Query psy9181
Match_columns 262
No_of_seqs 230 out of 1777
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 21:01:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9181.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9181hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0842|consensus 99.8 2E-19 4.3E-24 165.9 9.4 76 146-221 147-222 (307)
2 KOG0489|consensus 99.8 9.3E-20 2E-24 165.9 3.4 69 149-222 156-224 (261)
3 KOG0484|consensus 99.8 7.3E-20 1.6E-24 143.8 1.9 60 148-207 13-72 (125)
4 KOG0487|consensus 99.8 2.2E-19 4.8E-24 165.7 4.9 64 148-211 231-294 (308)
5 KOG0488|consensus 99.7 2.2E-18 4.7E-23 160.3 7.9 66 147-212 167-232 (309)
6 KOG0843|consensus 99.7 1.2E-18 2.7E-23 148.7 5.1 64 151-214 101-164 (197)
7 KOG0850|consensus 99.7 5.7E-18 1.2E-22 149.5 8.8 70 139-208 109-178 (245)
8 KOG0848|consensus 99.7 4.6E-18 9.9E-23 152.9 7.1 68 148-215 195-262 (317)
9 KOG0485|consensus 99.7 9.5E-18 2.1E-22 147.1 6.9 67 148-219 100-166 (268)
10 KOG0492|consensus 99.7 5.4E-18 1.2E-22 147.7 4.6 77 148-224 140-216 (246)
11 KOG2251|consensus 99.6 2E-16 4.3E-21 139.1 6.5 66 147-212 32-97 (228)
12 KOG0494|consensus 99.6 1.5E-16 3.2E-21 142.7 4.9 66 148-218 136-202 (332)
13 KOG0844|consensus 99.6 3.3E-16 7.1E-21 143.2 4.0 64 148-211 177-240 (408)
14 PF00046 Homeobox: Homeobox do 99.6 1.7E-16 3.6E-21 111.7 1.5 55 153-207 1-55 (57)
15 KOG4577|consensus 99.6 2.2E-16 4.9E-21 143.4 2.7 99 104-212 129-227 (383)
16 KOG0493|consensus 99.6 1.7E-15 3.7E-20 136.0 6.9 57 153-209 247-303 (342)
17 TIGR01565 homeo_ZF_HD homeobox 99.6 4.7E-15 1E-19 106.0 5.6 53 152-204 1-57 (58)
18 KOG0491|consensus 99.5 6E-16 1.3E-20 130.7 -0.7 58 150-207 98-155 (194)
19 KOG0486|consensus 99.5 2.4E-14 5.2E-19 131.4 5.7 72 149-225 109-180 (351)
20 smart00389 HOX Homeodomain. DN 99.5 1.9E-14 4.2E-19 100.3 3.2 55 153-207 1-55 (56)
21 KOG0483|consensus 99.5 2.2E-14 4.9E-19 125.6 3.5 60 156-215 54-113 (198)
22 COG5576 Homeodomain-containing 99.5 3.5E-14 7.6E-19 120.3 3.9 63 149-211 48-110 (156)
23 cd00086 homeodomain Homeodomai 99.4 4.1E-14 8.9E-19 99.2 2.6 54 154-207 2-55 (59)
24 KOG3802|consensus 99.4 2E-13 4.3E-18 129.1 4.8 136 76-212 204-354 (398)
25 KOG0847|consensus 99.3 4.1E-12 8.9E-17 112.0 7.6 68 148-220 163-230 (288)
26 KOG0490|consensus 99.3 9.7E-13 2.1E-17 115.6 3.6 64 149-217 57-120 (235)
27 KOG1168|consensus 99.2 7E-12 1.5E-16 114.4 3.4 151 62-212 201-369 (385)
28 KOG0849|consensus 99.1 5.9E-11 1.3E-15 112.6 6.4 69 144-217 168-236 (354)
29 KOG0775|consensus 98.4 3.7E-07 7.9E-12 83.2 4.7 59 150-208 165-232 (304)
30 KOG0490|consensus 98.2 8E-07 1.7E-11 78.0 2.8 63 146-208 147-209 (235)
31 KOG0774|consensus 98.1 3E-06 6.4E-11 77.0 4.6 60 152-211 188-250 (334)
32 PF05920 Homeobox_KN: Homeobox 98.0 8.4E-07 1.8E-11 58.9 -1.4 32 173-204 7-38 (40)
33 KOG2252|consensus 98.0 7.3E-06 1.6E-10 80.9 4.4 59 148-206 416-474 (558)
34 KOG1146|consensus 97.2 0.0003 6.5E-09 75.6 4.0 63 150-212 901-963 (1406)
35 KOG0773|consensus 95.1 0.023 4.9E-07 53.5 3.9 56 152-207 239-297 (342)
36 PF11569 Homez: Homeodomain le 94.9 0.0087 1.9E-07 42.6 0.4 41 164-204 10-50 (56)
37 KOG3623|consensus 94.1 0.029 6.3E-07 57.8 2.3 44 164-207 568-611 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 90.3 0.26 5.6E-06 34.3 2.5 46 153-203 1-46 (53)
39 PF04967 HTH_10: HTH DNA bindi 62.8 8.5 0.00018 26.9 2.7 38 159-196 1-40 (53)
40 KOG1146|consensus 45.6 22 0.00048 39.6 3.8 54 152-205 444-497 (1406)
41 COG3413 Predicted DNA binding 40.0 26 0.00055 30.7 2.7 39 158-196 155-195 (215)
42 PF01527 HTH_Tnp_1: Transposas 37.0 26 0.00056 25.0 1.9 42 154-200 2-44 (76)
