Query 021194
Match_columns 316
No_of_seqs 286 out of 1487
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 08:20:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021194.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021194hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.8 8.1E-21 1.8E-25 172.2 6.7 105 54-164 47-151 (198)
2 KOG0842 Transcription factor t 99.7 1.2E-16 2.7E-21 153.0 7.5 67 56-122 150-218 (307)
3 KOG0489 Transcription factor z 99.6 7.9E-17 1.7E-21 151.5 2.9 63 55-117 157-219 (261)
4 KOG0488 Transcription factor B 99.6 3.9E-16 8.4E-21 150.3 7.7 55 64-118 179-233 (309)
5 KOG0487 Transcription factor A 99.6 6.2E-16 1.3E-20 148.3 4.6 64 56-119 234-297 (308)
6 KOG0843 Transcription factor E 99.6 1.3E-15 2.9E-20 135.7 4.9 64 56-119 101-164 (197)
7 KOG0484 Transcription factor P 99.6 2.7E-15 5.8E-20 123.6 5.0 61 57-117 17-77 (125)
8 KOG0850 Transcription factor D 99.6 5.4E-15 1.2E-19 136.1 7.4 61 56-116 121-181 (245)
9 PF00046 Homeobox: Homeobox do 99.6 3.1E-15 6.8E-20 108.6 4.0 57 58-114 1-57 (57)
10 KOG0485 Transcription factor N 99.5 2.7E-15 5.8E-20 137.3 4.4 60 58-117 103-164 (268)
11 KOG0493 Transcription factor E 99.5 2.2E-14 4.7E-19 134.3 6.6 62 58-119 247-308 (342)
12 KOG0492 Transcription factor M 99.5 3.6E-14 7.8E-19 129.2 6.7 61 56-116 143-203 (246)
13 KOG0848 Transcription factor C 99.5 8.7E-15 1.9E-19 137.3 2.7 54 64-117 206-259 (317)
14 KOG2251 Homeobox transcription 99.5 3.7E-14 8E-19 129.9 4.7 63 56-118 36-98 (228)
15 KOG0494 Transcription factor C 99.5 4.9E-14 1.1E-18 131.9 5.6 56 64-119 148-203 (332)
16 cd00086 homeodomain Homeodomai 99.4 2.1E-13 4.6E-18 98.5 4.3 57 59-115 2-58 (59)
17 smart00389 HOX Homeodomain. DN 99.4 2.5E-13 5.4E-18 97.6 4.2 55 59-113 2-56 (56)
18 COG5576 Homeodomain-containing 99.4 3.3E-13 7.1E-18 118.7 5.0 64 55-118 49-112 (156)
19 KOG4577 Transcription factor L 99.4 3.1E-13 6.6E-18 128.2 4.1 97 52-149 162-258 (383)
20 TIGR01565 homeo_ZF_HD homeobox 99.3 2.4E-12 5.2E-17 96.0 5.8 52 58-109 2-57 (58)
21 KOG3802 Transcription factor O 99.2 6.1E-12 1.3E-16 123.7 5.2 61 56-116 293-353 (398)
22 KOG0486 Transcription factor P 99.2 4.9E-12 1.1E-16 121.1 4.1 57 64-120 119-175 (351)
23 KOG0844 Transcription factor E 99.2 3.5E-12 7.5E-17 121.8 3.0 61 58-118 182-242 (408)
24 KOG0847 Transcription factor, 99.2 3.2E-12 6.9E-17 117.5 1.8 63 54-116 164-226 (288)
25 KOG0491 Transcription factor B 99.2 1.8E-12 3.8E-17 114.6 -0.1 57 61-117 104-160 (194)
26 KOG0490 Transcription factor, 99.0 1E-10 2.2E-15 105.4 3.4 62 55-116 58-119 (235)
27 KOG0849 Transcription factor P 98.8 2.8E-09 6.2E-14 104.6 3.9 61 57-117 176-236 (354)
28 KOG1168 Transcription factor A 98.8 3.1E-09 6.8E-14 101.3 3.7 64 53-116 305-368 (385)
29 KOG0775 Transcription factor S 98.6 2.8E-08 6.1E-13 94.1 3.9 51 64-114 183-233 (304)
30 KOG0774 Transcription factor P 98.0 2.4E-06 5.2E-11 80.8 2.8 60 57-116 188-250 (334)
31 PF05920 Homeobox_KN: Homeobox 98.0 1.6E-06 3.6E-11 60.1 0.9 34 78-111 7-40 (40)
32 KOG0490 Transcription factor, 97.8 2.4E-05 5.1E-10 70.5 4.0 61 57-117 153-213 (235)
33 KOG2252 CCAAT displacement pro 97.6 4.1E-05 8.8E-10 78.7 4.0 57 56-112 419-475 (558)
34 PF02183 HALZ: Homeobox associ 97.4 0.00026 5.6E-09 50.4 4.1 44 115-164 1-44 (45)
35 KOG1146 Homeobox protein [Gene 97.2 0.00026 5.5E-09 78.9 3.4 62 56-117 902-963 (1406)
36 KOG0773 Transcription factor M 96.0 0.0059 1.3E-07 59.3 3.6 56 63-118 245-303 (342)
37 PF11569 Homez: Homeodomain le 95.2 0.0062 1.3E-07 45.4 0.4 41 69-109 10-50 (56)
38 KOG3623 Homeobox transcription 91.6 0.13 2.8E-06 55.3 2.9 48 69-116 568-615 (1007)
39 PF04218 CENP-B_N: CENP-B N-te 90.0 0.35 7.5E-06 35.2 3.1 47 58-109 1-47 (53)
40 PRK09413 IS2 repressor TnpA; R 85.0 3.4 7.4E-05 34.5 6.6 43 60-107 9-52 (121)
41 PF02183 HALZ: Homeobox associ 73.9 4.2 9.1E-05 28.9 3.1 34 124-163 3-36 (45)
42 PF04967 HTH_10: HTH DNA bindi 65.8 5.6 0.00012 29.2 2.4 38 64-101 1-40 (53)
43 KOG4196 bZIP transcription fac 63.5 43 0.00094 29.2 7.7 73 62-150 22-105 (135)
44 cd06171 Sigma70_r4 Sigma70, re 61.7 6.9 0.00015 25.9 2.1 42 64-110 11-52 (55)
45 KOG1146 Homeobox protein [Gene 60.1 2.8 6.1E-05 48.0 -0.1 59 61-119 448-506 (1406)
46 smart00340 HALZ homeobox assoc 58.1 12 0.00026 26.6 2.8 27 128-160 7-33 (44)
47 PF04545 Sigma70_r4: Sigma-70, 57.7 8.7 0.00019 26.7 2.1 39 63-106 4-42 (50)
48 PF01527 HTH_Tnp_1: Transposas 55.0 10 0.00022 28.2 2.3 43 60-107 3-46 (76)
49 cd00569 HTH_Hin_like Helix-tur 53.0 18 0.00038 21.2 2.8 37 63-104 5-41 (42)
50 smart00340 HALZ homeobox assoc 51.3 23 0.0005 25.2 3.3 33 116-148 2-34 (44)
51 COG3413 Predicted DNA binding 47.8 17 0.00037 33.0 3.0 47 63-111 155-203 (215)
52 PF00170 bZIP_1: bZIP transcri 47.6 50 0.0011 24.4 4.9 30 121-150 28-57 (64)
53 PF13443 HTH_26: Cro/C1-type H 47.1 12 0.00026 26.9 1.4 34 86-119 12-45 (63)
54 PF08281 Sigma70_r4_2: Sigma-7 44.8 17 0.00036 25.5 1.9 41 64-109 11-51 (54)
55 KOG4005 Transcription factor X 44.2 41 0.0009 32.3 4.9 45 106-150 82-128 (292)
56 PRK03975 tfx putative transcri 44.0 22 0.00049 31.1 2.9 48 61-114 4-51 (141)
57 PF01763 Herpes_UL6: Herpesvir 42.4 36 0.00078 36.2 4.6 39 261-300 477-515 (557)
58 PF10224 DUF2205: Predicted co 40.8 75 0.0016 25.4 5.2 44 114-163 18-61 (80)
59 smart00338 BRLZ basic region l 39.8 80 0.0017 23.3 5.0 28 123-150 30-57 (65)
60 PF09607 BrkDBD: Brinker DNA-b 38.1 23 0.00051 26.7 1.8 43 62-106 4-47 (58)
