Query psy18046
Match_columns 141
No_of_seqs 178 out of 1246
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 21:05:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18046.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18046hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0842|consensus 99.5 8.9E-14 1.9E-18 111.7 9.7 52 90-141 148-199 (307)
2 KOG0489|consensus 99.5 5.8E-15 1.3E-19 116.9 2.6 50 92-141 156-205 (261)
3 KOG0488|consensus 99.5 3.4E-14 7.4E-19 114.9 4.8 55 87-141 164-218 (309)
4 KOG0850|consensus 99.4 1.2E-13 2.6E-18 106.3 3.9 54 88-141 115-168 (245)
5 KOG0484|consensus 99.4 1.2E-13 2.5E-18 94.8 0.5 50 92-141 14-63 (125)
6 KOG0487|consensus 99.4 2.3E-12 5.1E-17 103.6 8.0 54 88-141 228-281 (308)
7 TIGR01565 homeo_ZF_HD homeobox 99.3 2.7E-12 5.9E-17 79.9 4.6 47 95-141 1-51 (58)
8 KOG2251|consensus 99.3 3.1E-12 6.8E-17 98.0 5.0 52 90-141 32-83 (228)
9 KOG0843|consensus 99.3 3.8E-12 8.1E-17 94.9 3.8 49 93-141 100-148 (197)
10 KOG0485|consensus 99.3 8.2E-12 1.8E-16 95.7 5.3 50 92-141 101-150 (268)
11 KOG0486|consensus 99.2 3.1E-11 6.7E-16 96.7 7.5 49 93-141 110-158 (351)
12 KOG0848|consensus 99.2 2.4E-11 5.1E-16 95.6 6.0 55 87-141 191-245 (317)
13 KOG0492|consensus 99.2 2.1E-11 4.5E-16 92.9 4.0 52 90-141 139-190 (246)
14 KOG0494|consensus 99.1 6.6E-11 1.4E-15 92.9 5.9 50 92-141 138-187 (332)
15 KOG0493|consensus 99.1 1.8E-10 4E-15 90.5 8.1 46 96-141 247-292 (342)
16 KOG0844|consensus 99.1 1.2E-10 2.5E-15 93.3 4.0 49 93-141 179-227 (408)
17 PF00046 Homeobox: Homeobox do 98.9 1.1E-09 2.3E-14 67.2 2.3 45 96-140 1-45 (57)
18 KOG0491|consensus 98.7 1.2E-09 2.6E-14 80.7 -0.7 48 94-141 99-146 (194)
19 smart00389 HOX Homeodomain. DN 98.7 1.8E-08 3.9E-13 61.2 3.5 45 96-140 1-45 (56)
20 cd00086 homeodomain Homeodomai 98.6 6.4E-08 1.4E-12 59.1 3.4 44 97-140 2-45 (59)
21 KOG0490|consensus 98.5 6.7E-08 1.5E-12 74.0 3.0 50 92-141 57-106 (235)
22 KOG0849|consensus 98.5 1.5E-07 3.2E-12 77.7 4.4 55 87-141 168-222 (354)
23 COG5576 Homeodomain-containing 97.9 2.2E-05 4.7E-10 58.0 5.1 47 95-141 51-97 (156)
24 KOG0847|consensus 97.9 5.5E-06 1.2E-10 64.1 1.5 50 92-141 164-213 (288)
25 KOG0483|consensus 97.7 2.3E-05 4.9E-10 60.0 3.0 41 101-141 56-96 (198)
26 KOG4577|consensus 97.7 2.9E-05 6.4E-10 62.3 3.5 47 95-141 167-213 (383)
27 KOG3802|consensus 97.7 5.5E-05 1.2E-09 62.9 4.5 49 93-141 292-340 (398)
28 KOG2252|consensus 97.0 0.00067 1.5E-08 58.5 3.9 46 94-139 419-464 (558)
29 KOG0490|consensus 95.9 0.0092 2E-07 45.5 3.7 51 91-141 149-199 (235)
30 KOG1168|consensus 94.7 0.019 4.1E-07 46.4 1.9 49 93-141 307-355 (385)
31 PF05920 Homeobox_KN: Homeobox 93.9 0.019 4.2E-07 32.8 0.3 25 116-140 7-31 (40)
32 KOG0774|consensus 93.4 0.084 1.8E-06 42.2 3.2 44 96-139 189-235 (334)
33 KOG0775|consensus 93.0 0.14 2.9E-06 41.2 3.8 42 98-139 170-220 (304)
34 PF04218 CENP-B_N: CENP-B N-te 85.8 1.6 3.5E-05 26.1 3.7 40 96-140 1-40 (53)
35 KOG1146|consensus 81.4 3.8 8.2E-05 39.5 5.8 48 94-141 902-949 (1406)
36 PF04967 HTH_10: HTH DNA bindi 73.9 2.9 6.3E-05 25.3 2.0 37 102-138 1-39 (53)
37 COG3413 Predicted DNA binding 53.5 15 0.00033 27.9 3.0 37 101-137 155-193 (215)
38 PF08880 QLQ: QLQ; InterPro: 51.8 13 0.00028 20.8 1.8 15 101-115 2-16 (37)
39 PF11569 Homez: Homeodomain le 47.7 8.7 0.00019 23.6 0.7 34 107-140 10-43 (56)
40 PF08280 HTH_Mga: M protein tr 44.6 12 0.00026 22.6 0.9 32 105-140 6-37 (59)
41 COG4367 Uncharacterized protei 38.5 22 0.00048 23.9 1.6 37 102-138 3-39 (97)
42 PF13936 HTH_38: Helix-turn-he 37.7 18 0.00038 20.6 0.9 35 100-139 3-37 (44)
43 PTZ00183 centrin; Provisional 37.6 1.1E+02 0.0023 21.1 5.2 42 93-134 2-48 (158)
44 KOG0773|consensus 35.6 53 0.0012 26.7 3.8 46 95-140 239-287 (342)
45 PF04545 Sigma70_r4: Sigma-70, 33.2 29 0.00063 19.8 1.4 34 102-140 5-38 (50)
46 PF12824 MRP-L20: Mitochondria 28.1 91 0.002 23.1 3.6 40 98-139 82-121 (164)
47 PRK15183 Vi polysaccharide bio 23.1 84 0.0018 22.0 2.4 38 100-137 94-131 (143)
48 PF01527 HTH_Tnp_1: Transposas 23.0 64 0.0014 19.7 1.7 37 97-138 2-39 (76)
49 PF02796 HTH_7: Helix-turn-hel 22.9 51 0.0011 18.6 1.1 33 102-139 6-38 (45)
No 1
>KOG0842|consensus
Probab=99.51 E-value=8.9e-14 Score=111.73 Aligned_cols=52 Identities=37% Similarity=0.532 Sum_probs=49.1
Q ss_pred CCCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 90 NKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 90 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
...+++||.|..||..|..|||++|..++|++.++|++||..|+||++||||
T Consensus 148 t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKI 199 (307)
