Query psy8133
Match_columns 99
No_of_seqs 128 out of 1114
Neff 9.6
Searched_HMMs 46136
Date Fri Aug 16 19:26:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8133.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8133hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0614|consensus 99.8 1.6E-19 3.5E-24 125.6 4.9 99 1-99 204-302 (732)
2 KOG1113|consensus 99.7 7.2E-18 1.6E-22 112.2 2.4 99 1-99 172-270 (368)
3 PLN03192 Voltage-dependent pot 99.2 7.4E-11 1.6E-15 87.6 9.7 82 1-82 424-509 (823)
4 PF00027 cNMP_binding: Cyclic 99.2 8.8E-11 1.9E-15 64.7 6.7 61 1-61 26-91 (91)
5 TIGR03697 NtcA_cyano global ni 99.2 4E-10 8.8E-15 70.3 8.6 73 1-73 20-99 (193)
6 PRK10402 DNA-binding transcrip 99.1 6.1E-10 1.3E-14 71.5 8.7 69 1-69 58-131 (226)
7 PRK09392 ftrB transcriptional 99.1 5.5E-10 1.2E-14 71.9 8.5 70 1-70 57-130 (236)
8 PRK11753 DNA-binding transcrip 99.1 1E-09 2.2E-14 69.4 9.5 69 1-69 47-121 (211)
9 COG0664 Crp cAMP-binding prote 99.1 6E-10 1.3E-14 69.8 7.9 70 1-70 50-124 (214)
10 cd00038 CAP_ED effector domain 99.0 1.9E-09 4.1E-14 61.0 7.1 65 1-65 44-113 (115)
11 PRK09391 fixK transcriptional 98.8 7.9E-08 1.7E-12 62.0 8.5 68 1-71 65-137 (230)
12 KOG0498|consensus 98.8 1.5E-08 3.3E-13 74.2 5.4 72 1-72 469-546 (727)
13 PRK11161 fumarate/nitrate redu 98.7 1.2E-07 2.7E-12 60.9 8.3 69 1-70 64-137 (235)
14 smart00100 cNMP Cyclic nucleot 98.6 3E-07 6.4E-12 52.1 7.6 67 1-67 44-117 (120)
15 COG2905 Predicted signal-trans 98.6 1.6E-07 3.6E-12 66.7 7.1 74 1-74 57-131 (610)
16 KOG0500|consensus 98.6 4.1E-07 9E-12 63.8 8.9 67 1-67 357-431 (536)
17 PRK13918 CRP/FNR family transc 98.6 2.4E-07 5.2E-12 58.2 6.9 51 1-52 35-90 (202)
18 KOG0614|consensus 98.5 6.1E-08 1.3E-12 68.8 2.8 64 1-64 322-392 (732)
19 KOG0499|consensus 98.5 3.1E-07 6.7E-12 65.9 6.2 74 1-74 577-659 (815)
20 KOG1113|consensus 98.4 5.9E-07 1.3E-11 60.7 4.4 62 1-63 290-353 (368)
21 PLN02868 acyl-CoA thioesterase 98.2 5.4E-06 1.2E-10 57.8 7.0 57 1-59 58-118 (413)
22 KOG0501|consensus 97.8 1.9E-05 4.1E-10 57.1 2.7 68 1-68 598-667 (971)
23 KOG2968|consensus 97.6 8.6E-05 1.9E-09 55.9 4.3 54 9-62 432-485 (1158)
24 KOG2968|consensus 97.5 9.7E-05 2.1E-09 55.6 3.7 64 11-74 550-613 (1158)
25 PF04831 Popeye: Popeye protei 97.2 0.0049 1.1E-07 37.5 7.3 64 1-64 56-124 (153)
26 PRK11832 putative DNA-binding 97.0 0.0072 1.6E-07 38.8 7.2 60 1-60 50-110 (207)
27 KOG2378|consensus 96.3 0.0046 1E-07 43.8 3.2 43 17-59 1-44 (573)
28 KOG3542|consensus 86.7 1.1 2.4E-05 34.1 3.7 59 1-59 332-391 (1283)
29 KOG0498|consensus 80.5 4.3 9.2E-05 31.1 4.6 36 63-98 413-448 (727)
30 COG2905 Predicted signal-trans 77.8 3.3 7.1E-05 30.8 3.3 32 67-98 5-36 (610)
31 PRK09392 ftrB transcriptional 76.6 3.5 7.6E-05 26.4 3.0 32 68-99 6-37 (236)
32 KOG3179|consensus 76.4 1 2.3E-05 29.1 0.5 79 13-91 133-223 (245)
33 PLN02868 acyl-CoA thioesterase 74.8 4.4 9.5E-05 28.6 3.3 33 67-99 6-38 (413)
34 PF05899 Cupin_3: Protein of u 72.4 4.1 8.9E-05 21.6 2.1 21 1-21 34-54 (74)
35 PF10330 Stb3: Putative Sin3 b 61.5 27 0.00059 19.6 4.4 41 50-90 9-50 (92)
36 COG3450 Predicted enzyme of th 61.3 12 0.00025 22.0 2.6 21 1-21 72-92 (116)
37 PLN03192 Voltage-dependent pot 60.7 16 0.00036 28.2 4.0 36 64-99 369-404 (823)
38 PF10539 Dev_Cell_Death: Devel 54.0 46 0.001 20.0 5.2 51 30-90 78-128 (130)
39 cd06942 NR_LBD_Sex_1_like The 47.7 62 0.0013 20.2 4.5 36 56-91 7-42 (191)
40 cd06953 NR_LBD_DHR4_like The l 45.2 80 0.0017 20.2 5.5 36 56-91 32-67 (213)
41 COG1220 HslU ATP-dependent pro 41.2 77 0.0017 22.7 4.4 53 42-94 331-383 (444)
42 PF07883 Cupin_2: Cupin domain 39.6 52 0.0011 16.3 4.6 20 1-21 28-47 (71)
43 cd06940 NR_LBD_REV_ERB The lig 39.0 98 0.0021 19.4 5.5 34 58-91 19-52 (189)
44 TIGR02930 vnfG_nitrog V-contai 38.1 56 0.0012 19.0 2.9 32 64-95 59-90 (109)
45 PF00842 Ala_racemase_C: Alani 37.8 60 0.0013 19.2 3.2 29 11-48 10-38 (129)
46 KOG2297|consensus 37.3 31 0.00067 24.2 2.1 72 14-89 78-151 (412)
47 smart00767 DCD DCD is a plant 37.3 95 0.0021 18.7 4.9 53 30-92 78-130 (132)
48 PF10474 DUF2451: Protein of u 37.3 42 0.0009 22.1 2.6 52 39-93 182-233 (234)
49 TIGR02929 anfG_nitrog Fe-only 37.2 59 0.0013 18.9 2.9 32 64-95 59-90 (109)
50 KOG4410|consensus 36.3 87 0.0019 21.7 4.0 42 13-54 173-221 (396)
51 cd06949 NR_LBD_ER Ligand bindi 36.3 1.2E+02 0.0027 19.7 5.8 41 50-90 31-71 (235)
52 PRK09943 DNA-binding transcrip 36.3 1.1E+02 0.0023 19.0 4.5 43 1-47 137-179 (185)
53 TIGR03214 ura-cupin putative a 35.2 1.2E+02 0.0027 20.1 4.7 43 1-47 89-131 (260)
54 PF03139 AnfG_VnfG: Vanadium/a 34.7 67 0.0014 18.7 2.9 32 64-95 62-93 (112)
55 COG3718 IolB Uncharacterized e 33.6 76 0.0016 21.3 3.3 37 15-51 63-112 (270)
56 cd06939 NR_LBD_ROR_like The li 33.1 1.4E+02 0.0031 19.5 5.8 43 49-91 46-88 (241)
57 KOG0066|consensus 31.8 46 0.001 24.8 2.3 37 35-71 762-798 (807)
58 PF07943 PBP5_C: Penicillin-bi 31.5 88 0.0019 16.6 4.5 37 11-47 3-39 (91)
59 PRK07539 NADH dehydrogenase su 30.6 99 0.0022 18.8 3.4 45 50-94 8-52 (154)
60 PRK13290 ectC L-ectoine syntha 29.6 1.2E+02 0.0027 17.7 5.7 42 1-47 64-106 (125)
61 cd06941 NR_LBD_DmE78_like The 29.3 1.5E+02 0.0032 18.5 5.3 34 58-91 9-42 (195)
62 cd06929 NR_LBD_F1 Ligand-bindi 27.8 1.4E+02 0.0031 17.9 4.5 32 60-91 11-42 (174)
63 cd06935 NR_LBD_TR The ligand b 27.5 1.8E+02 0.004 19.0 5.2 35 57-91 58-92 (243)
64 PRK07571 bidirectional hydroge 27.2 1.2E+02 0.0026 18.9 3.4 45 50-94 22-66 (169)
65 PF05678 VQ: VQ motif; InterP 26.2 73 0.0016 14.0 2.7 19 41-59 4-22 (31)
66 cd04759 Rib_hydrolase ADP-ribo 25.2 1.4E+02 0.003 20.0 3.5 28 1-28 147-175 (242)
67 cd07070 NR_LBD_SF-1 The ligand 24.2 2.1E+02 0.0046 18.6 4.7 31 61-91 48-78 (237)
68 cd06938 NR_LBD_EcR The ligand 24.1 2.1E+02 0.0045 18.5 5.4 31 61-91 49-79 (231)
69 PF11699 CENP-C_C: Mif2/CENP-C 23.5 1.4E+02 0.0031 16.3 3.2 20 1-21 42-61 (85)
70 cd06954 NR_LBD_LXR The ligand 23.0 2.2E+02 0.0048 18.4 5.5 29 63-91 55-83 (236)
71 PRK05988 formate dehydrogenase 22.9 1.7E+02 0.0037 17.9 3.5 46 49-94 8-53 (156)
72 cd06936 NR_LBD_Fxr The ligand 22.8 2.2E+02 0.0048 18.3 5.4 31 61-91 46-76 (221)
73 COG3228 Uncharacterized protei 21.7 1.8E+02 0.0039 19.6 3.5 28 65-92 21-48 (266)
74 cd06944 NR_LBD_Ftz-F1_like The 21.4 2.4E+02 0.0053 18.3 5.1 31 61-91 48-78 (237)
75 PF10742 DUF2555: Protein of u 21.2 87 0.0019 16.0 1.6 22 77-98 6-27 (57)
76 PF04962 KduI: KduI/IolB famil 20.4 2.8E+02 0.0061 18.6 4.8 48 1-48 56-106 (261)
77 cd06933 NR_LBD_VDR The ligand 20.4 2.6E+02 0.0056 18.2 5.5 33 58-90 44-76 (238)
78 PF04518 Effector_1: Effector 20.2 2.1E+02 0.0046 20.5 3.8 35 59-93 218-252 (379)
79 cd06946 NR_LBD_ERR The ligand 20.1 2.5E+02 0.0054 17.9 5.6 32 61-92 37-68 (221)
No 1
>KOG0614|consensus
Probab=99.78 E-value=1.6e-19 Score=125.57 Aligned_cols=99 Identities=60% Similarity=1.031 Sum_probs=96.5
Q ss_pred CeEEEEECCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCC
Q psy8133 1 GRVEVSRENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDL 80 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l 80 (99)
|++.|+++++.+..+++|..|||.+++++++|++|++|.+++.+|.|+++.|+.+++.....+...+.+|++.+++|.++
T Consensus 204 G~~~V~~~g~ll~~m~~gtvFGELAILynctRtAsV~alt~~~lWaidR~vFq~IM~~tg~~r~~~~~~fLrsv~~~q~l 283 (732)
T KOG0614|consen 204 GELQVSREGKLLGKMGAGTVFGELAILYNCTRTASVRALTDVRLWAIDREVFQAIMMRTGLERHEQYMNFLRSVPLFQNL 283 (732)
T ss_pred ceEEEeeCCeeeeccCCchhhhHHHHHhCCcchhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccC
Confidence 78889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHhHhhhccCCC
Q psy8133 81 PEETLIKISDVLEESLGSA 99 (99)
Q Consensus 81 ~~~~~~~l~~~~~~~~~~a 99 (99)
+++.+.++++.+..++|.|
T Consensus 284 ~Ee~L~KiaD~le~~~Yd~ 302 (732)
T KOG0614|consen 284 PEELLLKIADVLEEEYYDA 302 (732)
T ss_pred CHHHHHHHHHHHHHHhhcC
Confidence 9999999999999999975
No 2
>KOG1113|consensus
Probab=99.69 E-value=7.2e-18 Score=112.24 Aligned_cols=99 Identities=36% Similarity=0.633 Sum_probs=95.8
Q ss_pred CeEEEEECCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCC
Q psy8133 1 GRVEVSRENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDL 80 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l 80 (99)
|+++|.+++..+..++||++|||.+|+.+.||.+|+.|.+++.+|.|++..|.+++..+....++++..+++.+++++++
T Consensus 172 Gt~dVyv~~~~v~~~~~g~sFGElALmyn~PRaATv~a~t~~klWgldr~SFrrIi~~s~~kkrkMy~~~l~s~pil~~l 251 (368)
T KOG1113|consen 172 GTFDVYVNGTYVTTYSPGGSFGELALMYNPPRAATVVAKSLKKLWGLDRTSFRRIIMKSCIKKRKMYEPFLESVPILESL 251 (368)
T ss_pred ceEEEEECCeEEeeeCCCCchhhhHhhhCCCcccceeeccccceEEEeeceeEEEeeccchhhhhhhhhhhhcchhhHHH
Confidence 78888899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHhHhhhccCCC
Q psy8133 81 PEETLIKISDVLEESLGSA 99 (99)
Q Consensus 81 ~~~~~~~l~~~~~~~~~~a 99 (99)
..-++.++++.+..+.|+.