61 PF00170 bZIP_1: bZIP transcri 37.5 97 0.0021 22.8 5.1 37 113-149 27-63 (64)
62 PF00424 REV: REV protein (ant 35.8 43 0.00093 27.5 3.2 33 69-117 14-48 (91)
63 PF10668 Phage_terminase: Phag 35.7 13 0.00027 28.2 0.1 20 86-105 24-43 (60)
64 TIGR02937 sigma70-ECF RNA poly 33.9 38 0.00082 26.9 2.6 45 64-113 111-155 (158)
65 PRK09646 RNA polymerase sigma 33.4 42 0.0009 29.5 3.0 45 64-113 143-187 (194)
66 PRK09652 RNA polymerase sigma 32.3 41 0.0009 28.3 2.7 45 64-113 129-173 (182)
67 PRK09642 RNA polymerase sigma 32.2 46 0.001 27.9 3.0 46 64-114 107-152 (160)
68 KOG0709 CREB/ATF family transc 31.8 1.4E+02 0.003 31.2 6.8 13 63-75 220-232 (472)
69 PF13936 HTH_38: Helix-turn-he 31.0 19 0.00042 24.9 0.4 39 62-105 3-41 (44)
70 PF06156 DUF972: Protein of un 30.6 85 0.0018 26.2 4.2 43 117-165 13-55 (107)
71 PF06005 DUF904: Protein of un 30.4 1.5E+02 0.0032 23.0 5.3 34 117-150 23-56 (72)
72 PRK12526 RNA polymerase sigma 29.7 51 0.0011 29.4 3.0 46 64-114 154-199 (206)
73 PRK06759 RNA polymerase factor 29.7 46 0.001 27.6 2.6 43 64-111 107-149 (154)
74 PF00196 GerE: Bacterial regul 28.6 44 0.00096 23.8 2.0 45 63-113 3-47 (58)
75 PRK12514 RNA polymerase sigma 28.4 60 0.0013 27.8 3.1 46 64-114 130-175 (179)
76 PF07716 bZIP_2: Basic region 27.9 1.5E+02 0.0032 21.2 4.6 19 132-150 31-49 (54)
77 PRK11924 RNA polymerase sigma 27.3 70 0.0015 26.8 3.3 46 64-114 126-171 (179)
78 KOG3119 Basic region leucine z 27.3 1E+02 0.0022 29.6 4.7 39 109-150 208-246 (269)
79 PRK12512 RNA polymerase sigma 26.9 60 0.0013 27.9 2.9 46 64-114 132-177 (184)
80 PF15058 Speriolin_N: Sperioli 26.9 36 0.00078 31.6 1.5 39 126-164 5-43 (200)
81 PRK09644 RNA polymerase sigma 25.8 73 0.0016 27.0 3.1 46 64-114 109-154 (165)
82 TIGR02985 Sig70_bacteroi1 RNA 25.2 67 0.0015 26.3 2.8 44 64-112 114-157 (161)
83 TIGR02989 Sig-70_gvs1 RNA poly 25.2 62 0.0013 26.9 2.5 42 64-110 112-153 (159)
84 PRK09648 RNA polymerase sigma 25.2 66 0.0014 27.9 2.8 42 64-110 140-181 (189)
85 PRK12530 RNA polymerase sigma 25.0 82 0.0018 27.6 3.4 46 64-114 135-180 (189)
86 PRK12515 RNA polymerase sigma 24.8 79 0.0017 27.5 3.2 46 64-114 132-177 (189)
87 smart00338 BRLZ basic region l 24.7 1.9E+02 0.0042 21.2 4.9 35 115-149 29-63 (65)
88 PRK12519 RNA polymerase sigma 24.4 57 0.0012 28.4 2.2 45 64-113 142-186 (194)
89 PF02796 HTH_7: Helix-turn-hel 24.1 49 0.0011 22.8 1.4 38 63-105 5-42 (45)
90 TIGR02948 SigW_bacill RNA poly 24.0 64 0.0014 27.6 2.5 45 64-113 137-181 (187)
91 PRK13169 DNA replication intia 24.0 1.5E+02 0.0032 25.0 4.6 42 117-164 13-54 (110)
92 TIGR02999 Sig-70_X6 RNA polyme 23.7 75 0.0016 27.2 2.8 45 64-113 135-179 (183)
93 PF12824 MRP-L20: Mitochondria 23.7 3.2E+02 0.007 24.4 6.9 45 61-107 83-127 (164)
94 COG4467 Regulator of replicati 22.9 1.8E+02 0.0039 24.8 4.7 42 117-164 13-54 (114)
95 TIGR02959 SigZ RNA polymerase 22.8 80 0.0017 27.1 2.9 43 64-111 101-143 (170)
96 PRK13729 conjugal transfer pil 22.7 2.8E+02 0.0062 29.1 7.1 41 116-162 80-120 (475)
97 PRK05602 RNA polymerase sigma 22.6 72 0.0016 27.6 2.5 46 64-114 129-174 (186)
98 KOG4571 Activating transcripti 22.6 1.7E+02 0.0037 28.8 5.2 27 124-150 253-279 (294)
99 PRK00118 putative DNA-binding 22.3 82 0.0018 26.2 2.6 45 64-113 18-62 (104)
100 smart00421 HTH_LUXR helix_turn 22.2 77 0.0017 21.2 2.1 38 64-107 4-41 (58)
101 PF13518 HTH_28: Helix-turn-he 22.0 39 0.00084 23.0 0.6 24 86-109 14-37 (52)
102 PHA02955 hypothetical protein; 22.0 1.1E+02 0.0024 28.8 3.7 43 65-107 59-102 (213)
103 PRK06811 RNA polymerase factor 21.6 79 0.0017 27.6 2.6 47 64-115 132-178 (189)
104 TIGR02939 RpoE_Sigma70 RNA pol 21.5 67 0.0014 27.6 2.1 44 64-112 139-182 (190)
105 PRK09639 RNA polymerase sigma 21.3 1.1E+02 0.0023 25.8 3.2 45 64-114 113-157 (166)
106 PF08172 CASP_C: CASP C termin 21.2 3.4E+02 0.0074 25.8 6.9 49 109-163 90-138 (248)
107 PRK12541 RNA polymerase sigma 21.1 75 0.0016 26.7 2.3 44 64-112 113-156 (161)
108 PRK09047 RNA polymerase factor 20.7 99 0.0021 25.7 2.9 42 64-110 107-148 (161)
109 PRK04217 hypothetical protein; 20.6 97 0.0021 26.0 2.8 44 63-111 42-85 (110)
110 PF06005 DUF904: Protein of un 20.3 2.6E+02 0.0056 21.7 4.9 31 120-150 19-49 (72)
111 PRK12546 RNA polymerase sigma 20.2 67 0.0014 28.4 1.9 46 64-114 114-159 (188)
112 PRK12538 RNA polymerase sigma 20.2 1E+02 0.0022 28.4 3.2 46 64-114 172-217 (233)
113 cd04761 HTH_MerR-SF Helix-Turn 20.1 36 0.00078 22.9 0.1 23 87-109 3-25 (49)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.82 E-value=8.1e-21 Score=172.23 Aligned_cols=105 Identities=59% Similarity=0.873 Sum_probs=94.7
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHHHHHHHHhhhHHHhh
Q 021194 54 GGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALKL 133 (316)
Q Consensus 54 ~g~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~~~~~lk~~~~~L~~ 133 (316)
+....+|++||+.+|+..||..|+.+.++.+.+|..||++|||.+|||+|||||||||||.++++.++..||..++.|+.
T Consensus 47 ~~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~ 126 (198)
T KOG0483|consen 47 GSKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRS 126 (198)
T ss_pred ccccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhh
Confidence 34456778889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhchHHHHHHHHHhhcccccchhhhhhccc
Q 021194 134 NYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (316)
Q Consensus 134 ~~~sl~~en~~L~~e~~~~~~d~~lk~~L~~ 164 (316)
+++.++.++..|..++. .++.+...
