Query psy7087
Match_columns 162
No_of_seqs 222 out of 1271
Neff 7.4
Searched_HMMs 46136
Date Fri Aug 16 17:46:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7087.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7087hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.6 3.7E-16 8.1E-21 108.9 1.4 53 110-162 11-63 (125)
2 KOG0850|consensus 99.5 8.6E-14 1.9E-18 109.3 7.8 54 109-162 115-168 (245)
3 KOG2251|consensus 99.4 1.5E-13 3.3E-18 107.4 4.3 51 112-162 33-83 (228)
4 KOG0488|consensus 99.4 2.3E-13 5E-18 112.7 4.8 54 109-162 165-218 (309)
5 KOG0489|consensus 99.4 8E-14 1.7E-18 113.2 1.8 49 114-162 157-205 (261)
6 KOG0843|consensus 99.4 1.6E-12 3.4E-17 98.8 7.3 48 115-162 101-148 (197)
7 KOG0842|consensus 99.4 8E-13 1.7E-17 108.7 5.3 52 111-162 148-199 (307)
8 TIGR01565 homeo_ZF_HD homeobox 99.3 2.3E-12 5.1E-17 81.7 4.8 46 117-162 2-51 (58)
9 KOG0487|consensus 99.2 9.5E-12 2.1E-16 102.4 3.4 50 113-162 232-281 (308)
10 KOG0485|consensus 99.1 3.5E-11 7.6E-16 94.1 3.8 50 113-162 101-150 (268)
11 KOG0848|consensus 99.1 5.4E-11 1.2E-15 95.5 4.9 52 111-162 194-245 (317)
12 KOG0494|consensus 99.1 6.7E-11 1.5E-15 94.6 5.3 51 112-162 136-187 (332)
13 KOG0492|consensus 99.1 4.3E-11 9.3E-16 93.0 4.0 52 111-162 139-190 (246)
14 KOG0486|consensus 99.1 1E-10 2.2E-15 95.7 3.9 49 114-162 110-158 (351)
15 KOG0493|consensus 99.0 1.5E-10 3.3E-15 92.7 3.9 46 117-162 247-292 (342)
16 PF00046 Homeobox: Homeobox do 98.9 1E-09 2.2E-14 68.8 2.5 46 117-162 1-46 (57)
17 KOG0844|consensus 98.8 2.3E-09 4.9E-14 87.7 2.8 51 112-162 177-227 (408)
18 KOG0490|consensus 98.7 7.8E-09 1.7E-13 81.4 3.0 50 113-162 57-106 (235)
19 smart00389 HOX Homeodomain. DN 98.7 1.6E-08 3.4E-13 62.9 3.6 46 117-162 1-46 (56)
20 KOG0491|consensus 98.7 2.9E-09 6.3E-14 80.2 -0.3 48 114-161 98-145 (194)
21 cd00086 homeodomain Homeodomai 98.6 5.5E-08 1.2E-12 60.8 3.5 45 118-162 2-46 (59)
22 KOG0849|consensus 98.6 4.6E-08 1E-12 82.7 3.9 53 110-162 170-222 (354)
23 COG5576 Homeodomain-containing 98.2 1.5E-06 3.3E-11 65.6 4.7 49 114-162 49-97 (156)
24 KOG0847|consensus 97.8 7.2E-06 1.6E-10 64.7 1.4 51 112-162 163-213 (288)
25 KOG0483|consensus 97.7 2.2E-05 4.7E-10 61.4 2.8 42 121-162 55-96 (198)
26 KOG3802|consensus 97.7 4.8E-05 1E-09 64.6 4.5 48 115-162 293-340 (398)
27 KOG4577|consensus 97.4 0.00016 3.4E-09 59.3 3.8 49 114-162 165-213 (383)
28 KOG2252|consensus 97.1 0.00058 1.3E-08 60.2 4.4 49 113-161 417-465 (558)
29 KOG0490|consensus 96.1 0.005 1.1E-07 48.2 3.0 51 112-162 149-199 (235)
30 KOG1168|consensus 95.7 0.0056 1.2E-07 50.4 1.8 48 115-162 308-355 (385)
31 KOG0774|consensus 93.5 0.081 1.7E-06 43.1 3.4 45 116-160 188-235 (334)
32 PF05920 Homeobox_KN: Homeobox 93.0 0.034 7.4E-07 32.4 0.4 25 137-161 7-31 (40)
33 KOG0775|consensus 91.0 0.42 9.2E-06 39.2 4.6 43 118-160 169-220 (304)
34 PF04218 CENP-B_N: CENP-B N-te 85.1 1.7 3.7E-05 26.6 3.6 39 117-160 1-39 (53)
35 PF04967 HTH_10: HTH DNA bindi 83.7 0.93 2E-05 28.0 2.0 37 123-159 1-39 (53)
36 KOG1146|consensus 81.8 1.1 2.3E-05 44.0 2.5 48 115-162 902-949 (1406)
37 COG3413 Predicted DNA binding 64.2 5.2 0.00011 31.3 2.1 38 122-159 155-194 (215)
38 PF13936 HTH_38: Helix-turn-he 52.5 7.5 0.00016 22.6 0.9 35 121-160 3-37 (44)
39 COG4367 Uncharacterized protei 51.7 11 0.00024 25.9 1.7 37 123-159 3-39 (97)
40 PF08280 HTH_Mga: M protein tr 51.5 9.7 0.00021 23.5 1.4 32 126-161 6-37 (59)
41 PF04545 Sigma70_r4: Sigma-70, 50.5 11 0.00023 22.2 1.4 35 122-161 4-38 (50)
42 PF12824 MRP-L20: Mitochondria 48.5 24 0.00052 26.8 3.4 40 119-160 82-121 (164)
43 PF11569 Homez: Homeodomain le 48.2 8.8 0.00019 24.0 0.8 34 128-161 10-43 (56)
44 PF08880 QLQ: QLQ; InterPro: 45.4 18 0.00039 20.6 1.7 17 122-138 2-18 (37)
45 PF02796 HTH_7: Helix-turn-hel 35.0 31 0.00067 19.9 1.7 33 123-160 6-38 (45)
46 KOG0773|consensus 34.4 55 0.0012 27.3 3.7 47 116-162 239-288 (342)
47 PF01527 HTH_Tnp_1: Transposas 32.2 43 0.00094 21.0 2.2 37 118-159 2-39 (76)
48 cd00569 HTH_Hin_like Helix-tur 31.5 70 0.0015 15.7 2.7 33 123-160 6-38 (42)
49 TIGR03879 near_KaiC_dom probab 30.2 8.2 0.00018 25.4 -1.5 30 132-161 21-50 (73)
50 PF00196 GerE: Bacterial regul 28.7 39 0.00084 20.4 1.4 34 122-161 3-36 (58)
51 PRK13558 bacterio-opsin activa 24.6 54 0.0012 29.6 2.2 39 121-159 606-646 (665)
52 cd08315 Death_TRAILR_DR4_DR5 D 24.1 60 0.0013 22.2 1.9 31 130-160 5-36 (96)
53 PF08281 Sigma70_r4_2: Sigma-7 23.8 18 0.00039 21.4 -0.8 24 138-161 21-44 (54)
54 cd06171 Sigma70_r4 Sigma70, re 21.6 79 0.0017 17.5 1.8 34 123-161 11-44 (55)
55 PF08279 HTH_11: HTH domain; 21.5 66 0.0014 18.9 1.5 17 145-161 17-33 (55)
56 cd08318 Death_NMPP84 Death dom 21.0 94 0.002 20.6 2.3 32 122-160 4-35 (86)
57 PF04539 Sigma70_r3: Sigma-70 20.7 38 0.00083 21.5 0.3 17 145-161 22-38 (78)
No 1
>KOG0484|consensus
Probab=99.58 E-value=3.7e-16 Score=108.86 Aligned_cols=53 Identities=92% Similarity=1.224 Sum_probs=50.6
Q ss_pred cccccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 110 LTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 110 ~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