43 PF11632 LcnG-beta: Lactococci 33.4 12 0.00025 23.8 -0.4 9 16-24 1-9 (35)
44 PF10668 Phage_terminase: Phag 33.3 13 0.00028 26.8 -0.2 19 182-200 25-43 (60)
45 KOG3623|consensus 32.9 36 0.00078 36.0 2.8 58 150-207 624-681 (1007)
46 cd00569 HTH_Hin_like Helix-tur 31.2 59 0.0013 18.1 2.6 36 159-199 6-41 (42)
47 KOG3755|consensus 29.0 8.3 0.00018 39.6 -2.4 60 152-211 691-758 (769)
48 PF08280 HTH_Mga: M protein tr 28.3 39 0.00083 23.6 1.6 34 161-198 5-38 (59)
49 PRK03975 tfx putative transcri 27.2 42 0.00091 28.1 1.8 42 157-204 5-46 (141)
50 PF09607 BrkDBD: Brinker DNA-b 26.8 48 0.001 23.8 1.8 45 156-201 3-47 (58)
51 cd06171 Sigma70_r4 Sigma70, re 26.7 27 0.00058 22.1 0.5 41 158-203 10-50 (55)
52 COG4367 Uncharacterized protei 26.2 50 0.0011 25.8 1.9 39 158-196 2-40 (97)
53 PF04545 Sigma70_r4: Sigma-70, 22.5 55 0.0012 21.6 1.4 38 158-200 4-41 (50)
54 PF13936 HTH_38: Helix-turn-he 20.2 54 0.0012 21.5 0.9 36 157-197 3-38 (44)
No 1
>KOG0842|consensus
Probab=99.79 E-value=2e-19 Score=165.89 Aligned_cols=76 Identities=22% Similarity=0.245 Sum_probs=65.5
Q ss_pred ccCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhcCCCC
Q psy9181 146 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYKNPQF 221 (262)
Q Consensus 146 ~~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k~~~~ 221 (262)
....+++||.|..||..|+.+||+.|..++|++..||++||..|.||++||||||||||.|.||+...+.......
T Consensus 147 ~t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~ 222 (307)
T KOG0842|consen 147 QTGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLL 222 (307)
T ss_pred ccccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccC
Confidence 3446678888999999999999999999999999999999999999999999999999999766665555444333
No 2
>KOG0489|consensus
Probab=99.77 E-value=9.3e-20 Score=165.87 Aligned_cols=69 Identities=30% Similarity=0.345 Sum_probs=62.4
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhcCCCCC
Q psy9181 149 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYKNPQFQ 222 (262)
Q Consensus 149 ~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k~~~~~ 222 (262)
..+.||.||.||..|+.+||++|..|+|+++..|.|||..|+|+|+|||||||||| +||||+.+.....
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRR-----MK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRR-----MKWKKENKAKSSQ 224 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHH-----HHHHHhhcccccc
Confidence 34578999999999999999999999999999999999999999999999999999 7777777765544
No 3
>KOG0484|consensus
Probab=99.77 E-value=7.3e-20 Score=143.82 Aligned_cols=60 Identities=53% Similarity=0.694 Sum_probs=56.5
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccc
Q psy9181 148 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRR 207 (262)
Q Consensus 148 ~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~ 207 (262)
..+|.||.||.||..||.+||+.|...+||++..|++||.++.|++..|||||||||+|.
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKf 72 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKF 72 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHH
Confidence 356789999999999999999999999999999999999999999999999999999554
No 4
>KOG0487|consensus
Probab=99.77 E-value=2.2e-19 Score=165.68 Aligned_cols=64 Identities=23% Similarity=0.262 Sum_probs=59.2
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhh
Q psy9181 148 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLAL 211 (262)
Q Consensus 148 ~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~K 211 (262)
..++.|+||..||+.|+.+||++|-.|.|++.+.|.+|++.|+|++|||||||||||+|+||..