T Consensus 127 ~~~~Lq~e~~eL~~~~~------~~~~~~~~ 151 (198)
T KOG0483|consen 127 ENDRLQSEVQELVAELS------SLKREMQK 151 (198)
T ss_pred hhhHHHHHHHHHHHHHh------hhhhhhcc
Confidence 99999999888888887 55554443
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.66 E-value=1.2e-16 Score=153.00 Aligned_cols=67 Identities=37% Similarity=0.584 Sum_probs=60.0
Q ss_pred CCCCCCCc--CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHHHHH
Q 021194 56 HVSEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYG 122 (316)
Q Consensus 56 ~~krkRrR--fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~~~~ 122 (316)
.++|||+| |+..|+.+||+.|...+|++..+|+.||..|.|+++||||||||||-|.||+++++.+.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 44455555 99999999999999999999999999999999999999999999999999998776543
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.63 E-value=7.9e-17 Score=151.51 Aligned_cols=63 Identities=33% Similarity=0.688 Sum_probs=57.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 55 g~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
+..|+.|+.||..|+.+||+.|..++|++..+|.+||..|.|+++||||||||||+||||...
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 445556666999999999999999999999999999999999999999999999999998764
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.63 E-value=3.9e-16 Score=150.28 Aligned_cols=55 Identities=44% Similarity=0.723 Sum_probs=53.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHH
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~ 118 (316)
||..|+..||+.|++.+|++..+|.+||+.|||+..||++||||||+|||++..+
T Consensus 179 FT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 179 FSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred hhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999998754
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.59 E-value=6.2e-16 Score=148.26 Aligned_cols=64 Identities=33% Similarity=0.497 Sum_probs=57.7
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHH
Q 021194 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (316)
Q Consensus 56 ~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~ 119 (316)
..||||..+|..|+.+||+.|-.|.|++.+.|.+|++.|+|++|||+|||||||.|.||...+.
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 3445555699999999999999999999999999999999999999999999999999977543
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.58 E-value=1.3e-15 Score=135.74 Aligned_cols=64 Identities=34% Similarity=0.487 Sum_probs=57.9
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHH
Q 021194 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (316)
Q Consensus 56 ~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~ 119 (316)
+.|+.|+.||.+|+..||..|+.++|....+|++||+.|+|++.||+|||||||.|.||.+.+.
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 3444555599999999999999999999999999999999999999999999999999987654
No 7
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.56 E-value=2.7e-15 Score=123.62 Aligned_cols=61 Identities=26% Similarity=0.472 Sum_probs=55.5
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 57 ~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
+++-|+.||..|+..||+.|...+||++-.|++||.+++|++.+|||||||||+|.||+..
T Consensus 17 QRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3344455999999999999999999999999999999999999999999999999998754
No 8
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.56 E-value=5.4e-15 Score=136.09 Aligned_cols=61 Identities=34% Similarity=0.579 Sum_probs=55.2
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHH
Q 021194 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (316)
Q Consensus 56 ~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq 116 (316)
+.|+.|+.++.-||+.|.+.|++++|+.-.+|.+||..|||+..||||||||||.|.||..
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 3344455599999999999999999999999999999999999999999999999999864
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.55 E-value=3.1e-15 Score=108.61 Aligned_cols=57 Identities=42% Similarity=0.647 Sum_probs=54.0
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 58 krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++|++||.+|+..|+..|..++||+..++..||.++||+..+|++||+|||+++|+
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 356777999999999999999999999999999999999999999999999999885
No 10
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.55 E-value=2.7e-15 Score=137.27 Aligned_cols=60 Identities=42% Similarity=0.666 Sum_probs=55.2
Q ss_pred CCCCCc--CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 58 SEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 58 krkRrR--fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
+|||+| |+..|+..||..|+..+|++..+|..||++|.|++.||+|||||||.|||++-.
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 444444 999999999999999999999999999999999999999999999999999753
No 11
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.51 E-value=2.2e-14 Score=134.34 Aligned_cols=62 Identities=32% Similarity=0.610 Sum_probs=55.7
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHH
Q 021194 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (316)
Q Consensus 58 krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~ 119 (316)
|+.|+-||.+||+.|+..|+.++|++...|.+||.+|||.+.||+|||||+|+|.||..-.+
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence 33444599999999999999999999999999999999999999999999999999865433
No 12
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.49 E-value=3.6e-14 Score=129.15 Aligned_cols=61 Identities=31% Similarity=0.500 Sum_probs=56.0
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHH
Q 021194 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (316)
Q Consensus 56 ~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq 116 (316)
..++.|+.||..|+..||+.|+..+|+++.+|.+++..|.|++.||+|||||||+|.|+-+
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 3445556699999999999999999999999999999999999999999999999999865
No 13
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.49 E-value=8.7e-15 Score=137.26 Aligned_cols=54 Identities=41% Similarity=0.602 Sum_probs=52.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
+|..|+-+||+.|..++|.++.+|.+||..|||++|||||||||||||+||...
T Consensus 206 YTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred ecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999998653
No 14
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.46 E-value=3.7e-14 Score=129.93 Aligned_cols=63 Identities=27% Similarity=0.435 Sum_probs=57.8
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHH
Q 021194 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (316)
Q Consensus 56 ~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~ 118 (316)
+.+|.|++|+-.|+.+||..|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|+++..
T Consensus 36 kqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred hcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 345556679999999999999999999999999999999999999999999999999998754
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.46 E-value=4.9e-14 Score=131.85 Aligned_cols=56 Identities=30% Similarity=0.542 Sum_probs=53.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHH
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~ 119 (316)
||..|+..||+.|+..+||+...|+-||.++.|.+.+|+|||||||+||||++.+.
T Consensus 148 FT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 148 FTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred hhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 99999999999999999999999999999999999999999999999999987654
No 16
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.40 E-value=2.1e-13 Score=98.48 Aligned_cols=57 Identities=46% Similarity=0.738 Sum_probs=53.1
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhH
Q 021194 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (316)
Q Consensus 59 rkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkk 115 (316)
+++..++..|+..|+..|..++||+..++..||.++||++.||++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 345669999999999999999999999999999999999999999999999998764
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.40 E-value=2.5e-13 Score=97.65 Aligned_cols=55 Identities=45% Similarity=0.792 Sum_probs=51.2
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 59 rkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
+.|.+|+.+|+..|+..|..++||+..++..||..+||+..||+.||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 3455699999999999999999999999999999999999999999999998764
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.38 E-value=3.3e-13 Score=118.70 Aligned_cols=64 Identities=33% Similarity=0.568 Sum_probs=59.3
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHH
Q 021194 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (316)
Q Consensus 55 g~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~ 118 (316)
...+++|+|.|.+|+.+|++.|..++||+...|..|+..|+|+++-|+|||||||++.|+....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 4567778889999999999999999999999999999999999999999999999999987644
No 19
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.37 E-value=3.1e-13 Score=128.16 Aligned_cols=97 Identities=23% Similarity=0.344 Sum_probs=78.8
Q ss_pred cCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHHHHHHHHhhhHHH
Q 021194 52 ESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDAL 131 (316)
Q Consensus 52 ~~~g~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~~~~~lk~~~~~L 131 (316)
+..+..|+.|+.+|+.|++.|+..|+..++|....|++|+.++||..|+|||||||||||.|+-+...-...|.+.+..+
T Consensus 162 ~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsm 241 (383)
T KOG4577|consen 162 EGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSM 241 (383)
T ss_pred ccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHh
Confidence 44566777788899999999999999999999999999999999999999999999999999977666666777777666
Q ss_pred hhhhhchHHHHHHHHHhh
Q 021194 132 KLNYDSLQHDNEALLKET 149 (316)
Q Consensus 132 ~~~~~sl~~en~~L~~e~ 149 (316)
+.. .+.+.|+..-..|+
T Consensus 242 K~s-gs~r~ekdsd~sel 258 (383)
T KOG4577|consen 242 KRS-GSSRAEKDSDDSEL 258 (383)
T ss_pred hcc-CCcccccccccCcc
Confidence 665 44455544433343
No 20
>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=99.32 E-value=2.4e-12 Score=96.03 Aligned_cols=52 Identities=15% Similarity=0.360 Sum_probs=48.9
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHhCCCccceeeechhhH
Q 021194 58 SEKKRRLSVDQVKALEKNFEVENK----LEPERKVKLAQELGLQPRQVAVWFQNRR 109 (316)
Q Consensus 58 krkRrRfT~~Ql~~LE~~F~~~~y----Ps~~~r~~LA~~LgLs~rQVqVWFQNRR 109 (316)
++.|+.||.+|+..|+..|+.++| |+...+.+||..+||++++|+|||||-+
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 566777999999999999999999 9999999999999999999999999964
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.24 E-value=6.1e-12 Score=123.69 Aligned_cols=61 Identities=31% Similarity=0.436 Sum_probs=54.9
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHH
Q 021194 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (316)
Q Consensus 56 ~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq 116 (316)
++||||+.|.......||+.|.+|++|+..++..||.+|+|.+.+|+|||||||.|.||-.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 3444555599999999999999999999999999999999999999999999999998753
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.23 E-value=4.9e-12 Score=121.07 Aligned_cols=57 Identities=26% Similarity=0.559 Sum_probs=54.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHHH
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERD 120 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~~ 120 (316)
||..|+..||..|+++.||+...|++||..++|++.+|+|||.|||+||||++....
