Query 006400
Match_columns 647
No_of_seqs 191 out of 1210
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 22:45:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006400.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006400hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03131 hypothetical protein; 100.0 1E-167 2E-172 1356.3 41.9 615 1-644 1-633 (705)
2 PLN03119 putative ADP-ribosyla 100.0 1E-151 2E-156 1223.6 39.1 573 1-644 1-579 (648)
3 KOG0702 Predicted GTPase-activ 100.0 3.9E-36 8.4E-41 322.5 27.0 440 1-642 1-454 (524)
4 KOG0703 Predicted GTPase-activ 100.0 1.4E-35 3E-40 304.0 7.3 118 5-125 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 2.9E-35 6.2E-40 266.7 8.1 111 12-123 2-115 (116)
6 smart00105 ArfGap Putative GTP 100.0 2.1E-33 4.5E-38 253.3 10.1 106 21-126 1-109 (112)
7 COG5347 GTPase-activating prot 100.0 1.7E-30 3.7E-35 271.4 8.8 117 8-124 5-125 (319)
8 KOG0704 ADP-ribosylation facto 99.9 4.5E-28 9.7E-33 252.3 11.0 86 7-92 3-91 (386)
9 PLN03114 ADP-ribosylation fact 99.9 1.5E-25 3.2E-30 234.9 11.0 116 11-126 10-130 (395)
10 KOG0706 Predicted GTPase-activ 99.9 5.7E-25 1.2E-29 235.0 7.2 85 8-92 8-95 (454)
11 KOG0705 GTPase-activating prot 99.9 7.6E-24 1.7E-28 231.1 7.0 116 11-127 501-619 (749)
12 KOG0521 Putative GTPase activa 99.8 7.1E-21 1.5E-25 218.5 4.0 115 13-127 416-534 (785)
13 KOG1117 Rho- and Arf-GTPase ac 99.6 1.6E-16 3.4E-21 179.6 3.7 109 15-124 290-403 (1186)
14 KOG0818 GTPase-activating prot 99.6 8.1E-17 1.8E-21 174.4 0.5 133 18-150 3-146 (669)
15 PLN03131 hypothetical protein; 96.8 0.094 2E-06 60.5 19.1 39 330-373 359-398 (705)
16 PLN03119 putative ADP-ribosyla 95.8 0.51 1.1E-05 54.4 18.2 39 358-396 318-357 (648)
17 KOG0702 Predicted GTPase-activ 94.6 0.058 1.2E-06 60.7 5.9 142 150-301 1-144 (524)
18 KOG0521 Putative GTPase activa 89.1 0.11 2.4E-06 61.8 -0.1 67 20-88 627-697 (785)
19 PRK12495 hypothetical protein; 76.3 1.7 3.7E-05 45.0 2.2 37 12-52 29-67 (226)
20 PF00643 zf-B_box: B-box zinc 75.8 1.7 3.8E-05 32.6 1.6 40 22-63 2-42 (42)
21 PRK00085 recO DNA repair prote 56.6 9.7 0.00021 38.5 3.1 31 20-50 146-177 (247)
22 TIGR00613 reco DNA repair prot 56.6 6.9 0.00015 39.4 2.0 33 20-52 144-177 (241)
23 TIGR02419 C4_traR_proteo phage 51.0 9.1 0.0002 32.2 1.5 33 20-53 28-62 (63)
24 COG1734 DksA DnaK suppressor p 49.2 10 0.00022 36.0 1.7 30 24-53 81-111 (120)
25 PRK13715 conjugal transfer pro 43.9 11 0.00024 32.8 0.9 31 23-53 34-65 (73)
26 COG1381 RecO Recombinational D 42.3 13 0.00028 38.6 1.4 30 21-50 152-182 (251)
27 PRK11019 hypothetical protein; 42.3 16 0.00035 33.0 1.8 33 22-55 35-69 (88)
28 PHA00080 DksA-like zinc finger 38.6 16 0.00034 31.7 1.1 32 21-53 29-62 (72)
29 KOG2057 Predicted equilibrativ 38.2 43 0.00093 37.1 4.5 81 349-429 327-419 (499)