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 3467788999999999999999999999999999999999999999999999999999985444
No 5
>KOG0488|consensus
Probab=99.75 E-value=2.2e-18 Score=160.27 Aligned_cols=66 Identities=32% Similarity=0.351 Sum_probs=59.0
Q ss_pred cCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhH
Q psy9181 147 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALW 212 (262)
Q Consensus 147 ~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kw 212 (262)
...+|+|+.||.||..||.+||+.|++++|++..+|++||+.|||+..|||+||||||+|.||.+-
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 344788889999999999999999999999999999999999999999999999999955544443
No 6
>KOG0843|consensus
Probab=99.74 E-value=1.2e-18 Score=148.75 Aligned_cols=64 Identities=31% Similarity=0.383 Sum_probs=60.4
Q ss_pred CCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHH
Q psy9181 151 KPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVA 214 (262)
Q Consensus 151 k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr 214 (262)
+.+|.||.||.+||..||..|+.++|..-.+|++||+.|+|++.||||||||||.|.||.+.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 7889999999999999999999999999999999999999999999999999999987766654
No 7
>KOG0850|consensus
Probab=99.74 E-value=5.7e-18 Score=149.49 Aligned_cols=70 Identities=27% Similarity=0.328 Sum_probs=62.6
Q ss_pred CCCCcccccCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccch
Q psy9181 139 ENDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRP 208 (262)
Q Consensus 139 ~~~~~~~~~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~k 208 (262)
+..+.....+.+|.|++||.|+..||..|.+.|++++|+...+|.+||..|||+.+||||||||||.|.|
T Consensus 109 E~~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~K 178 (245)
T KOG0850|consen 109 EPSERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFK 178 (245)
T ss_pred CcceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHH
Confidence 3344455667788899999999999999999999999999999999999999999999999999997763
No 8
>KOG0848|consensus
Probab=99.73 E-value=4.6e-18 Score=152.87 Aligned_cols=68 Identities=22% Similarity=0.227 Sum_probs=61.4
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHH
Q psy9181 148 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAE 215 (262)
Q Consensus 148 ~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~ 215 (262)
+.+.+-+-|.+||+.|..+||++|..++|..+..+.|||..|+|+||||||||||||+|++|.+.|+.
T Consensus 195 KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 195 KTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred eeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 34455567899999999999999999999999999999999999999999999999999987776664
No 9
>KOG0485|consensus
Probab=99.72 E-value=9.5e-18 Score=147.05 Aligned_cols=67 Identities=25% Similarity=0.385 Sum_probs=61.9
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhcCC
Q psy9181 148 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYKNP 219 (262)
Q Consensus 148 ~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k~~ 219 (262)
...++||.||+|+..|+..||..|+..+|++..+|..||++|.|+|+|||||||||| .||||+....
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRR-----nKwKRq~aad 166 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRR-----NKWKRQYAAD 166 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhh-----HHHHHHHhhh
Confidence 456788899999999999999999999999999999999999999999999999999 8888877643
No 10
>KOG0492|consensus
Probab=99.71 E-value=5.4e-18 Score=147.70 Aligned_cols=77 Identities=22% Similarity=0.227 Sum_probs=69.2
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhcCCCCCCC
Q psy9181 148 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYKNPQFQSE 224 (262)
Q Consensus 148 ~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k~~~~~s~ 224 (262)
+.+..|++||.||..||..||+.|+..+|+++.+|.+++..|.|+++||||||||||+|.||.+-.+.+|..+....
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~kmaa~~ 216 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKLKMAAKS 216 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHhhhhhcc
Confidence 34556788999999999999999999999999999999999999999999999999999988888887877665444
No 11
>KOG2251|consensus
Probab=99.64 E-value=2e-16 Score=139.09 Aligned_cols=66 Identities=44% Similarity=0.564 Sum_probs=60.4
Q ss_pred cCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhH
Q psy9181 147 RRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALW 212 (262)
Q Consensus 147 ~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kw 212 (262)
...+|.||.||.||..|+++||..|.+++||+...|++||.+|+|.+.+|||||.|||+|.|+.++
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 567889999999999999999999999999999999999999999999999999999966544443
No 12
>KOG0494|consensus
Probab=99.64 E-value=1.5e-16 Score=142.71 Aligned_cols=66 Identities=47% Similarity=0.650 Sum_probs=58.3
Q ss_pred CCCCCCCC-CCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhcC
Q psy9181 148 RKPKPRRN-RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYKN 218 (262)
Q Consensus 148 ~~~k~RR~-Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k~ 218 (262)
+++++||. ||.||..|+.+||+.|+..+||+...|+.||.++.|+|.+||||||||| +||||.+|.
T Consensus 136 kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRR-----AKWRk~Ek~ 202 (332)
T KOG0494|consen 136 KKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRR-----AKWRKTEKR 202 (332)
T ss_pred ccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhh-----HHhhhhhhh
Confidence 34444554 9999999999999999999999999999999999999999999999999 667776664
No 13
>KOG0844|consensus
Probab=99.61 E-value=3.3e-16 Score=143.23 Aligned_cols=64 Identities=30% Similarity=0.318 Sum_probs=58.3
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhh
Q psy9181 148 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLAL 211 (262)
Q Consensus 148 ~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~K 211 (262)
....-||.||.||.+|+..||++|.+..|-++..|.|||..|+|+|..|||||||||+|.||++
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 3445689999999999999999999999999999999999999999999999999998875443
No 14
>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=99.61 E-value=1.7e-16 Score=111.69 Aligned_cols=55 Identities=36% Similarity=0.498 Sum_probs=52.6
Q ss_pred CCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccc
Q psy9181 153 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRR 207 (262)
Q Consensus 153 RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~ 207 (262)
||+|+.||.+|+..||..|..++||+..+++.||..+||++.+|++||||||+|.