T Consensus 252 ~k~er~kv~dal~~k~y~~ 270 (368)
T KOG1113|consen 252 EKLERAKVADALGTKSYKD 270 (368)
T ss_pred HHHHHHhhhcccceeeccC
Confidence 9999999999999999874
No 3
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=99.24 E-value=7.4e-11 Score=87.63 Aligned_cols=82 Identities=21% Similarity=0.303 Sum_probs=72.8
Q ss_pred CeEEEEE----CCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCC
Q psy8133 1 GRVEVSR----ENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPI 76 (99)
Q Consensus 1 G~v~v~~----~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~ 76 (99)
|.|++.. .+.++..+++|++|||.+++.+.|++++++|.+.|+++.|++++|.++++.+|.....++.++++++..
T Consensus 424 G~V~i~~~~~~~e~~l~~l~~Gd~FGE~~~l~~~p~~~t~ra~~~s~ll~l~~~~f~~ll~~~p~d~~~i~~~~l~~~~~ 503 (823)
T PLN03192 424 GEVEIIDSEGEKERVVGTLGCGDIFGEVGALCCRPQSFTFRTKTLSQLLRLKTSTLIEAMQTRQEDNVVILKNFLQHHKE 503 (823)
T ss_pred cEEEEEEecCCcceeeEEccCCCEecchHHhcCCCCCCeEEEcccEEEEEEEHHHHHHHHHHhhHHHHHHHHHHHHHhhh
Confidence 7788754 224688999999999999999999999999999999999999999999999999999999999998877
Q ss_pred CCCCCH
Q psy8133 77 FKDLPE 82 (99)
Q Consensus 77 ~~~l~~ 82 (99)
++++..
T Consensus 504 l~~l~v 509 (823)
T PLN03192 504 LHDLNV 509 (823)
T ss_pred hccccH
Confidence 766543
No 4
>PF00027 cNMP_binding: Cyclic nucleotide-binding domain; InterPro: IPR000595 Proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues [, , ]. The best studied of these proteins is the prokaryotic catabolite gene activator (also known as the cAMP receptor protein) (gene crp) where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure. There are six invariant amino acids in this domain, three of which are glycine residues that are thought to be essential for maintenance of the structural integrity of the beta-barrel. cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain. The cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain. The cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section. Vertebrate cyclic nucleotide-gated ion-channels also contain this domain. Two such cations channels have been fully characterised, one is found in rod cells where it plays a role in visual signal transduction.; PDB: 1O7F_A 2BYV_E 3E97_A 3U10_A 2H6B_A 3SHR_A 2OZ6_A 1WGP_A 3LA2_A 3LA3_B ....
Probab=99.21 E-value=8.8e-11 Score=64.65 Aligned_cols=61 Identities=30% Similarity=0.456 Sum_probs=53.6
Q ss_pred CeEEEEEC---Ce--EEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhH
Q psy8133 1 GRVEVSRE---NK--YLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGL 61 (99)
Q Consensus 1 G~v~v~~~---~~--~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~ 61 (99)
|.+++... +. .+..+++|++||+.+++.+.++.++++|.++|.++.||+++|.+++.++|.
T Consensus 26 G~v~~~~~~~~~~~~~~~~~~~g~~~g~~~~~~~~~~~~~~~a~~~~~~~~i~~~~~~~~~~~~p~ 91 (91)
T PF00027_consen 26 GEVKVSSINEDGKEQIIFFLGPGDIFGEIELLTGKPSPFTVIALTDSEVLRIPREDFLQLLQQDPE 91 (91)
T ss_dssp SEEEEEEETTTSEEEEEEEEETTEEESGHHHHHTSBBSSEEEESSSEEEEEEEHHHHHHHHHHSHH
T ss_pred CceEEEeceecceeeeecceeeeccccceeecCCCccEEEEEEccCEEEEEEeHHHHHHHHHhCcC
Confidence 66666542 22 578999999999999999999999999999999999999999999999874
No 5
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=99.16 E-value=4e-10 Score=70.29 Aligned_cols=73 Identities=18% Similarity=0.214 Sum_probs=59.5
Q ss_pred CeEEEEE---CC--eEEeeeCCCCeeeehhhhcCCc--ceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhc
Q psy8133 1 GRVEVSR---EN--KYLSTLAPGKVFGELAILYNCK--RTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKS 73 (99)
Q Consensus 1 G~v~v~~---~~--~~v~~l~~G~~fGe~~l~~~~~--~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~ 73 (99)
|.|++++ ++ ..+..++||++||+.+++.+.+ +.+++.|.++|.++.+|++.|..++.++|.+...++..+..+
T Consensus 20 G~v~~~~~~~~G~e~~l~~~~~g~~~G~~~~~~~~~~~~~~~~~A~~~~~v~~i~~~~~~~l~~~~p~l~~~~~~~l~~~ 99 (193)
T TIGR03697 20 GAVKLSRVYESGEEITVALLRENSVFGVLSLITGHRSDRFYHAVAFTRVELLAVPIEQVEKAIEEDPDLSMLLLQGLSSR 99 (193)
T ss_pred cEEEEEEeCCCCcEeeeEEccCCCEeeeeeeccCCCCccceEEEEecceEEEEeeHHHHHHHHHHChHHHHHHHHHHHHH
Confidence 7777765 22 2578899999999999998764 457899999999999999999999999998877666544433
No 6
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=99.13 E-value=6.1e-10 Score=71.52 Aligned_cols=69 Identities=14% Similarity=0.272 Sum_probs=59.2
Q ss_pred CeEEEEE---CC--eEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHH
Q psy8133 1 GRVEVSR---EN--KYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYND 69 (99)
Q Consensus 1 G~v~v~~---~~--~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~ 69 (99)
|.|++.. ++ ..+..+.||++||+.+++.+.++++++.|.++|.++.+|.+.|..++..+|.+...++..
T Consensus 58 G~v~v~~~~~~G~e~~~~~~~~g~~~G~~~~~~~~~~~~~~~A~~~~~i~~i~~~~~~~ll~~~p~~~~~~~~~ 131 (226)
T PRK10402 58 GRAKLYATLANGKVSLIDFFAAPCFIGEIELIDKDHETKAVQAIEECWCLALPMKDCRPLLLNDALFLRKLCKF 131 (226)
T ss_pred CEEEEEEECCCCCEeeeeecCCCCeEEeehhhcCCCCCccEEEeccEEEEEEEHHHHHHHHhcCHHHHHHHHHH
Confidence 6777765 22 267889999999999999999999999999999999999999999999999887655443
No 7
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=99.13 E-value=5.5e-10 Score=71.93 Aligned_cols=70 Identities=17% Similarity=0.196 Sum_probs=60.3
Q ss_pred CeEEEEE----CCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHH
Q psy8133 1 GRVEVSR----ENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDF 70 (99)
Q Consensus 1 G~v~v~~----~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~ 70 (99)
|.|++.. ++..+..+.+|++||+.+++.+.++.++++|.++|.++.||.+.|..++.++|.+...+...+
T Consensus 57 G~v~~~~~~~~~~~~i~~~~~g~~~g~~~~~~~~~~~~~~~A~~~~~~~~i~~~~~~~l~~~~p~l~~~~~~~l 130 (236)
T PRK09392 57 GLVELSASSQDRETTLAILRPVSTFILAAVVLDAPYLMSARTLTRSRVLMIPAELVREAMSEDPGFMRAVVFEL 130 (236)
T ss_pred CEEEEEEcCCCceEEEEEeCCCchhhhHHHhCCCCCceEEEEcCceEEEEEeHHHHHHHHHHCHHHHHHHHHHH
Confidence 6777754 224788899999999999999999999999999999999999999999999999877665444
No 8
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=99.12 E-value=1e-09 Score=69.44 Aligned_cols=69 Identities=28% Similarity=0.359 Sum_probs=57.2
Q ss_pred CeEEEEE---CC--eEEeeeCCCCeeeehhhhcC-CcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHH
Q psy8133 1 GRVEVSR---EN--KYLSTLAPGKVFGELAILYN-CKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYND 69 (99)
Q Consensus 1 G~v~v~~---~~--~~v~~l~~G~~fGe~~l~~~-~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~ 69 (99)
|.++++. ++ ..+..+++|++||+..++.+ .+++++++|.++|.++.|+.+.|..++.++|.+...++..
T Consensus 47 G~v~~~~~~~~g~~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~a~~~~~v~~i~~~~~~~l~~~~p~~~~~~~~~ 121 (211)
T PRK11753 47 GSVAVLIKDEEGKEMILSYLNQGDFIGELGLFEEGQERSAWVRAKTACEVAEISYKKFRQLIQVNPDILMALSAQ 121 (211)
T ss_pred CEEEEEEECCCCCEEEEEEcCCCCEEeehhhccCCCCceEEEEEcCcEEEEEEcHHHHHHHHHHCHHHHHHHHHH
Confidence 6777754 22 36788999999999999886 4688999999999999999999999999999886555433
No 9
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=99.11 E-value=6e-10 Score=69.84 Aligned_cols=70 Identities=29% Similarity=0.391 Sum_probs=58.0
Q ss_pred CeEEEEEC---C--eEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHH
Q psy8133 1 GRVEVSRE---N--KYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDF 70 (99)
Q Consensus 1 G~v~v~~~---~--~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~ 70 (99)
|.+++.+. + ..+..++||++||+.+++.+.+++++++|.++|.++.++++.|..++.+.|.+...+...+
T Consensus 50 G~v~~~~~~~~G~~~~~~~~~~g~~fg~~~l~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~p~l~~~l~~~~ 124 (214)
T COG0664 50 GIVKLYANTEDGREIILGFLGPGDFFGELALLGGDPRSASAVALTDVEVLEIPRKDFLELLAESPKLALALLRLL 124 (214)
T ss_pred eEEEEEEECCCCcEEEEEEecCCchhhhHHHhcCCCccceEEEcceEEEEEecHHHHHHHHhhCcHHHHHHHHHH
Confidence 56666552 2 3678899999999999999989999999999999999999999999987666665555444
No 10
>cd00038 CAP_ED effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of
Probab=99.03 E-value=1.9e-09 Score=61.01 Aligned_cols=65 Identities=34% Similarity=0.562 Sum_probs=56.6
Q ss_pred CeEEEEECC-----eEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHH
Q psy8133 1 GRVEVSREN-----KYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQA 65 (99)
Q Consensus 1 G~v~v~~~~-----~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~ 65 (99)
|.+++.... ..+..+.+|++||+..++.+.++..+++|.++|.+|.|+.+.|..++.++|.....
