Query 021367
Match_columns 313
No_of_seqs 297 out of 1486
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 02:24:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021367.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021367hhsearch_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 1.8E-21 4E-26 176.3 8.3 106 53-164 46-151 (198)
2 KOG0842 Transcription factor t 99.7 7.1E-17 1.5E-21 154.5 7.8 68 56-123 150-219 (307)
3 KOG0489 Transcription factor z 99.6 3.2E-17 6.9E-22 154.0 2.2 63 55-117 157-219 (261)
4 KOG0488 Transcription factor B 99.6 4.8E-16 1E-20 149.5 7.4 55 64-118 179-233 (309)
5 KOG0487 Transcription factor A 99.6 3.9E-16 8.5E-21 149.5 4.5 63 56-118 234-296 (308)
6 KOG0484 Transcription factor P 99.6 1.3E-15 2.8E-20 125.5 4.9 61 57-117 17-77 (125)
7 KOG0843 Transcription factor E 99.6 1.6E-15 3.4E-20 135.3 4.5 64 56-119 101-164 (197)
8 KOG0485 Transcription factor N 99.6 2.2E-15 4.7E-20 137.9 4.1 61 57-117 102-164 (268)
9 PF00046 Homeobox: Homeobox do 99.5 2.6E-15 5.7E-20 108.9 3.1 57 58-114 1-57 (57)
10 KOG0492 Transcription factor M 99.5 1.6E-14 3.5E-19 131.4 6.8 68 49-116 136-203 (246)
11 KOG0850 Transcription factor D 99.5 1.9E-14 4.1E-19 132.5 6.9 60 57-116 122-181 (245)
12 KOG0494 Transcription factor C 99.5 2.1E-14 4.6E-19 134.3 5.3 56 64-119 148-203 (332)
13 KOG2251 Homeobox transcription 99.5 3E-14 6.5E-19 130.5 4.7 63 56-118 36-98 (228)
14 KOG0493 Transcription factor E 99.5 6.7E-14 1.4E-18 131.1 6.3 61 59-119 248-308 (342)
15 KOG0848 Transcription factor C 99.4 2.8E-14 6.1E-19 133.9 2.7 53 64-116 206-258 (317)
16 COG5576 Homeodomain-containing 99.4 1.8E-13 3.8E-18 120.3 5.0 64 55-118 49-112 (156)
17 cd00086 homeodomain Homeodomai 99.4 1.8E-13 4E-18 98.6 3.5 57 59-115 2-58 (59)
18 smart00389 HOX Homeodomain. DN 99.4 2E-13 4.4E-18 98.0 3.3 55 59-113 2-56 (56)
19 KOG4577 Transcription factor L 99.4 1.2E-12 2.6E-17 124.3 8.0 98 52-150 162-259 (383)
20 TIGR01565 homeo_ZF_HD homeobox 99.3 2.1E-12 4.6E-17 96.3 5.8 52 58-109 2-57 (58)
21 KOG0844 Transcription factor E 99.3 6.2E-13 1.4E-17 126.9 3.0 60 59-118 183-242 (408)
22 KOG3802 Transcription factor O 99.3 4.5E-12 9.7E-17 124.6 5.6 60 57-116 294-353 (398)
23 KOG0486 Transcription factor P 99.2 6.9E-12 1.5E-16 120.1 4.7 57 64-120 119-175 (351)
24 KOG0491 Transcription factor B 99.2 2.1E-12 4.5E-17 114.2 -0.8 57 61-117 104-160 (194)
25 KOG0847 Transcription factor, 99.2 5.2E-12 1.1E-16 116.1 1.4 62 55-116 165-226 (288)
26 KOG0490 Transcription factor, 99.1 7.9E-11 1.7E-15 105.8 3.5 61 56-116 59-119 (235)
27 KOG1168 Transcription factor A 98.8 3.1E-09 6.8E-14 101.3 4.1 64 53-116 305-368 (385)
28 KOG0849 Transcription factor P 98.8 2.7E-09 6E-14 104.6 3.6 60 57-116 176-235 (354)
29 KOG0775 Transcription factor S 98.6 4.2E-08 9E-13 93.0 3.6 51 64-114 183-233 (304)
30 KOG0774 Transcription factor P 98.2 8.2E-07 1.8E-11 84.0 2.8 60 57-116 188-250 (334)
31 PF05920 Homeobox_KN: Homeobox 98.0 1.4E-06 3E-11 60.5 -0.0 34 78-111 7-40 (40)
32 KOG0490 Transcription factor, 97.8 2.4E-05 5.1E-10 70.4 3.9 61 57-117 153-213 (235)
33 KOG2252 CCAAT displacement pro 97.6 4.4E-05 9.5E-10 78.4 3.4 57 56-112 419-475 (558)
34 PF02183 HALZ: Homeobox associ 97.6 9.7E-05 2.1E-09 52.6 4.1 44 115-164 1-44 (45)
35 KOG1146 Homeobox protein [Gene 97.2 0.00019 4.2E-09 79.8 3.1 63 56-118 902-964 (1406)
36 KOG0773 Transcription factor M 95.8 0.0076 1.6E-07 58.4 3.3 56 62-117 244-302 (342)
37 PF11569 Homez: Homeodomain le 94.8 0.0061 1.3E-07 45.5 -0.5 42 68-109 9-50 (56)
38 KOG3623 Homeobox transcription 90.7 0.14 3.1E-06 55.0 2.1 52 64-116 564-615 (1007)
39 PF04218 CENP-B_N: CENP-B N-te 88.9 0.36 7.8E-06 35.1 2.4 47 58-109 1-47 (53)
40 PRK09413 IS2 repressor TnpA; R 85.5 1.8 3.8E-05 36.2 5.1 86 60-150 9-102 (121)
41 PF01763 Herpes_UL6: Herpesvir 77.2 2.8 6E-05 44.3 4.1 42 255-297 474-515 (557)
42 PF02183 HALZ: Homeobox associ 73.6 4.3 9.4E-05 28.9 3.1 26 125-150 4-29 (45)
43 KOG1146 Homeobox protein [Gene 72.1 2.2 4.9E-05 48.7 2.0 59 61-119 448-506 (1406)
44 smart00340 HALZ homeobox assoc 70.4 6.4 0.00014 28.0 3.3 28 116-150 2-29 (44)
45 PF04967 HTH_10: HTH DNA bindi 64.8 7.5 0.00016 28.6 2.9 38 64-101 1-40 (53)
46 KOG4196 bZIP transcription fac 60.5 50 0.0011 28.9 7.5 82 62-165 22-114 (135)
47 PF01527 HTH_Tnp_1: Transposas 53.9 3.2 7E-05 30.9 -0.7 43 60-106 3-45 (76)
48 PF00170 bZIP_1: bZIP transcri 53.6 36 0.00078 25.1 5.0 30 121-150 28-57 (64)
49 PF13443 HTH_26: Cro/C1-type H 52.7 6.6 0.00014 28.2 0.8 39 86-124 12-50 (63)
50 cd00569 HTH_Hin_like Helix-tur 52.4 15 0.00032 21.6 2.3 38 62-104 4-41 (42)
51 cd06171 Sigma70_r4 Sigma70, re 52.4 5.4 0.00012 26.4 0.3 41 64-109 11-51 (55)
52 PF04545 Sigma70_r4: Sigma-70, 52.2 8.1 0.00018 26.9 1.2 39 63-106 4-42 (50)
53 PF00170 bZIP_1: bZIP transcri 46.6 61 0.0013 23.9 5.3 40 110-149 24-63 (64)
54 PF06005 DUF904: Protein of un 45.4 65 0.0014 25.1 5.4 35 116-150 22-56 (72)
55 COG3413 Predicted DNA binding 44.9 20 0.00043 32.5 2.9 38 63-100 155-194 (215)
56 smart00338 BRLZ basic region l 41.8 74 0.0016 23.5 5.1 28 123-150 30-57 (65)
57 KOG4005 Transcription factor X 38.0 60 0.0013 31.3 4.9 43 106-148 82-126 (292)
58 PRK13729 conjugal transfer pil 38.0 1.3E+02 0.0027 31.6 7.6 36 115-150 79-114 (475)
59 PF00424 REV: REV protein (ant 37.2 36 0.00079 27.9 3.0 33 69-117 14-48 (91)
60 smart00338 BRLZ basic region l 36.3 1E+02 0.0022 22.7 5.0 37 113-149 27-63 (65)
61 PRK03975 tfx putative transcri 35.8 27 0.00059 30.6 2.2 48 61-114 4-51 (141)