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 55 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKE 55 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHh
Confidence 5789999999999999999999999999999999999999999999999999664
No 15
>KOG4577|consensus
Probab=99.60 E-value=2.2e-16 Score=143.37 Aligned_cols=99 Identities=21% Similarity=0.199 Sum_probs=80.3
Q ss_pred CCCCCCCCCCCCCccchhccchhhhhhhccccCCCCCCCcccccCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHH
Q psy9181 104 NLSQSQGGRGEDESKLTSKRHFWFAKLQMSIRVKSENDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVRE 183 (262)
Q Consensus 104 ~~~~s~~~~~~des~~~s~~~~~~s~~~~s~~~~s~~~~~~~~~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~ 183 (262)
.+...++..-|+|.+..|+.+|..+..-.-. .-......+|+||.+|..||+.|+..|+..+.|.+..|+
T Consensus 129 ~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~----------~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVRE 198 (383)
T KOG4577|consen 129 QLATGDEFYLMEDARLVCKDDYETAKQKHCN----------ELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVRE 198 (383)
T ss_pred ccccCCeeEEeccceeehhhhHHHHHhcccc----------ccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHH
Confidence 4555677778999999999998533221110 111233467899999999999999999999999999999
Q ss_pred HHHHHcCCCCCcceeccccccccchhhhH
Q psy9181 184 ELAKKVCLSEARVQVSMMILFVRRPLALW 212 (262)
Q Consensus 184 ~LA~~lgLserqVqVWFQNRRaK~kr~Kw 212 (262)
+|+.++||..|.|||||||||||+||.|.
T Consensus 199 QLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 199 QLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred HhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 99999999999999999999999986553
No 16
>KOG0493|consensus
Probab=99.59 E-value=1.7e-15 Score=136.04 Aligned_cols=57 Identities=26% Similarity=0.403 Sum_probs=54.4
Q ss_pred CCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchh
Q psy9181 153 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPL 209 (262)
Q Consensus 153 RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr 209 (262)
+|+||.||.+||+.|+.+|+.|+|+....|.+||.+|+|.|.||||||||+|+|.||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKK 303 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKK 303 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhh
Confidence 689999999999999999999999999999999999999999999999999988643
No 17
>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=99.56 E-value=4.7e-15 Score=105.98 Aligned_cols=53 Identities=17% Similarity=0.199 Sum_probs=51.0
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCCCCcceecccccc
Q psy9181 152 PRRNRTTFNSHQLNALEKVFERTHY----PDAFVREELAKKVCLSEARVQVSMMILF 204 (262)
Q Consensus 152 ~RR~Rt~fT~~Ql~~LE~~F~~~~y----ps~~~R~~LA~~lgLserqVqVWFQNRR 204 (262)
+||.||.||.+|+..||..|+.++| |+..++++||..|||++++|||||||-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3789999999999999999999999 9999999999999999999999999974
No 18
>KOG0491|consensus
Probab=99.54 E-value=6e-16 Score=130.69 Aligned_cols=58 Identities=36% Similarity=0.481 Sum_probs=54.6
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccc
Q psy9181 150 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRR 207 (262)
Q Consensus 150 ~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~ 207 (262)
-++|+.||+|+..|+..||+.|+.++|++..+|.|||..|+|++.|||.||||||+|.
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~ 155 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKH 155 (194)
T ss_pred HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 3457789999999999999999999999999999999999999999999999999776
No 19
>KOG0486|consensus
Probab=99.49 E-value=2.4e-14 Score=131.44 Aligned_cols=72 Identities=42% Similarity=0.534 Sum_probs=65.1
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhcCCCCCCCC
Q psy9181 149 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYKNPQFQSEN 225 (262)
Q Consensus 149 ~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k~~~~~s~~ 225 (262)
-.|+||.||.||.+|+++||..|++++||+...|++||..++|+|..|+|||.||| +||||++++.+....+
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrr-----akwrkrErN~~ae~~k 180 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRR-----AKWRKRERNQQAELAK 180 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccch-----hhhhhhhhhHHHHhhh
Confidence 34889999999999999999999999999999999999999999999999999999 7888888876643333
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=1.9e-14 Score=100.27 Aligned_cols=55 Identities=44% Similarity=0.571 Sum_probs=51.7
Q ss_pred CCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccc
Q psy9181 153 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRR 207 (262)
Q Consensus 153 RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~ 207 (262)
++.|+.|+.+|+..|+..|..++||+..++..||..+||+..+|+.||+|||++.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 3567889999999999999999999999999999999999999999999999664
No 21
>KOG0483|consensus
Probab=99.47 E-value=2.2e-14 Score=125.60 Aligned_cols=60 Identities=23% Similarity=0.217 Sum_probs=53.8
Q ss_pred CCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHH
Q psy9181 156 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAE 215 (262)
Q Consensus 156 Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~ 215 (262)
+.+||.+|+..||..|+.+.++.+.++..||+.|||.+|||.|||||||||.|+++...+
T Consensus 54 k~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d 113 (198)
T KOG0483|consen 54 KRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKD 113 (198)
T ss_pred cccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhh
Confidence 345899999999999999999999999999999999999999999999999875554443
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.46 E-value=3.5e-14 Score=120.31 Aligned_cols=63 Identities=22% Similarity=0.295 Sum_probs=56.0
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhh
Q psy9181 149 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLAL 211 (262)
Q Consensus 149 ~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~K 211 (262)
....+++|++.|.+|+..|++.|+.++||+...|.+|+..++|+++-|||||||||++.|+..