...++|+||.||+||..||.+||+.|-++||||+.+|++||.+|+|+|.+|||
T Consensus 11 l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQV 63 (125)
T KOG0484|consen 11 LTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQV 63 (125)
T ss_pred hhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHH
Confidence 45688999999999999999999999999999999999999999999999986
No 2
>KOG0850|consensus
Probab=99.49 E-value=8.6e-14 Score=109.28 Aligned_cols=54 Identities=35% Similarity=0.517 Sum_probs=51.7
Q ss_pred ccccccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 109 VLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 109 ~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
.+.+.||.|+.||+|+..||..|.++|+++.|+..++|.|||+.|||+.+||||
T Consensus 115 ~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKI 168 (245)
T KOG0850|consen 115 PNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKI 168 (245)
T ss_pred cCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhh
Confidence 456788999999999999999999999999999999999999999999999998
No 3
>KOG2251|consensus
Probab=99.41 E-value=1.5e-13 Score=107.38 Aligned_cols=51 Identities=57% Similarity=0.860 Sum_probs=49.3
Q ss_pred cccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 112 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 112 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
..||+||.||+||..|+.+||..|.++.|||+.+|++||.+|+|+|.+|||
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV 83 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence 568899999999999999999999999999999999999999999999997
No 4
>KOG0488|consensus
Probab=99.40 E-value=2.3e-13 Score=112.75 Aligned_cols=54 Identities=35% Similarity=0.565 Sum_probs=50.3
Q ss_pred ccccccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 109 VLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 109 ~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
.....||+|+.||.||..||.+||+.|++.+|++..+|.+||++|||+++|||+
T Consensus 165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKt 218 (309)
T KOG0488|consen 165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKT 218 (309)
T ss_pred ccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHH
Confidence 344568889999999999999999999999999999999999999999999996
No 5
>KOG0489|consensus
Probab=99.40 E-value=8e-14 Score=113.17 Aligned_cols=49 Identities=41% Similarity=0.518 Sum_probs=47.2
Q ss_pred cccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 114 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 114 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
.+.||.||.||..|+.|||++|+.|+|+++.+|.|||..|+|+|+||||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKI 205 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKI 205 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHH
Confidence 4578999999999999999999999999999999999999999999998
No 6
>KOG0843|consensus
Probab=99.37 E-value=1.6e-12 Score=98.85 Aligned_cols=48 Identities=38% Similarity=0.580 Sum_probs=47.0
Q ss_pred ccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 115 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 115 k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
|.||.||.||.+||..||..|+.++|....+|++||+.|+|+|.||||
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkv 148 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKV 148 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhh
Confidence 788999999999999999999999999999999999999999999998
No 7
>KOG0842|consensus
Probab=99.36 E-value=8e-13 Score=108.66 Aligned_cols=52 Identities=40% Similarity=0.579 Sum_probs=49.0
Q ss_pred ccccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 111 TEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 111 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
..++++||.|..||..|..|||+.|..++|++.++|++||..|+||++||||
T Consensus 148 t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKI 199 (307)
T KOG0842|consen 148 TGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKI 199 (307)
T ss_pred cccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheee
Confidence 3466778889999999999999999999999999999999999999999999
No 8
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.32 E-value=2.3e-12 Score=81.67 Aligned_cols=46 Identities=20% Similarity=0.229 Sum_probs=44.9
Q ss_pred CCCCcccChHHHHHHHHhhhhcCC----CCHHHHHHHHHHcCCCCCcccC
Q psy7087 117 RRIRTTFTSAQLKELERAFQETHY----PDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 117 rr~Rt~ft~~Ql~~Le~~F~~~~y----p~~~~r~~LA~~l~L~e~qVkI 162 (162)
||.||.||.+|+..||..|++++| |+..+|++||..|||++.+|||
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKV 51 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKV 51 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeee
Confidence 789999999999999999999999 9999999999999999999997
No 9
>KOG0487|consensus
Probab=99.20 E-value=9.5e-12 Score=102.40 Aligned_cols=50 Identities=32% Similarity=0.424 Sum_probs=47.6
Q ss_pred ccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 113 KRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 113 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