T KOG0842|consen 148 TGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKI 199 (307)
T ss_pred cccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheee
Confidence 3466788899999999999999999999999999999999999999999998
No 2
>KOG0489|consensus
Probab=99.51 E-value=5.8e-15 Score=116.94 Aligned_cols=50 Identities=36% Similarity=0.569 Sum_probs=47.9
Q ss_pred CCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 92 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 92 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
..+.||.||+||..|++|||++|+.++|+++.+|.|||..|+|+|+||||
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKI 205 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKI 205 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHH
Confidence 45688999999999999999999999999999999999999999999998
No 3
>KOG0488|consensus
Probab=99.48 E-value=3.4e-14 Score=114.89 Aligned_cols=55 Identities=40% Similarity=0.617 Sum_probs=50.7
Q ss_pred CCCCCCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 87 GSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 87 ~~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.....++|+|+.||+||..||.+||++|++++|++...|.+||+.|||+.+||||
T Consensus 164 ~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKt 218 (309)
T KOG0488|consen 164 YQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKT 218 (309)
T ss_pred cccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHH
Confidence 3344568899999999999999999999999999999999999999999999996
No 4
>KOG0850|consensus
Probab=99.42 E-value=1.2e-13 Score=106.31 Aligned_cols=54 Identities=35% Similarity=0.630 Sum_probs=51.3
Q ss_pred CCCCCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 88 SANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 88 ~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
-+++++|.|+.||.|+..||..|.++|+++.|+..++|.+||+.|||+.+||||
T Consensus 115 ~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKI 168 (245)
T KOG0850|consen 115 PNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKI 168 (245)
T ss_pred cCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhh
Confidence 346688999999999999999999999999999999999999999999999998
No 5
>KOG0484|consensus
Probab=99.36 E-value=1.2e-13 Score=94.76 Aligned_cols=50 Identities=60% Similarity=0.946 Sum_probs=48.2
Q ss_pred CCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 92 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 92 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
++|+||.||+||..||.+||+.|...|||++..|++||.++.|+|.+|||
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQV 63 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQV 63 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHH
Confidence 57889999999999999999999999999999999999999999999986
No 6
>KOG0487|consensus
Probab=99.36 E-value=2.3e-12 Score=103.61 Aligned_cols=54 Identities=30% Similarity=0.412 Sum_probs=49.9
Q ss_pred CCCCCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 88 SANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 88 ~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.+...+..||+|..||..|+.|||++|..|.|+++..|.||++.|+|+|+||||
T Consensus 228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKI 281 (308)
T KOG0487|consen 228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKI 281 (308)
T ss_pred ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheee
Confidence 334457788999999999999999999999999999999999999999999998
No 7
>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=99.31 E-value=2.7e-12 Score=79.86 Aligned_cols=47 Identities=15% Similarity=0.225 Sum_probs=45.3
Q ss_pred CCCCCCccCHHHHHHHHHhhhcCCC----CCHHHHHHHHHHcCCCCCcccC
Q psy18046 95 IRRSRTTFTTYQLHQLERAFDKTQY----PDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 95 ~rr~Rt~ft~~Ql~~Le~~F~~~~y----~~~~~r~~LA~~l~L~e~qVKV 141 (141)
+||.||.||.+|+..||..|+.++| |+..+|.+||..|||++.+|||
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKV 51 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKV 51 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeee
Confidence 3789999999999999999999999 9999999999999999999997
No 8
>KOG2251|consensus
Probab=99.29 E-value=3.1e-12 Score=98.01 Aligned_cols=52 Identities=63% Similarity=0.900 Sum_probs=50.2
Q ss_pred CCCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 90 NKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 90 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
..++|.||.||.||..|+.+||+.|.+..||++..|++||.+|+|+|.+|||