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 344566777789999999999999999999999999999999999999999999998864443
No 23
>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=99.44 E-value=4.1e-14 Score=99.21 Aligned_cols=54 Identities=41% Similarity=0.554 Sum_probs=51.3
Q ss_pred CCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccc
Q psy9181 154 RNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRR 207 (262)
Q Consensus 154 R~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~ 207 (262)
+.|+.|+..|+..||..|..++||+..++..||..+||++.+|++||+|||++.
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 567889999999999999999999999999999999999999999999999664
No 24
>KOG3802|consensus
Probab=99.40 E-value=2e-13 Score=129.10 Aligned_cols=136 Identities=17% Similarity=0.062 Sum_probs=88.1
Q ss_pred CCchhhhhhhhhhccccCCCCCCCCC---CCCCCCCCCCCCCCCc---------cchhccch-hhhhhhcccc--CCCCC
Q psy9181 76 GNTVLEFVFWVWVDFTISAGNSSHLV---WGNLSQSQGGRGEDES---------KLTSKRHF-WFAKLQMSIR--VKSEN 140 (262)
Q Consensus 76 ~~~~~e~~~~p~~d~~~s~g~ss~~~---~g~~~~s~~~~~~des---------~~~s~~~~-~~s~~~~s~~--~~s~~ 140 (262)
....+|.|+..|++++++.|+..... -|.+.+...+. .... +-.||-+- ....++..+. .....
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQ-TTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~ 282 (398)
T KOG3802|consen 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQ-TTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSP 282 (398)
T ss_pred CHHHHHHHHHHHHhheeccccchhHHHHHHHhhhCcccch-hhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCC
Confidence 44567779999999999999865433 22211111111 0000 11111111 1122222111 11122
Q ss_pred CCcccccCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhH
Q psy9181 141 DDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALW 212 (262)
Q Consensus 141 ~~~~~~~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kw 212 (262)
...+.-....|+||+||.|.......||+.|.+|+.|+..+..+||.+|+|...+|+|||+|||.|+||..-
T Consensus 283 ~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 283 NSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred CCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 222222333478899999999999999999999999999999999999999999999999999988866553
No 25
>KOG0847|consensus
Probab=99.31 E-value=4.1e-12 Score=111.99 Aligned_cols=68 Identities=26% Similarity=0.406 Sum_probs=60.1
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhcCCC
Q psy9181 148 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYKNPQ 220 (262)
Q Consensus 148 ~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k~~~ 220 (262)
+..+++-.|..|+..|+..||+.|+..+|+-..+|.+||..+|+++.||+||||||| .||||+....+
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRR-----TKWRKkhAaEm 230 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRR-----TKWRKKHAAEM 230 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcch-----hhhhhhhccch
Confidence 345566678899999999999999999999999999999999999999999999999 77887655433
No 26
>KOG0490|consensus
Probab=99.31 E-value=9.7e-13 Score=115.55 Aligned_cols=64 Identities=36% Similarity=0.288 Sum_probs=59.4
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhc
Q psy9181 149 KPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYK 217 (262)
Q Consensus 149 ~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k 217 (262)
..++||.||.|+..|+++||+.|+..+||+...|+.||..+++++..||||||||| +||+++++
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrr-----ak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRR-----AKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhc-----Hhhhhhhc
Confidence 56788999999999999999999999999999999999999999999999999999 66777664
No 27
>KOG1168|consensus
Probab=99.21 E-value=7e-12 Score=114.39 Aligned_cols=151 Identities=19% Similarity=0.070 Sum_probs=101.4
Q ss_pred hhhhhcccCcCCCCCCchhhhhhhhhhccccCCCCCCCCC-----------CCCCCCCCCCCC----CCCccchhccchh
Q psy9181 62 TGLLLALLVTSDWVGNTVLEFVFWVWVDFTISAGNSSHLV-----------WGNLSQSQGGRG----EDESKLTSKRHFW 126 (262)
Q Consensus 62 ~g~~~~~~~ps~~~~~~~~e~~~~p~~d~~~s~g~ss~~~-----------~g~~~~s~~~~~----~des~~~s~~~~~ 126 (262)
++..++.+.+...++|..+|.|...|.++.+..|...-.. .|.++++.-.+- ..-..+..-....
T Consensus 201 a~~a~~~~~sD~dtDPReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLTLSHNNMiALKPIL 280 (385)
T KOG1168|consen 201 ARYAIAGPTSDMDTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPIL 280 (385)
T ss_pred hccccCCCCcccCCCHHHHHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeeccccCcchhhhHHH
Confidence 4555566777788899999999999999999998644322 333333332221 1111222222222
Q ss_pred hhhhhcccc---CCCCCCCcccccCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccc
Q psy9181 127 FAKLQMSIR---VKSENDDYDYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMIL 203 (262)
Q Consensus 127 ~s~~~~s~~---~~s~~~~~~~~~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNR 203 (262)
.+.++.... .+....+...--....++|+||.+-.-+...||.+|..++.|+.+....||++|+|....|+|||+|.