.++.||+|..||..|+.|||++|-.|.|+....|.||++.|+|+|+||||
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKI 281 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKI 281 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheee
Confidence 36678889999999999999999999999999999999999999999999
No 10
>KOG0485|consensus
Probab=99.13 E-value=3.5e-11 Score=94.06 Aligned_cols=50 Identities=30% Similarity=0.492 Sum_probs=47.1
Q ss_pred ccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 113 KRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 113 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
..++||.||.|+..|+..||..|+.++|++..+|..||++|.|+|.||||
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKI 150 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKI 150 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhh
Confidence 34567799999999999999999999999999999999999999999998
No 11
>KOG0848|consensus
Probab=99.13 E-value=5.4e-11 Score=95.50 Aligned_cols=52 Identities=29% Similarity=0.500 Sum_probs=48.0
Q ss_pred ccccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 111 TEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 111 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
.+.|.+-+.|.+||+.|+.|||++|..++|+.+.++.|||..|+|+|+||||
T Consensus 194 ~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKI 245 (317)
T KOG0848|consen 194 VKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKI 245 (317)
T ss_pred ceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhH
Confidence 3556666789999999999999999999999999999999999999999998
No 12
>KOG0494|consensus
Probab=99.13 E-value=6.7e-11 Score=94.64 Aligned_cols=51 Identities=57% Similarity=0.906 Sum_probs=46.0
Q ss_pred ccc-ccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 112 EKR-KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 112 ~~~-k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
+++ |+|+.||+||..|+.+||+.|++.||||+..|+-||.++.|+|.+|||
T Consensus 136 kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqV 187 (332)
T KOG0494|consen 136 KKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQV 187 (332)
T ss_pred ccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhH
Confidence 444 444559999999999999999999999999999999999999999987
No 13
>KOG0492|consensus
Probab=99.13 E-value=4.3e-11 Score=92.98 Aligned_cols=52 Identities=38% Similarity=0.606 Sum_probs=48.8
Q ss_pred ccccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 111 TEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 111 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
.+.+..|+.||.||..||..||+.|+..+|+++.+|.+++..|.|+|+||||
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKI 190 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKI 190 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheeh
Confidence 4556678899999999999999999999999999999999999999999998
No 14
>KOG0486|consensus
Probab=99.07 E-value=1e-10 Score=95.74 Aligned_cols=49 Identities=63% Similarity=0.842 Sum_probs=47.2
Q ss_pred cccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 114 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 114 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
+|+||.||.||..||++||..|++|+||+..+|+|||.-++|+|.+|+|
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrv 158 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRV 158 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhh
Confidence 4889999999999999999999999999999999999999999999986
No 15
>KOG0493|consensus
Probab=99.04 E-value=1.5e-10 Score=92.74 Aligned_cols=46 Identities=37% Similarity=0.603 Sum_probs=44.9
Q ss_pred CCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 117 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 117 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
||.||.||.+||..|+.+|+.|+|+....|.+||..|+|.|.||||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKI 292 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKI 292 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhH
Confidence 6889999999999999999999999999999999999999999998
No 16
>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=98.88 E-value=1e-09 Score=68.80 Aligned_cols=46 Identities=50% Similarity=0.695 Sum_probs=43.5
Q ss_pred CCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 117 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 117 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
||.|+.||.+|+..||..|..++||+..++++||..|||++.+|++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~ 46 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKN 46 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence 5789999999999999999999999999999999999999999863
No 17
>KOG0844|consensus
Probab=98.81 E-value=2.3e-09 Score=87.73 Aligned_cols=51 Identities=31% Similarity=0.493 Sum_probs=48.0
Q ss_pred cccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 112 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 112 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
....-||.||.||.+||-.||++|-+..|.++++|-|||..|+|+|..|||