62 PF08281 Sigma70_r4_2: Sigma-7 34.6 20 0.00043 25.1 0.9 41 64-109 11-51 (54)
63 PF10668 Phage_terminase: Phag 33.9 11 0.00024 28.5 -0.4 20 86-105 24-43 (60)
64 PF15058 Speriolin_N: Sperioli 33.0 67 0.0014 29.9 4.3 38 127-164 6-43 (200)
65 PF07716 bZIP_2: Basic region 32.9 1.1E+02 0.0025 21.8 4.7 19 132-150 31-49 (54)
66 PRK00888 ftsB cell division pr 31.9 1.2E+02 0.0027 25.0 5.4 46 101-147 17-62 (105)
67 KOG3119 Basic region leucine z 31.6 78 0.0017 30.3 4.7 39 109-150 208-246 (269)
68 PF10224 DUF2205: Predicted co 29.3 1.5E+02 0.0032 23.7 5.2 33 118-150 29-61 (80)
69 PF06156 DUF972: Protein of un 28.0 1.2E+02 0.0025 25.4 4.6 32 119-150 22-53 (107)
70 PRK09646 RNA polymerase sigma 27.7 48 0.001 29.1 2.4 45 64-113 143-187 (194)
71 PF06156 DUF972: Protein of un 27.5 1.2E+02 0.0026 25.3 4.6 47 115-167 11-57 (107)
72 KOG4571 Activating transcripti 26.6 1.3E+02 0.0027 29.7 5.2 40 110-150 240-279 (294)
73 TIGR02937 sigma70-ECF RNA poly 26.0 47 0.001 26.3 1.9 43 64-111 111-153 (158)
74 PRK09652 RNA polymerase sigma 25.9 48 0.001 27.9 2.0 42 64-110 129-170 (182)
75 KOG4343 bZIP transcription fac 25.8 1.1E+02 0.0024 32.7 4.9 29 122-150 305-333 (655)
76 PRK13169 DNA replication intia 25.4 1.4E+02 0.0029 25.2 4.5 32 119-150 22-53 (110)
77 PF06637 PV-1: PV-1 protein (P 25.3 2.6E+02 0.0056 28.8 7.2 15 136-150 352-366 (442)
78 PF09607 BrkDBD: Brinker DNA-b 24.7 41 0.00089 25.4 1.2 44 61-106 3-47 (58)
79 PRK06759 RNA polymerase factor 24.6 48 0.001 27.4 1.8 43 64-111 107-149 (154)
80 PF08187 Tetradecapep: Myoacti 24.1 32 0.00068 18.8 0.3 11 215-225 1-11 (14)
81 PRK09642 RNA polymerase sigma 23.5 65 0.0014 27.0 2.4 46 64-114 107-152 (160)
82 PRK00888 ftsB cell division pr 23.5 1.3E+02 0.0027 24.9 4.0 28 113-140 35-62 (105)
83 PRK12514 RNA polymerase sigma 23.4 68 0.0015 27.5 2.5 45 64-113 130-174 (179)
84 PRK12526 RNA polymerase sigma 23.3 58 0.0013 29.0 2.1 45 64-113 154-198 (206)
85 PF12824 MRP-L20: Mitochondria 23.1 1.7E+02 0.0037 26.2 5.1 45 60-106 82-126 (164)
86 PF06005 DUF904: Protein of un 22.7 2.3E+02 0.0049 22.1 5.0 30 121-150 20-49 (72)
87 PRK11924 RNA polymerase sigma 22.6 76 0.0016 26.5 2.6 45 64-113 126-170 (179)
88 PHA02955 hypothetical protein; 22.5 1E+02 0.0022 29.0 3.5 42 66-107 60-102 (213)
89 PRK13169 DNA replication intia 22.5 1.7E+02 0.0037 24.6 4.6 45 115-165 11-55 (110)
90 PF10224 DUF2205: Predicted co 22.4 2.1E+02 0.0045 22.9 4.8 46 112-163 16-61 (80)
91 PRK12512 RNA polymerase sigma 21.6 68 0.0015 27.6 2.2 45 64-113 132-176 (184)
92 PF13936 HTH_38: Helix-turn-he 21.3 27 0.00058 24.1 -0.4 39 62-105 3-41 (44)
93 PRK14127 cell division protein 20.9 1.8E+02 0.004 24.5 4.5 43 115-163 26-68 (109)
94 KOG0709 CREB/ATF family transc 20.8 2.8E+02 0.0062 29.0 6.6 32 63-94 220-253 (472)
95 PRK04217 hypothetical protein; 20.6 73 0.0016 26.7 2.1 40 63-107 42-81 (110)
96 cd01106 HTH_TipAL-Mta Helix-Tu 20.5 2.3E+02 0.0049 22.6 4.9 35 61-108 36-70 (103)
97 PRK09648 RNA polymerase sigma 20.4 72 0.0016 27.6 2.1 38 64-106 140-177 (189)
98 COG4467 Regulator of replicati 20.3 2E+02 0.0042 24.6 4.5 41 118-164 14-54 (114)
99 COG4026 Uncharacterized protei 20.2 1.3E+02 0.0028 28.9 3.8 30 120-149 150-179 (290)
100 PRK12519 RNA polymerase sigma 20.1 61 0.0013 28.1 1.5 45 64-113 142-186 (194)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.85 E-value=1.8e-21 Score=176.30 Aligned_cols=106 Identities=58% Similarity=0.868 Sum_probs=95.7
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHHHHHHHHHhhhHHHh
Q 021367 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALK 132 (313)
Q Consensus 53 ~~g~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~~~~~Lk~~~~~L~ 132 (313)
.+....+|++||+.+|+..||+.|+.+.++.+.+|..||++|||.+|||+|||||||||||.++++.+|+.||.+++.|+
T Consensus 46 ~~~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~ 125 (198)
T KOG0483|consen 46 NGSKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLR 125 (198)
T ss_pred cccccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHh
Confidence 34456677888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhchHHHHHHHHHhhhccccchhhhhhccc
Q 021367 133 LNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (313)
Q Consensus 133 ~e~dsL~~en~~L~~el~~~~~d~~lk~kL~~ 164 (313)
.+++.|+.++..|..++. .++...+.
T Consensus 126 ~~~~~Lq~e~~eL~~~~~------~~~~~~~~ 151 (198)
T KOG0483|consen 126 SENDRLQSEVQELVAELS------SLKREMQK 151 (198)
T ss_pred hhhhHHHHHHHHHHHHHh------hhhhhhcc
Confidence 999999999999988887 55554443
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.67 E-value=7.1e-17 Score=154.52 Aligned_cols=68 Identities=37% Similarity=0.576 Sum_probs=60.5
Q ss_pred CCCCCCCc--CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHHHHHHH
Q 021367 56 HVSEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGV 123 (313)
Q Consensus 56 ~~krKRrR--fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~~~~~ 123 (313)
.++|||+| |+..|+.+||+.|..++|++..+|+.||..|+|+++||||||||||-|.||+++++..+.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 34444445 999999999999999999999999999999999999999999999999999987776443
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.65 E-value=3.2e-17 Score=153.96 Aligned_cols=63 Identities=33% Similarity=0.688 Sum_probs=57.6
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHH
Q 021367 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (313)
Q Consensus 55 g~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (313)
+..||.|+.||..|+.+||+.|..++|++..+|.+||..|+|+++||+|||||||+||||...