T Consensus 119 FtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 119 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 999999999999999999999999999999999999999999999999999865544
No 23
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.23 E-value=3.5e-12 Score=121.84 Aligned_cols=61 Identities=34% Similarity=0.554 Sum_probs=55.6
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHH
Q 021194 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (316)
Q Consensus 58 krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~ 118 (316)
++=|+-||.+|+..||+.|-+.+|-+..+|.+||..|+|++..|||||||||.|+|++.+.
T Consensus 182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3334449999999999999999999999999999999999999999999999999998654
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.22 E-value=3.2e-12 Score=117.49 Aligned_cols=63 Identities=37% Similarity=0.683 Sum_probs=57.5
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHH
Q 021194 54 GGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (316)
Q Consensus 54 ~g~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq 116 (316)
+|+++..|..|+..|+..||..|+..+|+-.++|.+||..+|+++.||+|||||||.||||+.
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 355555566699999999999999999999999999999999999999999999999999875
No 25
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.21 E-value=1.8e-12 Score=114.57 Aligned_cols=57 Identities=39% Similarity=0.566 Sum_probs=53.7
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
|+.|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||.|.||.+.
T Consensus 104 Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 104 RTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred cccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 444999999999999999999999999999999999999999999999999998764
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.05 E-value=1e-10 Score=105.39 Aligned_cols=62 Identities=27% Similarity=0.302 Sum_probs=56.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHH
Q 021194 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (316)
Q Consensus 55 g~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq 116 (316)
.+.++.|+.|+..|++.||+.|+..+||+...|+.||..+++++..|+|||||||+||+++.
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 34455566699999999999999999999999999999999999999999999999999875
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.81 E-value=2.8e-09 Score=104.65 Aligned_cols=61 Identities=34% Similarity=0.570 Sum_probs=55.8
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 57 ~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
.++.|+.|+..|+..|++.|+.++||+...|++||.++++++..|+|||+|||++|++...
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3344566999999999999999999999999999999999999999999999999998753
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.80 E-value=3.1e-09 Score=101.27 Aligned_cols=64 Identities=28% Similarity=0.517 Sum_probs=58.3
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHH
Q 021194 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (316)
Q Consensus 53 ~~g~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq 116 (316)
.++.+||||+.+.+...+.||.+|...+.|+.+.+..||.+|+|.+.+|+|||+|.|+|.|+.+
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 4566777777798999999999999999999999999999999999999999999999988854
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.61 E-value=2.8e-08 Score=94.11 Aligned_cols=51 Identities=29% Similarity=0.428 Sum_probs=48.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
|...-+..|..+|..++||++.++.+||+.+||+..||-.||+|||+|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 677788899999999999999999999999999999999999999999883
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.04 E-value=2.4e-06 Score=80.83 Aligned_cols=60 Identities=28% Similarity=0.448 Sum_probs=54.0
Q ss_pred CCCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHH
Q 021194 57 VSEKKRRLSVDQVKALEKNFE---VENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (316)
Q Consensus 57 ~krkRrRfT~~Ql~~LE~~F~---~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq 116 (316)
.++||+.|+..-..+|..+|- .++||+.+.+++||+++|++..||..||.|+|-++||..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 456666799999999999996 588999999999999999999999999999999998754
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=98.02 E-value=1.6e-06 Score=60.06 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCCccceeeechhhHhh
Q 021194 78 VENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (316)
Q Consensus 78 ~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK 111 (316)
.++||+.+++..||.++||+..||..||-|.|.|
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 3789999999999999999999999999999964
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.76 E-value=2.4e-05 Score=70.53 Aligned_cols=61 Identities=31% Similarity=0.573 Sum_probs=54.6
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 57 ~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
.++.++.+...|+..+...|....+|+...+.+|+..+|++++.|++||||+|++.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3334445999999999999999999999999999999999999999999999999998653
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.64 E-value=4.1e-05 Score=78.68 Aligned_cols=57 Identities=21% Similarity=0.282 Sum_probs=51.2
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhh
Q 021194 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (316)
Q Consensus 56 ~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~ 112 (316)
..||.|..||..|...|..+|+.+++|+.+..+.|+.+|||....|.+||-|-|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 344444459999999999999999999999999999999999999999999988765
No 34
>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=97.38 E-value=0.00026 Score=50.43 Aligned_cols=44 Identities=55% Similarity=0.763 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhccc
Q 021194 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (316)
Q Consensus 115 kq~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L~~ 164 (316)
+|++++|..|+.+|+.|+.++++|..+|+.|++++. .|++++..
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~------~L~~kl~~ 44 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQ------ELKEKLQM 44 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHhhcC
Confidence 468999999999999999999999999999999999 89888753
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.17 E-value=0.00026 Score=78.88 Aligned_cols=62 Identities=27% Similarity=0.381 Sum_probs=57.4
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 56 ~~krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
.++..|++++..|+..+..+|....+|...+.+.|...+++.++.|++||||-|+|.|+..+
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 45566778999999999999999999999999999999999999999999999999998765
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.99 E-value=0.0059 Score=59.28 Aligned_cols=56 Identities=29% Similarity=0.357 Sum_probs=48.0
Q ss_pred cCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHH
Q 021194 63 RLSVDQVKALEKNFEV---ENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (316)
Q Consensus 63 RfT~~Ql~~LE~~F~~---~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~ 118 (316)
.+......+|+.+... .+||+...+..||+++||+..||.+||-|.|-|..+-..+
T Consensus 245 ~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 245 GLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred CCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHH
Confidence 4999999999988443 5799999999999999999999999999999887765543
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.19 E-value=0.0062 Score=45.43 Aligned_cols=41 Identities=24% Similarity=0.424 Sum_probs=31.1
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhH
Q 021194 69 VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (316)
Q Consensus 69 l~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRR 109 (316)
++-|+.+|...+++.......|..+.+|+..||+.||-.|+
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 46699999999999999999999999999999999996554
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=91.59 E-value=0.13 Score=55.28 Aligned_cols=48 Identities=23% Similarity=0.372 Sum_probs=44.6
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHH
Q 021194 69 VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (316)
Q Consensus 69 l~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq 116 (316)
...|..+|..|..|+.++...+|.+.||+.+.|++||+++++....-+
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 778999999999999999999999999999999999999999877654
No 39
>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=90.02 E-value=0.35 Score=35.16 Aligned_cols=47 Identities=21% Similarity=0.412 Sum_probs=34.5
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhH
Q 021194 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (316)
Q Consensus 58 krkRrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRR 109 (316)
+++|+.+|.++-..+-..++... ....||+++|++..+|..|..|+.
