Query psy16796
Match_columns 166
No_of_seqs 172 out of 1296
Neff 6.2
Searched_HMMs 46136
Date Fri Aug 16 22:18:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16796.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16796hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0842|consensus 99.7 1.7E-18 3.7E-23 147.7 3.8 68 74-141 149-216 (307)
2 KOG0489|consensus 99.7 7.3E-19 1.6E-23 147.4 0.5 66 75-140 156-221 (261)
3 KOG0850|consensus 99.7 5.1E-18 1.1E-22 139.0 3.3 62 71-132 115-176 (245)
4 KOG0487|consensus 99.7 7.6E-18 1.6E-22 143.8 3.3 61 75-135 232-292 (308)
5 KOG0843|consensus 99.7 8.5E-18 1.8E-22 133.4 2.9 65 76-140 100-164 (197)
6 KOG0488|consensus 99.7 4.6E-17 9.9E-22 139.7 3.4 65 73-137 167-233 (309)
7 KOG0484|consensus 99.7 2.5E-17 5.5E-22 120.7 1.4 59 74-132 13-71 (125)
8 TIGR01565 homeo_ZF_HD homeobox 99.6 3.4E-16 7.3E-21 103.9 5.2 52 79-130 2-57 (58)
9 KOG0492|consensus 99.6 1.8E-16 3.9E-21 128.5 3.6 64 73-136 139-202 (246)
10 KOG0485|consensus 99.5 2E-15 4.3E-20 123.3 2.2 58 76-133 102-161 (268)
11 KOG0848|consensus 99.5 3E-15 6.5E-20 125.2 1.4 59 76-134 197-255 (317)
12 KOG2251|consensus 99.5 1.1E-14 2.3E-19 118.9 4.6 60 73-132 32-91 (228)
13 PF00046 Homeobox: Homeobox do 99.5 8.8E-15 1.9E-19 95.2 1.2 54 79-132 1-54 (57)
14 KOG0493|consensus 99.4 3.2E-14 6.9E-19 118.9 2.8 55 78-132 246-300 (342)
15 KOG0494|consensus 99.4 4E-14 8.7E-19 118.2 3.2 58 77-134 140-199 (332)
16 KOG0491|consensus 99.4 2.7E-14 5.8E-19 112.3 -1.8 59 77-135 99-157 (194)
17 smart00389 HOX Homeodomain. DN 99.4 3.8E-13 8.3E-18 86.7 3.1 54 80-133 2-55 (56)
18 COG5576 Homeodomain-containing 99.3 6.6E-13 1.4E-17 104.1 3.6 64 76-139 49-112 (156)
19 cd00086 homeodomain Homeodomai 99.3 1.6E-12 3.5E-17 84.2 2.6 54 80-133 2-55 (59)
20 KOG0844|consensus 99.3 1.3E-12 2.9E-17 111.3 1.6 60 77-136 180-239 (408)
21 KOG0486|consensus 99.3 2.2E-12 4.8E-17 110.0 2.9 80 75-157 109-188 (351)
22 KOG4577|consensus 99.2 5.9E-12 1.3E-16 106.7 3.2 58 78-135 167-224 (383)
23 KOG0483|consensus 99.2 2.3E-11 4.9E-16 98.7 4.5 64 80-143 52-117 (198)
24 KOG0490|consensus 99.1 2E-11 4.3E-16 98.5 2.7 60 75-134 57-116 (235)
25 KOG3802|consensus 99.0 3.2E-10 6.9E-15 99.5 5.1 62 77-138 293-354 (398)
26 KOG0847|consensus 99.0 9.1E-11 2E-15 96.3 1.4 56 75-130 164-219 (288)
27 KOG0849|consensus 98.8 1.8E-09 3.9E-14 94.4 2.9 57 74-130 172-228 (354)
28 KOG1168|consensus 98.3 2.4E-07 5.2E-12 79.0 1.7 57 76-132 307-363 (385)
29 KOG2252|consensus 98.1 2.6E-06 5.7E-11 77.7 3.4 65 76-140 418-484 (558)
30 KOG0490|consensus 98.0 3.4E-06 7.4E-11 67.9 2.5 61 74-134 149-209 (235)
31 KOG0775|consensus 97.9 7.3E-06 1.6E-10 69.4 3.6 53 80-132 169-230 (304)
32 PF05920 Homeobox_KN: Homeobox 97.7 3.6E-06 7.8E-11 51.8 -1.3 32 99-130 7-38 (40)
33 KOG0774|consensus 97.3 0.00022 4.7E-09 60.4 3.6 53 78-130 188-243 (334)
34 KOG1146|consensus 97.2 0.00022 4.7E-09 70.8 2.3 55 78-132 903-957 (1406)
35 PF11569 Homez: Homeodomain le 95.0 0.0071 1.5E-07 39.9 0.1 40 90-129 10-49 (56)
36 KOG0773|consensus 94.0 0.059 1.3E-06 46.5 3.7 64 79-142 240-306 (342)
37 KOG3623|consensus 93.9 0.029 6.3E-07 53.6 1.6 46 90-135 568-613 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 87.6 0.67 1.5E-05 29.7 2.9 45 79-128 1-45 (53)
39 PF04967 HTH_10: HTH DNA bindi 61.8 11 0.00024 24.3 3.0 38 85-122 1-40 (53)
40 PF01527 HTH_Tnp_1: Transposas 41.6 6.8 0.00015 25.8 -0.5 45 81-129 3-47 (76)
41 COG3413 Predicted DNA binding 40.8 29 0.00064 27.8 3.0 38 84-121 155-194 (215)
42 TIGR03879 near_KaiC_dom probab 37.7 4.8 0.0001 27.8 -1.8 35 94-128 21-55 (73)