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 445555666999999999999999999999999999999999999999999999999998653
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.62 E-value=4.8e-16 Score=149.48 Aligned_cols=55 Identities=44% Similarity=0.723 Sum_probs=53.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e 118 (313)
||..|+..||+.|++.+|++..+|.+||+.|||+..||++||||||+|||+...+
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 9999999999999999999999999999999999999999999999999997654
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.60 E-value=3.9e-16 Score=149.51 Aligned_cols=63 Identities=33% Similarity=0.504 Sum_probs=57.5
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHH
Q 021367 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (313)
Q Consensus 56 ~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e 118 (313)
..||||..+|..|+.+||+.|-.|.|++.+.|.+|++.|+|++|||+|||||||+|.||...+
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 345556669999999999999999999999999999999999999999999999999997653
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.58 E-value=1.3e-15 Score=125.55 Aligned_cols=61 Identities=26% Similarity=0.472 Sum_probs=55.4
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHH
Q 021367 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (313)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (313)
+++-|+.||..|+..||+.|...+||+.-.|++||.++.|++.+|||||||||+|.|++..
T Consensus 17 QRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 17 QRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3444555999999999999999999999999999999999999999999999999998653
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.57 E-value=1.6e-15 Score=135.29 Aligned_cols=64 Identities=34% Similarity=0.487 Sum_probs=57.9
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHHH
Q 021367 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (313)
Q Consensus 56 ~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~ 119 (313)
+.|+.|+.||.+|+..||..|+.++|....+|++||+.|+|++.||+|||||||.|.|+.+.+.
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 3444555699999999999999999999999999999999999999999999999999987653
No 8
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.55 E-value=2.2e-15 Score=137.94 Aligned_cols=61 Identities=41% Similarity=0.640 Sum_probs=55.6
Q ss_pred CCCCCCc--CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHH
Q 021367 57 VSEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (313)
Q Consensus 57 ~krKRrR--fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (313)
.++||+| |+..|+..||..|+..+|++..+|..||.+|.|++.||+|||||||.|||++-.
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 3444544 999999999999999999999999999999999999999999999999999753
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=99.54 E-value=2.6e-15 Score=108.87 Aligned_cols=57 Identities=42% Similarity=0.647 Sum_probs=54.0
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhH
Q 021367 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (313)
Q Consensus 58 krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kk 114 (313)
+++|++||.+|+.+|+..|..++||+..+++.||.+|||++.+|++||+|||+++|+
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 456778999999999999999999999999999999999999999999999999885
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.52 E-value=1.6e-14 Score=131.40 Aligned_cols=68 Identities=29% Similarity=0.475 Sum_probs=59.1
Q ss_pred CcccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 49 CLEESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 49 ~~~~~~g~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
|........|+.|+.||.+|+..||+.|...+|+++.+|.+++..|.|++.||+|||||||+|.|+-|
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 33333344555566699999999999999999999999999999999999999999999999999865
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.51 E-value=1.9e-14 Score=132.52 Aligned_cols=60 Identities=35% Similarity=0.586 Sum_probs=54.5
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
.|+.|+.++.-||..|.+.|++++|+-..+|.+||..|||+.+||+|||||||.|.||..
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 333445599999999999999999999999999999999999999999999999999854
No 12
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.49 E-value=2.1e-14 Score=134.33 Aligned_cols=56 Identities=30% Similarity=0.542 Sum_probs=53.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHHH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~ 119 (313)
||..|+..||+.|+..+||+...|+-||.++.|++.+|+|||||||+||||+....
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 99999999999999999999999999999999999999999999999999976543
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.47 E-value=3e-14 Score=130.51 Aligned_cols=63 Identities=27% Similarity=0.435 Sum_probs=57.5
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHH
Q 021367 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (313)
Q Consensus 56 ~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e 118 (313)
+.+|.|++|+..|+++||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|+++..
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 344556679999999999999999999999999999999999999999999999999987643
No 14
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.46 E-value=6.7e-14 Score=131.13 Aligned_cols=61 Identities=33% Similarity=0.620 Sum_probs=55.3
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHHH
Q 021367 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (313)
Q Consensus 59 rKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~ 119 (313)
+.|+-||.+||+.|+..|+.++|++..+|.+||.+|||.+.||+|||||+|+|.||..-.+
T Consensus 248 RPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 248 RPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK 308 (342)
T ss_pred CccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence 3344499999999999999999999999999999999999999999999999999876443
No 15
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.45 E-value=2.8e-14 Score=133.87 Aligned_cols=53 Identities=42% Similarity=0.626 Sum_probs=51.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
+|..|.-+||+.|..++|.++.+|.+||..|||++|||+|||||||||+||.+
T Consensus 206 YTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999865
No 16
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.41 E-value=1.8e-13 Score=120.30 Aligned_cols=64 Identities=33% Similarity=0.568 Sum_probs=59.4
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHH
Q 021367 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (313)
Q Consensus 55 g~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e 118 (313)
...+++|+|.|.+|+.+|++.|+.++||+...|.+|+..|+|+++-|+|||||||++.|+....
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 4567778889999999999999999999999999999999999999999999999999987643
No 17
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.40 E-value=1.8e-13 Score=98.65 Aligned_cols=57 Identities=46% Similarity=0.738 Sum_probs=53.2
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHH
Q 021367 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (313)
Q Consensus 59 rKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkk 115 (313)
+++..++..|+.+|+..|..++||+..++..||.++||++.+|++||+|||++.++.
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 345679999999999999999999999999999999999999999999999998763
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.39 E-value=2e-13 Score=97.96 Aligned_cols=55 Identities=45% Similarity=0.792 Sum_probs=51.2
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhh
Q 021367 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (313)
Q Consensus 59 rKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~K 113 (313)
+.|.+++.+|+.+|+..|..++||+..++..||..+||+..+|+.||+|||++.|
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 3456699999999999999999999999999999999999999999999998764
No 19
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.37 E-value=1.2e-12 Score=124.25 Aligned_cols=98 Identities=22% Similarity=0.335 Sum_probs=79.8
Q ss_pred cCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHHHHHHHHHhhhHHH
Q 021367 52 ESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDAL 131 (313)
Q Consensus 52 ~~~g~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~~~~~Lk~~~~~L 131 (313)
+..+..|+.|+.+|+.|++.|+..|...++|....|++|+.++||..|+|||||||||||.|+-+...-...|.+.+..+
T Consensus 162 ~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsm 241 (383)
T KOG4577|consen 162 EGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSM 241 (383)
T ss_pred ccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHh
Confidence 34456777788899999999999999999999999999999999999999999999999999977666666787777777
Q ss_pred hhhhhchHHHHHHHHHhhh
Q 021367 132 KLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 132 ~~e~dsL~~en~~L~~el~ 150 (313)
+.. .+-+.|+..-..|+.