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 35566699998888888888775 577899999999999999998753
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=84.99 E-value=3.4 Score=34.48 Aligned_cols=43 Identities=21% Similarity=0.402 Sum_probs=29.1
Q ss_pred CCCcCCHHHHH-HHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechh
Q 021194 60 KKRRLSVDQVK-ALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (316)
Q Consensus 60 kRrRfT~~Ql~-~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQN 107 (316)
++++|+.++.. ++...+.. . ....++|+++|+++.+|..|.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~-g----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEP-G----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcC-C----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35567777654 44444442 2 24567899999999999999754
No 41
>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=73.92 E-value=4.2 Score=28.95 Aligned_cols=34 Identities=41% Similarity=0.645 Sum_probs=23.3
Q ss_pred HHhhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhcc
Q 021194 124 LKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (316)
Q Consensus 124 lk~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L~ 163 (316)
+...|+.|+..++.|..++++|..|+. .|+.++.
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~------~L~aev~ 36 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENE------KLRAEVQ 36 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHH
Confidence 345667777777777777777777776 6666553
No 42
>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=65.82 E-value=5.6 Score=29.24 Aligned_cols=38 Identities=26% Similarity=0.285 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCccce
Q 021194 64 LSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQV 101 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~y--Ps~~~r~~LA~~LgLs~rQV 101 (316)
+|..|..+|...|+..-| |-.....+||.++|+++.-|
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 588999999999998765 55667889999999998653
No 43
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=63.49 E-value=43 Score=29.23 Aligned_cols=73 Identities=27% Similarity=0.328 Sum_probs=42.7
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHh-CCCccceeeechhhHhhh----------hhHHHHHHHHHHHhhhHH
Q 021194 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQEL-GLQPRQVAVWFQNRRARW----------KTKQLERDYGVLKANYDA 130 (316)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~L-gLs~rQVqVWFQNRRaK~----------Kkkq~~~~~~~lk~~~~~ 130 (316)
.+|+.+++..+ ..| +|=++| |++...|-.|=|.||+-. |+-+.. ..|...+..
T Consensus 22 d~lsDd~Lvsm------------SVR-eLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk---~eLE~~k~~ 85 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVR-ELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQK---HELEKEKAE 85 (135)
T ss_pred CCcCHHHHHHh------------hHH-HHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH---HHHHHHHHH
Confidence 46898888777 222 334444 888888888888887532 222222 223333344
Q ss_pred HhhhhhchHHHHHHHHHhhc
Q 021194 131 LKLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 131 L~~~~~sl~~en~~L~~e~~ 150 (316)
|..+.+.|..++..+..|+.
T Consensus 86 L~qqv~~L~~e~s~~~~E~d 105 (135)
T KOG4196|consen 86 LQQQVEKLKEENSRLRRELD 105 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 55555666666666666665
No 44
>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=61.67 E-value=6.9 Score=25.90 Aligned_cols=42 Identities=14% Similarity=0.128 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRa 110 (316)
++..+..++...|... ....++|..+|++...|..|....+.
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6777888887777433 24567899999999999988865443
No 45
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=60.12 E-value=2.8 Score=48.01 Aligned_cols=59 Identities=20% Similarity=0.095 Sum_probs=52.2
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhHHHHH
Q 021194 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (316)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~ 119 (316)
++|++.-|..+|..+|....+|.-.++..++.-||+..|.+-.||++++.+|.+...+.
T Consensus 448 s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~ 506 (1406)
T KOG1146|consen 448 SKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRL 506 (1406)
T ss_pred hhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccc
Confidence 44588889999999999999999999999999999999999999999998888766543
No 46
>smart00340 HALZ homeobox associated leucin zipper.
Probab=58.13 E-value=12 Score=26.59 Aligned_cols=27 Identities=33% Similarity=0.377 Sum_probs=20.0
Q ss_pred hHHHhhhhhchHHHHHHHHHhhcccccchhhhh
Q 021194 128 YDALKLNYDSLQHDNEALLKETIVHETDHQNKA 160 (316)
Q Consensus 128 ~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~ 160 (316)
++.|+.-+++|..||.+|++|+. +|+.
T Consensus 7 Ce~LKrcce~LteeNrRL~ke~~------eLra 33 (44)
T smart00340 7 CELLKRCCESLTEENRRLQKEVQ------ELRA 33 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHh
Confidence 34555667777888888888888 7765
No 47
>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=57.71 E-value=8.7 Score=26.72 Aligned_cols=39 Identities=13% Similarity=0.183 Sum_probs=29.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeech
Q 021194 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (316)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQ 106 (316)
.+++.+..+|...|... ..-.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHH
Confidence 37888999999998333 3567899999999988876654
No 48
>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=55.01 E-value=10 Score=28.18 Aligned_cols=43 Identities=26% Similarity=0.451 Sum_probs=28.5
Q ss_pred CCCcCCHHHHHHHHHhh-hhcCCCCHHHHHHHHHHhCCCccceeeechh
Q 021194 60 KKRRLSVDQVKALEKNF-EVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (316)
Q Consensus 60 kRrRfT~~Ql~~LE~~F-~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQN 107 (316)
++++||+++...+-..+ ... .....+|+++|+++.++..|-.-
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHH
Confidence 45679998877766655 333 46788999999999999888743
No 49
>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=52.96 E-value=18 Score=21.24 Aligned_cols=37 Identities=14% Similarity=0.337 Sum_probs=25.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeee
Q 021194 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVW 104 (316)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVW 104 (316)
.++.++...+...|... . ...++|..+|++...|..|
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHh
Confidence 36777777676666533 2 4567889999988877666
No 50
>smart00340 HALZ homeobox associated leucin zipper.
Probab=51.29 E-value=23 Score=25.22 Aligned_cols=33 Identities=27% Similarity=0.251 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHh
Q 021194 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLKE 148 (316)
Q Consensus 116 q~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e 148 (316)
+.+.++.-||..++.|..+|..|++|.+.|++-
T Consensus 2 QTEvdCe~LKrcce~LteeNrRL~ke~~eLral 34 (44)
T smart00340 2 QTEVDCELLKRCCESLTEENRRLQKEVQELRAL 34 (44)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 567889999999999999999999998888754
No 51
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=47.81 E-value=17 Score=32.99 Aligned_cols=47 Identities=23% Similarity=0.238 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCccceeeechhhHhh
Q 021194 63 RLSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (316)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~y--Ps~~~r~~LA~~LgLs~rQVqVWFQNRRaK 111 (316)
.+|+.|+++|...|...-| |-.....+||+++|+++.- +|.-=|||.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHH
Confidence 4999999999999998764 6666788899999999864 333334443
No 52
>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=47.65 E-value=50 Score=24.38 Aligned_cols=30 Identities=23% Similarity=0.281 Sum_probs=18.3
Q ss_pred HHHHHhhhHHHhhhhhchHHHHHHHHHhhc
Q 021194 121 YGVLKANYDALKLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 121 ~~~lk~~~~~L~~~~~sl~~en~~L~~e~~ 150 (316)
...|......|..+++.|..++..|..++.
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~ 57 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEIQ 57 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555556666666666666666666665
No 53
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.09 E-value=12 Score=26.92 Aligned_cols=34 Identities=15% Similarity=0.261 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCccceeeechhhHhhhhhHHHHH
Q 021194 86 RKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (316)
Q Consensus 86 ~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~~~ 119 (316)
....||+.+|++..+|..|+.++.....-....+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ 45 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEK 45 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHH
Confidence 5678999999999999999987765555544433
No 54
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=44.85 E-value=17 Score=25.45 Aligned_cols=41 Identities=17% Similarity=0.173 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhH
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRR 109 (316)
+++.+..++...|-.+ -.-.++|..+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5667777776665544 3677899999999999999986433
No 55
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=44.16 E-value=41 Score=32.31 Aligned_cols=45 Identities=31% Similarity=0.371 Sum_probs=27.4
Q ss_pred hhhHhhhhhH--HHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhc
Q 021194 106 QNRRARWKTK--QLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 106 QNRRaK~Kkk--q~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~ 150 (316)
|+-|.|.|-+ +++.+...|-..++.|..+|+.|+..|+.|..++.