43 PF13384 HTH_23: Homeodomain-l 30.3 11 0.00024 22.8 -0.9 31 105-137 17-47 (50)
44 cd04761 HTH_MerR-SF Helix-Turn 27.3 16 0.00034 21.8 -0.6 22 109-130 4-25 (49)
45 cd00569 HTH_Hin_like Helix-tur 27.0 79 0.0017 15.9 2.5 36 85-125 6-41 (42)
46 PF06056 Terminase_5: Putative 26.6 9.9 0.00022 24.8 -1.6 32 106-137 14-45 (58)
47 KOG1146|consensus 25.4 20 0.00043 37.0 -0.5 51 78-128 444-494 (1406)
48 PF10668 Phage_terminase: Phag 24.7 20 0.00043 23.8 -0.5 27 107-133 24-50 (60)
49 PF08281 Sigma70_r4_2: Sigma-7 24.5 7.9 0.00017 23.9 -2.3 29 101-129 22-50 (54)
50 PF09607 BrkDBD: Brinker DNA-b 22.3 62 0.0013 21.4 1.5 37 90-128 12-48 (58)
51 PF04545 Sigma70_r4: Sigma-70, 22.0 48 0.001 20.1 1.0 40 84-128 4-43 (50)
52 PF08280 HTH_Mga: M protein tr 21.7 55 0.0012 20.9 1.2 33 88-124 6-38 (59)
53 PF08880 QLQ: QLQ; InterPro: 21.3 85 0.0018 18.7 1.9 17 83-99 1-17 (37)
54 PF13518 HTH_28: Helix-turn-he 20.7 36 0.00077 20.4 0.2 22 107-128 14-35 (52)
55 PF13411 MerR_1: MerR HTH fami 20.5 26 0.00056 22.5 -0.6 20 109-128 4-23 (69)
No 1
>KOG0842|consensus
Probab=99.73 E-value=1.7e-18 Score=147.66 Aligned_cols=68 Identities=25% Similarity=0.426 Sum_probs=60.2
Q ss_pred cCCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCCchhhh
Q psy16796 74 KNGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGEDEEEE 141 (166)
Q Consensus 74 ~~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~~~~~ 141 (166)
..+++||.|..||..|+.+||+.|..++|+++++|++||..|+||++||||||||+|-|=+..+.+..
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 34567888999999999999999999999999999999999999999999999998877666554443
No 2
>KOG0489|consensus
Probab=99.72 E-value=7.3e-19 Score=147.45 Aligned_cols=66 Identities=53% Similarity=0.739 Sum_probs=58.9
Q ss_pred CCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCCchhh
Q psy16796 75 NGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGEDEEE 140 (166)
Q Consensus 75 ~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~~~~ 140 (166)
....||.||.||..||.+||+.|+.|+|+++..|.+||..|+|+++||||||||+|+|.+..+.+.
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~ 221 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAK 221 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccc
Confidence 356789999999999999999999999999999999999999999999999999777766544443
No 3
>KOG0850|consensus
Probab=99.70 E-value=5.1e-18 Score=138.99 Aligned_cols=62 Identities=34% Similarity=0.478 Sum_probs=57.4
Q ss_pred hhhcCCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccc
Q psy16796 71 EEKKNGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEE 132 (166)
Q Consensus 71 ~~~~~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~k 132 (166)
.+++++|.|++||+|+..||..|.+.|+.+.|+-.++|.+||..||||.+||||||||+|.|
T Consensus 115 ~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK 176 (245)
T KOG0850|consen 115 PNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSK 176 (245)
T ss_pred cCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHH
Confidence 45667888999999999999999999999999999999999999999999999999996543
No 4
>KOG0487|consensus
Probab=99.69 E-value=7.6e-18 Score=143.79 Aligned_cols=61 Identities=39% Similarity=0.597 Sum_probs=57.2
Q ss_pred CCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccC
Q psy16796 75 NGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEG 135 (166)
Q Consensus 75 ~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~ 135 (166)
.+..|++|+.||..|+.+||+.|-.|.|++...|.+|++.|+||++||||||||+|+|++.