T Consensus 242 K~s-gs~r~ekdsd~sel~ 259 (383)
T KOG4577|consen 242 KRS-GSSRAEKDSDDSELS 259 (383)
T ss_pred hcc-CCcccccccccCccc
Confidence 665 445555554344443
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=99.33 E-value=2.1e-12 Score=96.34 Aligned_cols=52 Identities=15% Similarity=0.360 Sum_probs=48.9
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHhCCCCceeeeeccchh
Q 021367 58 SEKKRRLSVDQVKALEKNFEVENK----LEPERKVKLAQELGLQPRQVAVWFQNRR 109 (313)
Q Consensus 58 krKRrRfT~~Ql~~LE~~F~~~~y----Ps~~~reeLA~~LgLserQVqVWFQNRR 109 (313)
++.|+.||.+|+..||..|+.+.| |+...+.+||..|||++++|+|||||-+
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 556777999999999999999999 9999999999999999999999999964
No 21
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.32 E-value=6.2e-13 Score=126.89 Aligned_cols=60 Identities=35% Similarity=0.564 Sum_probs=55.3
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHH
Q 021367 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (313)
Q Consensus 59 rKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e 118 (313)
|-|+-||.+|+..||+.|-+.+|.+..+|.+||..|+|++..|+|||||||+|+|++.+.
T Consensus 183 RYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 183 RYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 334459999999999999999999999999999999999999999999999999997753
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.26 E-value=4.5e-12 Score=124.57 Aligned_cols=60 Identities=32% Similarity=0.439 Sum_probs=54.5
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
+||||+.+......+||+.|.+|++|+..++..||.+|+|...+|+|||||||.|.||-.
T Consensus 294 kRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 294 KRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 344455599999999999999999999999999999999999999999999999999854
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.23 E-value=6.9e-12 Score=120.07 Aligned_cols=57 Identities=26% Similarity=0.559 Sum_probs=54.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHHHH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERD 120 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~~ 120 (313)
||.+|+..||..|++++||+...|++||..++|++.+|+|||.|||+|||++.....
T Consensus 119 FtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 119 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 999999999999999999999999999999999999999999999999999876554
No 24
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.19 E-value=2.1e-12 Score=114.22 Aligned_cols=57 Identities=39% Similarity=0.566 Sum_probs=53.5
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHH
Q 021367 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (313)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (313)
|+.|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.+.
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 344999999999999999999999999999999999999999999999999998764
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.18 E-value=5.2e-12 Score=116.14 Aligned_cols=62 Identities=37% Similarity=0.692 Sum_probs=56.3
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 55 g~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
|+++..|..|+..|+..||+.|+..+|+-..+|.+||..+|+++.||+|||||||+||||+.
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 44444455599999999999999999999999999999999999999999999999999875
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.06 E-value=7.9e-11 Score=105.80 Aligned_cols=61 Identities=28% Similarity=0.335 Sum_probs=56.2
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 56 ~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
..++.|+.|+..|++.||+.|+..+||+...++.||..+++++..|+|||||||++|+++.
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 4455566699999999999999999999999999999999999999999999999999865
No 27
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.81 E-value=3.1e-09 Score=101.29 Aligned_cols=64 Identities=28% Similarity=0.517 Sum_probs=58.1
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 53 ~~g~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
.++.+||||+.+-....+.||.+|..++.|+.+.+..||++|+|...+|+|||||.|+|.|+.+
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 4556677777788899999999999999999999999999999999999999999999988854
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.80 E-value=2.7e-09 Score=104.60 Aligned_cols=60 Identities=35% Similarity=0.591 Sum_probs=55.3
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
.+++|+.|+..|+..||+.|+.++||+...|++||.++++++..|+|||+|||++|++..
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 344456699999999999999999999999999999999999999999999999999865
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.56 E-value=4.2e-08 Score=92.96 Aligned_cols=51 Identities=29% Similarity=0.428 Sum_probs=48.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kk 114 (313)
|...-...|..+|..++||++.+|.+||+.+||+..||-.||+|||+|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 677778899999999999999999999999999999999999999999883
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.19 E-value=8.2e-07 Score=83.98 Aligned_cols=60 Identities=28% Similarity=0.448 Sum_probs=54.5
Q ss_pred CCCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 57 VSEKKRRLSVDQVKALEKNFE---VENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~---~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
.+||||.|+..-.++|..+|. .++||+.+.+++||+++|++..||-.||.|+|-++||..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 456677799999999999996 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=97.98 E-value=1.4e-06 Score=60.45 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCCCceeeeeccchhhH
Q 021367 78 VENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (313)
Q Consensus 78 ~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK 111 (313)
.++||+.+++..||.++||+..||..||-|.|.|
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 4789999999999999999999999999999875
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.75 E-value=2.4e-05 Score=70.35 Aligned_cols=61 Identities=31% Similarity=0.573 Sum_probs=54.7
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHH
Q 021367 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (313)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (313)
.++.++.++..|+..++..|...++|+...+.+|+..+|++++.|++||||+|++.++...
T Consensus 153 ~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 153 PRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3334455999999999999999999999999999999999999999999999999998653
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.58 E-value=4.4e-05 Score=78.40 Aligned_cols=57 Identities=21% Similarity=0.282 Sum_probs=51.3
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHh
Q 021367 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (313)
Q Consensus 56 ~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~ 112 (313)
..|+.|..||..|.+.|...|+.+++|+.+..+.|+.+|||....|..||-|-|.|.
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 344444559999999999999999999999999999999999999999999998765
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=97.58 E-value=9.7e-05 Score=52.63 Aligned_cols=44 Identities=55% Similarity=0.763 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhhccccchhhhhhccc
Q 021367 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (313)
Q Consensus 115 kq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~~~~~d~~lk~kL~~ 164 (313)
+|++++|+.|+++|+.|+.+|++|..||+.|+.++. .|++++..
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 478999999999999999999999999999999999 89888754
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.22 E-value=0.00019 Score=79.78 Aligned_cols=63 Identities=27% Similarity=0.380 Sum_probs=57.7
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHH
Q 021367 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (313)
Q Consensus 56 ~~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e 118 (313)
.++.+|++++..|+..+..+|....+|...+.+.|...+++.++.|+|||||-|+|.|+..+.
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhc
Confidence 455567779999999999999999999999999999999999999999999999999987753
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.78 E-value=0.0076 Score=58.43 Aligned_cols=56 Identities=29% Similarity=0.364 Sum_probs=47.7
Q ss_pred CcCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHH
Q 021367 62 RRLSVDQVKALEKNFEV---ENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (313)
Q Consensus 62 rRfT~~Ql~~LE~~F~~---~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (313)
+.+....+.+|+.+... .+||+...+..||.++||+..||..||-|.|-|..+-..
T Consensus 244 ~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 244 RGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 34999999999988543 579999999999999999999999999999887666544
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=94.84 E-value=0.0061 Score=45.50 Aligned_cols=42 Identities=24% Similarity=0.421 Sum_probs=31.0
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchh
Q 021367 68 QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (313)
Q Consensus 68 Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRR 109 (313)
.+..|+++|...+++.......|..+.+|+..||+.||-.|+
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 356699999999999999999999999999999999996553
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=90.68 E-value=0.14 Score=54.98 Aligned_cols=52 Identities=21% Similarity=0.345 Sum_probs=46.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq 116 (313)
|+.. +..|..+|..|..|+.++...+|.+.||+.+.|++||+++++....-+
T Consensus 564 ~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred cCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 4433 788999999999999999999999999999999999999999877654
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=88.90 E-value=0.36 Score=35.08 Aligned_cols=47 Identities=21% Similarity=0.412 Sum_probs=34.3
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchh
Q 021367 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (313)
Q Consensus 58 krKRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRR 109 (313)
+++|+.+|.++-..+-..++... ....||+++|++..+|..|..|+.