T Consensus 44 G~v~~~~~~~~g~~~~~~~~~~g~~~g~~~~~~~~~~~~~~~a~~~~~~~~i~~~~~~~~~~~~~~~~~~ 113 (115)
T cd00038 44 GSVEVYKLDEDGREQIVGFLGPGDLFGELALLGNGPRSATVRALTDSELLVLPRSDFRRLLQEYPELARR 113 (115)
T ss_pred CEEEEEEECCCCcEEEEEecCCccCcChHHHhcCCCCCceEEEcCceEEEEEeHHHHHHHHHHCcHhHHh
Confidence 667775522 46788999999999999988999999999999999999999999999999887654
No 11
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=98.77 E-value=7.9e-08 Score=61.96 Aligned_cols=68 Identities=21% Similarity=0.199 Sum_probs=55.2
Q ss_pred CeEEEEE---CC--eEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHh
Q psy8133 1 GRVEVSR---EN--KYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFL 71 (99)
Q Consensus 1 G~v~v~~---~~--~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l 71 (99)
|.|++.. ++ ..+..+.+|++||+. .+.++.+++.|.++|.++.|+.+.|..++..+|.+...++..+.
T Consensus 65 G~vkl~~~~~~G~e~i~~~~~~Gd~fG~~---~~~~~~~~~~A~~ds~v~~i~~~~f~~l~~~~p~l~~~l~~~l~ 137 (230)
T PRK09391 65 GAVRTYRLLSDGRRQIGAFHLPGDVFGLE---SGSTHRFTAEAIVDTTVRLIKRRSLEQAAATDVDVARALLSLTA 137 (230)
T ss_pred CEEEEEEECCCCcEEEEEEecCCceeccc---CCCcCCeEEEEcCceEEEEEEHHHHHHHHhhChHHHHHHHHHHH
Confidence 6777765 23 267778999999964 45678899999999999999999999999999988776654443
No 12
>KOG0498|consensus
Probab=98.76 E-value=1.5e-08 Score=74.17 Aligned_cols=72 Identities=19% Similarity=0.364 Sum_probs=61.8
Q ss_pred CeEEEEECC----eEEeeeCCCCeee-ehhhhcC-CcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhh
Q psy8133 1 GRVEVSREN----KYLSTLAPGKVFG-ELAILYN-CKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLK 72 (99)
Q Consensus 1 G~v~v~~~~----~~v~~l~~G~~fG-e~~l~~~-~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~ 72 (99)
|.+++...+ ..+..+++||+|| |...... .|.++||+|.+.|+++.|.+++|..+++.++..+..++.+.++
T Consensus 469 G~le~~~~~~g~~~~~~~L~~Gd~~GeEl~~~~~~~p~t~TVralt~~el~~L~~~dL~~V~~~f~~~~~~~l~~~~r 546 (727)
T KOG0498|consen 469 GSLESITTDGGGFFVVAILGPGDFFGEELLTWCLDLPQTRTVRALTYCELFRLSADDLKEVLQQFRRLGSKFLQHTFR 546 (727)
T ss_pred eeEEEEEccCCceEEEEEecCCCccchHHHHHHhcCCCCceeehhhhhhHHhccHHHHHHHHHHhHHHHHHHHHhHHH
Confidence 677776644 5889999999999 8877776 8889999999999999999999999999999888887774443
No 13
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=98.73 E-value=1.2e-07 Score=60.93 Aligned_cols=69 Identities=13% Similarity=0.072 Sum_probs=54.5
Q ss_pred CeEEEEEC---C--eEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHH
Q psy8133 1 GRVEVSRE---N--KYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDF 70 (99)
Q Consensus 1 G~v~v~~~---~--~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~ 70 (99)
|.|++... + ..+..+.||++||+.+++. .+++.++.|.++|.++.||++.|.+++.++|.+...++..+
T Consensus 64 G~v~~~~~~~~G~e~i~~~~~~gd~~g~~~~~~-~~~~~~~~a~~~~~i~~ip~~~f~~l~~~~p~~~~~~~~~~ 137 (235)
T PRK11161 64 GTIKSYTITEQGDEQITGFHLAGDLVGFDAIGS-GQHPSFAQALETSMVCEIPFETLDDLSGKMPKLRQQIMRLM 137 (235)
T ss_pred ceEEEEEECCCCCEEEEEeccCCceeccccccC-CCCcceEEEeccEEEEEEEHHHHHHHHHHChHHHHHHHHHH
Confidence 67777652 2 3677789999999987654 45567899999999999999999999999998876655433
No 14
>smart00100 cNMP Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases.
Probab=98.65 E-value=3e-07 Score=52.09 Aligned_cols=67 Identities=28% Similarity=0.368 Sum_probs=55.0
Q ss_pred CeEEEEEC-----CeEEeeeCCCCeeeehhhh--cCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHH
Q psy8133 1 GRVEVSRE-----NKYLSTLAPGKVFGELAIL--YNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEY 67 (99)
Q Consensus 1 G~v~v~~~-----~~~v~~l~~G~~fGe~~l~--~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~ 67 (99)
|.+++... ...+..+.+|++||+..++ ...++..++.+.++|.++.++.+.+...+..++......+
T Consensus 44 G~v~~~~~~~~g~~~~~~~~~~g~~~g~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~ 117 (120)
T smart00100 44 GEVRVYKVLEDGREQILGILGPGDFFGELALLTNSRRAASATAVALELATLLRIDFRDFLQLLQENPQLLLELL 117 (120)
T ss_pred eEEEEEEECCCCceEEEEeecCCceechhhhccCCCcccceEEEEEeeEEEEccCHHHHHHHHHHhHHHHHHHH
Confidence 56666542 2378889999999999998 4567789999999999999999999999998887765544
No 15
>COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]
Probab=98.63 E-value=1.6e-07 Score=66.75 Aligned_cols=74 Identities=20% Similarity=0.313 Sum_probs=62.5
Q ss_pred CeEEEE-ECCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcC
Q psy8133 1 GRVEVS-RENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSV 74 (99)
Q Consensus 1 G~v~v~-~~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~ 74 (99)
|.|++. .+++++..+..||+||-.+++.+.+-+..+.|.+|+.||.||++.|.+++.++|.++.....+.-+++
T Consensus 57 G~vev~~~~g~v~~~~~~gdlFg~~~l~~~~~~~~~~~aeedsl~y~lp~s~F~ql~~~n~~f~~ff~~~~akR~ 131 (610)
T COG2905 57 GVVEVRSDGGEVLDRLAAGDLFGFSSLFTELNKQRYMAAEEDSLCYLLPKSVFMQLMEENPEFADFFLRSLAKRL 131 (610)
T ss_pred ceeeEEcCCCeeeeeeccCccccchhhcccCCCcceeEeeccceEEecCHHHHHHHHHhCcHHHHHHHHHHHHHH
Confidence 667764 45678999999999999999998888888999999999999999999999999998776654444443
No 16
>KOG0500|consensus
Probab=98.62 E-value=4.1e-07 Score=63.77 Aligned_cols=67 Identities=24% Similarity=0.399 Sum_probs=56.6
Q ss_pred CeEEEEEC-C-eEEeeeCCCCeeeehhhhc------CCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHH
Q psy8133 1 GRVEVSRE-N-KYLSTLAPGKVFGELAILY------NCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEY 67 (99)
Q Consensus 1 G~v~v~~~-~-~~v~~l~~G~~fGe~~l~~------~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~ 67 (99)
|.+.|..+ + .....++.|++|||.+++. +.+|+++++.+..+.+++++++++.+.+.++|+.+....
T Consensus 357 G~L~Vv~dDg~t~~~~L~~G~~FGEisIlni~g~~~gNRRtanvrSvGYSDlfvLskdDl~~aL~eYP~a~~~L~ 431 (536)
T KOG0500|consen 357 GKLAVVADDGVTVFVTLKAGSVFGEISILNIKGNKNGNRRTANVRSVGYSDLFVLSKDDLWEALSEYPDARKRLE 431 (536)
T ss_pred cEEEEEecCCcEEEEEecCCceeeeeEEEEEcCcccCCcceeeeeeeccceeeEeeHHHHHHHHHhCCHHHHHHH
Confidence 45555443 3 4678899999999999983 678999999999999999999999999999998876655
No 17
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=98.61 E-value=2.4e-07 Score=58.25 Aligned_cols=51 Identities=25% Similarity=0.398 Sum_probs=41.8
Q ss_pred CeEEEEE---CC--eEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHH
Q psy8133 1 GRVEVSR---EN--KYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCF 52 (99)
Q Consensus 1 G~v~v~~---~~--~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f 52 (99)
|.|++.. ++ ..+..+.|||+||+.+++ +.++++++.|.++|.++.|+++.|
T Consensus 35 G~vr~~~~~~~G~e~~l~~~~~Gd~~G~~~~~-~~~~~~~~~A~~~~~v~~i~~~~~ 90 (202)
T PRK13918 35 GLVRLHTVDDEGNALTLRYVRPGEYFGEEALA-GAERAYFAEAVTDSRIDVLNPALM 90 (202)
T ss_pred eEEEEEEECCCCCEEEEEEecCCCeechHHhc-CCCCCceEEEcCceEEEEEEHHHc
Confidence 6777755 22 367888999999997654 578899999999999999998776
No 18
>KOG0614|consensus
Probab=98.53 E-value=6.1e-08 Score=68.75 Aligned_cols=64 Identities=30% Similarity=0.471 Sum_probs=55.6
Q ss_pred CeEEEEECC------eEEeeeCCCCeeeehhhhcCCcceeEEEEccc-eEEEEECHHHHHHHHHhhhHHHH
Q psy8133 1 GRVEVSREN------KYLSTLAPGKVFGELAILYNCKRTATIKAASD-CKLWAIERQCFQTIMMRTGLIRQ 64 (99)
Q Consensus 1 G~v~v~~~~------~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~-~~~~~i~~~~f~~~l~~~~~~~~ 64 (99)
|+|.+.+.+ ..++.++.||+|||.+++....|+++++|..+ ..|+.|+++.|.+++.....++.