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV 83 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence 5678999999999999999999999999999999999999999999999997
No 9
>KOG0843|consensus
Probab=99.26 E-value=3.8e-12 Score=94.95 Aligned_cols=49 Identities=43% Similarity=0.541 Sum_probs=47.4
Q ss_pred CCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 93 RKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 93 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.+.||.||+||.+||..||..|+.++|+...+|++||+.|+|++.||||
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkv 148 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKV 148 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhh
Confidence 3788999999999999999999999999999999999999999999998
No 10
>KOG0485|consensus
Probab=99.25 E-value=8.2e-12 Score=95.69 Aligned_cols=50 Identities=32% Similarity=0.539 Sum_probs=47.3
Q ss_pred CCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 92 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 92 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
..++||.||+|+..|+..||..|+.++|++..+|..||++|.|+|+||||
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKI 150 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKI 150 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhh
Confidence 34567899999999999999999999999999999999999999999997
No 11
>KOG0486|consensus
Probab=99.22 E-value=3.1e-11 Score=96.71 Aligned_cols=49 Identities=49% Similarity=0.774 Sum_probs=47.1
Q ss_pred CCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 93 RKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 93 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
+|+||.||.||..|++|||..|++++||+...|+|||..++|+|.+|+|
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrv 158 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRV 158 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhh
Confidence 4789999999999999999999999999999999999999999999976
No 12
>KOG0848|consensus
Probab=99.21 E-value=2.4e-11 Score=95.61 Aligned_cols=55 Identities=31% Similarity=0.489 Sum_probs=49.9
Q ss_pred CCCCCCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 87 GSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 87 ~~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
+...+-|-+-|.|.+||..|.+|||++|+..+|+++.++.|||..|+|+|+||||
T Consensus 191 g~~~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKI 245 (317)
T KOG0848|consen 191 GQNVKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKI 245 (317)
T ss_pred CCCceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhH
Confidence 3444556667899999999999999999999999999999999999999999998
No 13
>KOG0492|consensus
Probab=99.17 E-value=2.1e-11 Score=92.90 Aligned_cols=52 Identities=40% Similarity=0.624 Sum_probs=48.5
Q ss_pred CCCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 90 NKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 90 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.+.+..|+.||.||..||..||+.|..+.|+++.+|.+++..|.|||+||||
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKI 190 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKI 190 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheeh
Confidence 4455568899999999999999999999999999999999999999999998
No 14
>KOG0494|consensus
Probab=99.15 E-value=6.6e-11 Score=92.86 Aligned_cols=50 Identities=50% Similarity=0.844 Sum_probs=45.6
Q ss_pred CCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 92 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 92 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.+|+|+.||.||..|+.+||+.|+..+||+...|+-||.++.|+|.+|+|
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqV 187 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQV 187 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhH
Confidence 33455559999999999999999999999999999999999999999987
No 15
>KOG0493|consensus
Probab=99.14 E-value=1.8e-10 Score=90.47 Aligned_cols=46 Identities=35% Similarity=0.622 Sum_probs=44.7
Q ss_pred CCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 96 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 96 rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
||.||+||.+||..|+++|+.++|++..+|.+||+.|+|.|.||||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKI 292 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKI 292 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhH
Confidence 5789999999999999999999999999999999999999999997
No 16
>KOG0844|consensus
Probab=99.06 E-value=1.2e-10 Score=93.31 Aligned_cols=49 Identities=35% Similarity=0.550 Sum_probs=46.9
