|consen 250 KEALLGELEGLEKRNEELKDQA 271 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555555555555443
No 61
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=33.80 E-value=9.8 Score=41.86 Aligned_cols=60 Identities=15% Similarity=0.217 Sum_probs=0.0
Q ss_pred CCCCCccCCHHHHHHHHHH-HhhcCCCCHHHHHHHHHHcCCCc-------cceeecccchhhhhhhhh
Q 015772 231 STRKKLRLSKQQSAFLEES-FKEHTTLTPKQKLALAKQLNLRP-------RQVEVWFQNRRARTKLKQ 290 (400)
Q Consensus 231 ~rRkRtrfT~~Ql~~LE~~-F~~~~yPs~~~R~eLA~~LgLse-------rQVqvWFQNRRaK~Krkq 290 (400)
.||++.+|-..|..++... |.+++.+......+--.++.|.+ +-|+.||.|||.++|+-+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 62
>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=32.52 E-value=14 Score=28.74 Aligned_cols=19 Identities=16% Similarity=0.461 Sum_probs=17.0
Q ss_pred HHHHHHHHcCCCccceeec
Q 015772 260 QKLALAKQLNLRPRQVEVW 278 (400)
Q Consensus 260 ~R~eLA~~LgLserQVqvW 278 (400)
.-.+||.+||+++.+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 4567899999999999999
No 63
>PF15234 LAT: Linker for activation of T-cells
Probab=30.22 E-value=1.1e+02 Score=29.26 Aligned_cols=10 Identities=50% Similarity=0.610 Sum_probs=7.9
Q ss_pred cccccccCCC
Q 015772 68 IIQQLDLLPN 77 (400)
Q Consensus 68 ~~~~~~~~~~ 77 (400)
++-|-||||.
T Consensus 70 plsqPDLLpI 79 (230)
T PF15234_consen 70 PLSQPDLLPI 79 (230)
T ss_pred CCCCcccccC
Confidence 4678888887
No 64
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=28.89 E-value=48 Score=31.19 Aligned_cols=38 Identities=21% Similarity=0.176 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHcCCCccc
Q 015772 237 RLSKQQSAFLEESFKEHT--TLTPKQKLALAKQLNLRPRQ 274 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~--yPs~~~R~eLA~~LgLserQ 274 (400)
.+|..|+++|...|+..= ||-.....+||++||+++.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 699999999999998554 47777788999999998754
No 65
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=28.43 E-value=79 Score=26.76 Aligned_cols=37 Identities=19% Similarity=0.321 Sum_probs=19.6
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhhhhhhhh
Q 015772 243 SAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 293 (400)
Q Consensus 243 l~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~Krkq~~~ 293 (400)
+.+.+-.|+.|+||...--.. | -.|||.+||+++.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHH
Confidence 445556688999997441111 1 158999998765443
No 66
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.37 E-value=42 Score=28.39 Aligned_cols=40 Identities=20% Similarity=0.274 Sum_probs=31.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccee
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVE 276 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVq 276 (400)
.++++|.+.-...|+.+--.+.-..+++|.+||+++..|+
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 3567888877777777777777889999999999885543
No 67
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=27.87 E-value=1.4e+02 Score=25.76 Aligned_cols=36 Identities=36% Similarity=0.314 Sum_probs=29.2
Q ss_pred hhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHh
Q 015772 289 KQTEVDCEYLKRCCETLTEENRRLQKELQELRALKS 324 (400)
Q Consensus 289 kq~~~~~e~l~~~~e~L~~En~~l~~e~~~l~al~~ 324 (400)
..+-.+.+.|+.....|.+||.+|+.|+..|+....
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~ 53 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRERLE 53 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566678888899999999999999999995543
No 68
>PHA02955 hypothetical protein; Provisional
Probab=27.50 E-value=72 Score=30.91 Aligned_cols=43 Identities=12% Similarity=0.176 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHcCCCccceeecccch
Q 015772 240 KQQSAFLEESFKEH-TTLTPKQKLALAKQLNLRPRQVEVWFQNR 282 (400)
Q Consensus 240 ~~Ql~~LE~~F~~~-~yPs~~~R~eLA~~LgLserQVqvWFQNR 282 (400)
..|+..|-+.|.+. ..+..++|.+++++||+....|..||.+.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 46677777777765 67888999999999999987789999764
No 69
>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=27.38 E-value=45 Score=24.04 Aligned_cols=41 Identities=15% Similarity=0.225 Sum_probs=26.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchh
Q 015772 238 LSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRR 283 (400)
Q Consensus 238 fT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRR 283 (400)
++..+..++...| .....-.++|..+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4555666665543 3445678899999999999999986443
No 70
>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=24.79 E-value=43 Score=24.77 Aligned_cols=45 Identities=11% Similarity=0.132 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhh
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTK 287 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~K 287 (400)
.||..++.+|.....- ....++|..+++++..|+.+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 5788888888766542 24678999999999999988877666554
No 71
>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=23.65 E-value=15 Score=29.72 Aligned_cols=36 Identities=14% Similarity=0.106 Sum_probs=27.2
Q ss_pred HHHHhhcCCCCHHHHHHHHHHcCCCccceeecccch
Q 015772 247 EESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNR 282 (400)
Q Consensus 247 E~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNR 282 (400)
+..|..++|-......+||..+|+++..|+.|+.+.