T Consensus 322 G~V~vtq~~e~~~q~~~lr~l~kGd~FGE~al~~edvRtAniia~~~gv~cl~lDresF~~liG~l~~l~e 392 (732)
T KOG0614|consen 322 GTVKVTQQDEGSTQPQELRTLNKGDYFGERALLGEDVRTANIIAQAPGVECLTLDRESFKKLIGDLEELKE 392 (732)
T ss_pred ceEEEeecCCCCCchhHHhhccccchhhHHHhhccCccchhhhccCCCceEEEecHHHHHHhcccHHHhhh
Confidence 677776532 36899999999999999999999999999997 99999999999999987776653
No 19
>KOG0499|consensus
Probab=98.52 E-value=3.1e-07 Score=65.90 Aligned_cols=74 Identities=28% Similarity=0.408 Sum_probs=58.2
Q ss_pred CeEEEEE---CCeEEeeeCCCCeeeehhhhc---CCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHH---HHHHh
Q psy8133 1 GRVEVSR---ENKYLSTLAPGKVFGELAILY---NCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAE---YNDFL 71 (99)
Q Consensus 1 G~v~v~~---~~~~v~~l~~G~~fGe~~l~~---~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~---~~~~l 71 (99)
|.|.|.- +..++..+..|..|||++|+. +.+|+++|+|..-|.+++++++++.+++..+|.-++-+ ...++
T Consensus 577 GqvQVlGGp~~~~Vl~tL~~GsVFGEISLLaigG~nRRTAnV~a~Gf~nLfvL~KkdLneil~~YP~sq~iLrkkAr~ll 656 (815)
T KOG0499|consen 577 GQVQVLGGPDGTKVLVTLKAGSVFGEISLLAIGGGNRRTANVVAHGFANLFVLDKKDLNEILVHYPDSQRILRKKARVLL 656 (815)
T ss_pred ceEEEecCCCCCEEEEEecccceeeeeeeeeecCCCccchhhhhcccceeeEecHhHHHHHHHhCccHHHHHHHHHHHHH
Confidence 4555543 235889999999999999995 67889999999999999999999999999988755333 33444
Q ss_pred hcC
Q psy8133 72 KSV 74 (99)
Q Consensus 72 ~~~ 74 (99)
++-
T Consensus 657 k~n 659 (815)
T KOG0499|consen 657 KQN 659 (815)
T ss_pred Hhc
Confidence 443
No 20
>KOG1113|consensus
Probab=98.37 E-value=5.9e-07 Score=60.74 Aligned_cols=62 Identities=31% Similarity=0.423 Sum_probs=51.7
Q ss_pred CeEEEEE--CCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHH
Q psy8133 1 GRVEVSR--ENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIR 63 (99)
Q Consensus 1 G~v~v~~--~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~ 63 (99)
|+|.+.+ ++..+ .++.||+|||.+++.+.||.+++.|.+...|..++++.|++++..-.++-
T Consensus 290 GEvdv~~~~~~v~v-kl~~~dyfge~al~~~~pr~Atv~a~~~~kc~~~dk~~ferllgpc~dil 353 (368)
T KOG1113|consen 290 GEVDVLKKRDGVEV-KLKKGDYFGELALLKNLPRAATVVAKGRLKCAKLDKPRFERLLGPCQDIL 353 (368)
T ss_pred cccchhhccCCeEE-EechhhhcchHHHHhhchhhceeeccCCceeeeeChHHHHHHhhHHHHHH
Confidence 4455432 23344 89999999999999999999999999999999999999999998765543
No 21
>PLN02868 acyl-CoA thioesterase family protein
Probab=98.24 E-value=5.4e-06 Score=57.79 Aligned_cols=57 Identities=21% Similarity=0.197 Sum_probs=47.7
Q ss_pred CeEEEEE----CCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhh
Q psy8133 1 GRVEVSR----ENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRT 59 (99)
Q Consensus 1 G~v~v~~----~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~ 59 (99)
|.|++.+ ++..+..+++|++||+. +.+.++.++++|.++|.++.|+++.|..+....
T Consensus 58 G~V~v~~~~~~ge~~l~~l~~Gd~fG~~--l~~~~~~~~~~A~~d~~v~~ip~~~~~~~~~~~ 118 (413)
T PLN02868 58 GEAEVSGPAEEESRPEFLLKRYDYFGYG--LSGSVHSADVVAVSELTCLVLPHEHCHLLSPKS 118 (413)
T ss_pred CEEEEEEECCCCcEEEEEeCCCCEeehh--hCCCCcccEEEECCCEEEEEEcHHHHhhhcccc
Confidence 7788765 23467889999999985 678899999999999999999999999776543
No 22
>KOG0501|consensus
Probab=97.77 E-value=1.9e-05 Score=57.11 Aligned_cols=68 Identities=22% Similarity=0.344 Sum_probs=55.0
Q ss_pred CeEEEEECCeEEeeeCCCCeeeehhhhcCC--cceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHH
Q psy8133 1 GRVEVSRENKYLSTLAPGKVFGELAILYNC--KRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYN 68 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~fGe~~l~~~~--~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~ 68 (99)
|+.+|..++++|+.++.||.||+..--... ...++++|.+.|.+..|.++.+...++-+..++.....
T Consensus 598 GSLEVIQDDEVVAILGKGDVFGD~FWK~~t~~qs~ANVRALTYcDLH~IKrd~Ll~VLdFYtAFanSFaR 667 (971)
T KOG0501|consen 598 GSLEVIQDDEVVAILGKGDVFGDEFWKENTLGQSAANVRALTYCDLHMIKRDKLLKVLDFYTAFANSFAR 667 (971)
T ss_pred cceEEeecCcEEEEeecCccchhHHhhhhhhhhhhhhhhhhhhhhhhHHhHHHHHHHHHHHHHHHHHhhh
Confidence 778888999999999999999986544332 23578999999999999999999999877666554433
No 23
>KOG2968|consensus
Probab=97.62 E-value=8.6e-05 Score=55.87 Aligned_cols=54 Identities=33% Similarity=0.429 Sum_probs=50.2
Q ss_pred CeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHH
Q psy8133 9 NKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLI 62 (99)
Q Consensus 9 ~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~ 62 (99)
+..+-.++||+.+|-.+++.+.+..++++|.++|.++.+++++|.+++.++|.+
T Consensus 432 ~~~~f~v~pG~ivgyla~lt~e~S~~tirArsdt~v~~isrs~l~~~~~~~p~I 485 (1158)
T KOG2968|consen 432 GMLLFVVGPGEIVGYLAILTNEPSFITIRARSDTRVLFISRSDLERFLDAEPLI 485 (1158)
T ss_pred cceEEEecCCceechhhhhcCCcceEEEEEecceEEEEeeHHHHHHHHHhCceE
Confidence 346778999999999999999999999999999999999999999999999944
No 24
>KOG2968|consensus
Probab=97.55 E-value=9.7e-05 Score=55.61 Aligned_cols=64 Identities=19% Similarity=0.259 Sum_probs=57.1
Q ss_pred EEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcC
Q psy8133 11 YLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSV 74 (99)
Q Consensus 11 ~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~ 74 (99)
.+..++.||.+|+..++.+.+|..|+.|+.++++..||..-|..+..++|..-.+..+-+.+++
T Consensus 550 i~~EygrGd~iG~~E~lt~~~R~tTv~AvRdSelariPe~l~~~ik~ryP~v~~rl~~ll~~~~ 613 (1158)
T KOG2968|consen 550 IVGEYGRGDLIGEVEMLTKQPRATTVMAVRDSELARIPEGLLNFIKLRYPQVVTRLIKLLAEKI 613 (1158)
T ss_pred hhhhccCcceeehhHHhhcCCccceEEEEeehhhhhccHHHHHHHHHhccHHHHHHHHHHHHHh
Confidence 6888999999999999999999999999999999999999999999999998776665444443
No 25
>PF04831 Popeye: Popeye protein conserved region; InterPro: IPR006916 The Popeye (POP) family of proteins, is restricted to vertebrates and is preferentially expressed in developing and adult striated muscle. It is represented by a conserved region which includes three potential transmembrane domains []. The strong conservation of POP genes during evolution and their preferential expression in heart and skeletal muscle suggest that these novel proteins may have an important function in these tissues in vertebrates.; GO: 0016020 membrane
Probab=97.16 E-value=0.0049 Score=37.55 Aligned_cols=64 Identities=20% Similarity=0.341 Sum_probs=50.3
Q ss_pred CeEEEEECCeEEeeeCCCCeeeehh-----hhcCCcceeEEEEccceEEEEECHHHHHHHHHhhhHHHH
Q psy8133 1 GRVEVSRENKYLSTLAPGKVFGELA-----ILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQ 64 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~fGe~~-----l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~ 64 (99)
|++.|+.++..++.+.|.++..--. .-.+..-..|+.|.++|..+..+|+.+..++.+.+.++.
T Consensus 56 Gr~~Vs~~g~fLH~I~p~qFlDSPEW~s~~~s~~~~FQVTitA~~~Cryl~W~R~kL~~~l~~~~~L~~ 124 (153)
T PF04831_consen 56 GRMRVSCDGRFLHYIYPYQFLDSPEWESLRPSEDDKFQVTITAEEDCRYLCWPREKLYLLLAKDPFLAA 124 (153)
T ss_pred CcEEEEECCEeeEeecccccccChhhhccccCCCCeEEEEEEEcCCcEEEEEEHHHHHHHHhhCHHHHH
Confidence 7888999998888777766554211 123556689999999999999999999999999887653
No 26
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=96.97 E-value=0.0072 Score=38.76 Aligned_cols=60 Identities=13% Similarity=0.210 Sum_probs=49.4
Q ss_pred CeEEEEEC-CeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEECHHHHHHHHHhhh
Q psy8133 1 GRVEVSRE-NKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIERQCFQTIMMRTG 60 (99)
Q Consensus 1 G~v~v~~~-~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~ 60 (99)
|.|.+.+. +-.+........||-...+.+....+..+|.++|.++.+|.++|..++.++.
T Consensus 50 G~vsirr~d~ll~~t~~aP~IlGl~~~~~~~~~~~~l~ae~~c~~~~i~~~~~~~iie~~~ 110 (207)
T PRK11832 50 GVISLRREENVLIGITQAPYIMGLADGLMKNDIPYKLISEGNCTGYHLPAKQTITLIEQNQ 110 (207)
T ss_pred ceEEEEecCCeEEEeccCCeEeecccccCCCCceEEEEEcCccEEEEeeHHHHHHHHHHhc
Confidence 66777443 3467788899999988777777767899999999999999999999998764
No 27
>KOG2378|consensus
Probab=96.30 E-value=0.0046 Score=43.80 Aligned_cols=43 Identities=28% Similarity=0.584 Sum_probs=38.4
Q ss_pred CCCeeeehhhhcCCcceeEEEEcc-ceEEEEECHHHHHHHHHhh
Q psy8133 17 PGKVFGELAILYNCKRTATIKAAS-DCKLWAIERQCFQTIMMRT 59 (99)
Q Consensus 17 ~G~~fGe~~l~~~~~~~~~~~a~~-~~~~~~i~~~~f~~~l~~~ 59 (99)
.||.||..++..+.||.++++..+ +|.++++++.+|.+++.+.
T Consensus 1 eGddfgklalvnd~praativl~ed~~~fl~vDk~~Fn~I~~~v 44 (573)
T KOG2378|consen 1 EGDDFGKLALVNDAPRAATIVLREDNCHFLRVDKHDFNRILHDV 44 (573)
T ss_pred CCcccchhccccccccccceeeecCCCcceeecHHHHHHHHHhh
Confidence 489999999999999999977666 5999999999999999654
No 28
>KOG3542|consensus
Probab=86.72 E-value=1.1 Score=34.13 Aligned_cols=59 Identities=22% Similarity=0.319 Sum_probs=42.6
Q ss_pred CeEEEEECCeEEeeeCCCCeeeehhhhcCCcceeEEEE-ccceEEEEECHHHHHHHHHhh
Q psy8133 1 GRVEVSRENKYLSTLAPGKVFGELAILYNCKRTATIKA-ASDCKLWAIERQCFQTIMMRT 59 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a-~~~~~~~~i~~~~f~~~l~~~ 59 (99)
|.|+|++.+.....+.-|++||-..-...+...-.+++ +.||++.+|...+|.+++...