Q ss_pred CCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 93 RKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 93 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
..-||.||+||.+||-.||++|-+..|.++++|.|||+.|+|+|..|||
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKV 227 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKV 227 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeeh
Confidence 4568999999999999999999999999999999999999999999997
No 17
>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=98.87 E-value=1.1e-09 Score=67.19 Aligned_cols=45 Identities=44% Similarity=0.663 Sum_probs=43.1
Q ss_pred CCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 96 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 96 rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
||.|+.||.+|+..||..|..++||+..++++||..|||+..+|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccc
Confidence 578999999999999999999999999999999999999999886
No 18
>KOG0491|consensus
Probab=98.74 E-value=1.2e-09 Score=80.66 Aligned_cols=48 Identities=38% Similarity=0.608 Sum_probs=45.7
Q ss_pred CCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 94 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 94 k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
++|+.||+|+..|+..||++|+.++|++.++|.|||..|+|++.|||.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKT 146 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKT 146 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHH
Confidence 567889999999999999999999999999999999999999999983
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.69 E-value=1.8e-08 Score=61.22 Aligned_cols=45 Identities=51% Similarity=0.788 Sum_probs=42.3
Q ss_pred CCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 96 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 96 rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
++.|+.|+..|+..|+..|..++||+..++.+||..+||+..+|+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVK 45 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 357888999999999999999999999999999999999999886
No 20
>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=98.56 E-value=6.4e-08 Score=59.10 Aligned_cols=44 Identities=48% Similarity=0.741 Sum_probs=41.9
Q ss_pred CCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 97 RSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 97 r~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
+.|+.|+..|+..||..|..++||+..++..||..+||++.+|+
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 56889999999999999999999999999999999999999986
No 21
>KOG0490|consensus
Probab=98.51 E-value=6.7e-08 Score=74.05 Aligned_cols=50 Identities=44% Similarity=0.454 Sum_probs=47.7
Q ss_pred CCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 92 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 92 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
..++||.||.|+.+|+.+||+.|++.|||+...|+.||..++++|..|||
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 56788999999999999999999999999999999999999999999986
No 22
>KOG0849|consensus
Probab=98.48 E-value=1.5e-07 Score=77.71 Aligned_cols=55 Identities=44% Similarity=0.622 Sum_probs=49.8
Q ss_pred CCCCCCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 87 GSANKPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 87 ~~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
......++.||.||.|+..|+..||+.|++++||++..|++||.+++|++..|+|
T Consensus 168 p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqv 222 (354)
T KOG0849|consen 168 PGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQV 222 (354)
T ss_pred ccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHH
Confidence 3445567788899999999999999999999999999999999999999988875
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=97.90 E-value=2.2e-05 Score=58.03 Aligned_cols=47 Identities=34% Similarity=0.449 Sum_probs=41.9
Q ss_pred CCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 95 IRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 95 ~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.++.|+.-|.+|+.-|++.|..++||+...|.+|+..|+++++-|||
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqI 97 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQI 97 (156)
T ss_pred CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhh
Confidence 33445555999999999999999999999999999999999999987
No 24
>KOG0847|consensus
Probab=97.87 E-value=5.5e-06 Score=64.09 Aligned_cols=50 Identities=38% Similarity=0.561 Sum_probs=46.5