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKV 227 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKV 227 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeeh
Confidence 445678999999999999999999999999999999999999999999997
No 18
>KOG0490|consensus
Probab=98.71 E-value=7.8e-09 Score=81.43 Aligned_cols=50 Identities=44% Similarity=0.537 Sum_probs=48.0
Q ss_pred ccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 113 KRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 113 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
+.++||.||.|+.+|+.+||+.|++.|||++..|+.||..++++|.+|||
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqv 106 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQV 106 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeeh
Confidence 56789999999999999999999999999999999999999999999997
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.70 E-value=1.6e-08 Score=62.86 Aligned_cols=46 Identities=50% Similarity=0.756 Sum_probs=42.6
Q ss_pred CCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 117 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 117 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
++.|+.|+.+|+..||..|..++||+..++.+||..+||+..+|++
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 3567889999999999999999999999999999999999999873
No 20
>KOG0491|consensus
Probab=98.68 E-value=2.9e-09 Score=80.15 Aligned_cols=48 Identities=33% Similarity=0.589 Sum_probs=45.3
Q ss_pred cccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 114 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 114 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
-++|+.||+|+..|+..||++|+..+|++..+|.|||..|+|++.|||
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVK 145 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVK 145 (194)
T ss_pred HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHH
Confidence 345778999999999999999999999999999999999999999997
No 21
>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=98.58 E-value=5.5e-08 Score=60.79 Aligned_cols=45 Identities=47% Similarity=0.703 Sum_probs=42.3
Q ss_pred CCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 118 RIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 118 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
+.|+.|+..|+..||..|..++||+..++.+||..+||++.+|++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 567899999999999999999999999999999999999999863
No 22
>KOG0849|consensus
Probab=98.57 E-value=4.6e-08 Score=82.71 Aligned_cols=53 Identities=47% Similarity=0.672 Sum_probs=49.3
Q ss_pred cccccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 110 LTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 110 ~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
...+++.||.||.|+..|+..||+.|++++||++..|++||.+++|+|.+|+|
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqv 222 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQV 222 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHH
Confidence 44677888899999999999999999999999999999999999999999875
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.24 E-value=1.5e-06 Score=65.58 Aligned_cols=49 Identities=29% Similarity=0.410 Sum_probs=44.3
Q ss_pred cccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 114 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 114 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
+..++.|+.-|.+|+..|++.|+.++||+..+|.+|+..|+|+++-|||
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqI 97 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQI 97 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhh
Confidence 3445566667999999999999999999999999999999999999998
No 24
>KOG0847|consensus
Probab=97.82 E-value=7.2e-06 Score=64.66 Aligned_cols=51 Identities=31% Similarity=0.519 Sum_probs=46.2
Q ss_pred cccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 112 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 112 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
+..+++-.|.+|+..||..||+.|+..+|+-..+|.+||-.||++|.||||
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkV 213 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKV 213 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHH
Confidence 334555678899999999999999999999999999999999999999987
No 25
>KOG0483|consensus
Probab=97.73 E-value=2.2e-05 Score=61.45 Aligned_cols=42 Identities=24% Similarity=0.339 Sum_probs=39.6
Q ss_pred cccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 121 TTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 121 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
..||.+|+..||+.|+..+++....+..||..|||.++||+|
T Consensus 55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVav 96 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAV 96 (198)
T ss_pred ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHH
Confidence 357999999999999999999999999999999999999986
No 26
>KOG3802|consensus
Probab=97.69 E-value=4.8e-05 Score=64.60 Aligned_cols=48 Identities=23% Similarity=0.299 Sum_probs=45.7