30 TIGR02890 spore_yteA sporulati 37.2 23 0.00051 34.9 2.2 42 10-53 74-117 (159)
31 PF11781 RRN7: RNA polymerase 36.8 18 0.0004 27.4 1.1 28 21-51 6-33 (36)
32 PF08271 TF_Zn_Ribbon: TFIIB z 36.2 11 0.00024 29.0 -0.2 27 25-52 2-28 (43)
33 PF01286 XPA_N: XPA protein N- 33.6 12 0.00025 28.5 -0.4 27 24-50 4-31 (34)
34 smart00401 ZnF_GATA zinc finge 32.1 28 0.00061 28.2 1.5 36 22-57 2-39 (52)
35 PRK10778 dksA RNA polymerase-b 30.1 63 0.0014 31.7 3.8 35 20-54 108-143 (151)
36 COG5145 RAD14 DNA excision rep 27.1 27 0.00058 36.8 0.7 32 21-53 114-147 (292)
37 cd07173 NR_DBD_AR DNA-binding 25.3 45 0.00098 29.4 1.8 31 22-55 2-32 (82)
38 cd07171 NR_DBD_ER DNA-binding 25.1 38 0.00082 29.8 1.2 31 22-55 2-32 (82)
39 TIGR00100 hypA hydrogenase nic 24.0 24 0.00051 32.8 -0.2 44 19-66 66-113 (115)
40 PRK03681 hypA hydrogenase nick 24.0 23 0.0005 32.9 -0.3 44 19-65 66-113 (114)
41 cd06968 NR_DBD_ROR DNA-binding 23.2 43 0.00093 30.3 1.2 31 22-55 4-34 (95)
42 KOG3362 Predicted BBOX Zn-fing 23.0 29 0.00062 34.3 0.1 34 21-55 116-150 (156)
43 COG1997 RPL43A Ribosomal prote 22.7 56 0.0012 29.8 1.8 30 21-52 33-62 (89)
44 COG2174 RPL34A Ribosomal prote 22.1 49 0.0011 30.4 1.3 35 17-51 28-79 (93)
45 PRK00564 hypA hydrogenase nick 21.2 29 0.00062 32.4 -0.3 44 20-66 68-115 (117)
46 PF00320 GATA: GATA zinc finge 21.2 43 0.00094 25.1 0.7 30 26-55 1-32 (36)
47 cd07170 NR_DBD_ERR DNA-binding 21.2 47 0.001 30.3 1.1 30 23-55 4-33 (97)
48 COG2719 SpoVR Uncharacterized 20.2 29 0.00063 39.6 -0.5 8 418-425 270-277 (495)
49 PRK11767 SpoVR family protein; 20.2 29 0.00063 40.1 -0.6 8 418-425 273-280 (498)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1e-167 Score=1356.35 Aligned_cols=615 Identities=60% Similarity=0.970 Sum_probs=589.1
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCCCceeecccCCCCHHHHHHHHhcC
Q 006400 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (647)
Q Consensus 1 M~srke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSItLD~Wt~eEVe~Lq~gG 80 (647)
|++||++|+++++|++|+++|+|++|||||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
T Consensus 1 m~SkkqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLghRVKSVTLD~WtdeEV~~Mk~gG 80 (705)
T PLN03131 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFTHRVKSVSMSKFTSQDVEALQNGG 80 (705)
T ss_pred CcchHHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccCcccccccCCCCCHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhhcCCcccCCCCCCCchHHHHHHHHHHHhhccccCCCCCCCCCCCccCCCCCcccccccCCCCCCCCCCCcc
Q 006400 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (647)
Q Consensus 81 N~rAN~iyea~~d~~~~~~P~~sd~~~~reFIraKYveKrF~~~k~~DkPpr~~q~l~~~~~e~rr~ssy~S~SQsPp~d 160 (647)
|++||+|||++|+..+.++|...+.+++|+|||.|||+|||+.....++|+++.+.++.++.++||.++||+++|||||+
T Consensus 81 N~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr~~syh~~SqSPpY~ 160 (705)