T Consensus 332 G~VEv~~PdGk~e~l~mGnSFG~~PT~dkqym~G~mRTkVDDCqFVciaqqDycrIln~v 391 (1283)
T KOG3542|consen 332 GCVEVVKPDGKREELKMGNSFGAEPTPDKQYMIGEMRTKVDDCQFVCIAQQDYCRILNTV 391 (1283)
T ss_pred ceEEEecCCCceEEeecccccCCCCCcchhhhhhhhheecccceEEEeehhhHHHHHHHH
Confidence 67788776666677999999997655443332223333 467999999999999999654
No 29
>KOG0498|consensus
Probab=80.51 E-value=4.3 Score=31.08 Aligned_cols=36 Identities=17% Similarity=0.316 Sum_probs=31.7
Q ss_pred HHHHHHHHhhcCCCCCCCCHHHHHHHHhHhhhccCC
Q psy8133 63 RQAEYNDFLKSVPIFKDLPEETLIKISDVLEESLGS 98 (99)
Q Consensus 63 ~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~~~~~ 98 (99)
.+.....+++++++|++.++.-+..|++.++.++|+
T Consensus 413 ~~hL~~~lv~~vpLF~~md~~~L~al~~rlk~~~f~ 448 (727)
T KOG0498|consen 413 KRHLCLDLVRKVPLFAGMDDGLLDALCSRLKPEYFT 448 (727)
T ss_pred HHHHhHHHHhhCchhhcCCHHHHHHHHHHhhhhccC
Confidence 344557889999999999999999999999999886
No 30
>COG2905 Predicted signal-transduction protein containing cAMP-binding and CBS domains [Signal transduction mechanisms]
Probab=77.85 E-value=3.3 Score=30.76 Aligned_cols=32 Identities=31% Similarity=0.468 Sum_probs=30.2
Q ss_pred HHHHhhcCCCCCCCCHHHHHHHHhHhhhccCC
Q psy8133 67 YNDFLKSVPIFKDLPEETLIKISDVLEESLGS 98 (99)
Q Consensus 67 ~~~~l~~~~~~~~l~~~~~~~l~~~~~~~~~~ 98 (99)
..+|+.+++-|+.+++.++.+|...+..++|+
T Consensus 5 ~~~Fl~~~pPF~~L~~eel~~L~~~l~v~yy~ 36 (610)
T COG2905 5 PDQFLQQHPPFSQLPAEELEQLMGALEVKYYR 36 (610)
T ss_pred HHHHHhcCCCcccCCHHHHHHHHhhhcccccc
Confidence 56899999999999999999999999999996
No 31
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=76.60 E-value=3.5 Score=26.38 Aligned_cols=32 Identities=16% Similarity=0.156 Sum_probs=28.8
Q ss_pred HHHhhcCCCCCCCCHHHHHHHHhHhhhccCCC
Q psy8133 68 NDFLKSVPIFKDLPEETLIKISDVLEESLGSA 99 (99)
Q Consensus 68 ~~~l~~~~~~~~l~~~~~~~l~~~~~~~~~~a 99 (99)
..+++.+++|..++..++..+...+....|++
T Consensus 6 ~~~l~~~~~f~~L~~~~~~~l~~~~~~~~~~~ 37 (236)
T PRK09392 6 LIRLRNLPLFADMADATFERLMRGAFLQRFPP 37 (236)
T ss_pred HHHHhcCccccCCCHHHHHHHHhhcceeecCC
Confidence 35889999999999999999999999988875
No 32
>KOG3179|consensus
Probab=76.44 E-value=1 Score=29.14 Aligned_cols=79 Identities=18% Similarity=0.120 Sum_probs=51.7
Q ss_pred eeeCCCCeeeehhhh-----------cCCcceeEEEEcc-ceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCC
Q psy8133 13 STLAPGKVFGELAIL-----------YNCKRTATIKAAS-DCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDL 80 (99)
Q Consensus 13 ~~l~~G~~fGe~~l~-----------~~~~~~~~~~a~~-~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l 80 (99)
....|+.+|||..-. .+-|-.++..|.+ +|++=..++.+=.-+++.||.....+...++.++.-....
T Consensus 133 ~~~~~~~yFG~~~~~l~IikcHqDevle~PE~a~llasSe~ceve~fs~~~~~l~fQGHPEyn~eil~~ivdrv~~~k~~ 212 (245)
T KOG3179|consen 133 DAEKPEKYFGEIPKSLNIIKCHQDEVLELPEGAELLASSEKCEVEMFSIEDHLLCFQGHPEYNKEILFEIVDRVLGTKLV 212 (245)
T ss_pred ecccchhhcccchhhhhHHhhcccceecCCchhhhhccccccceEEEEecceEEEecCCchhhHHHHHHHHHHHhcchhh
Confidence 346899999966221 2456667766554 4766555555545567889999999888888887766655
Q ss_pred CHHHHHHHHhH
Q psy8133 81 PEETLIKISDV 91 (99)
Q Consensus 81 ~~~~~~~l~~~ 91 (99)
..+...+...+
T Consensus 213 ~eef~~~ak~~ 223 (245)
T KOG3179|consen 213 EEEFAEKAKKT 223 (245)
T ss_pred HHHHHHHHHHh
Confidence 55554444333
No 33
>PLN02868 acyl-CoA thioesterase family protein
Probab=74.82 E-value=4.4 Score=28.60 Aligned_cols=33 Identities=33% Similarity=0.522 Sum_probs=29.5
Q ss_pred HHHHhhcCCCCCCCCHHHHHHHHhHhhhccCCC
Q psy8133 67 YNDFLKSVPIFKDLPEETLIKISDVLEESLGSA 99 (99)
Q Consensus 67 ~~~~l~~~~~~~~l~~~~~~~l~~~~~~~~~~a 99 (99)
+..+++++++|+.++..++.++...+..+.|++
T Consensus 6 ~~~~L~~~~~F~~L~~~~l~~l~~~~~~~~~~~ 38 (413)
T PLN02868 6 VVEFLGSVPLLQRLPSSSLKKIAEVVVPKRYGK 38 (413)
T ss_pred HHHHHhcCcccccCCHHHHHHHHHhceEEEECC
Confidence 456789999999999999999999999888874
No 34
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=72.40 E-value=4.1 Score=21.57 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=14.5
Q ss_pred CeEEEEECCeEEeeeCCCCee
Q psy8133 1 GRVEVSRENKYLSTLAPGKVF 21 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~f 21 (99)
|++.+...+.....+++||.|
T Consensus 34 G~v~it~~~G~~~~~~aGD~~ 54 (74)
T PF05899_consen 34 GEVTITDEDGETVTFKAGDAF 54 (74)
T ss_dssp EEEEEEETTTEEEEEETTEEE
T ss_pred eEEEEEECCCCEEEEcCCcEE
Confidence 566776644455778998876
No 35
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=61.51 E-value=27 Score=19.60 Aligned_cols=41 Identities=20% Similarity=0.251 Sum_probs=30.2
Q ss_pred HHHHHHHHhhhHHH-HHHHHHHhhcCCCCCCCCHHHHHHHHh
Q psy8133 50 QCFQTIMMRTGLIR-QAEYNDFLKSVPIFKDLPEETLIKISD 90 (99)
Q Consensus 50 ~~f~~~l~~~~~~~-~~~~~~~l~~~~~~~~l~~~~~~~l~~ 90 (99)
..+-++|-.+.+++ +.++..+...++-|+.+++....+|.-
T Consensus 9 ~~Lp~iLl~~GPLaIRhI~~~Lt~~vPgF~~ls~sKqRRLi~ 50 (92)
T PF10330_consen 9 YHLPEILLNHGPLAIRHITGYLTTSVPGFSDLSPSKQRRLIM 50 (92)
T ss_pred hhhHHHHHhcCcHHHHHHHHHHhccCCCcccCCHHHHHHHHH
Confidence 34455666666655 566778889999999999988777653
No 36
>COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]
Probab=61.31 E-value=12 Score=22.00 Aligned_cols=21 Identities=33% Similarity=0.522 Sum_probs=15.2
Q ss_pred CeEEEEECCeEEeeeCCCCee
Q psy8133 1 GRVEVSRENKYLSTLAPGKVF 21 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~f 21 (99)
|.+.+..++.....+++||.|
T Consensus 72 G~v~~T~d~Ge~v~~~aGD~~ 92 (116)
T COG3450 72 GRVEVTPDGGEPVEVRAGDSF 92 (116)
T ss_pred eEEEEECCCCeEEEEcCCCEE
Confidence 566666666666779999886
No 37
>PLN03192 Voltage-dependent potassium channel; Provisional
Probab=60.73 E-value=16 Score=28.19 Aligned_cols=36 Identities=17% Similarity=0.260 Sum_probs=30.2
Q ss_pred HHHHHHHhhcCCCCCCCCHHHHHHHHhHhhhccCCC
Q psy8133 64 QAEYNDFLKSVPIFKDLPEETLIKISDVLEESLGSA 99 (99)
Q Consensus 64 ~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~~~~~a 99 (99)
..+...+++++++|+++++..+..+...++.+.|+.
T Consensus 369 ~~l~~~~l~~~~lF~~~s~~~l~~L~~~~~~~~~~p 404 (823)
T PLN03192 369 QHLFLPVVEKVYLFKGVSREILLLLVTKMKAEYIPP 404 (823)
T ss_pred HHHHHHHHhhCcchhcCCHHHHHHHHHhhheeeeCC
Confidence 334456789999999999999999999999888863
No 38
>PF10539 Dev_Cell_Death: Development and cell death domain; InterPro: IPR013989 The DCD (Development and Cell Death) domain is found in plant proteins involved in development and cell death. The DCD domain is an ~130 amino acid long stretch that contains several mostly invariable motifs. These include a FGLP and a LFL motif at the N terminus and a PAQV and a PLxE motif towards the C terminus of the domain. The DCD domain is present in proteins with different architectures. Some of these proteins contain additional recognizable motifs, like the KELCH repeats or the ParB domain []. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone. The predicted secondary structure of the DCD domain is mostly composed of beta strands and confined by an alpha-helix at the N- and at the C terminus []. Proteins known to contain a DCD domain are listed below: Carrot B2 protein. Pea Gda-1 protein. Soybean N-rich protein (NRP).
Probab=54.05 E-value=46 Score=19.96 Aligned_cols=51 Identities=8% Similarity=-0.001 Sum_probs=38.1
Q ss_pred CcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHh
Q psy8133 30 CKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISD 90 (99)
Q Consensus 30 ~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~ 90 (99)
.+++++|+......+.-|+.+.|...+.++... .....-+|+..|..+|.+
T Consensus 78 ~~fPAQVrf~i~~~C~PL~E~~fk~aI~~Ny~~----------~~kF~~eLs~~Qv~~L~~ 128 (130)
T PF10539_consen 78 SPFPAQVRFRIRWDCPPLPESQFKPAIKDNYYD----------KNKFRFELSHQQVRKLLS 128 (130)
T ss_pred cccceEEEEEEeeeeecCCHHHHHHHHHHhCCC----------CCcccCcCCHHHHHHHHH
Confidence 588999999999999999999999988655332 334555677777666654
No 39
>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).
Probab=47.68 E-value=62 Score=20.21 Aligned_cols=36 Identities=22% Similarity=0.267 Sum_probs=27.2
Q ss_pred HHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 56 MMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 56 l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
+.+..........++.++++.|..++..+...|...
T Consensus 7 ~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~ 42 (191)
T cd06942 7 FAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKG 42 (191)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHH
Confidence 344445556677899999999999999987766543
No 40
>cd06953 NR_LBD_DHR4_like The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4. The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=45.24 E-value=80 Score=20.18 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=25.9
Q ss_pred HHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 56 MMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 56 l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
+.+.....-....++.++++.|.+++..+...|...
T Consensus 32 l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~ 67 (213)
T cd06953 32 LCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTT 67 (213)
T ss_pred HHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHH
Confidence 333334444556889999999999999987766543
No 41
>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=41.20 E-value=77 Score=22.71 Aligned_cols=53 Identities=15% Similarity=0.317 Sum_probs=41.1
Q ss_pred eEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhHhhh
Q psy8133 42 CKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDVLEE 94 (99)
Q Consensus 42 ~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~ 94 (99)
.++=.++.++|.++|.+...--.+++..+++-=..--.++.+.+.++++....