T Consensus 281 qaWLEeAE~a~keK~~~pd~~~l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQ 360 (385)
T KOG1168|consen 281 QAWLEEAEAAMKEKDTKPDINELLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQ 360 (385)
T ss_pred HHHHHHHHHHHHhhccCCchhhccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeecc
Confidence 333333221 11111111122233456789999999999999999999999999999999999999999999999999
Q ss_pred cccchhhhH
Q psy9181 204 FVRRPLALW 212 (262)
Q Consensus 204 RaK~kr~Kw 212 (262)
|.|.||.|.
T Consensus 361 RQKQKRm~~ 369 (385)
T KOG1168|consen 361 RQKQKRMKR 369 (385)
T ss_pred HHHHHHhhh
Confidence 988766553
No 28
>KOG0849|consensus
Probab=99.14 E-value=5.9e-11 Score=112.61 Aligned_cols=69 Identities=43% Similarity=0.533 Sum_probs=61.5
Q ss_pred ccccCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhHHHHhc
Q psy9181 144 DYERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALWVAEYK 217 (262)
Q Consensus 144 ~~~~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kwrr~~k 217 (262)
......++.||.||.|+..|++.||+.|+.++||+...|++||.++++++..|+|||+||| +||+|+..
T Consensus 168 p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrr-----a~~rr~~~ 236 (354)
T KOG0849|consen 168 PGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRR-----AKWRRQHR 236 (354)
T ss_pred ccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhh-----hhhhhccc
Confidence 3345567788889999999999999999999999999999999999999999999999999 55666663
No 29
>KOG0775|consensus
Probab=98.37 E-value=3.7e-07 Score=83.20 Aligned_cols=59 Identities=20% Similarity=0.189 Sum_probs=50.2
Q ss_pred CCCCCCCCcCCHHH---------HHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccch
Q psy9181 150 PKPRRNRTTFNSHQ---------LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRP 208 (262)
Q Consensus 150 ~k~RR~Rt~fT~~Q---------l~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~k 208 (262)
+|-.-+||....+| ...|...|..++||++.++.+||+.+||+..||-.||.|||.|.|
T Consensus 165 rKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 165 RKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred ccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 33344677766655 458999999999999999999999999999999999999998874
No 30
>KOG0490|consensus
Probab=98.20 E-value=8e-07 Score=77.98 Aligned_cols=63 Identities=43% Similarity=0.479 Sum_probs=57.9
Q ss_pred ccCCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccch
Q psy9181 146 ERRKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRP 208 (262)
Q Consensus 146 ~~~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~k 208 (262)
.....+.++.|+.++..|+..|+..|..+++|+...++.|+..++++++.|+|||||+|++.+
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~ 209 (235)
T KOG0490|consen 147 GPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLR 209 (235)
T ss_pred CCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHH
Confidence 445677888999999999999999999999999999999999999999999999999997753
No 31
>KOG0774|consensus
Probab=98.11 E-value=3e-06 Score=76.96 Aligned_cols=60 Identities=25% Similarity=0.346 Sum_probs=54.8
Q ss_pred CCCCCCcCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhh
Q psy9181 152 PRRNRTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLAL 211 (262)
Q Consensus 152 ~RR~Rt~fT~~Ql~~LE~~F~~---~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~K 211 (262)
.||+|..|+..-.++|...|.. ++||+.+++++||++++++..||-.||.|+|-+.||.-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 4788899999999999999974 88999999999999999999999999999998876543
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=97.96 E-value=8.4e-07 Score=58.85 Aligned_cols=32 Identities=28% Similarity=0.325 Sum_probs=27.7
Q ss_pred hcCCCCHHHHHHHHHHcCCCCCcceecccccc
Q psy9181 173 RTHYPDAFVREELAKKVCLSEARVQVSMMILF 204 (262)
Q Consensus 173 ~~~yps~~~R~~LA~~lgLserqVqVWFQNRR 204 (262)
.++||+..++++||..+||+..||..||-|.|
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 47999999999999999999999999999988
No 33
>KOG2252|consensus
Probab=97.95 E-value=7.3e-06 Score=80.90 Aligned_cols=59 Identities=19% Similarity=0.281 Sum_probs=54.4
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceecccccccc
Q psy9181 148 RKPKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVR 206 (262)
Q Consensus 148 ~~~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK 206 (262)
.....+|+|.+||..|...|...|+.+++|+.+..+.|+.+|+|....|..||-|-|.|
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 34456778999999999999999999999999999999999999999999999998855
No 34
>KOG1146|consensus
Probab=97.19 E-value=0.0003 Score=75.55 Aligned_cols=63 Identities=21% Similarity=0.148 Sum_probs=56.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccchhhhH
Q psy9181 150 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRRPLALW 212 (262)
Q Consensus 150 ~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~kr~Kw 212 (262)
-.+|+.||.++..||..|...|....||...+-+.|...+++..+.|+|||||-|+|.|+.+.