Q ss_pred CCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 92 PRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 92 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
..+++-.|.+|+..||+.||+.|+..+|+-.++|.+||..+|+++.||||
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkV 213 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKV 213 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHH
Confidence 35566789999999999999999999999999999999999999999987
No 25
>KOG0483|consensus
Probab=97.74 E-value=2.3e-05 Score=60.01 Aligned_cols=41 Identities=24% Similarity=0.358 Sum_probs=39.2
Q ss_pred ccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 101 TFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 101 ~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.||.+|+..||+.|+...|+...++..||..|||.++||+|
T Consensus 56 Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVav 96 (198)
T KOG0483|consen 56 RLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAV 96 (198)
T ss_pred cccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHH
Confidence 37999999999999999999999999999999999999986
No 26
>KOG4577|consensus
Probab=97.72 E-value=2.9e-05 Score=62.26 Aligned_cols=47 Identities=36% Similarity=0.473 Sum_probs=45.1
Q ss_pred CCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 95 IRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 95 ~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.+|+||++|..||+.|+.+++..+.|.++.|++|+..+||-.+.|||
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQV 213 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQV 213 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhh
Confidence 57899999999999999999999999999999999999999999987
No 27
>KOG3802|consensus
Probab=97.67 E-value=5.5e-05 Score=62.88 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=46.5
Q ss_pred CCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 93 RKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 93 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.|+||+||.|.......||+.|.+|..|+..+...||.+|+|-..+|+|
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRV 340 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRV 340 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEE
Confidence 3678899999999999999999999999999999999999999999886
No 28
>KOG2252|consensus
Probab=97.03 E-value=0.00067 Score=58.51 Aligned_cols=46 Identities=24% Similarity=0.418 Sum_probs=42.5
Q ss_pred CCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcc
Q psy18046 94 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 139 (141)
Q Consensus 94 k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qV 139 (141)
+.+|.|.+||..|...|.+.|+.++||+....+.|+.+|+|....|
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV 464 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTV 464 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHH
Confidence 4577899999999999999999999999999999999999987655
No 29
>KOG0490|consensus
Probab=95.92 E-value=0.0092 Score=45.49 Aligned_cols=51 Identities=47% Similarity=0.560 Sum_probs=46.8
Q ss_pred CCCCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 91 KPRKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 91 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
...+.++.|+.|+..|+..++..|....||....+..|+..+++++..|+|
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~ 199 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQV 199 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhh
Confidence 345678899999999999999999999999999999999999999988775
No 30
>KOG1168|consensus
Probab=94.70 E-value=0.019 Score=46.43 Aligned_cols=49 Identities=24% Similarity=0.306 Sum_probs=44.2
Q ss_pred CCCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 93 RKIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 93 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
..+||+||.+-.-....||+.|..++.|+......||.+|.|..-.|+|
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRV 355 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRV 355 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEE
Confidence 3467789999999999999999999999999999999999999988875
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=93.89 E-value=0.019 Score=32.84 Aligned_cols=25 Identities=28% Similarity=0.506 Sum_probs=19.8
Q ss_pred cCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 116 KTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 116 ~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
.++||+..++.+||..+||+..||.