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 344555555555668899999999999999998653
No 72
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.24 E-value=3.2e+02 Score=22.80 Aligned_cols=42 Identities=10% Similarity=0.112 Sum_probs=33.1
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCC-Cccceeeccc
Q 015772 235 KLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNL-RPRQVEVWFQ 280 (400)
Q Consensus 235 RtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgL-serQVqvWFQ 280 (400)
|.+|+.+....+-+.+....+ ....||+++|+ ...++..|-+
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 678999888777666665554 57889999996 9999998854
No 73
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=23.23 E-value=1.2e+02 Score=32.58 Aligned_cols=26 Identities=35% Similarity=0.657 Sum_probs=19.6
Q ss_pred eecc---cchhhhhhhhhhhhhHHHHHHh
Q 015772 276 EVWF---QNRRARTKLKQTEVDCEYLKRC 301 (400)
Q Consensus 276 qvWF---QNRRaK~Krkq~~~~~e~l~~~ 301 (400)
-+|| ||+.+|.+.++..++.+.|++.
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq~a 257 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQRA 257 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4588 8999999887777777666554
No 74
>PRK10072 putative transcriptional regulator; Provisional
Probab=22.40 E-value=59 Score=27.47 Aligned_cols=42 Identities=19% Similarity=0.150 Sum_probs=30.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhh
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRAR 285 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK 285 (400)
+.+...+..|..... . ...+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~g----l---TQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTG----L---KIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcC----C---CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 346666666644322 2 27789999999999999999887643
No 75
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.30 E-value=61 Score=22.53 Aligned_cols=40 Identities=15% Similarity=0.220 Sum_probs=28.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccch
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNR 282 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNR 282 (400)
.++..+..++...+. . ....++|..++++...|..|.+.-
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 367777777765432 1 246789999999999998887643
No 76
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=22.27 E-value=2.9e+02 Score=20.97 Aligned_cols=23 Identities=43% Similarity=0.653 Sum_probs=10.6
Q ss_pred HHHhhhhhHHHHHHHHHHHHHHH
Q 015772 298 LKRCCETLTEENRRLQKELQELR 320 (400)
Q Consensus 298 l~~~~e~L~~En~~l~~e~~~l~ 320 (400)
|......|..+|..|..++..|.
T Consensus 31 Le~~~~~L~~en~~L~~~~~~L~ 53 (64)
T PF00170_consen 31 LEEKVEELESENEELKKELEQLK 53 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344444455555554444443
No 77
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=21.88 E-value=58 Score=29.65 Aligned_cols=46 Identities=13% Similarity=0.133 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhh
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTK 287 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~K 287 (400)
.++..+..+|...|-.. ..-.++|+.||++...|++++..-|.+.|
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 46777777776654322 44678999999999999988855444444
No 78
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.60 E-value=34 Score=24.44 Aligned_cols=40 Identities=15% Similarity=0.119 Sum_probs=18.9
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecc
Q 015772 235 KLRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWF 279 (400)
Q Consensus 235 RtrfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWF 279 (400)
...||.+|...++..++.. ....+||+.||.+..-|..|.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 3568888888888886533 446679999999887776554
No 79
>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=21.57 E-value=69 Score=24.12 Aligned_cols=33 Identities=36% Similarity=0.439 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceee
Q 015772 241 QQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEV 277 (400)
Q Consensus 241 ~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqv 277 (400)
.|+..|+-.|. +...+.. +||..+|++++.|+.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 57888888888 6666644 899999999877653
No 80
>PRK04217 hypothetical protein; Provisional
Probab=21.48 E-value=68 Score=27.82 Aligned_cols=45 Identities=11% Similarity=0.028 Sum_probs=32.7
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhh
Q 015772 236 LRLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRAR 285 (400)
Q Consensus 236 trfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK 285 (400)
..++.+|..++...|...- ...+||+.+|++...|+..+..-+.+
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4578888888877664332 56789999999999888777544433
No 81
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=20.94 E-value=67 Score=26.51 Aligned_cols=46 Identities=15% Similarity=0.224 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhh
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTK 287 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~K 287 (400)
.++..|..+|...|-. .....+||+.+|+++..|+.|...-+.|.|
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3556666666544322 234668999999999999888765444443
No 82
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=20.88 E-value=73 Score=27.43 Aligned_cols=46 Identities=15% Similarity=0.143 Sum_probs=31.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccceeecccchhhhhh
Q 015772 237 RLSKQQSAFLEESFKEHTTLTPKQKLALAKQLNLRPRQVEVWFQNRRARTK 287 (400)
Q Consensus 237 rfT~~Ql~~LE~~F~~~~yPs~~~R~eLA~~LgLserQVqvWFQNRRaK~K 287 (400)
.++..+..++...|-.. ....+||..+|++...|+.|...-|.+.|
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 45666667666554322 34788999999999999998765444433
No 83
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=20.44 E-value=2.4e+02 Score=24.57 Aligned_cols=36 Identities=28% Similarity=0.181 Sum_probs=28.6
Q ss_pred hhhhhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHh
Q 015772 289 KQTEVDCEYLKRCCETLTEENRRLQKELQELRALKS 324 (400)
Q Consensus 289 kq~~~~~e~l~~~~e~L~~En~~l~~e~~~l~al~~ 324 (400)
..+-.+...|+.....|.+||..|+.|+..||....
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~ 53 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRERLE 53 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556677888899999999999999999995543
Done!