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK 292 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKK 292 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhh
Confidence 3567888999999999999999999999999999999999999999999999999988764
No 5
>KOG0843|consensus
Probab=99.69 E-value=8.5e-18 Score=133.40 Aligned_cols=65 Identities=34% Similarity=0.517 Sum_probs=61.2
Q ss_pred CCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCCchhh
Q psy16796 76 GLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGEDEEE 140 (166)
Q Consensus 76 ~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~~~~ 140 (166)
.+++|.||.||..||..||.+|..++|....+|..||..|+|++.||||||||+|.|.+...++.
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 37889999999999999999999999999999999999999999999999999999988777764
No 6
>KOG0488|consensus
Probab=99.65 E-value=4.6e-17 Score=139.67 Aligned_cols=65 Identities=38% Similarity=0.507 Sum_probs=58.3
Q ss_pred hcCCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc--ccccccCCc
Q psy16796 73 KKNGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV--AKEEEEGED 137 (166)
Q Consensus 73 ~~~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN--~k~ke~~~~ 137 (166)
..++|+|+.||.||..||..||+.|++..|++...|..||..||||..|||+|||| +|||+.-.+
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 34478889999999999999999999999999999999999999999999999999 566665433
No 7
>KOG0484|consensus
Probab=99.65 E-value=2.5e-17 Score=120.67 Aligned_cols=59 Identities=34% Similarity=0.423 Sum_probs=55.2
Q ss_pred cCCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccc
Q psy16796 74 KNGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEE 132 (166)
Q Consensus 74 ~~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~k 132 (166)
..++.||-||.||..||.+||+.|...|||+++.|++||..+.|++.+|||||||+|.|
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAK 71 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAK 71 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHH
Confidence 34678899999999999999999999999999999999999999999999999997744
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=99.63 E-value=3.4e-16 Score=103.89 Aligned_cols=52 Identities=17% Similarity=0.100 Sum_probs=50.7
Q ss_pred CCcccCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHcCCCCCCccccccccc
Q psy16796 79 RRLRTAYTNTQLLELEKEFHFNKY----LCRPRRIEIAASLDLTERQSDCKYYVAK 130 (166)
Q Consensus 79 rr~Rt~fT~~Ql~~Le~~F~~~~y----p~~~~R~~LA~~LgLse~qVkVWFQN~k 130 (166)
+|.||.||..|+..|+..|+.++| |+...|.+||..|||++++|+|||||.|
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 788999999999999999999999 9999999999999999999999999976
No 9
>KOG0492|consensus
Probab=99.62 E-value=1.8e-16 Score=128.48 Aligned_cols=64 Identities=33% Similarity=0.474 Sum_probs=58.1
Q ss_pred hcCCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCC
Q psy16796 73 KKNGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGE 136 (166)
Q Consensus 73 ~~~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~ 136 (166)
.+.+..|++||.||..||..||+.|...+|+++.+|.+++..|.||++||||||||+|.|.+.-
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 3456678899999999999999999999999999999999999999999999999999665543
No 10
>KOG0485|consensus
Probab=99.54 E-value=2e-15 Score=123.26 Aligned_cols=58 Identities=31% Similarity=0.484 Sum_probs=53.8
Q ss_pred CCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc--ccccc
Q psy16796 76 GLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV--AKEEE 133 (166)
Q Consensus 76 ~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN--~k~ke 133 (166)
.++++.||+|+..|+..||..|+..+|++..+|..||.+|.|+++|||||||| +|||.