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 32
>KOG0774|consensus
Probab=93.37 E-value=0.084 Score=42.20 Aligned_cols=44 Identities=27% Similarity=0.477 Sum_probs=39.6
Q ss_pred CCCCCccCHHHHHHHHHhhh---cCCCCCHHHHHHHHHHcCCCCCcc
Q psy18046 96 RRSRTTFTTYQLHQLERAFD---KTQYPDVFTREDLASRLDLSEARV 139 (141)
Q Consensus 96 rr~Rt~ft~~Ql~~Le~~F~---~~~y~~~~~r~~LA~~l~L~e~qV 139 (141)
||+|..|+..-...|...|. .++||+-.++++||.+-+++-.||
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQv 235 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQV 235 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhh
Confidence 67788999999999999986 478999999999999999998876
No 33
>KOG0775|consensus
Probab=93.00 E-value=0.14 Score=41.20 Aligned_cols=42 Identities=21% Similarity=0.305 Sum_probs=36.1
Q ss_pred CCCccCHHH---------HHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcc
Q psy18046 98 SRTTFTTYQ---------LHQLERAFDKTQYPDVFTREDLASRLDLSEARV 139 (141)
Q Consensus 98 ~Rt~ft~~Q---------l~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qV 139 (141)
+||.+..+| ...|...|..++||+..++.+||.++||+..||
T Consensus 170 PrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 170 PRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred CCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhh
Confidence 588765555 457888899999999999999999999999987
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=85.76 E-value=1.6 Score=26.14 Aligned_cols=40 Identities=18% Similarity=0.402 Sum_probs=29.2
Q ss_pred CCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 96 RRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 96 rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
||.|..+|-++-.++=..++... ...+||..+|++..+|.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~ 40 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVS 40 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHH
Confidence 46789999999998888888776 57789999999998763
No 35
>KOG1146|consensus
Probab=81.35 E-value=3.8 Score=39.49 Aligned_cols=48 Identities=21% Similarity=0.279 Sum_probs=44.2
Q ss_pred CCCCCCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcccC
Q psy18046 94 KIRRSRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQF 141 (141)
Q Consensus 94 k~rr~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVKV 141 (141)
.+|+.||.|+..||..+...|....|+...+-+.|-..++++.+.|+|
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 467889999999999999999999999999999999999999998875
No 36
>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=73.91 E-value=2.9 Score=25.27 Aligned_cols=37 Identities=30% Similarity=0.432 Sum_probs=28.4
Q ss_pred cCHHHHHHHHHhhhcCCC--CCHHHHHHHHHHcCCCCCc
Q psy18046 102 FTTYQLHQLERAFDKTQY--PDVFTREDLASRLDLSEAR 138 (141)
Q Consensus 102 ft~~Ql~~Le~~F~~~~y--~~~~~r~~LA~~l~L~e~q 138 (141)
+|..|...|...+...-| |-...-.+||..||++...
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 478899999999987766 3333457899999998743
No 37
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=53.49 E-value=15 Score=27.87 Aligned_cols=37 Identities=30% Similarity=0.436 Sum_probs=29.3
Q ss_pred ccCHHHHHHHHHhhhcCCC--CCHHHHHHHHHHcCCCCC
Q psy18046 101 TFTTYQLHQLERAFDKTQY--PDVFTREDLASRLDLSEA 137 (141)
Q Consensus 101 ~ft~~Ql~~Le~~F~~~~y--~~~~~r~~LA~~l~L~e~ 137 (141)
.+|..|+..|..+|...-| |-...-.+||..||++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISks 193 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKS 193 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHH
Confidence 7999999999999997754 333334689999999864
No 38
>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=51.84 E-value=13 Score=20.76 Aligned_cols=15 Identities=33% Similarity=0.394 Sum_probs=12.6
Q ss_pred ccCHHHHHHHHHhhh
Q psy18046 101 TFTTYQLHQLERAFD 115 (141)
Q Consensus 101 ~ft~~Ql~~Le~~F~ 115 (141)
.||..|+.+|+.-..
T Consensus 2 ~FT~~Ql~~L~~Qi~ 16 (37)
T PF08880_consen 2 PFTPAQLQELRAQIL 16 (37)
T ss_pred CCCHHHHHHHHHHHH
Confidence 699999999997644
No 39
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=47.73 E-value=8.7 Score=23.57 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=23.8
Q ss_pred HHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 107 LHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 107 l~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
+.-|++.|...+++.-..-..|..+.+|+..||+
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 4569999999999988888899999999998886
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=44.62 E-value=12 Score=22.63 Aligned_cols=32 Identities=28% Similarity=0.450 Sum_probs=22.3
Q ss_pred HHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 105 YQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 105 ~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
.|+.-|+-.+. +.+.+.. +||..++++++.|+
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 45666777777 6666554 88999999987764
No 41
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.53 E-value=22 Score=23.94 Aligned_cols=37 Identities=14% Similarity=0.218 Sum_probs=28.5
Q ss_pred cCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCc
Q psy18046 102 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEAR 138 (141)
Q Consensus 102 ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~q 138 (141)
+.++|+..-..+|+.+.-++.-.-+++|..|+.++-.