Q ss_pred ccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 115 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 115 k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
|+||+||.|....+..||+.|.+|.-|+..+..+||.+|+|...+|+|
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRV 340 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRV 340 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEE
Confidence 677889999999999999999999999999999999999999999986
No 27
>KOG4577|consensus
Probab=97.41 E-value=0.00016 Score=59.31 Aligned_cols=49 Identities=31% Similarity=0.406 Sum_probs=46.0
Q ss_pred cccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 114 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 114 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
...||+||++|..||+.|+..+....-|.+..|++|+..+||.-+.|||
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQV 213 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQV 213 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhh
Confidence 3458899999999999999999999999999999999999999999987
No 28
>KOG2252|consensus
Probab=97.12 E-value=0.00058 Score=60.19 Aligned_cols=49 Identities=24% Similarity=0.367 Sum_probs=44.4
Q ss_pred ccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 113 KRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 113 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
.-+.||.|.+||..|...|...|+.+++|+..+.+.|+.+|+|....|.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~ 465 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVI 465 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHH
Confidence 3456788999999999999999999999999999999999999887763
No 29
>KOG0490|consensus
Probab=96.10 E-value=0.005 Score=48.25 Aligned_cols=51 Identities=43% Similarity=0.570 Sum_probs=47.1
Q ss_pred cccccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 112 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 112 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
...+.++.|+.|+..|+..|+..|..+++|+...+++|+..+++++..|+|
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~ 199 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQV 199 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhh
Confidence 456778899999999999999999999999999999999999999998875
No 30
>KOG1168|consensus
Probab=95.73 E-value=0.0056 Score=50.41 Aligned_cols=48 Identities=27% Similarity=0.341 Sum_probs=43.7
Q ss_pred ccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 115 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 115 k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
.+||+||.+..-..+.||..|..+.-|+......||.+|+|....|+|
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRV 355 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRV 355 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEE
Confidence 346789999999999999999999999999999999999999988875
No 31
>KOG0774|consensus
Probab=93.52 E-value=0.081 Score=43.14 Aligned_cols=45 Identities=29% Similarity=0.462 Sum_probs=39.9
Q ss_pred cCCCCcccChHHHHHHHHhhh---hcCCCCHHHHHHHHHHcCCCCCcc
Q psy7087 116 QRRIRTTFTSAQLKELERAFQ---ETHYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 116 ~rr~Rt~ft~~Ql~~Le~~F~---~~~yp~~~~r~~LA~~l~L~e~qV 160 (162)
.||.|..|+..-...|...|. .++||+...+++||++-+++..||
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQv 235 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQV 235 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhh
Confidence 367788899999999999996 478999999999999999999887
No 32
>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=92.99 E-value=0.034 Score=32.43 Aligned_cols=25 Identities=24% Similarity=0.478 Sum_probs=19.8
Q ss_pred hcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 137 ETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 137 ~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
.++||+..++++||..+||+..||.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~ 31 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQIS 31 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 3789999999999999999998874
No 33
>KOG0775|consensus
Probab=91.00 E-value=0.42 Score=39.23 Aligned_cols=43 Identities=23% Similarity=0.285 Sum_probs=36.1
Q ss_pred CCCcccChH---------HHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcc
Q psy7087 118 RIRTTFTSA---------QLKELERAFQETHYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 118 r~Rt~ft~~---------Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qV 160 (162)
-+||++..+ -+..|...|..+.||...++.+||+.+||+..||
T Consensus 169 lPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 169 LPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred CCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhh
Confidence 357765444 4568888899999999999999999999999988
No 34
>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=85.13 E-value=1.7 Score=26.59 Aligned_cols=39 Identities=21% Similarity=0.396 Sum_probs=29.0
Q ss_pred CCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcc
Q psy7087 117 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 117 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qV 160 (162)
||.|..+|-++-.++-..++... ...+||..+|++..+|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv 39 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTV 39 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHH
Confidence 46788999999998888888776 5678999999999876
No 35
>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=83.68 E-value=0.93 Score=28.02 Aligned_cols=37 Identities=24% Similarity=0.376 Sum_probs=30.1
Q ss_pred cChHHHHHHHHhhhhcCC--CCHHHHHHHHHHcCCCCCc
Q psy7087 123 FTSAQLKELERAFQETHY--PDIYTREEIAMKIDLTEAR 159 (162)
Q Consensus 123 ft~~Ql~~Le~~F~~~~y--p~~~~r~~LA~~l~L~e~q 159 (162)
+|..|+..|...++..-| |-...-.+||..||++...
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st 39 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKST 39 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHH
Confidence 578899999999998776 5455668999999998754
No 36
>KOG1146|consensus
Probab=81.76 E-value=1.1 Score=43.97 Aligned_cols=48 Identities=23% Similarity=0.303 Sum_probs=43.8
Q ss_pred ccCCCCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 115 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 115 k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
.+|+.||.++..||..|...|....||...+-+.|-..++++.+.|+|
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~v 949 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQV 949 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHH
Confidence 356789999999999999999999999999999999999999998875
No 37
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=64.25 E-value=5.2 Score=31.26 Aligned_cols=38 Identities=18% Similarity=0.376 Sum_probs=31.8
Q ss_pred ccChHHHHHHHHhhhhcCC--CCHHHHHHHHHHcCCCCCc
Q psy7087 122 TFTSAQLKELERAFQETHY--PDIYTREEIAMKIDLTEAR 159 (162)
Q Consensus 122 ~ft~~Ql~~Le~~F~~~~y--p~~~~r~~LA~~l~L~e~q 159 (162)
.+|..|++.|...|...-| |-...-.+||..||++...
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 6999999999999998765 5555667999999998753
No 38
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=52.49 E-value=7.5 Score=22.64 Aligned_cols=35 Identities=17% Similarity=0.317 Sum_probs=15.9
Q ss_pred cccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcc
Q psy7087 121 TTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 121 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qV 160 (162)
..+|.+|...++...+.. ....+||..||.+...|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV 37 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTV 37 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHH
Confidence 457888888888776544 35668999999987654
No 39
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.71 E-value=11 Score=25.86 Aligned_cols=37 Identities=22% Similarity=0.255 Sum_probs=26.0
Q ss_pred cChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCc
Q psy7087 123 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEAR 159 (162)
Q Consensus 123 ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~q 159 (162)
+.++|++.-...|+.|.-++.-..+++|..|+.++-.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~ 39 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVK 39 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHH
Confidence 3556666666666666656666778999999998753
No 40
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=51.50 E-value=9.7 Score=23.52 Aligned_cols=32 Identities=28% Similarity=0.468 Sum_probs=23.1
Q ss_pred HHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 126 AQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 126 ~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
.|+.-|+-.+. +...... +||..|+++++.|+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 46677777777 6666554 89999999998764
No 41
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=50.51 E-value=11 Score=22.22 Aligned_cols=35 Identities=20% Similarity=0.326 Sum_probs=24.6
Q ss_pred ccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 122 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 122 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
.+++.+...|...|... ..-.++|..+|+++..|+
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~ 38 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVR 38 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHH
Confidence 35677778888777333 256799999999987764
No 42
>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=48.46 E-value=24 Score=26.79 Aligned_cols=40 Identities=25% Similarity=0.414 Sum_probs=32.1
Q ss_pred CCcccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcc
Q psy7087 119 IRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 119 ~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qV 160 (162)
....+|.+++.++.+.-..+ |..+.|..||.++|++..-|
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV 121 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFV 121 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHH
Confidence 34689999999998765544 67789999999999987544
No 43