T Consensus 82 QtaRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~ 128 (292)
T KOG4005|consen 82 QTARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNH 128 (292)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhH
Confidence 4445444433 33444555666777777777777777777766655
No 56
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=43.99 E-value=22 Score=31.08 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=35.9
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
...+++.|..+|... ... ....++|..+|++...|..|-++.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345899999999873 322 246689999999999999999865555443
No 57
>PF01763 Herpes_UL6: Herpesvirus UL6 like; InterPro: IPR002660 This family consists of various proteins from the Herpesviridae that are similar to Human herpesvirus 1 (HHV-1) UL6 virion protein. UL6 is essential for cleavage and packaging of the viral genome [].; GO: 0006323 DNA packaging
Probab=42.40 E-value=36 Score=36.17 Aligned_cols=39 Identities=31% Similarity=0.383 Sum_probs=33.3
Q ss_pred ceeeeEeeccccccccceeeeccccccchhhhhhhHHHHH
Q 021194 261 SLINFRLTASNSQNQRTRLSLSRWKSTISLVMRPAISSLM 300 (316)
Q Consensus 261 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 300 (316)
-+.||+++- +.-||-++++++-=.+||+++.-|-..+++
T Consensus 477 l~RtFKL~r-~vnNQGqe~sI~YSn~TIslll~Pf~~~Il 515 (557)
T PF01763_consen 477 LFRTFKLRR-VVNNQGQEVSISYSNYTISLLLGPFFFSIL 515 (557)
T ss_pred HHHHccccc-ccCCCCceEEEEechhhHHHHHHHHHHHHh
Confidence 457899874 678999999999999999999999877654
No 58
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=40.78 E-value=75 Score=25.36 Aligned_cols=44 Identities=18% Similarity=0.218 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhcc
Q 021194 114 TKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (316)
Q Consensus 114 kkq~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L~ 163 (316)
+..+.++...|+...+.|....+.++.+++.|..++. .|+.++.
T Consensus 18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~------~Lq~YI~ 61 (80)
T PF10224_consen 18 KEELIQEILELQDSLEALSDRVEEVKEENEKLESENE------YLQQYIG 61 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHH
Confidence 3344455556666666676777777777777777776 6666553
No 59
>smart00338 BRLZ basic region leucin zipper.
Probab=39.76 E-value=80 Score=23.27 Aligned_cols=28 Identities=21% Similarity=0.287 Sum_probs=17.4
Q ss_pred HHHhhhHHHhhhhhchHHHHHHHHHhhc
Q 021194 123 VLKANYDALKLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 123 ~lk~~~~~L~~~~~sl~~en~~L~~e~~ 150 (316)
.|......|...+..|..+...|..++.
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~l~~e~~ 57 (65)
T smart00338 30 ELERKVEQLEAENERLKKEIERLRRELE 57 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555666666666666666666666
No 60
>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=38.12 E-value=23 Score=26.69 Aligned_cols=43 Identities=21% Similarity=0.377 Sum_probs=22.8
Q ss_pred CcCCHHH-HHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeech
Q 021194 62 RRLSVDQ-VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (316)
Q Consensus 62 rRfT~~Q-l~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQ 106 (316)
+.|+... +.+++.++ ....--...|.. |+++|+++++|+-|-+
T Consensus 4 rsy~~~FKL~Vv~~a~-~~~nc~~~~RAa-arkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAE-KDNNCKGNQRAA-ARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ----HHHHHHHHHHHH-H-TTTTT-HHHH-HHHTTS-HHHHHHHHT
T ss_pred cccChHHHHHHHHHHH-HccchhhhHHHH-HHHhCccHHHHHHHHH
Confidence 3465544 44444444 333333344554 9999999999998875
No 61
>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=37.49 E-value=97 Score=22.79 Aligned_cols=37 Identities=22% Similarity=0.337 Sum_probs=25.7
Q ss_pred hhHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhh
Q 021194 113 KTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKET 149 (316)
Q Consensus 113 Kkkq~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~ 149 (316)
.-..++.....|...++.|...+..+..+...|..++
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 27 YIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3344556667777777777777777777777777664
No 62
>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=35.78 E-value=43 Score=27.46 Aligned_cols=33 Identities=27% Similarity=0.605 Sum_probs=19.4
Q ss_pred HHHHHHhhhhcCCCCHHH--HHHHHHHhCCCccceeeechhhHhhhhhHHH
Q 021194 69 VKALEKNFEVENKLEPER--KVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (316)
Q Consensus 69 l~~LE~~F~~~~yPs~~~--r~~LA~~LgLs~rQVqVWFQNRRaK~Kkkq~ 117 (316)
+...+-.|+.++||.+.- +.. .|||.+||+.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~aR----------------RnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQAR----------------RNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HHHH----------------HHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccccc----------------cchhhhHHHHHH
Confidence 344555688999997542 222 589999998764
No 63
>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=35.74 E-value=13 Score=28.19 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCCccceeeec
Q 021194 86 RKVKLAQELGLQPRQVAVWF 105 (316)
Q Consensus 86 ~r~~LA~~LgLs~rQVqVWF 105 (316)
.-.+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45678999999999999885
No 64
>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=33.89 E-value=38 Score=26.94 Aligned_cols=45 Identities=16% Similarity=0.181 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
+++.|...+...|-.. ....++|..+|+++..|..|...-+.+.|
T Consensus 111 L~~~~~~ii~~~~~~g-----~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLEG-----LSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5666666665554322 24568999999999999887765444433
No 65
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.36 E-value=42 Score=29.47 Aligned_cols=45 Identities=13% Similarity=0.119 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
+++.+..+|...|-.+ ..-.++|..||++...|+++...-|.+.|
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 7777777776655433 25668899999999999888854444433
No 66
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=32.30 E-value=41 Score=28.29 Aligned_cols=45 Identities=13% Similarity=0.022 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
+++.+..++...|-.+ ..-.++|..+|+++..|+.|...-+.+.|
T Consensus 129 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 129 LPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 7788888887765432 24557899999999999988864444333
No 67
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=32.22 E-value=46 Score=27.92 Aligned_cols=46 Identities=13% Similarity=0.119 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.+..++...|-... .-.++|..+|+++..|+++...-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666655544332 45678999999999999988655554444
No 68
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=31.83 E-value=1.4e+02 Score=31.18 Aligned_cols=13 Identities=23% Similarity=0.355 Sum_probs=9.1
Q ss_pred cCCHHHHHHHHHh
Q 021194 63 RLSVDQVKALEKN 75 (316)
Q Consensus 63 RfT~~Ql~~LE~~ 75 (316)
+++.+....|.+.
T Consensus 220 ~LteeEkrLL~kE 232 (472)
T KOG0709|consen 220 VLTEEEKRLLTKE 232 (472)
T ss_pred eccHHHHHHHHhc
Confidence 4777777777665
No 69
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.00 E-value=19 Score=24.85 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=19.6
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeec
Q 021194 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (316)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWF 105 (316)
+.+|.+|...++..++.. ....+||+.+|.++.-|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 458889999999887644 356679999999988776554
No 70
>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=30.63 E-value=85 Score=26.20 Aligned_cols=43 Identities=26% Similarity=0.320 Sum_probs=25.8
Q ss_pred HHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhcccc
Q 021194 117 LERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRD 165 (316)
Q Consensus 117 ~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L~~~ 165 (316)
.+.+...+-.....|+.....+..+|..|+.|+. .|+++|.+.
T Consensus 13 le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~------~Lr~~l~~~ 55 (107)
T PF06156_consen 13 LEQQLGQLLEELEELKKQLQELLEENARLRIENE------HLRERLEEL 55 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHH
Confidence 3444455555555666666666666666666666 666666543
No 71
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=30.38 E-value=1.5e+02 Score=23.05 Aligned_cols=34 Identities=29% Similarity=0.374 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhc
Q 021194 117 LERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 117 ~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~ 150 (316)
++.+...|+..+..+..++..|..+|..|+.+..