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 345778999999999999999999999999999999999999999999999999988654443
No 35
>KOG0773|consensus
Probab=95.08 E-value=0.023 Score=53.49 Aligned_cols=56 Identities=21% Similarity=0.175 Sum_probs=46.7
Q ss_pred CCCCCCcCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCCCCcceeccccccccc
Q psy9181 152 PRRNRTTFNSHQLNALEKVFER---THYPDAFVREELAKKVCLSEARVQVSMMILFVRR 207 (262)
Q Consensus 152 ~RR~Rt~fT~~Ql~~LE~~F~~---~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~ 207 (262)
..|++..+.......|+..... .+||+..++..||.++||+..||..||-|.|.|.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~ 297 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRL 297 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhccccc
Confidence 4455567888888888866433 5799999999999999999999999999999553
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=94.88 E-value=0.0087 Score=42.56 Aligned_cols=41 Identities=17% Similarity=0.126 Sum_probs=31.2
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceecccccc
Q psy9181 164 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILF 204 (262)
Q Consensus 164 l~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRR 204 (262)
+..|+++|...+++....-..|..+.+|+..||+.||--|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 46699999999999999999999999999999999996654
No 37
>KOG3623|consensus
Probab=94.14 E-value=0.029 Score=57.75 Aligned_cols=44 Identities=16% Similarity=0.061 Sum_probs=41.4
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccc
Q psy9181 164 LNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRR 207 (262)
Q Consensus 164 l~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~ 207 (262)
+..|..+|..|..|+..+-..+|...||+.+.|++||+++++++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 77899999999999999999999999999999999999999664
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=90.34 E-value=0.26 Score=34.29 Aligned_cols=46 Identities=15% Similarity=0.249 Sum_probs=35.6
Q ss_pred CCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccc
Q psy9181 153 RRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMIL 203 (262)
Q Consensus 153 RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNR 203 (262)
||+|..+|-+|-..+=..++... ...+||+.+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 57888999999888888888777 46789999999999999999886
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=62.83 E-value=8.5 Score=26.94 Aligned_cols=38 Identities=26% Similarity=0.433 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCCCcc
Q psy9181 159 FNSHQLNALEKVFERTHY--PDAFVREELAKKVCLSEARV 196 (262)
Q Consensus 159 fT~~Ql~~LE~~F~~~~y--ps~~~R~~LA~~lgLserqV 196 (262)
+|+.|...|...++...| |-...-.+||..+|++..-+
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 588999999999998876 54556689999999998654
No 40
>KOG1146|consensus
Probab=45.64 E-value=22 Score=39.60 Aligned_cols=54 Identities=13% Similarity=0.087 Sum_probs=48.4
Q ss_pred CCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccc
Q psy9181 152 PRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFV 205 (262)
Q Consensus 152 ~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRa 205 (262)
.+-.|++++.-|...|...|+...||.-.++..++..|++..|.+..|||++++
T Consensus 444 ~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c 497 (1406)
T KOG1146|consen 444 PLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYC 497 (1406)
T ss_pred hhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHh
Confidence 344678899999999999999999999999999999999999999999999663
No 41
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=39.99 E-value=26 Score=30.72 Aligned_cols=39 Identities=21% Similarity=0.404 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCCCcc
Q psy9181 158 TFNSHQLNALEKVFERTHY--PDAFVREELAKKVCLSEARV 196 (262)
Q Consensus 158 ~fT~~Ql~~LE~~F~~~~y--ps~~~R~~LA~~lgLserqV 196 (262)
.+|+.|+..|...|+...| |-...-.+||+++|++...+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 6999999999999998875 65566689999999998653
No 42
>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=37.00 E-value=26 Score=24.97 Aligned_cols=42 Identities=14% Similarity=0.113 Sum_probs=25.3
Q ss_pred CCCCcCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHcCCCCCcceecc
Q psy9181 154 RNRTTFNSHQLNALEKVF-ERTHYPDAFVREELAKKVCLSEARVQVSM 200 (262)
Q Consensus 154 R~Rt~fT~~Ql~~LE~~F-~~~~yps~~~R~~LA~~lgLserqVqVWF 200 (262)
++|..||+++...+=..+ ... ....++|+.+|+++.++..|-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHH
Confidence 456779998877765555 322 355689999999998876554
No 43
>PF11632 LcnG-beta: Lactococcin G-beta; InterPro: IPR021089 This entry represents Lactococcin-G subunit beta with subunit alpha constitutes the two-peptide bacteriocin lactococcin G. This family of proteins represents the N-terminal domain which has an alpha-helical structure and is amphiphilic. Both peptides have a GxxxG motif which they use for interaction through a helix-helix structure []. It is thought to kill Lactococci [].; PDB: 2JPK_A 2JPM_A.
Probab=33.36 E-value=12 Score=23.77 Aligned_cols=9 Identities=33% Similarity=1.494 Sum_probs=6.1
Q ss_pred chhhhHHHH
Q psy9181 16 GRWGWAAWL 24 (262)
Q Consensus 16 ~~~~~~~~~ 24 (262)
+.|+|.+|+
T Consensus 1 ~~~~wl~w~ 9 (35)
T PF11632_consen 1 KPWKWLPWV 9 (35)
T ss_dssp --HHHHCCC
T ss_pred CCccccccc
Confidence 468899986
No 44
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=33.30 E-value=13 Score=26.77 Aligned_cols=19 Identities=21% Similarity=0.314 Sum_probs=16.6
Q ss_pred HHHHHHHcCCCCCcceecc
Q psy9181 182 REELAKKVCLSEARVQVSM 200 (262)
Q Consensus 182 R~~LA~~lgLserqVqVWF 200 (262)
-.+||.+||+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 3579999999999999884
No 45
>KOG3623|consensus
Probab=32.93 E-value=36 Score=36.02 Aligned_cols=58 Identities=14% Similarity=0.100 Sum_probs=42.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccccccc
Q psy9181 150 PKPRRNRTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILFVRR 207 (262)
Q Consensus 150 ~k~RR~Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRRaK~ 207 (262)
..+-+.|+....++-..|...++.+--+...+-..++.++...+..|+|||++|+...