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 35666799998888888888765 578899999999999999998753
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=85.47 E-value=1.8 Score=36.16 Aligned_cols=86 Identities=15% Similarity=0.190 Sum_probs=46.8
Q ss_pred CCCcCCHHHHH-HHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHh-------hHHHHHHHHHHHHhhhHHH
Q 021367 60 KKRRLSVDQVK-ALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW-------KTKQLERDYGVLKANYDAL 131 (313)
Q Consensus 60 KRrRfT~~Ql~-~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~-------Kkkq~e~~~~~Lk~~~~~L 131 (313)
++++|+.++.. ++...+... ....++|+++|+++.+|..|.+.-+... +..........+......|
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-----~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L 83 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-----MTVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKEL 83 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHH
Confidence 35567777644 444444422 2456789999999999999965432110 0000001112233444555
Q ss_pred hhhhhchHHHHHHHHHhhh
Q 021367 132 KLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 132 ~~e~dsL~~en~~L~~el~ 150 (313)
+.+...++.|++.|++...
T Consensus 84 ~~el~~L~~E~diLKKa~~ 102 (121)
T PRK09413 84 QRLLGKKTMENELLKEAVE 102 (121)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6666666666666666554
No 41
>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=77.24 E-value=2.8 Score=44.26 Aligned_cols=42 Identities=29% Similarity=0.337 Sum_probs=36.4
Q ss_pred ccccceeeEeeccccccccceeeeccccccchhhhhhhHHHHH
Q 021367 255 FRASLINFRLTASNSQNQRTRLSLSRWKSTISLVMRPAISSLM 297 (313)
Q Consensus 255 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 297 (313)
|+-=+-||.++. ..-||-++++++-=.+||+++.-|-..+++
T Consensus 474 E~El~RtFKL~r-~vnNQGqe~sI~YSn~TIslll~Pf~~~Il 515 (557)
T PF01763_consen 474 EQELFRTFKLRR-VVNNQGQEVSISYSNYTISLLLGPFFFSIL 515 (557)
T ss_pred HHHHHHHccccc-ccCCCCceEEEEechhhHHHHHHHHHHHHh
Confidence 666788999986 567999999999999999999999877654
No 42
>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=73.56 E-value=4.3 Score=28.89 Aligned_cols=26 Identities=46% Similarity=0.713 Sum_probs=14.7
Q ss_pred HhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 125 KANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 125 k~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
...|+.|+..++.|..++++|..+..
T Consensus 4 E~Dy~~LK~~yd~Lk~~~~~L~~E~~ 29 (45)
T PF02183_consen 4 ERDYDALKASYDSLKAEYDSLKKENE 29 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555555555555
No 43
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=72.06 E-value=2.2 Score=48.74 Aligned_cols=59 Identities=20% Similarity=0.095 Sum_probs=52.3
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhHHHHHH
Q 021367 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (313)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~ 119 (313)
++|++.-|...|...|+...+|.-.+...++..|++..|.+-.||++++.+|.....+.
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 44688899999999999999999999999999999999999999999888888765543
No 44
>smart00340 HALZ homeobox associated leucin zipper.
Probab=70.39 E-value=6.4 Score=28.01 Aligned_cols=28 Identities=39% Similarity=0.423 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 116 q~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
+.+-+++-||... ++|..||.+|++|+.
T Consensus 2 QTEvdCe~LKrcc-------e~LteeNrRL~ke~~ 29 (44)
T smart00340 2 QTEVDCELLKRCC-------ESLTEENRRLQKEVQ 29 (44)
T ss_pred chHHHHHHHHHHH-------HHHHHHHHHHHHHHH
Confidence 4567777777765 555666777777777
No 45
>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=64.81 E-value=7.5 Score=28.58 Aligned_cols=38 Identities=26% Similarity=0.285 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCCcee
Q 021367 64 LSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQV 101 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~y--Ps~~~reeLA~~LgLserQV 101 (313)
+|..|.++|...|+..-| |-.....+||++||+++.-|
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 55666889999999998653
No 46
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=60.46 E-value=50 Score=28.88 Aligned_cols=82 Identities=24% Similarity=0.257 Sum_probs=47.8
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHH-HHhCCCCceeeeeccchhhH----------hhHHHHHHHHHHHHhhhHH
Q 021367 62 RRLSVDQVKALEKNFEVENKLEPERKVKLA-QELGLQPRQVAVWFQNRRAR----------WKTKQLERDYGVLKANYDA 130 (313)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yPs~~~reeLA-~~LgLserQVqVWFQNRRaK----------~Kkkq~e~~~~~Lk~~~~~ 130 (313)
.+|+.+++..+ ..| +|= +.-|++...|-.|=|.||+- .|+-+ +...|.+.+..
T Consensus 22 d~lsDd~Lvsm------------SVR-eLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~---Qk~eLE~~k~~ 85 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVR-ELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQ---QKHELEKEKAE 85 (135)
T ss_pred CCcCHHHHHHh------------hHH-HHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHH---HHHHHHHHHHH
Confidence 46888888776 222 233 33478888888888877752 22222 22334444455
Q ss_pred HhhhhhchHHHHHHHHHhhhccccchhhhhhcccc
Q 021367 131 LKLNYDSLQHDNEALLKETIVHETDHQNKATLDRD 165 (313)
Q Consensus 131 L~~e~dsL~~en~~L~~el~~~~~d~~lk~kL~~~ 165 (313)
|..+.+.|..|+..+..|+. .++.+...-
T Consensus 86 L~qqv~~L~~e~s~~~~E~d------a~k~k~e~l 114 (135)
T KOG4196|consen 86 LQQQVEKLKEENSRLRRELD------AYKSKYEAL 114 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHH------HHHHHHHHH
Confidence 66666666666666666666 555554433
No 47
>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=53.86 E-value=3.2 Score=30.92 Aligned_cols=43 Identities=23% Similarity=0.384 Sum_probs=28.0
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeecc
Q 021367 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (313)
Q Consensus 60 KRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQ 106 (313)
++++||+++...+-..+.. ......++|+++|+++.++..|-.
T Consensus 3 ~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHH
Confidence 4567999887766666521 235788899999999999888863
No 48
>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=53.62 E-value=36 Score=25.11 Aligned_cols=30 Identities=23% Similarity=0.281 Sum_probs=17.7
Q ss_pred HHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 121 YGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 121 ~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
...|......|..+++.|..++..|..++.
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 344555556666666666666666666655
No 49
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=52.66 E-value=6.6 Score=28.25 Aligned_cols=39 Identities=15% Similarity=0.202 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCCceeeeeccchhhHhhHHHHHHHHHHH
Q 021367 86 RKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVL 124 (313)
Q Consensus 86 ~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~e~~~~~L 124 (313)
...+||+.+|++..+|..|+.++...+....+.+-+..|
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKAL 50 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHc
Confidence 467899999999999999998876666665555544443
No 50
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=52.40 E-value=15 Score=21.55 Aligned_cols=38 Identities=13% Similarity=0.317 Sum_probs=26.0
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeee
Q 021367 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVW 104 (313)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVW 104 (313)
+.++.++...+...|.... ...++|+.+|++...|..|
T Consensus 4 ~~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 4 PKLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CcCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHh
Confidence 3467777777766665322 4567889999988777665
No 51
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=52.39 E-value=5.4 Score=26.42 Aligned_cols=41 Identities=15% Similarity=0.134 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRR 109 (313)
++..+..++...|... ....++|..+|++...|..|....+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6777888887776433 2456789999999999988875443
No 52
>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=52.24 E-value=8.1 Score=26.86 Aligned_cols=39 Identities=13% Similarity=0.183 Sum_probs=28.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeecc
Q 021367 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (313)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQ 106 (313)
.+++.+..+|...|..+ ..-.++|..+|++...|+.+..
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 37888999999988332 3567899999999988776543
No 53
>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=46.64 E-value=61 Score=23.90 Aligned_cols=40 Identities=20% Similarity=0.308 Sum_probs=28.3
Q ss_pred hHhhHHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhh
Q 021367 110 ARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKET 149 (313)
Q Consensus 110 aK~Kkkq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el 149 (313)
-+..-..++.....|...++.|...+..|..+...|..++
T Consensus 24 Kk~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 24 KKQYIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3344445566777777788888888888888877777664
No 54
>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=45.41 E-value=65 Score=25.08 Aligned_cols=35 Identities=29% Similarity=0.348 Sum_probs=22.5
Q ss_pred HHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 116 q~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
.++.+...|+..+..|..+++.|..+|..|+.+..