T Consensus 23 Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~ 56 (72)
T PF06005_consen 23 LQMENEELKEKNNELKEENEELKEENEQLKQERN 56 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555556666666666655544
No 72
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=29.75 E-value=51 Score=29.41 Aligned_cols=46 Identities=22% Similarity=0.175 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.|..++...|-.+ ....++|..+|++...|+++...-|.+.++
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666666544322 256789999999999998877544444433
No 73
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=29.71 E-value=46 Score=27.59 Aligned_cols=43 Identities=16% Similarity=0.119 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK 111 (316)
+++.+..++...|-.+ ....++|..+|++...|+.|...-|.+
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 6777777776655433 246789999999999999987644443
No 74
>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=28.61 E-value=44 Score=23.84 Aligned_cols=45 Identities=16% Similarity=0.179 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
+||+.++.+|.....-. ...++|..+|++++.|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 47888888887766543 5678999999999999887766555443
No 75
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=28.36 E-value=60 Score=27.81 Aligned_cols=46 Identities=13% Similarity=0.260 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.+..++...|-.. ....+||..+|+++..|+++...-|.+.|+
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 5666666665555322 246789999999999999888655544443
No 76
>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=27.85 E-value=1.5e+02 Score=21.19 Aligned_cols=19 Identities=26% Similarity=0.387 Sum_probs=9.3
Q ss_pred hhhhhchHHHHHHHHHhhc
Q 021194 132 KLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 132 ~~~~~sl~~en~~L~~e~~ 150 (316)
......|..+|..|..++.
T Consensus 31 e~~~~~L~~en~~L~~~i~ 49 (54)
T PF07716_consen 31 EQEVQELEEENEQLRQEIA 49 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3344445555555555554
No 77
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=27.32 E-value=70 Score=26.79 Aligned_cols=46 Identities=17% Similarity=0.174 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.+..++...|..+ ..-.+||..+|+++..|..|...-|.+.|+
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5566666665554322 245789999999999999988655544443
No 78
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=27.30 E-value=1e+02 Score=29.55 Aligned_cols=39 Identities=28% Similarity=0.317 Sum_probs=21.6
Q ss_pred HhhhhhHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhc
Q 021194 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 109 RaK~Kkkq~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~ 150 (316)
|.+.++++.+.+ .+.....|..+++.|+.+.+.|++|+.
T Consensus 208 kSR~~~k~~~~e---~~~r~~~leken~~lr~~v~~l~~el~ 246 (269)
T KOG3119|consen 208 KSRDKRKQKEDE---MAHRVAELEKENEALRTQVEQLKKELA 246 (269)
T ss_pred HhhhhHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455443322 233345566666666666667766666
No 79
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=26.93 E-value=60 Score=27.94 Aligned_cols=46 Identities=15% Similarity=0.047 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.+..++...|-.. ..-.+||..+|++...|+.++..-|.+.|.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6777777777765443 246689999999999999988655555443
No 80
>PF15058 Speriolin_N: Speriolin N terminus
Probab=26.92 E-value=36 Score=31.58 Aligned_cols=39 Identities=28% Similarity=0.446 Sum_probs=25.8
Q ss_pred hhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhccc
Q 021194 126 ANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (316)
Q Consensus 126 ~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L~~ 164 (316)
.+|+.+++..+.+..||+.|+++++.-..+++||.-|.+
T Consensus 5 ~~yeGlrhqierLv~ENeeLKKlVrLirEN~eLksaL~e 43 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKKLVRLIRENHELKSALGE 43 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 356666777777777777777777655555567765543
No 81
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=25.79 E-value=73 Score=26.97 Aligned_cols=46 Identities=22% Similarity=0.073 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.+..++...|-.. ....++|..+|+++..|++|.+.-|.+.|+
T Consensus 109 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 109 LPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666665443222 246789999999999999988655544443
No 82
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=25.18 E-value=67 Score=26.31 Aligned_cols=44 Identities=16% Similarity=0.101 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~ 112 (316)
++..+..++...|-.. ....++|..+|+++..|+.+...-|.+.
T Consensus 114 L~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALKEL 157 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5566666665544322 2456789999999999988775444433
No 83
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=25.15 E-value=62 Score=26.90 Aligned_cols=42 Identities=21% Similarity=0.190 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRa 110 (316)
+++.+..++...|-.. ..-.++|..+|++...|+++...-|.
T Consensus 112 L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 112 LPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 6777777776654332 35677899999999999987653333
No 84
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.15 E-value=66 Score=27.88 Aligned_cols=42 Identities=24% Similarity=0.136 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRa 110 (316)
+++.|..++...|-.+ ....+||..+|++...|+.+...-|.
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6777777777655443 35678999999999999887743333
No 85
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.01 E-value=82 Score=27.60 Aligned_cols=46 Identities=15% Similarity=0.200 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.|..++.-.|-.. ..-.++|..+|+++..|+++...-|.+.|+
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666776666655433 246689999999999999988644444443
No 86
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.77 E-value=79 Score=27.47 Aligned_cols=46 Identities=13% Similarity=0.171 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.+..+|...|-.. ..-.++|..+|+++..|++....-|.+.|+
T Consensus 132 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6777777776655433 245678999999999998877655544444
No 87
>smart00338 BRLZ basic region leucin zipper.
Probab=24.73 E-value=1.9e+02 Score=21.18 Aligned_cols=35 Identities=31% Similarity=0.407 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhh
Q 021194 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKET 149 (316)
Q Consensus 115 kq~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~ 149 (316)
..++.+...|...+..|......+..++..|..++
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 29 EELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34455666666666777777777777777666654
No 88
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=24.43 E-value=57 Score=28.38 Aligned_cols=45 Identities=18% Similarity=0.200 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
+++.+..++...|-. .....++|..+|++...|+.|...-|.+.|
T Consensus 142 L~~~~~~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAYYE-----GLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhhhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 555555555544322 235668899999999999999865444444
No 89
>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=24.11 E-value=49 Score=22.77 Aligned_cols=38 Identities=16% Similarity=0.367 Sum_probs=26.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeec
Q 021194 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (316)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWF 105 (316)
.++.+|...+...+... ....+||+.+|++...|..|+
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 37777777777777765 247789999999988776544
No 90
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.05 E-value=64 Score=27.58 Aligned_cols=45 Identities=11% Similarity=0.073 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
+++.+..++...|-. ...-.++|..+|+++..|+++.+.-|.+.|
T Consensus 137 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 137 LPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 666666666654332 234667899999999999988865444443
No 91
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=24.00 E-value=1.5e+02 Score=24.99 Aligned_cols=42 Identities=33% Similarity=0.411 Sum_probs=24.8
Q ss_pred HHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhccc
Q 021194 117 LERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (316)
Q Consensus 117 ~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L~~ 164 (316)
.+.+...+-.....|+.....+..+|..|+.|+. .|+.+|.+
T Consensus 13 le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~------~Lr~~l~~ 54 (110)
T PRK13169 13 LEQNLGVLLKELGALKKQLAELLEENTALRLEND------KLRERLEE 54 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHH
Confidence 3444444455555566666666666666666666 66666654
No 92
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=23.71 E-value=75 Score=27.21 Aligned_cols=45 Identities=22% Similarity=0.198 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
+++.|..++...|-.+ ..-.++|..+|+++..|++....-|.+.|
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 5555555555544333 24567899999999999988764444433
No 93
>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=23.69 E-value=3.2e+02 Score=24.44 Aligned_cols=45 Identities=18% Similarity=0.213 Sum_probs=35.7
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechh
Q 021194 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (316)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQN 107 (316)
+..+|++++..+.+.-..+ |..-.+..||+++|+++.-|.+-..-
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~ 127 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPA 127 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCC
Confidence 3459999999998887766 55667899999999999877765543
No 94
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=22.86 E-value=1.8e+02 Score=24.75 Aligned_cols=42 Identities=36% Similarity=0.415 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhccc
Q 021194 117 LERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (316)
Q Consensus 117 ~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L~~ 164 (316)
.+...+++-+...+++..-.++..+|-.|+-|+. .|+.+|..