T PLN03131 81 NQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRRACSYHSYSQSPPYD 160 (705)
T ss_pred cHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccccccccCCCcCCCcc
Confidence 99999999999998877888888888999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCccccccccccCCCCCCCCCCCCCCcc
Q 006400 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (647)
Q Consensus 161 ~~~Edrr~~k~~~~l~Rkpgsd~~~~~gk~s~~~~sP~r~s~~~~~DRfa~e~s~~r~sdfs~s~~g~~~k~~~~sp~~~ 240 (647)
|+||||||||+...++|+||+++++|.|||++|++||+|+.+||+||||+||++++|++||+++++|+++|.+.+|||++
T Consensus 161 ~~yedrRygk~~~~~~R~pg~d~~~~~~k~~~~~~SP~r~~d~~~eDrf~ne~~~~r~~d~s~ss~~~~~r~~~~SP~~~ 240 (705)
T PLN03131 161 FQYEDRRYGKQAGILTRKPGSDRGLNVGKMASFICSPTRLNDRMFEDRFANEGSVSGVSDYSVSSGGDLVRSGAESPNFQ 240 (705)
T ss_pred cccccccccccccccccCCccccccccccccccccCchhhhhhhhhcccccCCCCcccccccccccccccccCCCCCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCcccccccccccccCC-----------CCCCCCCCCCccccCCCccccCCCccccccccCCCCccCCCCCcc
Q 006400 241 KDAGFNSPPVQLSRDVSSLKANFK-----------RDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQ 309 (647)
Q Consensus 241 Kd~~~ssp~v~~~~~~~~~~~~~~-----------~~~~~~~~~qrt~ss~S~~s~~~~~~~~k~~~s~sl~d~~~~~~~ 309 (647)
|++. +||||+++|+|||+.++.. +.++|++++|||+|+||+||+||+++++|++||+|||||.+|+++
T Consensus 241 k~~~-~Sp~v~p~r~ilg~n~~~~~v~~~s~~~~~~~~~~~~~~Qrt~Ssgs~gS~dg~s~s~Ks~~s~sL~D~~~e~~~ 319 (705)
T PLN03131 241 KDIA-FSPPIQPPKDILGEDVQQRRIDLFSAALCKQGAEGCPHIQRSASLGSIGSFDSLSVSIKSFNSGSLADIVAEAEQ 319 (705)
T ss_pred cccC-CCCCcccchhhccccccccccCCCcccccccccccccccccccccCcccccCCCccceeecccccccccccCccc
Confidence 9975 5789988999999765544 457999999999999999999999999999999999999999999
Q ss_pred CcCCCCCcccccCCCCCCCCcCccccCCCCCCCCCCCCCCCCCCccCCCccccc-cccccccccCCCCCCCCCCCCCCCC
Q 006400 310 AAGAPLDKISTFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTS 388 (647)
Q Consensus 310 ~~~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlf~~p~~~~~-~v~~f~~~~~~~~~s~~~~q~~q~~ 388 (647)
+++++|.|+.+.++..+...+.++|+|++||+|+++..++++|||||+|+|+.| +|||||-+++..++++|.+|+.||+
T Consensus 320 ~~~~~q~k~~~~~~~~~~~~~~s~d~f~~~v~p~~~~~~a~pIDLFqlp~ts~a~~vdlf~~s~l~~~p~~n~~q~~qts 399 (705)
T PLN03131 320 AAGNHQDKMPAFPRMAGSGSHASLDHFKAPVAPEAAAPMAPPIDLFQLPATSPAPPVDLFEIPPLDPAPAINAYQPPQTS 399 (705)
T ss_pred cccccccccCCccccccccccccccccccccccccccccCCchhhhhccCCCCCCcccccccCcccCCCccccCCCCccc
Confidence 999999999999999999999999999999999999999999999999999988 9999999999999999999999999
Q ss_pred CCCCcccc-cccCCCccccccCCCCCCCCCCCCCcccccCCCCCCCCCCccCcccccccCCCCCCCCCCCCCCCCCCCCC
Q 006400 389 SPSSLNFF-QITEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQW 467 (647)
Q Consensus 389 ~~~~~d~f-~~~~~~~~~~~~~~~~~~~~~~n~gwatfd~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 467 (647)