T Consensus 22 ~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~ 56 (72)
T PF06005_consen 22 LLQMENEELKEKNNELKEENEELKEENEQLKQERN 56 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 34555666666666666667777777777766554
No 55
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=44.92 E-value=20 Score=32.54 Aligned_cols=38 Identities=21% Similarity=0.250 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCCce
Q 021367 63 RLSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQ 100 (313)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~y--Ps~~~reeLA~~LgLserQ 100 (313)
.+|..|+++|...|...-| |-.....+||+++|+++.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 4999999999999998764 6566688999999999854
No 56
>smart00338 BRLZ basic region leucin zipper.
Probab=41.85 E-value=74 Score=23.46 Aligned_cols=28 Identities=21% Similarity=0.287 Sum_probs=16.1
Q ss_pred HHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 123 VLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 123 ~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
.|......|..++..|..+...|..++.
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~l~~e~~ 57 (65)
T smart00338 30 ELERKVEQLEAENERLKKEIERLRRELE 57 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444455556666666666666666665
No 57
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=38.04 E-value=60 Score=31.26 Aligned_cols=43 Identities=33% Similarity=0.337 Sum_probs=20.0
Q ss_pred cchhhHhhHHHH--HHHHHHHHhhhHHHhhhhhchHHHHHHHHHh
Q 021367 106 QNRRARWKTKQL--ERDYGVLKANYDALKLNYDSLQHDNEALLKE 148 (313)
Q Consensus 106 QNRRaK~Kkkq~--e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~e 148 (313)
|+-|.|.|-+.. +.+...|...++.|..+++.|+..|+.|..+
T Consensus 82 QtaRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~ 126 (292)
T KOG4005|consen 82 QTARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAK 126 (292)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 444554443332 3333344445555555555555544444443
No 58
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=37.99 E-value=1.3e+02 Score=31.60 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 115 kq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
..++++.+.+++..+.+......+.+..+.|+.++.
T Consensus 79 sELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~ 114 (475)
T PRK13729 79 AQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNA 114 (475)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence 334444444444333333333333433344444444
No 59
>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=37.24 E-value=36 Score=27.89 Aligned_cols=33 Identities=30% Similarity=0.662 Sum_probs=19.6
Q ss_pred HHHHHHhhhhcCCCCHH--HHHHHHHHhCCCCceeeeeccchhhHhhHHHH
Q 021367 69 VKALEKNFEVENKLEPE--RKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (313)
Q Consensus 69 l~~LE~~F~~~~yPs~~--~reeLA~~LgLserQVqVWFQNRRaK~Kkkq~ 117 (313)
+...+-.|+.++||... .+.. .|||.+|++.+.
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 34555568899999744 2222 589999998764
No 60
>smart00338 BRLZ basic region leucin zipper.
Probab=36.27 E-value=1e+02 Score=22.74 Aligned_cols=37 Identities=30% Similarity=0.390 Sum_probs=26.0
Q ss_pred hHHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhh
Q 021367 113 KTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKET 149 (313)
Q Consensus 113 Kkkq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el 149 (313)
....++.....|...+..|....+.|..++..|..++
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3344556667777777777777777777777777665
No 61
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=35.82 E-value=27 Score=30.55 Aligned_cols=48 Identities=19% Similarity=0.154 Sum_probs=35.5
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhH
Q 021367 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (313)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kk 114 (313)
...+++.|..+|.. +... ....++|..||++...|..|-++.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~l-r~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRL-RERG-----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHH-HHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34589999999977 3222 346689999999999999998755554443
No 62
>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=34.61 E-value=20 Score=25.05 Aligned_cols=41 Identities=17% Similarity=0.173 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRR 109 (313)
+++.+..++.-.|... ..-.++|..+|+++..|+.|.+.-|
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 5666666666655433 4677899999999999999886433
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=33.95 E-value=11 Score=28.48 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCCceeeeec
Q 021367 86 RKVKLAQELGLQPRQVAVWF 105 (313)
Q Consensus 86 ~reeLA~~LgLserQVqVWF 105 (313)
.-.+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45679999999999999884
No 64
>PF15058 Speriolin_N: Speriolin N terminus
Probab=32.95 E-value=67 Score=29.86 Aligned_cols=38 Identities=29% Similarity=0.452 Sum_probs=22.7
Q ss_pred hhHHHhhhhhchHHHHHHHHHhhhccccchhhhhhccc
Q 021367 127 NYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (313)
Q Consensus 127 ~~~~L~~e~dsL~~en~~L~~el~~~~~d~~lk~kL~~ 164 (313)
+|+.+++..+.+..||..|++++++-..+++||.-|.+
T Consensus 6 ~yeGlrhqierLv~ENeeLKKlVrLirEN~eLksaL~e 43 (200)
T PF15058_consen 6 NYEGLRHQIERLVRENEELKKLVRLIRENHELKSALGE 43 (200)
T ss_pred chHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555666666666666666666644455566665443
No 65
>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=32.94 E-value=1.1e+02 Score=21.82 Aligned_cols=19 Identities=26% Similarity=0.387 Sum_probs=8.8
Q ss_pred hhhhhchHHHHHHHHHhhh
Q 021367 132 KLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 132 ~~e~dsL~~en~~L~~el~ 150 (313)
......|..+|..|..++.
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 3333444445555554444
No 66
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=31.92 E-value=1.2e+02 Score=24.95 Aligned_cols=46 Identities=15% Similarity=0.231 Sum_probs=21.6
Q ss_pred eeeeccchhhHhhHHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHH
Q 021367 101 VAVWFQNRRARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLK 147 (313)
Q Consensus 101 VqVWFQNRRaK~Kkkq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~ 147 (313)
...||++.-- .+-.+++++...+++.++.++.+++.|+.+...|+.
T Consensus 17 y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 17 YSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 4468865411 112223344445555555555555555555544443
No 67
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=31.57 E-value=78 Score=30.27 Aligned_cols=39 Identities=28% Similarity=0.317 Sum_probs=20.5
Q ss_pred hhHhhHHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 109 RaK~Kkkq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
|.+.|+++.+.+ .+.....|..+++.|+.+...|++++.
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 455555544322 233334555666666666666666665
No 68
>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=29.33 E-value=1.5e+02 Score=23.69 Aligned_cols=33 Identities=18% Similarity=0.213 Sum_probs=17.5
Q ss_pred HHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 118 ERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 118 e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
+.....|-.+.+.++.+++.|+.+|+.|+.-+.
T Consensus 29 Q~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~ 61 (80)
T PF10224_consen 29 QDSLEALSDRVEEVKEENEKLESENEYLQQYIG 61 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444445555555556666666655555443
No 69
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=27.97 E-value=1.2e+02 Score=25.36 Aligned_cols=32 Identities=22% Similarity=0.199 Sum_probs=15.2
Q ss_pred HHHHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 119 RDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 119 ~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
.+.+.||.....|..+|..|+-||+.|+..+.
T Consensus 22 ~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~ 53 (107)
T PF06156_consen 22 EELEELKKQLQELLEENARLRIENEHLRERLE 53 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444444444444443
No 70
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=27.68 E-value=48 Score=29.05 Aligned_cols=45 Identities=13% Similarity=0.119 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~K 113 (313)
+++.+..+|.-.|-.+ ..-.++|..||++...|+++...-|.+.|
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 7777777776655333 34668999999999999887754444333
No 71
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=27.47 E-value=1.2e+02 Score=25.32 Aligned_cols=47 Identities=26% Similarity=0.340 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhhccccchhhhhhccccCC
Q 021367 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRDQE 167 (313)
Q Consensus 115 kq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~~~~~d~~lk~kL~~~~~ 167 (313)
.+.+.....+-.....|+.....+..||..|+.|.. .|+.+|.+...