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=48.20 E-value=8.8 Score=24.00 Aligned_cols=34 Identities=15% Similarity=0.185 Sum_probs=23.7
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 128 LKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 128 l~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
++-|+..|...+++.-..-.+|..+.+|+..||+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr 43 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVR 43 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHH
Confidence 4569999999999988888899999999988875
No 44
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=45.44 E-value=18 Score=20.57 Aligned_cols=17 Identities=41% Similarity=0.497 Sum_probs=13.5
Q ss_pred ccChHHHHHHHHhhhhc
Q psy7087 122 TFTSAQLKELERAFQET 138 (162)
Q Consensus 122 ~ft~~Ql~~Le~~F~~~ 138 (162)
.||..|+.+||.-...-
T Consensus 2 ~FT~~Ql~~L~~Qi~ay 18 (37)
T PF08880_consen 2 PFTPAQLQELRAQILAY 18 (37)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 69999999999765433
No 45
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=35.01 E-value=31 Score=19.94 Aligned_cols=33 Identities=21% Similarity=0.431 Sum_probs=21.4
Q ss_pred cChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcc
Q psy7087 123 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 123 ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qV 160 (162)
++.+|+.++...+... ....+||..+|++...|
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~Tv 38 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTV 38 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHH
Confidence 5665666666666655 24678999999987654
No 46
>KOG0773|consensus
Probab=34.42 E-value=55 Score=27.29 Aligned_cols=47 Identities=15% Similarity=0.194 Sum_probs=35.7
Q ss_pred cCCCCcccChHHHHHHHHhh-h--hcCCCCHHHHHHHHHHcCCCCCcccC
Q psy7087 116 QRRIRTTFTSAQLKELERAF-Q--ETHYPDIYTREEIAMKIDLTEARVQK 162 (162)
Q Consensus 116 ~rr~Rt~ft~~Ql~~Le~~F-~--~~~yp~~~~r~~LA~~l~L~e~qVkI 162 (162)
..|.+..|.......|+... + ...||.-..+..|+..+||+..||.+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~N 288 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSN 288 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCc
Confidence 34455577777777777663 3 24699999999999999999998753
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=32.21 E-value=43 Score=21.01 Aligned_cols=37 Identities=14% Similarity=0.236 Sum_probs=21.3
Q ss_pred CCCcccChHHHHHHHHhh-hhcCCCCHHHHHHHHHHcCCCCCc
Q psy7087 118 RIRTTFTSAQLKELERAF-QETHYPDIYTREEIAMKIDLTEAR 159 (162)
Q Consensus 118 r~Rt~ft~~Ql~~Le~~F-~~~~yp~~~~r~~LA~~l~L~e~q 159 (162)
+.|..||.++...+-... ... ....++|..+||+..+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~ 39 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPST 39 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeeccccccccc
Confidence 456789999888776554 332 3567889999987654
No 48
>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=31.55 E-value=70 Score=15.65 Aligned_cols=33 Identities=21% Similarity=0.393 Sum_probs=20.4
Q ss_pred cChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcc
Q psy7087 123 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 123 ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qV 160 (162)
++..+...+...+.... ...+++..++++...|
T Consensus 6 ~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv 38 (42)
T cd00569 6 LTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTL 38 (42)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHH
Confidence 45666666655565332 4557888888876543
No 49
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=30.16 E-value=8.2 Score=25.43 Aligned_cols=30 Identities=30% Similarity=0.155 Sum_probs=21.7
Q ss_pred HHhhhhcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 132 ERAFQETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 132 e~~F~~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
+..|...+|.......+||..|++++..|+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk 50 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVR 50 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHH
Confidence 344555555555567899999999997765
No 50
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=28.70 E-value=39 Score=20.37 Aligned_cols=34 Identities=26% Similarity=0.373 Sum_probs=22.8
Q ss_pred ccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 122 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 122 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
.||..++..|+....-. ...++|..+++++..|+
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~ 36 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVK 36 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHH
Confidence 46777888777655543 46788888888876654
No 51
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.62 E-value=54 Score=29.55 Aligned_cols=39 Identities=23% Similarity=0.424 Sum_probs=33.3
Q ss_pred cccChHHHHHHHHhhhhcCC--CCHHHHHHHHHHcCCCCCc
Q psy7087 121 TTFTSAQLKELERAFQETHY--PDIYTREEIAMKIDLTEAR 159 (162)
Q Consensus 121 t~ft~~Ql~~Le~~F~~~~y--p~~~~r~~LA~~l~L~e~q 159 (162)
..+|..|...|+..+...-| |-...-++||..||++...