T Consensus 331 VEL~~Lt~~Df~rILtep~~sLikQY~aLlkTE~v~l~FtddaI~~iAeiA~~ 383 (444)
T COG1220 331 VELDALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIAYQ 383 (444)
T ss_pred EEcccCCHHHHHHHHcCcchHHHHHHHHHHhhcCeeEEecHHHHHHHHHHHHH
Confidence 56678999999999987766667778888877767677888888887765543
No 42
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=39.58 E-value=52 Score=16.34 Aligned_cols=20 Identities=20% Similarity=0.423 Sum_probs=11.8
Q ss_pred CeEEEEECCeEEeeeCCCCee
Q psy8133 1 GRVEVSRENKYLSTLAPGKVF 21 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~f 21 (99)
|++.+..+++ ...+++||.+
T Consensus 28 G~~~~~~~~~-~~~l~~Gd~~ 47 (71)
T PF07883_consen 28 GEGTLTVDGE-RVELKPGDAI 47 (71)
T ss_dssp SEEEEEETTE-EEEEETTEEE
T ss_pred CCEEEEEccE-EeEccCCEEE
Confidence 4555554444 5567887754
No 43
>cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of
Probab=39.01 E-value=98 Score=19.37 Aligned_cols=34 Identities=21% Similarity=0.294 Sum_probs=25.7
Q ss_pred hhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 58 RTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 58 ~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
+........+.++.+++|.|.+++..+...|...
T Consensus 19 ~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~ 52 (189)
T cd06940 19 MSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKA 52 (189)
T ss_pred HHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHH
Confidence 3334455667899999999999999987766544
No 44
>TIGR02930 vnfG_nitrog V-containing nitrogenase, delta subunit. Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfG, represents the delta subunit of the V-containing (vanadium) alternative nitrogenase. It is homologous to AnfG, the delta subunit of the Fe-only nitrogenase.
Probab=38.10 E-value=56 Score=18.97 Aligned_cols=32 Identities=9% Similarity=0.344 Sum_probs=26.4
Q ss_pred HHHHHHHhhcCCCCCCCCHHHHHHHHhHhhhc
Q psy8133 64 QAEYNDFLKSVPIFKDLPEETLIKISDVLEES 95 (99)
Q Consensus 64 ~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~~ 95 (99)
..+...+-++.+.++.++.+++..+.+.++.+
T Consensus 59 v~la~~~k~rfpW~~~~~kdei~~l~~~lk~r 90 (109)
T TIGR02930 59 KNLASDIKERFPWISELDKDQILELVESVKKR 90 (109)
T ss_pred HHHHHHHHHhCcHHHhCCHHHHHHHHHHHHHH
Confidence 34457788999999999999999998877654
No 45
>PF00842 Ala_racemase_C: Alanine racemase, C-terminal domain; InterPro: IPR011079 Alanine racemase (5.1.1.1 from EC) plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins [,]. The molecular structure of alanine racemase from Bacillus stearothermophilus (Geobacillus stearothermophilus) was determined by X-ray crystallography to a resolution of 1.9 A []. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N terminus, and a C-terminal domain essentially composed of beta-strand. The pyridoxal 5'-phosphate (PLP) cofactor lies in and above the mouth of the alpha/beta barrel and is covalently linked via an aldimine linkage to a lysine residue, which is at the C terminus of the first beta-strand of the alpha/beta barrel.; GO: 0008784 alanine racemase activity, 0006522 alanine metabolic process; PDB: 3HUR_A 4A3Q_B 3S46_A 1RCQ_A 3CO8_A 1VFT_B 1VFH_A 1VFS_B 2DY3_B 4ECL_C ....
Probab=37.77 E-value=60 Score=19.16 Aligned_cols=29 Identities=17% Similarity=0.314 Sum_probs=18.3
Q ss_pred EEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEEC
Q psy8133 11 YLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAIE 48 (99)
Q Consensus 11 ~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i~ 48 (99)
.++.+.+|+..|- ..+.+|..++.+..++
T Consensus 10 ~v~~v~~G~~VgY---------g~~~~a~~~~~iavv~ 38 (129)
T PF00842_consen 10 QVREVPKGETVGY---------GRTYRAPRDTRIAVVP 38 (129)
T ss_dssp EEEEE-TT-EESG---------GGSEE-SSSEEEEEES
T ss_pred EEEEeCCCCCCcC---------CCEEECCCCeEEEEEE
Confidence 5788999999884 4555566677776665
No 46
>KOG2297|consensus
Probab=37.30 E-value=31 Score=24.17 Aligned_cols=72 Identities=21% Similarity=0.202 Sum_probs=37.5
Q ss_pred eeCCCCeeeehhhhcCCcce-eEEEEc-cceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHH
Q psy8133 14 TLAPGKVFGELAILYNCKRT-ATIKAA-SDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKIS 89 (99)
Q Consensus 14 ~l~~G~~fGe~~l~~~~~~~-~~~~a~-~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~ 89 (99)
.+.||..-++ .+.+++ +.+.+. ++-+.+.-....|..++...+.+....-...-+-+..++.+++.++.+|+
T Consensus 78 ~~~pg~~~sd----dge~~t~~cvfda~e~~E~i~~~~qvf~KliRRykyLeK~fE~e~~k~Llflk~F~e~Er~KLA 151 (412)
T KOG2297|consen 78 RLQPGGVKSD----DGERHTSYCVFDAEEKREAIRNSVQVFQKLIRRYKYLEKNFENEMRKFLLFLKLFEENERKKLA 151 (412)
T ss_pred ccCCCCcccc----ccCccCceeEeecCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCHHHHHHHH
Confidence 3455555443 233554 555543 34555555666777777766655433222222223355566666666665
No 47
>smart00767 DCD DCD is a plant specific domain in proteins involved in development and programmed cell death. The domain is shared by several proteins in the Arabidopsis and the rice genomes, which otherwise show a different protein architecture. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone.
Probab=37.29 E-value=95 Score=18.71 Aligned_cols=53 Identities=8% Similarity=0.103 Sum_probs=38.3
Q ss_pred CcceeEEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhHh
Q psy8133 30 CKRTATIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDVL 92 (99)
Q Consensus 30 ~~~~~~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~ 92 (99)
.++++.|+....-.+.-|+.+.|...+.++..- .....-.|+-.|-.+|++.+
T Consensus 78 s~fPaQVrf~i~~~C~PL~E~~f~~aI~~nY~~----------~~kF~~eLs~~Qv~~L~~LF 130 (132)
T smart00767 78 SRFPAQVRFRIRKDCKPLPESEFRSAILENYDG----------PSKFRFELSHAQVLRLLDLF 130 (132)
T ss_pred CccCcEEEEEEeeeecCCCHHHHHHHHHHhCcC----------CccccccCCHHHHHHHHHHh
Confidence 468999999999999999999999777655322 23445567777766666544
No 48
>PF10474 DUF2451: Protein of unknown function C-terminus (DUF2451); InterPro: IPR019514 This protein is found in eukaryotes but its function is not known. The N-terminal domain of some members is PF10475 from PFAM (DUF2450).
Probab=37.25 E-value=42 Score=22.06 Aligned_cols=52 Identities=6% Similarity=0.093 Sum_probs=37.3
Q ss_pred ccceEEEEECHHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhHhh
Q psy8133 39 ASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDVLE 93 (99)
Q Consensus 39 ~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~ 93 (99)
.+....+.+|.+++.+++.+|+....+.+.+++...... ++.++.++...++
T Consensus 182 e~YIKAyYl~e~e~~~W~~~h~eYs~~ql~~Lv~~~~~~---~kk~r~~ll~~ie 233 (234)
T PF10474_consen 182 ENYIKAYYLPEEELEEWIRTHTEYSKKQLVGLVNCAAAS---KKKTRQRLLNAIE 233 (234)
T ss_pred HHHHHHHcCCHHHHHHHHHhCcccCHHHHHHHHHHHHHh---hHHHHHHHHHHhh
Confidence 445677889999999999999777777777666654443 6666767665543
No 49
>TIGR02929 anfG_nitrog Fe-only nitrogenase, delta subunit. Nitrogenase, also called dinitrogenase, is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, AnfG, represents the delta subunit of the Fe-only alternative nitrogenase. It is homologous to VnfG, the delta subunit of the V-containing (vanadium) nitrogenase.
Probab=37.16 E-value=59 Score=18.86 Aligned_cols=32 Identities=13% Similarity=0.330 Sum_probs=26.3
Q ss_pred HHHHHHHhhcCCCCCCCCHHHHHHHHhHhhhc
Q psy8133 64 QAEYNDFLKSVPIFKDLPEETLIKISDVLEES 95 (99)
Q Consensus 64 ~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~~ 95 (99)
..+...+-++.+.++.++.+++..+.+.++.+
T Consensus 59 v~la~~~k~rfpW~~~~~kdei~~l~~~lk~r 90 (109)
T TIGR02929 59 VTLAGAYKRRFPWLEDMTKDEIKTLMQALHEK 90 (109)
T ss_pred HHHHHHHHHhCcHHHhCCHHHHHHHHHHHHHH
Confidence 34457788999999999999999998877654
No 50
>KOG4410|consensus
Probab=36.31 E-value=87 Score=21.66 Aligned_cols=42 Identities=24% Similarity=0.451 Sum_probs=28.5
Q ss_pred eeeCCCCeeeehh--hh----cCCcceeEEEEccceEEEE-ECHHHHHH
Q psy8133 13 STLAPGKVFGELA--IL----YNCKRTATIKAASDCKLWA-IERQCFQT 54 (99)
Q Consensus 13 ~~l~~G~~fGe~~--l~----~~~~~~~~~~a~~~~~~~~-i~~~~f~~ 54 (99)
..++.|+-|.+.. ++ .-.+.+--|..+.||++.- ||.+-|..
T Consensus 173 ~RiGkGeGfAdLeygmli~mGAi~~~TpvVTiVHDcQvVD~iP~el~~~ 221 (396)
T KOG4410|consen 173 YRIGKGEGFADLEYGMLIEMGAITPKTPVVTIVHDCQVVDSIPPELFQK 221 (396)
T ss_pred eeeccCCchhhhhhHHHHHhcccCCCCceEEEEecceeeccCCHHHHhh
Confidence 5688999998653 22 1234444566778999987 88887764
No 51
>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal doma
Probab=36.30 E-value=1.2e+02 Score=19.71 Aligned_cols=41 Identities=12% Similarity=0.216 Sum_probs=29.5
Q ss_pred HHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHh
Q psy8133 50 QCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISD 90 (99)
Q Consensus 50 ~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~ 90 (99)
......+.+..........++.++++.|..++..+...|..