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~------~Lr~~l~~~~~ 57 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENE------HLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHhc
Confidence 456677778888889999999999999999999999 89999976643
No 72
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=26.58 E-value=1.3e+02 Score=29.68 Aligned_cols=40 Identities=18% Similarity=0.306 Sum_probs=22.1
Q ss_pred hHhhHHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 110 ARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 110 aK~Kkkq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
+|+|.|+. .+.+.+-.+...|...|+.|+..-..|.+|+.
T Consensus 240 tRYRqKkR-ae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ 279 (294)
T KOG4571|consen 240 TRYRQKKR-AEKEALLGELEGLEKRNEELKDQASELEREIR 279 (294)
T ss_pred HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444332 23333444456666666666666666666666
No 73
>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=26.01 E-value=47 Score=26.31 Aligned_cols=43 Identities=16% Similarity=0.167 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK 111 (313)
+++.|..++...|-. .....++|..+|+++..|..|...-+.+
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 566666666554432 2345689999999999988777544433
No 74
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=25.87 E-value=48 Score=27.85 Aligned_cols=42 Identities=14% Similarity=0.012 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRa 110 (313)
+++.+..++...|-.. ....++|..+|+++..|+.|...-+.
T Consensus 129 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~ 170 (182)
T PRK09652 129 LPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRARE 170 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7777777777665322 24567999999999999888763333
No 75
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=25.75 E-value=1.1e+02 Score=32.69 Aligned_cols=29 Identities=24% Similarity=0.233 Sum_probs=23.2
Q ss_pred HHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 122 GVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 122 ~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
..|+.+..+|-.+++.|+.||..|+.++.
T Consensus 305 ~~Le~rLq~ll~Ene~Lk~ENatLk~qL~ 333 (655)
T KOG4343|consen 305 LGLEARLQALLSENEQLKKENATLKRQLD 333 (655)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence 46777778888888888888888888775
No 76
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=25.36 E-value=1.4e+02 Score=25.25 Aligned_cols=32 Identities=22% Similarity=0.322 Sum_probs=15.6
Q ss_pred HHHHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 119 RDYGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 119 ~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
.+.+.||.....+..+|..|+-||+.|+..+.
T Consensus 22 ~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~ 53 (110)
T PRK13169 22 KELGALKKQLAELLEENTALRLENDKLRERLE 53 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555444455555555555555544444
No 77
>PF06637 PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 This family consists of several PV-1 (PLVAP) proteins, which seem to be specific to mammals. PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms []. The function of this family is unknown.
Probab=25.28 E-value=2.6e+02 Score=28.76 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=7.9
Q ss_pred hchHHHHHHHHHhhh
Q 021367 136 DSLQHDNEALLKETI 150 (313)
Q Consensus 136 dsL~~en~~L~~el~ 150 (313)
..|+.+++.|.+++.
T Consensus 352 aaLrkerd~L~keLe 366 (442)
T PF06637_consen 352 AALRKERDSLAKELE 366 (442)
T ss_pred HHHHHHHHHHHHHHH
Confidence 345555555555554
No 78
>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=24.70 E-value=41 Score=25.41 Aligned_cols=44 Identities=20% Similarity=0.436 Sum_probs=22.1
Q ss_pred CCcCCHH-HHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeecc
Q 021367 61 KRRLSVD-QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (313)
Q Consensus 61 RrRfT~~-Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQ 106 (313)
|+.|+.. -+.+++..+. ...--...|. -|++.|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~-~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK-DNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHH-ccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 3345554 3455555443 3222223344 49999999999998864
No 79
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.62 E-value=48 Score=27.42 Aligned_cols=43 Identities=16% Similarity=0.119 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK 111 (313)
+++.+..++...|-.+ ....++|..+|+++..|+.|...-|.+
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 6677777766555433 346789999999999999887543333
No 80
>PF08187 Tetradecapep: Myoactive tetradecapeptides family; InterPro: IPR012619 This entry consists of myoactive tetradecapeptides that are isolated from the gut of Earthworms, Eisenia foetida (Common brandling worm) and Pheretima vittata (Earthworm). These peptides were termed ETP and PTP respectively. Both peptides showed a potent excitatory action on spontaneous contractions of the anterior gut. These peptides show similarity to Molluscan tetradecapeptides and Arthropodan tridecapeptides [].; GO: 0005184 neuropeptide hormone activity, 0007218 neuropeptide signaling pathway, 0005576 extracellular region
Probab=24.05 E-value=32 Score=18.83 Aligned_cols=11 Identities=45% Similarity=0.676 Sum_probs=7.7
Q ss_pred CCCCCCCCCcc
Q 021367 215 DLKDGSSDSDS 225 (313)
Q Consensus 215 ~~~~gs~dsds 225 (313)
+|+||+.|-=|
T Consensus 1 gf~dg~adris 11 (14)
T PF08187_consen 1 GFRDGSADRIS 11 (14)
T ss_pred Cccccchhhhh
Confidence 48899887433
No 81
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=23.49 E-value=65 Score=26.98 Aligned_cols=46 Identities=13% Similarity=0.122 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhhH
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~Kk 114 (313)
+++.+..++.-.|-.. -.-.++|..+|+++..|+++...-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5556566555544322 235589999999999999887644444443
No 82
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=23.47 E-value=1.3e+02 Score=24.89 Aligned_cols=28 Identities=25% Similarity=0.262 Sum_probs=12.7
Q ss_pred hHHHHHHHHHHHHhhhHHHhhhhhchHH
Q 021367 113 KTKQLERDYGVLKANYDALKLNYDSLQH 140 (313)
Q Consensus 113 Kkkq~e~~~~~Lk~~~~~L~~e~dsL~~ 140 (313)
+....+++...+++.+..|..+.+.|+.
T Consensus 35 q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 35 QVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3333444444444444445444444443
No 83
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=23.37 E-value=68 Score=27.46 Aligned_cols=45 Identities=13% Similarity=0.261 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~K 113 (313)
+++.+..++.-.|-. .....++|..+|+++..|+++...-|.+.|
T Consensus 130 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 130 LEKDRAAAVRRAYLE-----GLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 555666555555422 234678999999999999887764444443
No 84
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.28 E-value=58 Score=28.98 Aligned_cols=45 Identities=22% Similarity=0.179 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~K 113 (313)
+++.|..++...|-.+ ....++|..+|+++..|+++...-|.+.+
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5556666665443222 34668999999999999887754444333
No 85
>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=23.09 E-value=1.7e+02 Score=26.16 Aligned_cols=45 Identities=20% Similarity=0.239 Sum_probs=36.0
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeecc
Q 021367 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (313)
Q Consensus 60 KRrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQ 106 (313)
++..+|.+++..+.+.-..+ |..-.+..||++.|+++.-|.+-..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~ 126 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAP 126 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcC
Confidence 34459999999998887766 5667789999999999887776554
No 86
>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=22.70 E-value=2.3e+02 Score=22.06 Aligned_cols=30 Identities=27% Similarity=0.393 Sum_probs=13.8
Q ss_pred HHHHHhhhHHHhhhhhchHHHHHHHHHhhh
Q 021367 121 YGVLKANYDALKLNYDSLQHDNEALLKETI 150 (313)
Q Consensus 121 ~~~Lk~~~~~L~~e~dsL~~en~~L~~el~ 150 (313)
+..|+...+.|+..+..+..++..|..+..