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t 646 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRST 646 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 46999999999999998887 6666778999999998753
No 52
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=24.06 E-value=60 Score=22.24 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=19.8
Q ss_pred HHHHhhhhc-CCCCHHHHHHHHHHcCCCCCcc
Q psy7087 130 ELERAFQET-HYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 130 ~Le~~F~~~-~yp~~~~r~~LA~~l~L~e~qV 160 (162)
.|...|..- .......-.+|+++|||++..|
T Consensus 5 ~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I 36 (96)
T cd08315 5 TLRRSFDHFIKEVPFDSWNRLMRQLGLSENEI 36 (96)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHH
Confidence 455555443 2334445668999999998765
No 53
>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=23.79 E-value=18 Score=21.41 Aligned_cols=24 Identities=25% Similarity=0.303 Sum_probs=15.2
Q ss_pred cCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 138 THYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 138 ~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
-+|.....-.++|..+|+++..|+
T Consensus 21 l~~~~g~s~~eIa~~l~~s~~~v~ 44 (54)
T PF08281_consen 21 LRYFQGMSYAEIAEILGISESTVK 44 (54)
T ss_dssp HHHTS---HHHHHHHCTS-HHHHH
T ss_pred HHHHHCcCHHHHHHHHCcCHHHHH
Confidence 344455578899999999987765
No 54
>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=21.65 E-value=79 Score=17.45 Aligned_cols=34 Identities=18% Similarity=0.242 Sum_probs=21.7
Q ss_pred cChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCccc
Q psy7087 123 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 161 (162)
Q Consensus 123 ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVk 161 (162)
++..+...++..+. ....-.++|..+|+++..|+
T Consensus 11 l~~~~~~~~~~~~~-----~~~~~~~ia~~~~~s~~~i~ 44 (55)
T cd06171 11 LPEREREVILLRFG-----EGLSYEEIAEILGISRSTVR 44 (55)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHH
Confidence 45566666655442 22346688999999887663
No 55
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=21.50 E-value=66 Score=18.91 Aligned_cols=17 Identities=18% Similarity=0.423 Sum_probs=12.3
Q ss_pred HHHHHHHHcCCCCCccc
Q psy7087 145 TREEIAMKIDLTEARVQ 161 (162)
Q Consensus 145 ~r~~LA~~l~L~e~qVk 161 (162)
.-.+||..|+++.+.|+
T Consensus 17 t~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 17 TAKELAEELGVSRRTIR 33 (55)
T ss_dssp EHHHHHHHCTS-HHHHH
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45689999999987653
No 56
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.00 E-value=94 Score=20.64 Aligned_cols=32 Identities=9% Similarity=0.253 Sum_probs=21.0
Q ss_pred ccChHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCCCcc
Q psy7087 122 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 160 (162)
Q Consensus 122 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qV 160 (162)
..|.+|+..+....- ..-++||..||+++..|
T Consensus 4 ~~t~~~l~~ia~~iG-------~~Wk~Lar~LGls~~dI 35 (86)
T cd08318 4 PVTGEQITVFANKLG-------EDWKTLAPHLEMKDKEI 35 (86)
T ss_pred CCCHHHHHHHHHHHh-------hhHHHHHHHcCCCHHHH
Confidence 357777777653222 23567999999988655
No 57
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 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 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; 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: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=20.65 E-value=38 Score=21.52 Aligned_cols=17 Identities=35% Similarity=0.503 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCCCCccc
Q psy7087 145 TREEIAMKIDLTEARVQ 161 (162)
Q Consensus 145 ~r~~LA~~l~L~e~qVk 161 (162)
+.++||..||++...|+
T Consensus 22 t~eEiA~~lgis~~~v~ 38 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVR 38 (78)
T ss_dssp BHHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHcccHHHHH
Confidence 66799999999986653
Done!