T Consensus 31 ~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk 71 (235)
T cd06949 31 ASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLE 71 (235)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHH
Confidence 34444444555555666789999999999999998776654
No 52
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=36.25 E-value=1.1e+02 Score=18.98 Aligned_cols=43 Identities=14% Similarity=0.271 Sum_probs=23.1
Q ss_pred CeEEEEECCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEE
Q psy8133 1 GRVEVSRENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAI 47 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i 47 (99)
|++.+..+++ ...+++||++= +-.+.+..+.....+++.++.+
T Consensus 137 G~~~~~~~~~-~~~l~~Gd~~~---~~~~~~H~~~n~~~~~~~~l~~ 179 (185)
T PRK09943 137 GEIVLTINGQ-DYHLVAGQSYA---INTGIPHSFSNTSAGICRIISA 179 (185)
T ss_pred eEEEEEECCE-EEEecCCCEEE---EcCCCCeeeeCCCCCCeEEEEE
Confidence 5566655553 45688988752 2224444444433445655554
No 53
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=35.24 E-value=1.2e+02 Score=20.09 Aligned_cols=43 Identities=23% Similarity=0.248 Sum_probs=22.8
Q ss_pred CeEEEEECCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEE
Q psy8133 1 GRVEVSRENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAI 47 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i 47 (99)
|++.+..+++. ..+++||++= +-.+.+....-...+++.++.+
T Consensus 89 G~l~v~~~g~~-~~L~~Gd~~y---~pa~~~H~~~N~~~~~a~~l~v 131 (260)
T TIGR03214 89 GEVNVTAEGET-HELREGGYAY---LPPGSKWTLANAQAEDARFFLY 131 (260)
T ss_pred CEEEEEECCEE-EEECCCCEEE---ECCCCCEEEEECCCCCEEEEEE
Confidence 56666555543 4799998863 2223343333333445666544
No 54
>PF03139 AnfG_VnfG: Vanadium/alternative nitrogenase delta subunit; InterPro: IPR004349 The nitrogenase complex 1.18.6.1 from EC catalyses the conversion of molecular nitrogen to ammonia (nitrogen fixation). The complex is hexameric, consisting of 2 alpha, 2 beta, and 2 delta subunits. This family represents the delta subunit of a group of nitrogenases that do not utilise molybdenum (Mo) as a cofactor, but instead use either vanadium (V nitrogenases), or iron (alternative nitrogenases). ; GO: 0016163 nitrogenase activity, 0009399 nitrogen fixation, 0055114 oxidation-reduction process
Probab=34.71 E-value=67 Score=18.74 Aligned_cols=32 Identities=13% Similarity=0.276 Sum_probs=26.2
Q ss_pred HHHHHHHhhcCCCCCCCCHHHHHHHHhHhhhc
Q psy8133 64 QAEYNDFLKSVPIFKDLPEETLIKISDVLEES 95 (99)
Q Consensus 64 ~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~~ 95 (99)
.-+...+-++.+.+..++.+++..+.+.++.+
T Consensus 62 v~la~~~k~rfpW~~~~~k~ei~~lm~~lk~r 93 (112)
T PF03139_consen 62 VCLAEAFKERFPWINEMSKDEIKSLMQGLKER 93 (112)
T ss_pred HHHHHHHHHcCcHHHHCCHHHHHHHHHHHHHH
Confidence 34457788999999999999999998877654
No 55
>COG3718 IolB Uncharacterized enzyme involved in inositol metabolism [Carbohydrate transport and metabolism]
Probab=33.59 E-value=76 Score=21.26 Aligned_cols=37 Identities=19% Similarity=0.295 Sum_probs=23.7
Q ss_pred eCCCCeeeeh----hhhcCCc---------ceeEEEEccceEEEEECHHH
Q psy8133 15 LAPGKVFGEL----AILYNCK---------RTATIKAASDCKLWAIERQC 51 (99)
Q Consensus 15 l~~G~~fGe~----~l~~~~~---------~~~~~~a~~~~~~~~i~~~~ 51 (99)
-..|..||++ +.|.+.| +.+++.|.+++++..-....
T Consensus 63 s~~g~~f~~iG~R~SvFe~~p~~~vYvp~g~~~~vtA~t~~~vAvC~AP~ 112 (270)
T COG3718 63 SAHGSTFGEIGTRMSVFERKPPDSVYVPAGSAFSVTATTDLEVAVCSAPG 112 (270)
T ss_pred eeccchHhhcccccccccCCCCCeEEecCCceEEEEeecceEEEEEeCCC
Confidence 3456666654 3555533 46889999998887765443
No 56
>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely r
Probab=33.09 E-value=1.4e+02 Score=19.53 Aligned_cols=43 Identities=16% Similarity=0.144 Sum_probs=30.2
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 49 RQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 49 ~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
......-+...-......+.++-+++|.|..|+.++...|...
T Consensus 46 ~~~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~ 88 (241)
T cd06939 46 REEMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKA 88 (241)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHH
Confidence 3344444444544556777899999999999999987666543
No 57
>KOG0066|consensus
Probab=31.83 E-value=46 Score=24.76 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=30.2
Q ss_pred EEEEccceEEEEECHHHHHHHHHhhhHHHHHHHHHHh
Q psy8133 35 TIKAASDCKLWAIERQCFQTIMMRTGLIRQAEYNDFL 71 (99)
Q Consensus 35 ~~~a~~~~~~~~i~~~~f~~~l~~~~~~~~~~~~~~l 71 (99)
..+..++|.+|++....+.++-..+..+.+..+..+-
T Consensus 762 RLi~eT~C~LwVvE~Q~i~eIdGdFeDYkkEVLdaLG 798 (807)
T KOG0066|consen 762 RLIVETDCNLWVVENQGIDEIDGDFEDYKKEVLDALG 798 (807)
T ss_pred ceeeecCceEEEEccCChhhccccHHHHHHHHHHHHH
Confidence 3667899999999999999998888888877766543
No 58
>PF07943 PBP5_C: Penicillin-binding protein 5, C-terminal domain; InterPro: IPR012907 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry contains proteins that are annotated as penicillin-binding protein 5 and 6. These belong to MEROPS peptidase family S11 (D-Ala-D-Ala carboxypeptidase A family, clan SE). Penicillin-binding protein 5 expressed by Escherichia coli functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (IPR001967 from INTERPRO) is the catalytic domain. The C-terminal domain, this entry, is organised into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides []. ; GO: 0009002 serine-type D-Ala-D-Ala carboxypeptidase activity, 0006508 proteolysis; PDB: 3A3J_A 3MFD_B 1XP4_D 3MZD_A 1NZU_A 1NJ4_A 1Z6F_A 3MZF_A 1NZO_A 3MZE_A ....
Probab=31.48 E-value=88 Score=16.62 Aligned_cols=37 Identities=16% Similarity=0.158 Sum_probs=29.7
Q ss_pred EEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEE
Q psy8133 11 YLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAI 47 (99)
Q Consensus 11 ~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i 47 (99)
....+..|+.++...+..+......+.+.++..++.-
T Consensus 3 ~~~l~~kg~~~~~~~v~~g~~~~v~l~~~~d~~~~~~ 39 (91)
T PF07943_consen 3 TVKLLKKGQPVATVPVKKGKKKTVPLVAKEDIYITVP 39 (91)
T ss_dssp EEEEE-TTCESEEEEEESCSSSEEEEEESSGEEEEEE
T ss_pred cEEEeCCCCEEEEEEECCCCcCEEEEEECCCEEEEEE
Confidence 3566889999999999988888899999988877663
No 59
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=30.65 E-value=99 Score=18.77 Aligned_cols=45 Identities=13% Similarity=0.063 Sum_probs=29.6
Q ss_pred HHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhHhhh
Q psy8133 50 QCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDVLEE 94 (99)
Q Consensus 50 ~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~ 94 (99)
+.+.+++.+++..+..++.-+..-...+..+++..+..+++.+..
T Consensus 8 ~~~~~i~~~~~~~~~~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v 52 (154)
T PRK07539 8 AAIEREIAKYPRPRSAVIPALKIVQEQRGWVPDEAIEAVADYLGM 52 (154)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhCc
Confidence 467788888875555444433333356788888888888877653
No 60
>PRK13290 ectC L-ectoine synthase; Reviewed
Probab=29.59 E-value=1.2e+02 Score=17.73 Aligned_cols=42 Identities=19% Similarity=0.380 Sum_probs=22.3
Q ss_pred CeEEEE-ECCeEEeeeCCCCeeeehhhhcCCcceeEEEEccceEEEEE
Q psy8133 1 GRVEVS-RENKYLSTLAPGKVFGELAILYNCKRTATIKAASDCKLWAI 47 (99)
Q Consensus 1 G~v~v~-~~~~~v~~l~~G~~fGe~~l~~~~~~~~~~~a~~~~~~~~i 47 (99)
|+..+. .++.....+++||+|- .....+..+.+.+++.++.+
T Consensus 64 G~~~~~~i~~g~~~~L~aGD~i~-----~~~~~~H~~~N~e~~~~l~v 106 (125)
T PRK13290 64 GEGEVEDLATGEVHPIRPGTMYA-----LDKHDRHYLRAGEDMRLVCV 106 (125)
T ss_pred CEEEEEEcCCCEEEEeCCCeEEE-----ECCCCcEEEEcCCCEEEEEE
Confidence 455555 3334456789998864 22222333444467666554
No 61
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=29.28 E-value=1.5e+02 Score=18.51 Aligned_cols=34 Identities=18% Similarity=0.237 Sum_probs=25.8
Q ss_pred hhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 58 RTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 58 ~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
+........+.++.+++|.|+.++..+...|...
T Consensus 9 ~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~ 42 (195)
T cd06941 9 EALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKA 42 (195)
T ss_pred HHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHH
Confidence 3444455667889999999999999987776644
No 62
>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=27.79 E-value=1.4e+02 Score=17.90 Aligned_cols=32 Identities=22% Similarity=0.335 Sum_probs=24.6
Q ss_pred hHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 60 GLIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 60 ~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
.........++.+.++.|..|+..+...|...
T Consensus 11 ~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~ 42 (174)
T cd06929 11 MTVAIRRVVEFAKRIPGFRELSQEDQIALLKG 42 (174)
T ss_pred HHHHHHHHHhhccCCcCcccCChhHHHHHHHh
Confidence 33445566789999999999999987776543
No 63
>cd06935 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors. The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), a
Probab=27.52 E-value=1.8e+02 Score=19.01 Aligned_cols=35 Identities=26% Similarity=0.327 Sum_probs=26.0
Q ss_pred HhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 57 MRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 57 ~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
.+...........+.+++|.|..|+..+...|...
T Consensus 58 ~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~ 92 (243)
T cd06935 58 TKIITPAITRVVDFAKKLPMFTELPCEDQIILLKG 92 (243)
T ss_pred HHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHH
Confidence 34444555667899999999999999987666543
No 64
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=27.21 E-value=1.2e+02 Score=18.93 Aligned_cols=45 Identities=18% Similarity=0.241 Sum_probs=30.1
Q ss_pred HHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhHhhh
Q psy8133 50 QCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDVLEE 94 (99)
Q Consensus 50 ~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~ 94 (99)
+.+..++.+++..+..++.-+-.-...+..+++..+..+++.+..
T Consensus 22 ~~i~~ii~~~~~~~~~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v 66 (169)
T PRK07571 22 KVLEATMKRNQYRQDALIEVLHKAQELFGYLERDLLLYVARQLKL 66 (169)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCc
Confidence 356777788876555554444333357788888888888877653
No 65
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=26.25 E-value=73 Score=14.01 Aligned_cols=19 Identities=11% Similarity=0.195 Sum_probs=15.3
Q ss_pred ceEEEEECHHHHHHHHHhh
Q psy8133 41 DCKLWAIERQCFQTIMMRT 59 (99)
Q Consensus 41 ~~~~~~i~~~~f~~~l~~~ 59 (99)
...++..+..+|..++++.
T Consensus 4 ~p~vi~~d~~~Fr~lVQ~L 22 (31)
T PF05678_consen 4 PPTVIHTDPSNFRALVQRL 22 (31)
T ss_pred CCEEEEeCHHHHHHHHHHh
Confidence 4578889999999988764
No 66
>cd04759 Rib_hydrolase ADP-ribosyl cyclase (also known as cyclic ADP-ribose hydrolase or CD38) synthesizes the second messenger cyclic-ADP ribose (cADPR), which in turn releases calcium from internal stores. Mammals possess two membrane proteins, CD38 and BST-1/CD157, which exhibit ADP-ribosyl cyclase function, as well as intracellular soluble ADP-ribose cyclases. CD38 is involved in differentiation, adhesion, and cell proliferation, as well as diseases such as AIDS, diabetes, and B-cell chronic lymphocytic leukemia. The extramembrane domain of CD38 acts as a multifunctional enzyme and can synthesize cADPR from NAD+, hydrolyze NAD+, and cADPR to ADPR, as well as catalyze the exchange of the nicotinamide group of NADP+ with nicotinic acid under acidic conditions to yield NAADP+ (nicotinic acid-adenine dinucleotide phosphate), a metabolite involved in Ca2+ mobilization from acidic stores.