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKR 161 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKR 161 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHH
Confidence 46788999999999999999999999999999999999999999999999999 45554
No 11
>KOG0848|consensus
Probab=99.51 E-value=3e-15 Score=125.20 Aligned_cols=59 Identities=39% Similarity=0.580 Sum_probs=53.7
Q ss_pred CCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccccc
Q psy16796 76 GLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEE 134 (166)
Q Consensus 76 ~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~ 134 (166)
+.+-+-|.+||.+|+.+||+.|..++|+++..+.+||..|||++|||||||||+|.||-
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKER 255 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKER 255 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHH
Confidence 34445689999999999999999999999999999999999999999999999887653
No 12
>KOG2251|consensus
Probab=99.51 E-value=1.1e-14 Score=118.85 Aligned_cols=60 Identities=28% Similarity=0.272 Sum_probs=56.5
Q ss_pred hcCCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccc
Q psy16796 73 KKNGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEE 132 (166)
Q Consensus 73 ~~~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~k 132 (166)
..+++.||.||.||..|+.+||..|...+||+...|++||.+|+|.+.+|+|||.|+|.|
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK 91 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAK 91 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccch
Confidence 456788999999999999999999999999999999999999999999999999998743
No 13
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.48 E-value=8.8e-15 Score=95.19 Aligned_cols=54 Identities=37% Similarity=0.470 Sum_probs=51.3
Q ss_pred CCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccc
Q psy16796 79 RRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEE 132 (166)
Q Consensus 79 rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~k 132 (166)
|+.|+.||..|+..|+..|..++||+...+..||..|||+..+|++||+|+|.+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHH
Confidence 578999999999999999999999999999999999999999999999997754
No 14
>KOG0493|consensus
Probab=99.45 E-value=3.2e-14 Score=118.94 Aligned_cols=55 Identities=38% Similarity=0.530 Sum_probs=52.0
Q ss_pred CCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccc
Q psy16796 78 PRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEE 132 (166)
Q Consensus 78 ~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~k 132 (166)
-+|+||.||..||..|...|..|+|++...|..||..|+|.+.||||||||.|.|
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAK 300 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAK 300 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhh
Confidence 3689999999999999999999999999999999999999999999999997654
No 15
>KOG0494|consensus
Probab=99.45 E-value=4e-14 Score=118.22 Aligned_cols=58 Identities=29% Similarity=0.278 Sum_probs=52.1
Q ss_pred CCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccc--ccccc
Q psy16796 77 LPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVA--KEEEE 134 (166)
Q Consensus 77 k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~--k~ke~ 134 (166)
++|+.||.||..|+..||..|...+||+.+.|+-||..+.|++.+|+|||||+ ||++.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~ 199 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKT 199 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhh
Confidence 44455999999999999999999999999999999999999999999999994 45543
No 16
>KOG0491|consensus
Probab=99.38 E-value=2.7e-14 Score=112.28 Aligned_cols=59 Identities=32% Similarity=0.501 Sum_probs=55.5
Q ss_pred CCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccC
Q psy16796 77 LPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEG 135 (166)
Q Consensus 77 k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~ 135 (166)
++++.||+|+..|+..|+..|+..+|++.++|.+||..|+|++.|||.||||+|+|++.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999988764
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.36 E-value=3.8e-13 Score=86.65 Aligned_cols=54 Identities=44% Similarity=0.543 Sum_probs=50.5
Q ss_pred CcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccc
Q psy16796 80 RLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEE 133 (166)
Q Consensus 80 r~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke 133 (166)
+.|+.|+..|+..|+..|..++||+...+..||..+||+..+|++||+|+|.+.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 567889999999999999999999999999999999999999999999987543
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.34 E-value=6.6e-13 Score=104.05 Aligned_cols=64 Identities=23% Similarity=0.389 Sum_probs=56.8
Q ss_pred CCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCCchh
Q psy16796 76 GLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGEDEE 139 (166)
Q Consensus 76 ~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~~~ 139 (166)
+..++.|++.|..|+..|++.|..++||+...|..|+..|+|+++-|||||||+|.++++.-+.
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 4567778889999999999999999999999999999999999999999999977666555444
No 19
>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=99.28 E-value=1.6e-12 Score=84.22 Aligned_cols=54 Identities=44% Similarity=0.519 Sum_probs=50.4
Q ss_pred CcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccc
Q psy16796 80 RLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEE 133 (166)
Q Consensus 80 r~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke 133 (166)
+.|+.|+..++..|+..|..++||+...+..||..+||+..+|++||+|+|.+.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKL 55 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 467899999999999999999999999999999999999999999999977554
No 20
>KOG0844|consensus
Probab=99.26 E-value=1.3e-12 Score=111.32 Aligned_cols=60 Identities=38% Similarity=0.577 Sum_probs=56.2
Q ss_pred CCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCC
Q psy16796 77 LPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGE 136 (166)
Q Consensus 77 k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~ 136 (166)
.-||-||.||..|+..||+.|-+-.|.+++.|-+||..|+|++..|||||||+|+|.+..
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 357889999999999999999999999999999999999999999999999999987653
No 21
>KOG0486|consensus
Probab=99.26 E-value=2.2e-12 Score=110.05 Aligned_cols=80 Identities=30% Similarity=0.278 Sum_probs=64.2
Q ss_pred CCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCCchhhhhhchHHHHHHhhh
Q psy16796 75 NGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGEDEEEEEEGEEEAKEQEQK 154 (166)
Q Consensus 75 ~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~~~~~~~~~~~a~~~~~~ 154 (166)
-.|+||-||+||.+||.+||..|.+|+||+...|++||..++|++.+|+|||.|+|.|--..|--++ ++.||-+=+-
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~---ae~~k~~f~~ 185 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ---AELAKGGFGP 185 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH---HHhhhcCCcc
Confidence 3478999999999999999999999999999999999999999999999999996655444433333 2355555444
Q ss_pred hhc
Q psy16796 155 QVG 157 (166)
Q Consensus 155 ~~~ 157 (166)
+++
T Consensus 186 ~~~ 188 (351)
T KOG0486|consen 186 QFL 188 (351)
T ss_pred ccc
Confidence 443
No 22
>KOG4577|consensus
Probab=99.22 E-value=5.9e-12 Score=106.70 Aligned_cols=58 Identities=21% Similarity=0.253 Sum_probs=55.0
Q ss_pred CCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccC
Q psy16796 78 PRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEG 135 (166)
Q Consensus 78 ~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~ 135 (166)
.+|+||.+|..||..|..+|...+.|.+..|+.|+..+||.-+.|||||||+|.||+.