T Consensus 624 ~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstp 681 (1007)
T KOG3623|consen 624 ERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTP 681 (1007)
T ss_pred CCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCC
Confidence 3344556777777778888888877766655555556667888899999999998654
No 46
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=31.23 E-value=59 Score=18.06 Aligned_cols=36 Identities=11% Similarity=0.248 Sum_probs=23.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceec
Q psy9181 159 FNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVS 199 (262)
Q Consensus 159 fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVW 199 (262)
++..+...+...+.... ...++|..++++...|..|
T Consensus 6 ~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 6 LTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHh
Confidence 56666666666665332 3457888999887766555
No 47
>KOG3755|consensus
Probab=28.98 E-value=8.3 Score=39.58 Aligned_cols=60 Identities=13% Similarity=0.017 Sum_probs=0.0
Q ss_pred CCCCCCcCCHHHHHHHHHH-HhhcCCCCHHHHHHHHHHcCCCC-------Ccceeccccccccchhhh
Q psy9181 152 PRRNRTTFNSHQLNALEKV-FERTHYPDAFVREELAKKVCLSE-------ARVQVSMMILFVRRPLAL 211 (262)
Q Consensus 152 ~RR~Rt~fT~~Ql~~LE~~-F~~~~yps~~~R~~LA~~lgLse-------rqVqVWFQNRRaK~kr~K 211 (262)
.|+++..|-.+|..++... |-+++.++...-.+--..+.+.+ .-|+.||.|||.++||.|
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 48
>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=28.30 E-value=39 Score=23.55 Aligned_cols=34 Identities=32% Similarity=0.415 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCccee
Q psy9181 161 SHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQV 198 (262)
Q Consensus 161 ~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqV 198 (262)
..|+..|+-.+. +...+.. +||..++++++.|+-
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 357888888888 6666655 799999999988764
No 49
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=27.24 E-value=42 Score=28.12 Aligned_cols=42 Identities=21% Similarity=0.188 Sum_probs=32.7
Q ss_pred CcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceecccccc
Q psy9181 157 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMILF 204 (262)
Q Consensus 157 t~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNRR 204 (262)
..+|+.|...|... ... ....++|..+|++...|+.|-++.+
T Consensus 5 ~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 5 SFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred cCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56889999999773 222 2456899999999999999998655
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=26.78 E-value=48 Score=23.77 Aligned_cols=45 Identities=16% Similarity=0.108 Sum_probs=22.0
Q ss_pred CCcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccc
Q psy9181 156 RTTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMM 201 (262)
Q Consensus 156 Rt~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQ 201 (262)
|..|+..--...-..|.....--...| ..|+++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 344555543333333433332222233 359999999999999975
No 51
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=26.69 E-value=27 Score=22.08 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=28.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceeccccc
Q psy9181 158 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSMMIL 203 (262)
Q Consensus 158 ~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWFQNR 203 (262)
.+++.+...++..|... ..-.++|..+|++...|..|...-
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35667777776665322 235678999999999998887543
No 52
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.20 E-value=50 Score=25.82 Aligned_cols=39 Identities=15% Similarity=0.221 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcc
Q psy9181 158 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARV 196 (262)
Q Consensus 158 ~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqV 196 (262)
.++++|...-...|+.+--++.-..+++|..|+.++-.|
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 467888888888888888888888889999999888433
No 53
>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=22.47 E-value=55 Score=21.57 Aligned_cols=38 Identities=13% Similarity=0.216 Sum_probs=27.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcceecc
Q psy9181 158 TFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQVSM 200 (262)
Q Consensus 158 ~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVqVWF 200 (262)
.+++.|...|...|.... .-.++|..+|++...|+...
T Consensus 4 ~L~~~er~vi~~~y~~~~-----t~~eIa~~lg~s~~~V~~~~ 41 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGL-----TLEEIAERLGISRSTVRRIL 41 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCC-----CHHHHHHHHCCcHHHHHHHH
Confidence 467888899988883322 35689999999998887554
No 54
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=20.15 E-value=54 Score=21.52 Aligned_cols=36 Identities=22% Similarity=0.353 Sum_probs=16.6
Q ss_pred CcCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCCcce
Q psy9181 157 TTFNSHQLNALEKVFERTHYPDAFVREELAKKVCLSEARVQ 197 (262)
Q Consensus 157 t~fT~~Ql~~LE~~F~~~~yps~~~R~~LA~~lgLserqVq 197 (262)
..+|.+|...++..++.. ....+||+.+|.+...|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~ 38 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVS 38 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHH
Confidence 457888888888876644 244579999998876654
Done!