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 4667777777777777777777788999999998743
No 42
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=37.67 E-value=18 Score=20.57 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=15.1
Q ss_pred CccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcc
Q psy18046 100 TTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 139 (141)
Q Consensus 100 t~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qV 139 (141)
..+|..|...++...... ....+||..||.+...|
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 346777888888765543 35567999999887544
No 43
>PTZ00183 centrin; Provisional
Probab=37.61 E-value=1.1e+02 Score=21.06 Aligned_cols=42 Identities=26% Similarity=0.235 Sum_probs=31.1
Q ss_pred CCCCCCCCccCHHHHHHHHHhhhc-----CCCCCHHHHHHHHHHcCC
Q psy18046 93 RKIRRSRTTFTTYQLHQLERAFDK-----TQYPDVFTREDLASRLDL 134 (141)
Q Consensus 93 ~k~rr~Rt~ft~~Ql~~Le~~F~~-----~~y~~~~~r~~LA~~l~L 134 (141)
+|++..+..|+..|+.+++..|.. +.+++..+-..+...+++
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 2 RKRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred CccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 456667899999999999999864 456777766665666554
No 44
>KOG0773|consensus
Probab=35.62 E-value=53 Score=26.66 Aligned_cols=46 Identities=22% Similarity=0.234 Sum_probs=35.7
Q ss_pred CCCCCCccCHHHHHHHHHh-hh--cCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 95 IRRSRTTFTTYQLHQLERA-FD--KTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 95 ~rr~Rt~ft~~Ql~~Le~~-F~--~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
..|.+..+.......|+.. |+ ..+||+-.....||..+||+..||.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~ 287 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVS 287 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCC
Confidence 4455567778888878766 33 2479999999999999999999874
No 45
>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=33.22 E-value=29 Score=19.77 Aligned_cols=34 Identities=21% Similarity=0.334 Sum_probs=23.0
Q ss_pred cCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCccc
Q psy18046 102 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARVQ 140 (141)
Q Consensus 102 ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qVK 140 (141)
++..+...|...|... ..-.++|..+|++...|+
T Consensus 5 L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~ 38 (50)
T PF04545_consen 5 LPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVR 38 (50)
T ss_dssp S-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHH
T ss_pred CCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHH
Confidence 4666777777777333 245689999999987664
No 46
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=28.06 E-value=91 Score=23.13 Aligned_cols=40 Identities=23% Similarity=0.395 Sum_probs=31.6
Q ss_pred CCCccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcc
Q psy18046 98 SRTTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 139 (141)
Q Consensus 98 ~Rt~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qV 139 (141)
....+|.+++.++.+.-..+ |....|..||.++||+..-|
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 34679999999998766544 56678999999999987544
No 47
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=23.06 E-value=84 Score=22.01 Aligned_cols=38 Identities=16% Similarity=0.215 Sum_probs=28.8
Q ss_pred CccCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCC
Q psy18046 100 TTFTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEA 137 (141)
Q Consensus 100 t~ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~ 137 (141)
--++..-.++|..+|-...---..-|++||.++|+.+.
T Consensus 94 yflsesgmeelqdrfmns~st~yrwrke~a~kfgvr~p 131 (143)
T PRK15183 94 YFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREP 131 (143)
T ss_pred hhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCC
Confidence 34567777889988876665555678899999998774
No 48
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=23.03 E-value=64 Score=19.72 Aligned_cols=37 Identities=16% Similarity=0.236 Sum_probs=20.3
Q ss_pred CCCCccCHHHHHHHHHhh-hcCCCCCHHHHHHHHHHcCCCCCc
Q psy18046 97 RSRTTFTTYQLHQLERAF-DKTQYPDVFTREDLASRLDLSEAR 138 (141)
Q Consensus 97 r~Rt~ft~~Ql~~Le~~F-~~~~y~~~~~r~~LA~~l~L~e~q 138 (141)
+.|..||.++...+=... ... ....++|..+|++..+
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 456788998887765554 222 3556788888887644
No 49
>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=22.88 E-value=51 Score=18.57 Aligned_cols=33 Identities=12% Similarity=0.381 Sum_probs=20.4
Q ss_pred cCHHHHHHHHHhhhcCCCCCHHHHHHHHHHcCCCCCcc
Q psy18046 102 FTTYQLHQLERAFDKTQYPDVFTREDLASRLDLSEARV 139 (141)
Q Consensus 102 ft~~Ql~~Le~~F~~~~y~~~~~r~~LA~~l~L~e~qV 139 (141)
++.+|+.++...+... ....++|..+|++...|
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 4665666666666555 25668899999987544
Done!