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKR 224 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKR 224 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHh
Confidence 4889999999999999999999999999999999999999999999999998887764
No 23
>KOG0483|consensus
Probab=99.17 E-value=2.3e-11 Score=98.66 Aligned_cols=64 Identities=25% Similarity=0.236 Sum_probs=56.1
Q ss_pred CcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc--ccccccCCchhhhhh
Q psy16796 80 RLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV--AKEEEEGEDEEEEEE 143 (166)
Q Consensus 80 r~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN--~k~ke~~~~~~~~~~ 143 (166)
+...+||..|+..||..|+...|+.+..+..||..|||.++||.||||| +|||-+.-|-+..-+
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~L 117 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESL 117 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHH
Confidence 3445699999999999999999999999999999999999999999999 667777666666555
No 24
>KOG0490|consensus
Probab=99.14 E-value=2e-11 Score=98.51 Aligned_cols=60 Identities=23% Similarity=0.190 Sum_probs=54.9
Q ss_pred CCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccccc
Q psy16796 75 NGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEE 134 (166)
Q Consensus 75 ~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~ 134 (166)
..+.|+.||.|+..|+.+|++.|...|||+...|..||..+++++..|+|||||++.+.-
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r 116 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDR 116 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhh
Confidence 456789999999999999999999999999999999999999999999999999665443
No 25
>KOG3802|consensus
Probab=99.01 E-value=3.2e-10 Score=99.49 Aligned_cols=62 Identities=23% Similarity=0.161 Sum_probs=57.6
Q ss_pred CCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCCch
Q psy16796 77 LPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGEDE 138 (166)
Q Consensus 77 k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~~ 138 (166)
++|++||.+.......||.+|..|..|+..+...||..|+|....|+|||+|+|-|++.-..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 67888999999999999999999999999999999999999999999999998888776443
No 26
>KOG0847|consensus
Probab=99.01 E-value=9.1e-11 Score=96.31 Aligned_cols=56 Identities=30% Similarity=0.532 Sum_probs=52.0
Q ss_pred CCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccc
Q psy16796 75 NGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAK 130 (166)
Q Consensus 75 ~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k 130 (166)
.++++..|..|+..|+..|+..|+...|+-..+|.+||..+|+++.||+|||||+|
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRR 219 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRR 219 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcch
Confidence 45667778899999999999999999999999999999999999999999999954
No 27
>KOG0849|consensus
Probab=98.82 E-value=1.8e-09 Score=94.41 Aligned_cols=57 Identities=25% Similarity=0.229 Sum_probs=53.0
Q ss_pred cCCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccc
Q psy16796 74 KNGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAK 130 (166)
Q Consensus 74 ~~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k 130 (166)
..++.+|.||.|+..|+..|+..|..++||+...|+.||..++|++.+|+|||+|++
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrr 228 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRR 228 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhh
Confidence 345667889999999999999999999999999999999999999999999999955
No 28
>KOG1168|consensus
Probab=98.30 E-value=2.4e-07 Score=79.00 Aligned_cols=57 Identities=21% Similarity=0.243 Sum_probs=52.1
Q ss_pred CCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccc
Q psy16796 76 GLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEE 132 (166)
Q Consensus 76 ~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~k 132 (166)
.-++|+||.+..-.-+.||++|..++-|+......+|.+|.|-.-.|+|||+|||.|
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK 363 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 363 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence 346788999999999999999999999999999999999999999999999998844
No 29
>KOG2252|consensus
Probab=98.07 E-value=2.6e-06 Score=77.68 Aligned_cols=65 Identities=18% Similarity=0.178 Sum_probs=55.7
Q ss_pred CCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc--ccccccCCchhh
Q psy16796 76 GLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV--AKEEEEGEDEEE 140 (166)
Q Consensus 76 ~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN--~k~ke~~~~~~~ 140 (166)
-..+++|++||..|...|..+|..+.+|+......|+.+|+|....|..||-| +|...++-+++.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~~~~~dd~ 484 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLDKKVDDDS 484 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhccccccccCc
Confidence 34677899999999999999999999999999999999999999999999999 443444444443
No 30
>KOG0490|consensus
Probab=98.00 E-value=3.4e-06 Score=67.92 Aligned_cols=61 Identities=28% Similarity=0.296 Sum_probs=55.8
Q ss_pred cCCCCCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccccc
Q psy16796 74 KNGLPRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEE 134 (166)
Q Consensus 74 ~~~k~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~ 134 (166)
...+.++.|+.|+..|+..|...|..+++|+...+..|+..+|++.+.|+|||||.+.+..