Probab=25.16 E-value=1.4e+02 Score=19.98 Aligned_cols=28 Identities=21% Similarity=0.278 Sum_probs=21.3
Q ss_pred CeEEEEECCeEEe-eeCCCCeeeehhhhc
Q psy8133 1 GRVEVSRENKYLS-TLAPGKVFGELAILY 28 (99)
Q Consensus 1 G~v~v~~~~~~v~-~l~~G~~fGe~~l~~ 28 (99)
|.|.|.-++.... -+.++.+||...+..
T Consensus 147 G~V~VmLNGS~~~~af~~~S~Fg~vElp~ 175 (242)
T cd04759 147 GVVHVMLNGSASGGAFRNNSTFGSVEIPN 175 (242)
T ss_pred CeEEEEEcCCCCCCCcCCCCceeeEEccc
Confidence 6777777776555 789999999877664
No 67
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=24.22 E-value=2.1e+02 Score=18.63 Aligned_cols=31 Identities=13% Similarity=0.142 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 61 LIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 61 ~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
...-.....+.++++.|+.|+..+...|...
T Consensus 48 ~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~ 78 (237)
T cd07070 48 DQTFISIVDWARRCMVFKELEVADQMTLLQN 78 (237)
T ss_pred HHHHHHHHHHHHhCCChhhCCHHHHHHHHHH
Confidence 3344456789999999999999987766543
No 68
>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcript
Probab=24.11 E-value=2.1e+02 Score=18.49 Aligned_cols=31 Identities=23% Similarity=0.373 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 61 LIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 61 ~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
......+.++.++++.|..|+..+...|...
T Consensus 49 ~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~ 79 (231)
T cd06938 49 ILTVQLIVEFAKRLPGFDKLSREDQITLLKA 79 (231)
T ss_pred HHHHHHHHHHHhcCCccccCChhHHHHHHHH
Confidence 3444556899999999999999987766544
No 69
>PF11699 CENP-C_C: Mif2/CENP-C like; PDB: 2VPV_B.
Probab=23.51 E-value=1.4e+02 Score=16.35 Aligned_cols=20 Identities=30% Similarity=0.561 Sum_probs=10.6
Q ss_pred CeEEEEECCeEEeeeCCCCee
Q psy8133 1 GRVEVSRENKYLSTLAPGKVF 21 (99)
Q Consensus 1 G~v~v~~~~~~v~~l~~G~~f 21 (99)
|.|++.-++... .+.+|++|
T Consensus 42 G~v~Vti~~~~f-~v~~G~~F 61 (85)
T PF11699_consen 42 GKVEVTIHETSF-VVTKGGSF 61 (85)
T ss_dssp SEEEEEETTEEE-EEETT-EE
T ss_pred CEEEEEEcCcEE-EEeCCCEE
Confidence 556665555332 36777776
No 70
>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee
Probab=23.03 E-value=2.2e+02 Score=18.37 Aligned_cols=29 Identities=31% Similarity=0.391 Sum_probs=23.3
Q ss_pred HHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 63 RQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 63 ~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
....+.++.++++.|..|+..+...|...
T Consensus 55 ~i~~~VefaK~lP~F~~L~~~DQi~LLK~ 83 (236)
T cd06954 55 SVQEIVDFAKQLPGFLTLTREDQIALLKA 83 (236)
T ss_pred HHHHHHHHHcCCCCcccCChHHHHHHHHH
Confidence 44457889999999999999987776644
No 71
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=22.93 E-value=1.7e+02 Score=17.91 Aligned_cols=46 Identities=15% Similarity=0.135 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhHhhh
Q psy8133 49 RQCFQTIMMRTGLIRQAEYNDFLKSVPIFKDLPEETLIKISDVLEE 94 (99)
Q Consensus 49 ~~~f~~~l~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~~ 94 (99)
.+.+.+++..++..+..++.-+-.-...+..++...+..+++.+..
T Consensus 8 ~~~i~~ii~~y~~~~~~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v 53 (156)
T PRK05988 8 AARIAAIIAEHKHLEGALLPILHAIQDEFGYVPEDAVPVIAEALNL 53 (156)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCC
Confidence 3466778877776554444333333356778888888888877653
No 72
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=22.84 E-value=2.2e+02 Score=18.31 Aligned_cols=31 Identities=23% Similarity=0.260 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 61 LIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 61 ~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
........++.++++.|+.|+..+...|...
T Consensus 46 ~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~ 76 (221)
T cd06936 46 TSHVQVLVEFTKGLPGFETLDHEDQIALLKG 76 (221)
T ss_pred HHHHHHHHHHHhCCCchhhCChhHHHHHHHH
Confidence 3445556889999999999999987766543
No 73
>COG3228 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.71 E-value=1.8e+02 Score=19.56 Aligned_cols=28 Identities=11% Similarity=0.274 Sum_probs=22.8
Q ss_pred HHHHHHhhcCCCCCCCCHHHHHHHHhHh
Q psy8133 65 AEYNDFLKSVPIFKDLPEETLIKISDVL 92 (99)
Q Consensus 65 ~~~~~~l~~~~~~~~l~~~~~~~l~~~~ 92 (99)
..+...+.+++++-.|++.+..+|....
T Consensus 21 ~~W~~~l~~lP~l~~L~~~e~~RL~~~a 48 (266)
T COG3228 21 PLWQAALSNLPLLLCLSPQEQRRLVELA 48 (266)
T ss_pred hHHHHHHhcCCcccCCCHHHHHHHHHHH
Confidence 4567788889999999999988886543
No 74
>cd06944 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors. The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not
Probab=21.40 E-value=2.4e+02 Score=18.30 Aligned_cols=31 Identities=13% Similarity=0.161 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhhcCCCCCCCCHHHHHHHHhH
Q psy8133 61 LIRQAEYNDFLKSVPIFKDLPEETLIKISDV 91 (99)
Q Consensus 61 ~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~ 91 (99)
.........+.++++.|++++..+...|...
T Consensus 48 ~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~ 78 (237)
T cd06944 48 DQTLFSIVEWARNSVFFKELKVDDQMKLLQN 78 (237)
T ss_pred HHHHHHHHHHHHhCCChhcCCHHHHHHHHHH
Confidence 3334446789999999999999987766543
No 75
>PF10742 DUF2555: Protein of unknown function (DUF2555); InterPro: IPR019678 This entry represents conserved proteins found in Cyanobacteria. The function is not known.
Probab=21.23 E-value=87 Score=15.98 Aligned_cols=22 Identities=27% Similarity=0.324 Sum_probs=16.8
Q ss_pred CCCCCHHHHHHHHhHhhhccCC
Q psy8133 77 FKDLPEETLIKISDVLEESLGS 98 (99)
Q Consensus 77 ~~~l~~~~~~~l~~~~~~~~~~ 98 (99)
+..+++.....|+..++...|+
T Consensus 6 ~~~~t~~~va~LA~RLE~DdY~ 27 (57)
T PF10742_consen 6 LAAFTEEDVAKLAKRLEEDDYP 27 (57)
T ss_pred HhhcCHHHHHHHHHhhhhccCC
Confidence 4567777888888888888775
No 76
>PF04962 KduI: KduI/IolB family; InterPro: IPR021120 The KduI/IolB family of enzymes includes 5-keto 4-deoxyuronate isomerase (KduI) and 5-deoxy-glucuronate isomerase (IolB). KduI is involved in pectin degradation by free-living soil bacteria that use pectin as a carbon source, breaking it down to 2-keto-3-deoxygluconate, which can ultimately be converted to pyruvate. KduI catalyses the fourth step in pectin degradation, namely the interconversion of 5-keto-4-deoxyuronate and 2,5-diketo-3-dexoygluconate []. KduI has a TIM-barrel fold []. IolB is one of several bacterial proteins encoded by the inositol operon (iolABCDEFGHIJ) in Bacillus subtilis that are involved in myo-inositol catabolism. The enzyme is responsible for isomerization of 5-deoxy-D-glucuronic acid by IolB to produce 2-deoxy-5-keto-D-gluconic acid []. IolBs possess a cupin-like structure.; GO: 0016861 intramolecular oxidoreductase activity, interconverting aldoses and ketoses, 0008152 metabolic process; PDB: 1YWK_B 2QJV_B 1X8M_A 1XRU_A.
Probab=20.45 E-value=2.8e+02 Score=18.60 Aligned_cols=48 Identities=15% Similarity=0.209 Sum_probs=23.3
Q ss_pred CeEEEEECC-eEEeeeCCCCeeeehh--hhcCCcceeEEEEccceEEEEEC
Q psy8133 1 GRVEVSREN-KYLSTLAPGKVFGELA--ILYNCKRTATIKAASDCKLWAIE 48 (99)
Q Consensus 1 G~v~v~~~~-~~v~~l~~G~~fGe~~--l~~~~~~~~~~~a~~~~~~~~i~ 48 (99)
|.+.+..++ ..-..-++-+.|.+.. +....-....+.|.++++++...
T Consensus 56 G~~~v~~~g~~~~~l~~R~~vF~~~~d~lYvp~g~~~~i~a~~~ae~~~~s 106 (261)
T PF04962_consen 56 GKATVTVDGEEFYELGGRESVFDGPPDALYVPRGTKVVIFASTDAEFAVCS 106 (261)
T ss_dssp SSEEEEETTEEEEEE-TTSSGGGS--EEEEE-TT--EEEEESSTEEEEEEE
T ss_pred CEEEEEeCCceEEEecccccccCCCCcEEEeCCCCeEEEEEcCCCEEEEEc
Confidence 455555555 3333334445554332 22233345777888888888653
No 77
>cd06933 NR_LBD_VDR The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily. The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and
Probab=20.41 E-value=2.6e+02 Score=18.23 Aligned_cols=33 Identities=24% Similarity=0.269 Sum_probs=24.4
Q ss_pred hhhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHh
Q psy8133 58 RTGLIRQAEYNDFLKSVPIFKDLPEETLIKISD 90 (99)
Q Consensus 58 ~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~ 90 (99)
+........+.++.++++.|.+++..+...|..
T Consensus 44 ~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk 76 (238)
T cd06933 44 DLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLK 76 (238)
T ss_pred HHHHHHHHHHHHHHcCCCccccCChHHHHHHHH
Confidence 333344555689999999999999988666653
No 78
>PF04518 Effector_1: Effector from type III secretion system; InterPro: IPR007606 This family contains several uncharacterised chlamydial proteins.
Probab=20.24 E-value=2.1e+02 Score=20.50 Aligned_cols=35 Identities=23% Similarity=0.125 Sum_probs=29.2
Q ss_pred hhHHHHHHHHHHhhcCCCCCCCCHHHHHHHHhHhh
Q psy8133 59 TGLIRQAEYNDFLKSVPIFKDLPEETLIKISDVLE 93 (99)
Q Consensus 59 ~~~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~~ 93 (99)
++..+...+.+++.++.-...++..|+.++.+.+.
T Consensus 218 ~~~~A~~~l~~~~~~V~~d~~lT~~Qk~~l~d~l~ 252 (379)
T PF04518_consen 218 SCERAKAVLNKQLARVKADAKLTSEQKSELLDSLN 252 (379)
T ss_pred HHHHHHHHHHHHHHHHhcccccCHHHHHHHHHHHH
Confidence 45556777889999999999999999999987654
No 79
>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-
Probab=20.10 E-value=2.5e+02 Score=17.90 Aligned_cols=32 Identities=13% Similarity=0.099 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhhcCCCCCCCCHHHHHHHHhHh
Q psy8133 61 LIRQAEYNDFLKSVPIFKDLPEETLIKISDVL 92 (99)
Q Consensus 61 ~~~~~~~~~~l~~~~~~~~l~~~~~~~l~~~~ 92 (99)
........++.++++.|+.++..+...|....
T Consensus 37 ~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~ 68 (221)
T cd06946 37 DRELVVIIGWAKHIPGFSSLSLNDQMSLLQSA 68 (221)
T ss_pred HHHHHHHHHHHHhCCCcccCCHHHHHHHHHHH
Confidence 34445567899999999999999877765443
Done!