T Consensus 13 le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe------~LR~RL~~ 54 (114)
T COG4467 13 LEEQLGVLLAELGGLKQHLGSLVEENTALRLENE------KLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHH------HHHHHhCC
Confidence 3445555555666666777777777777777777 78888876
No 95
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=22.77 E-value=80 Score=27.09 Aligned_cols=43 Identities=19% Similarity=0.158 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK 111 (316)
+++.+..+|.-.|-.. ....++|..+|+++..|+++.+.-|.+
T Consensus 101 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~ 143 (170)
T TIGR02959 101 LPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKK 143 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 6777777777665433 246678999999999998877543333
No 96
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=22.65 E-value=2.8e+02 Score=29.07 Aligned_cols=41 Identities=17% Similarity=0.244 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhc
Q 021194 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATL 162 (316)
Q Consensus 116 q~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L 162 (316)
++++++..++...+.+......+.+..+.|+.++. .|+.++
T Consensus 80 ELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~------~Lk~Ql 120 (475)
T PRK13729 80 QMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNA------ALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH------HHHHHH
Confidence 33444444443333233333334444444555555 555554
No 97
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=22.61 E-value=72 Score=27.58 Aligned_cols=46 Identities=11% Similarity=0.134 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.+..++...|-.. ..-.+||..+|++...|+.+...-|.+.|+
T Consensus 129 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 129 LPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 5666666665544322 245678999999999999887544444433
No 98
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=22.59 E-value=1.7e+02 Score=28.80 Aligned_cols=27 Identities=19% Similarity=0.281 Sum_probs=16.9
Q ss_pred HHhhhHHHhhhhhchHHHHHHHHHhhc
Q 021194 124 LKANYDALKLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 124 lk~~~~~L~~~~~sl~~en~~L~~e~~ 150 (316)
+-.....|...|+.|+.+-..|.+|++
T Consensus 253 l~ge~~~Le~rN~~LK~qa~~lerEI~ 279 (294)
T KOG4571|consen 253 LLGELEGLEKRNEELKDQASELEREIR 279 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334446666666666666666666666
No 99
>PRK00118 putative DNA-binding protein; Validated
Probab=22.27 E-value=82 Score=26.18 Aligned_cols=45 Identities=13% Similarity=0.102 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~K 113 (316)
++..|..++...|.... ...+||..+|+++..|..|...-|.+.|
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 56777777766665542 4567999999999999998864444333
No 100
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.20 E-value=77 Score=21.16 Aligned_cols=38 Identities=21% Similarity=0.289 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQN 107 (316)
++..+...+...+. . ....++|..+|++...|..|.+.
T Consensus 4 l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 4 LTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 67778887765432 2 24578899999999998887753
No 101
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.04 E-value=39 Score=23.02 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCCccceeeechhhH
Q 021194 86 RKVKLAQELGLQPRQVAVWFQNRR 109 (316)
Q Consensus 86 ~r~~LA~~LgLs~rQVqVWFQNRR 109 (316)
...++|.++|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 455689999999999999986433
No 102
>PHA02955 hypothetical protein; Provisional
Probab=22.00 E-value=1.1e+02 Score=28.76 Aligned_cols=43 Identities=7% Similarity=0.131 Sum_probs=34.4
Q ss_pred CHHHHHHHHHhhhhc-CCCCHHHHHHHHHHhCCCccceeeechh
Q 021194 65 SVDQVKALEKNFEVE-NKLEPERKVKLAQELGLQPRQVAVWFQN 107 (316)
Q Consensus 65 T~~Ql~~LE~~F~~~-~yPs~~~r~~LA~~LgLs~rQVqVWFQN 107 (316)
...|+..|-+.|... ..+.+++|.+++++||+....|..||.+
T Consensus 59 a~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 59 EEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 346777777777665 6788899999999999999878888865
No 103
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.58 E-value=79 Score=27.59 Aligned_cols=47 Identities=15% Similarity=0.266 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhhH
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kkk 115 (316)
+++.+..++.-.|-.. ....+||..+|++...|+...+.-|.+.|++
T Consensus 132 L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 132 LEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 6777777776554322 2456889999999999887765444444443
No 104
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=21.49 E-value=67 Score=27.57 Aligned_cols=44 Identities=16% Similarity=-0.006 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~ 112 (316)
+++.+..++.-.|- ....-.++|..+|+++..|+++...-|.+-
T Consensus 139 L~~~~r~v~~l~~~-----~~~s~~EIA~~lgis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 139 LPEDLRTAITLREL-----EGLSYEDIARIMDCPVGTVRSRIFRAREAI 182 (190)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 44555555544332 223467899999999999988875444333
No 105
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.32 E-value=1.1e+02 Score=25.75 Aligned_cols=45 Identities=13% Similarity=0.270 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.+..+|.-.| ... .-.+||..+|+++..|+.+...-|.+.|+
T Consensus 113 L~~~~r~il~l~~-~g~-----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF-SGY-----SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH-cCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6777777777666 332 45678999999999999888544444443
No 106
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=21.18 E-value=3.4e+02 Score=25.82 Aligned_cols=49 Identities=20% Similarity=0.251 Sum_probs=36.9
Q ss_pred HhhhhhHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhcccccchhhhhhcc
Q 021194 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (316)
Q Consensus 109 RaK~Kkkq~~~~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~~~~~d~~lk~~L~ 163 (316)
|=|.|..+++.+...++.....|+.+.++|+.||..|=+.++ .|+..-.
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiR------ylqSY~~ 138 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIR------YLQSYNN 138 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHhhCcc
Confidence 344455666777777888888899999999999999988887 6555443
No 107
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=21.12 E-value=75 Score=26.70 Aligned_cols=44 Identities=16% Similarity=0.089 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~ 112 (316)
+++.|..++.-.|-.+ ..-.++|..+|++...|+.+...-|.+-
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L 156 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKET 156 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 6666666666654333 2456789999999999888775444433
No 108
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=20.70 E-value=99 Score=25.72 Aligned_cols=42 Identities=14% Similarity=0.102 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRa 110 (316)
+++.|..++.-.|-... .-.++|..+|++...|++....-|.
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 107 LPARQREAFLLRYWEDM-----DVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred CCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 77777777776554332 3567899999999999887653333
No 109
>PRK04217 hypothetical protein; Provisional
Probab=20.60 E-value=97 Score=26.00 Aligned_cols=44 Identities=11% Similarity=0.079 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhh
Q 021194 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (316)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK 111 (316)
.++.+|..++...|...- ...+||+.+|++...|...+..-+.+
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 388999888877765443 56789999999999888777544433
No 110
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=20.25 E-value=2.6e+02 Score=21.72 Aligned_cols=31 Identities=26% Similarity=0.381 Sum_probs=17.0
Q ss_pred HHHHHHhhhHHHhhhhhchHHHHHHHHHhhc
Q 021194 120 DYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (316)
Q Consensus 120 ~~~~lk~~~~~L~~~~~sl~~en~~L~~e~~ 150 (316)
.+..|+...+.|+..+..+..++..|..++.
T Consensus 19 ti~~Lq~e~eeLke~n~~L~~e~~~L~~en~ 49 (72)
T PF06005_consen 19 TIALLQMENEELKEKNNELKEENEELKEENE 49 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 3445555555555555555555555555555
No 111
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=20.22 E-value=67 Score=28.42 Aligned_cols=46 Identities=22% Similarity=0.042 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
+++.|..++.-.|-.. ....++|..+|++...|+++...-|.+.|+
T Consensus 114 Lp~~~r~v~~L~~~~g-----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 114 LPDEQREALILVGASG-----FSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred CCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666665554322 245678999999999999988755544443
No 112
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.18 E-value=1e+02 Score=28.37 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeechhhHhhhhh
Q 021194 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (316)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~r~~LA~~LgLs~rQVqVWFQNRRaK~Kk 114 (316)
++..|..++.-.|-.. ..-.+||..+|++...|+++.+.-|.+.|+
T Consensus 172 Lp~~~R~v~~L~~~eg-----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 172 LPEQQRIAVILSYHEN-----MSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5555555554444322 245688999999999999888655544443
No 113
>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=20.10 E-value=36 Score=22.89 Aligned_cols=23 Identities=17% Similarity=0.167 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCccceeeechhhH
Q 021194 87 KVKLAQELGLQPRQVAVWFQNRR 109 (316)
Q Consensus 87 r~~LA~~LgLs~rQVqVWFQNRR 109 (316)
..++|+.+|++++.|+.|.++..
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35789999999999999976543
Done!