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~ 209 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLR 209 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHH
Confidence 4467788999999999999999999999999999999999999999999999999776553
No 31
>KOG0775|consensus
Probab=97.94 E-value=7.3e-06 Score=69.38 Aligned_cols=53 Identities=19% Similarity=0.148 Sum_probs=44.9
Q ss_pred CcccCCCHH---------HHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccc
Q psy16796 80 RLRTAYTNT---------QLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEE 132 (166)
Q Consensus 80 r~Rt~fT~~---------Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~k 132 (166)
-+||..... -+..|..-|..++||++.++.+||..+||+..||-.||.|+|.+
T Consensus 169 lPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR 230 (304)
T KOG0775|consen 169 LPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQR 230 (304)
T ss_pred CCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence 357765544 45688888999999999999999999999999999999996644
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=97.73 E-value=3.6e-06 Score=51.78 Aligned_cols=32 Identities=22% Similarity=0.321 Sum_probs=27.0
Q ss_pred hcCCCCHHHHHHHHHHcCCCCCCccccccccc
Q psy16796 99 FNKYLCRPRRIEIAASLDLTERQSDCKYYVAK 130 (166)
Q Consensus 99 ~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k 130 (166)
.++||+..++..||..+||+..||..||-|+|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaR 38 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINAR 38 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhH
Confidence 47899999999999999999999999999965
No 33
>KOG0774|consensus
Probab=97.31 E-value=0.00022 Score=60.42 Aligned_cols=53 Identities=21% Similarity=0.230 Sum_probs=48.2
Q ss_pred CCCcccCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHcCCCCCCccccccccc
Q psy16796 78 PRRLRTAYTNTQLLELEKEFH---FNKYLCRPRRIEIAASLDLTERQSDCKYYVAK 130 (166)
Q Consensus 78 ~rr~Rt~fT~~Ql~~Le~~F~---~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k 130 (166)
.||+|..|+..-...|...|. .|+||+...+++||.+.+++..||-.||.|.+
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkr 243 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKR 243 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccce
Confidence 366788999999999999997 57899999999999999999999999999944
No 34
>KOG1146|consensus
Probab=97.15 E-value=0.00022 Score=70.81 Aligned_cols=55 Identities=15% Similarity=0.146 Sum_probs=51.1
Q ss_pred CCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccccccc
Q psy16796 78 PRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEE 132 (166)
Q Consensus 78 ~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~k 132 (166)
+|+.|+.++..||..|...|....||.....+.|...++|..+.|+|||||.+.+
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~ 957 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAK 957 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhh
Confidence 5678999999999999999999999999999999999999999999999996643
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=94.97 E-value=0.0071 Score=39.87 Aligned_cols=40 Identities=15% Similarity=0.056 Sum_probs=30.2
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccc
Q psy16796 90 LLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVA 129 (166)
Q Consensus 90 l~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~ 129 (166)
+..|+.+|...+++.-.....|+...+|+..||+.||--+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~ 49 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAER 49 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHh
Confidence 4579999999999999999999999999999999999763
No 36
>KOG0773|consensus
Probab=94.02 E-value=0.059 Score=46.52 Aligned_cols=64 Identities=16% Similarity=0.096 Sum_probs=48.1
Q ss_pred CCcccCCCHHHHHHHHHH-hh--hcCCCCHHHHHHHHHHcCCCCCCcccccccccccccCCchhhhh
Q psy16796 79 RRLRTAYTNTQLLELEKE-FH--FNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEGEDEEEEE 142 (166)
Q Consensus 79 rr~Rt~fT~~Ql~~Le~~-F~--~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~~~~~~ 142 (166)
.|++..|.......|..- |+ ..+||+......||..+||+..||-.||-|+|.+.--+.-+.+=
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~ 306 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEEMY 306 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHHHH
Confidence 344456767766666643 22 24699999999999999999999999999988777766655443
No 37
>KOG3623|consensus
Probab=93.89 E-value=0.029 Score=53.59 Aligned_cols=46 Identities=15% Similarity=0.070 Sum_probs=41.8
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccccccccC
Q psy16796 90 LLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVAKEEEEG 135 (166)
Q Consensus 90 l~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~ 135 (166)