T Consensus 20 i~~Lq~e~eeLke~n~~L~~e~~~L~~en~ 49 (72)
T PF06005_consen 20 IALLQMENEELKEKNNELKEENEELKEENE 49 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 344444444444444444444444444444
No 87
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=22.60 E-value=76 Score=26.53 Aligned_cols=45 Identities=18% Similarity=0.172 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~K 113 (313)
+++.+..++...|.. ...-.+||..+|+++..|..|...-|.+.|
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 555555555554432 234578999999999999998864444444
No 88
>PHA02955 hypothetical protein; Provisional
Probab=22.50 E-value=1e+02 Score=29.01 Aligned_cols=42 Identities=7% Similarity=0.132 Sum_probs=34.0
Q ss_pred HHHHHHHHHhhhhc-CCCCHHHHHHHHHHhCCCCceeeeeccc
Q 021367 66 VDQVKALEKNFEVE-NKLEPERKVKLAQELGLQPRQVAVWFQN 107 (313)
Q Consensus 66 ~~Ql~~LE~~F~~~-~yPs~~~reeLA~~LgLserQVqVWFQN 107 (313)
..|+..|-+.|... .-+.+++|.+++++||+....|..||.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 46777777777665 6788999999999999999778888865
No 89
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=22.47 E-value=1.7e+02 Score=24.62 Aligned_cols=45 Identities=31% Similarity=0.364 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhhccccchhhhhhcccc
Q 021367 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDRD 165 (313)
Q Consensus 115 kq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~~~~~d~~lk~kL~~~ 165 (313)
.+++.....+-+....|+.....+..+|..|+.|.. .|+.+|.+.
T Consensus 11 ~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~------~Lr~~l~~~ 55 (110)
T PRK13169 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRLEND------KLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHh
Confidence 456677777888889999999999999999999998 899999754
No 90
>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=22.38 E-value=2.1e+02 Score=22.89 Aligned_cols=46 Identities=17% Similarity=0.187 Sum_probs=37.9
Q ss_pred hhHHHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhhccccchhhhhhcc
Q 021367 112 WKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (313)
Q Consensus 112 ~Kkkq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~~~~~d~~lk~kL~ 163 (313)
..+..+.++...|+...+.|....+.++.+++.|+.+.. -|+..+.
T Consensus 16 e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~------~Lq~YI~ 61 (80)
T PF10224_consen 16 EEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENE------YLQQYIG 61 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHH
Confidence 344556677888899999999999999999999999998 7777664
No 91
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.63 E-value=68 Score=27.58 Aligned_cols=45 Identities=16% Similarity=0.044 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~K 113 (313)
+++.+..++.-.|-.. ..-.+||..+|++...|+.++..-|.+.|
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 6666767766655433 34668999999999999988765554444
No 92
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.25 E-value=27 Score=24.13 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=18.8
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeec
Q 021367 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (313)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWF 105 (313)
+.+|.+|...++..++.. ....+||+.||.++..|..|.
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 458888999998887643 456679999999887765543
No 93
>PRK14127 cell division protein GpsB; Provisional
Probab=20.89 E-value=1.8e+02 Score=24.45 Aligned_cols=43 Identities=14% Similarity=0.272 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhhccccchhhhhhcc
Q 021367 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLD 163 (313)
Q Consensus 115 kq~e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~~~~~d~~lk~kL~ 163 (313)
..-......+-..++.+..++..|+.++..|+.++. +++.++.
T Consensus 26 ~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~------e~~~~~~ 68 (109)
T PRK14127 26 DEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVD------ELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHhhc
Confidence 333444445555666666777777777777777777 6666554
No 94
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=20.75 E-value=2.8e+02 Score=29.00 Aligned_cols=32 Identities=9% Similarity=0.238 Sum_probs=18.0
Q ss_pred cCCHHHHHHHHHh-hhh-cCCCCHHHHHHHHHHh
Q 021367 63 RLSVDQVKALEKN-FEV-ENKLEPERKVKLAQEL 94 (313)
Q Consensus 63 RfT~~Ql~~LE~~-F~~-~~yPs~~~reeLA~~L 94 (313)
.+|.+....|.+. |-. ..+|-...-+++-++.
T Consensus 220 ~LteeEkrLL~kEG~slPs~lPLTKaEEriLKrv 253 (472)
T KOG0709|consen 220 VLTEEEKRLLTKEGYSLPSKLPLTKAEERILKRV 253 (472)
T ss_pred eccHHHHHHHHhccCcCcccCCchHHHHHHHHHH
Confidence 4888888888776 333 2345544444444433
No 95
>PRK04217 hypothetical protein; Provisional
Probab=20.62 E-value=73 Score=26.74 Aligned_cols=40 Identities=10% Similarity=0.033 Sum_probs=30.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccc
Q 021367 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (313)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQN 107 (313)
.++.+|..++...|...- ...+||+.+|++...|...+..
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 488999888877765443 5678999999999888776643
No 96
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=20.51 E-value=2.3e+02 Score=22.60 Aligned_cols=35 Identities=14% Similarity=0.308 Sum_probs=22.8
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccch
Q 021367 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNR 108 (313)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNR 108 (313)
.+.|+..++..|..... .+.+|++..+|+-++...
T Consensus 36 ~R~y~~~di~~l~~i~~-------------lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 36 YRLYTEEDLERLQQILF-------------LKELGFSLKEIKELLKDP 70 (103)
T ss_pred ceeeCHHHHHHHHHHHH-------------HHHcCCCHHHHHHHHHcC
Confidence 34599999999865433 345566666666666543
No 97
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=20.36 E-value=72 Score=27.60 Aligned_cols=38 Identities=24% Similarity=0.151 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeecc
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQ 106 (313)
+++.|..++...|-.. ....+||..+|++...|+.+..
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ 177 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQH 177 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 6777777776655443 3467899999999999888764
No 98
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=20.25 E-value=2e+02 Score=24.56 Aligned_cols=41 Identities=34% Similarity=0.392 Sum_probs=21.5
Q ss_pred HHHHHHHHhhhHHHhhhhhchHHHHHHHHHhhhccccchhhhhhccc
Q 021367 118 ERDYGVLKANYDALKLNYDSLQHDNEALLKETIVHETDHQNKATLDR 164 (313)
Q Consensus 118 e~~~~~Lk~~~~~L~~e~dsL~~en~~L~~el~~~~~d~~lk~kL~~ 164 (313)
+....++-+...+++..-.++..||..|+-|.. .|+.+|.+
T Consensus 14 e~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe------~LR~RL~~ 54 (114)
T COG4467 14 EEQLGVLLAELGGLKQHLGSLVEENTALRLENE------KLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHH------HHHHHhCC
Confidence 333444444445555555555555555555555 56666655
No 99
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=20.21 E-value=1.3e+02 Score=28.91 Aligned_cols=30 Identities=20% Similarity=0.273 Sum_probs=13.1
Q ss_pred HHHHHHhhhHHHhhhhhchHHHHHHHHHhh
Q 021367 120 DYGVLKANYDALKLNYDSLQHDNEALLKET 149 (313)
Q Consensus 120 ~~~~Lk~~~~~L~~e~dsL~~en~~L~~el 149 (313)
+...|...++.+..+++.++....+|..+.
T Consensus 150 EkeeL~~eleele~e~ee~~erlk~le~E~ 179 (290)
T COG4026 150 EKEELLKELEELEAEYEEVQERLKRLEVEN 179 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444444443
No 100
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=20.07 E-value=61 Score=28.13 Aligned_cols=45 Identities=20% Similarity=0.261 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCCceeeeeccchhhHhh
Q 021367 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (313)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~reeLA~~LgLserQVqVWFQNRRaK~K 113 (313)
+++.+..++...| .......++|..+|++...|+.|...-|.+.|
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4455555554433 22335678999999999999998864444433
Done!