+..|.+.|..|.+|+..+...+|...||+.+.|++||++.+.++-.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~s 613 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMS 613 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhh
Confidence 7789999999999999999999999999999999999997665543
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=87.62 E-value=0.67 Score=29.68 Aligned_cols=45 Identities=18% Similarity=0.214 Sum_probs=34.7
Q ss_pred CCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc
Q psy16796 79 RRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV 128 (166)
Q Consensus 79 rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN 128 (166)
++.|..+|-.+-..+-..++... ....||..+|++..+|.-|..|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHC
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHh
Confidence 46788899999888888887776 5778999999999999999988
No 39
>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=61.78 E-value=11 Score=24.25 Aligned_cols=38 Identities=18% Similarity=0.222 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCCCCCc
Q psy16796 85 YTNTQLLELEKEFHFNKY--LCRPRRIEIAASLDLTERQS 122 (166)
Q Consensus 85 fT~~Ql~~Le~~F~~~~y--p~~~~R~~LA~~LgLse~qV 122 (166)
+|..|+..|..++...-| |-...-..||..||++..-|
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 578899999999998776 66667788999999987643
No 40
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=41.60 E-value=6.8 Score=25.78 Aligned_cols=45 Identities=13% Similarity=0.031 Sum_probs=29.0
Q ss_pred cccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccccccc
Q psy16796 81 LRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYVA 129 (166)
Q Consensus 81 ~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN~ 129 (166)
.|..||..+-..+-..+. ........+|..+||++..|..|-.--
T Consensus 3 ~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHHHH
Confidence 466788888777665552 223466789999999999999997653
No 41
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=40.80 E-value=29 Score=27.82 Aligned_cols=38 Identities=18% Similarity=0.267 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCCCCC
Q psy16796 84 AYTNTQLLELEKEFHFNKY--LCRPRRIEIAASLDLTERQ 121 (166)
Q Consensus 84 ~fT~~Ql~~Le~~F~~~~y--p~~~~R~~LA~~LgLse~q 121 (166)
.+|..|+..|..+|...-| |-...-..||..||++..-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 7999999999999998875 7677777899999998764
No 42
>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=37.68 E-value=4.8 Score=27.79 Aligned_cols=35 Identities=20% Similarity=0.070 Sum_probs=27.9
Q ss_pred HHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc
Q psy16796 94 EKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV 128 (166)
Q Consensus 94 e~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN 128 (166)
+..|...+|.......++|..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 44566666656667789999999999999999875
No 43
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=30.32 E-value=11 Score=22.83 Aligned_cols=31 Identities=23% Similarity=0.036 Sum_probs=17.6
Q ss_pred HHHHHHHHHHcCCCCCCcccccccccccccCCc
Q psy16796 105 RPRRIEIAASLDLTERQSDCKYYVAKEEEEGED 137 (166)
Q Consensus 105 ~~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~ 137 (166)
......+|..||++...|.-|... +++.|.+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr--~~~~G~~ 47 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKR--YREEGLE 47 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT----------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH--ccccccc
Confidence 345678899999999999999875 4455554
No 44
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.25 E-value=16 Score=21.76 Aligned_cols=22 Identities=9% Similarity=-0.070 Sum_probs=18.6
Q ss_pred HHHHHHcCCCCCCccccccccc
Q psy16796 109 IEIAASLDLTERQSDCKYYVAK 130 (166)
Q Consensus 109 ~~LA~~LgLse~qVkVWFQN~k 130 (166)
.++|..+|+++..|+.|.++-.
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCCC
Confidence 4689999999999999987743
No 45
>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=27.03 E-value=79 Score=15.93 Aligned_cols=36 Identities=19% Similarity=0.077 Sum_probs=23.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCcccc
Q psy16796 85 YTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCK 125 (166)
Q Consensus 85 fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVW 125 (166)
++......+...|... + ....+|..+|++...|..|
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHh
Confidence 4555566565555432 2 3457788999888777666
No 46
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=26.59 E-value=9.9 Score=24.82 Aligned_cols=32 Identities=19% Similarity=-0.162 Sum_probs=27.0
Q ss_pred HHHHHHHHHcCCCCCCcccccccccccccCCc
Q psy16796 106 PRRIEIAASLDLTERQSDCKYYVAKEEEEGED 137 (166)
Q Consensus 106 ~~R~~LA~~LgLse~qVkVWFQN~k~ke~~~~ 137 (166)
..-.++|..||++...|..|-+--+|.+..+.
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~ 45 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKDRYKWDELLPI 45 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHHhhCccccCch
Confidence 34567999999999999999998888877665
No 47
>KOG1146|consensus
Probab=25.43 E-value=20 Score=36.98 Aligned_cols=51 Identities=16% Similarity=0.026 Sum_probs=43.2
Q ss_pred CCCcccCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc
Q psy16796 78 PRRLRTAYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV 128 (166)
Q Consensus 78 ~rr~Rt~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN 128 (166)
.+-.|++++..|...|...|....||.-..+..++..|++..+.+-.||++
T Consensus 444 ~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~ 494 (1406)
T KOG1146|consen 444 PLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQS 494 (1406)
T ss_pred hhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccch
Confidence 455688899999999999999999999999999999999999994444444
No 48
>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=24.75 E-value=20 Score=23.83 Aligned_cols=27 Identities=22% Similarity=0.112 Sum_probs=22.6
Q ss_pred HHHHHHHHcCCCCCCcccccccccccc
Q psy16796 107 RRIEIAASLDLTERQSDCKYYVAKEEE 133 (166)
Q Consensus 107 ~R~~LA~~LgLse~qVkVWFQN~k~ke 133 (166)
.-..||..||+++.+|..|=..-+|.+
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~~dkW~~ 50 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKSRDKWDE 50 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhhhcchhh
Confidence 455789999999999999987767765
No 49
>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=24.52 E-value=7.9 Score=23.92 Aligned_cols=29 Identities=24% Similarity=0.260 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHHHcCCCCCCcccccccc
Q psy16796 101 KYLCRPRRIEIAASLDLTERQSDCKYYVA 129 (166)
Q Consensus 101 ~yp~~~~R~~LA~~LgLse~qVkVWFQN~ 129 (166)
.|.....-.++|..+|++...|+.|....
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34455577899999999999999998763
No 50
>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=22.29 E-value=62 Score=21.41 Aligned_cols=37 Identities=19% Similarity=0.036 Sum_probs=21.5
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc
Q psy16796 90 LLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV 128 (166)
Q Consensus 90 l~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN 128 (166)
|..++.+...+.. -...|. .|+.+|++..+|+-|-+-
T Consensus 12 L~Vv~~a~~~~nc-~~~~RA-aarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 12 LKVVEYAEKDNNC-KGNQRA-AARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp HHHHHHHHH-TTT-TT-HHH-HHHHTTS-HHHHHHHHTT
T ss_pred HHHHHHHHHccch-hhhHHH-HHHHhCccHHHHHHHHHH
Confidence 4445444443332 122333 499999999999999764
No 51
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=21.98 E-value=48 Score=20.06 Aligned_cols=40 Identities=10% Similarity=-0.027 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccccccc
Q psy16796 84 AYTNTQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDCKYYV 128 (166)
Q Consensus 84 ~fT~~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkVWFQN 128 (166)
.+++.+...|...|.. ...-.++|..+|++...|+.+...
T Consensus 4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHHH
Confidence 3567777888777732 235678999999999988876554
No 52
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=21.74 E-value=55 Score=20.90 Aligned_cols=33 Identities=33% Similarity=0.422 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCCCCCccc
Q psy16796 88 TQLLELEKEFHFNKYLCRPRRIEIAASLDLTERQSDC 124 (166)
Q Consensus 88 ~Ql~~Le~~F~~~~yp~~~~R~~LA~~LgLse~qVkV 124 (166)
.|+..|+-.+. +...+.. .||..||++.+.|+.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 46677777777 6666554 899999999987764
No 53
>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=21.25 E-value=85 Score=18.68 Aligned_cols=17 Identities=29% Similarity=0.399 Sum_probs=13.3
Q ss_pred cCCCHHHHHHHHHHhhh
Q psy16796 83 TAYTNTQLLELEKEFHF 99 (166)
Q Consensus 83 t~fT~~Ql~~Le~~F~~ 99 (166)
..||..|+..|++-...
T Consensus 1 s~FT~~Ql~~L~~Qi~a 17 (37)
T PF08880_consen 1 SPFTPAQLQELRAQILA 17 (37)
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 36999999999876443
No 54
>PF13518 HTH_28: Helix-turn-helix domain
Probab=20.69 E-value=36 Score=20.40 Aligned_cols=22 Identities=14% Similarity=-0.038 Sum_probs=19.0
Q ss_pred HHHHHHHHcCCCCCCccccccc
Q psy16796 107 RRIEIAASLDLTERQSDCKYYV 128 (166)
Q Consensus 107 ~R~~LA~~LgLse~qVkVWFQN 128 (166)
....+|..+|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3456899999999999999976
No 55
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.54 E-value=26 Score=22.49 Aligned_cols=20 Identities=15% Similarity=-0.001 Sum_probs=17.0
Q ss_pred HHHHHHcCCCCCCccccccc
Q psy16796 109 IEIAASLDLTERQSDCKYYV 128 (166)
Q Consensus 109 ~~LA~~LgLse~qVkVWFQN 128 (166)
.++|..+|++...|+.|=..
T Consensus 4 ~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46899999999999999654
Done!