++++|||| +|+||++++++|++++||++||||||||||+++.++|++|++||+..+|+.....+.+||.++++.++|||
T Consensus 400 ~p~~~dlfag~~qqq~~~s~~~~~~~~s~pknegwa~fd~~~p~~s~~~~~n~t~~~v~~~~~~~~~~d~v~~~~~~~q~ 479 (705)
T PLN03131 400 LPSSIDLFGGITQQQSINSLDEKSPELSIPKNEGWATFDGIQPIASTPGNENLTPFSIGPSMAGSANFDQVPSLDKGMQW 479 (705)
T ss_pred CCccccccccccccCccccccccCcccCCccccCcccccCCCcccccCCcccccccccccccccCcchhhcccccccccc
Confidence 99999999 99999999999999999999999999999999988999999999888999776456799999999999999
Q ss_pred CcccCCCCCCCCCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccc--cccCCCCCCCC
Q 006400 468 PAFQNSGANGPSPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFD--DFTSHLPSEGF 545 (647)
Q Consensus 468 ~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~--ds~~~~~~~~~ 545 (647)
|+|+++.++.+ +.||++|.+++||||+|.. +++|+||||+ |+++++||+++
T Consensus 480 Pp~~~~~~~~s--------------------------~s~~~pW~~~~~~V~~~~~-~~~q~WnAF~~~ds~~~~~l~~~ 532 (705)
T PLN03131 480 PPFQNSSDEES--------------------------ASGPAPWLGDLHNVEAPDN-TSAQNWNAFEFDDSVAGIPLEGI 532 (705)
T ss_pred CCCcccccccc--------------------------cccCCcccccchhcccCCc-cCccccccccccccccccccccc
Confidence 99998877553 4577899999999999986 9999999999 99999999999
Q ss_pred CCCCCCcccCCCCCCCCCccccc-cccccCCCCCCcccCCCC--CCCCCCCCCCccCCCCCCCCCCcccccccccccCCC
Q 006400 546 KPNSEPHVDAYMPSPTPDQYLAI-VSQETNDDGNPRVASHDG--PPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKS 622 (647)
Q Consensus 546 ~~~~~~~~~~~~~~~t~~~~~~~-~~q~s~~dg~qr~ap~~~--f~~~~~ps~~v~gps~~p~~~~~mG~~~~~~~~~ks 622 (647)
++++++|++++++++.+ ||+++ ++||+++||+||+||+|+ |++|++|+.+|+||+|+|+++|+||++++|+++|||
T Consensus 533 ~~~s~~q~~~~~~~t~~-q~~~~~~~~d~~~d~~~r~~p~~~~~~~g~~~~~~~~~~ps~~~~~~~~~~~~~s~~~~~ks 611 (705)
T PLN03131 533 KQSSEPQTAANMPPTAD-QLIGCKALEDFNKDGIKRTAPHGQGELPGLDEPSDILAEPSYTPPAHPIMEHAQSHANDHKS 611 (705)
T ss_pred cccccccccccCCCCcc-cccccccccccccccccccCCCCCcCCCCCCCCCccccCCCCCccccccccccccccCccCC
Confidence 99999988766655555 99999 999999999999999999 999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCCCcccccc
Q 006400 623 TNPFDFPCDSDLEQNNMVWPRF 644 (647)
Q Consensus 623 tNPFDlPfdsD~e~~nMFm~~~ 644 (647)
+||||||||||+|++|||||+-
T Consensus 612 ~npfdl~~dsd~~~~~mf~d~s 633 (705)
T PLN03131 612 INPFDLPYDSDLEPGNMFLDMS 633 (705)
T ss_pred CCCcCCccccccCcccceeehH
Confidence 9999999999999999999973
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=1.1e-151 Score=1223.59 Aligned_cols=573 Identities=50% Similarity=0.767 Sum_probs=531.9
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCCCceeecccCCCCHHHHHHHHhcC
Q 006400 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (647)
Q Consensus 1 M~srke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSItLD~Wt~eEVe~Lq~gG 80 (647)
|++||++||++++|++|+++|+|++|||||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
T Consensus 1 M~SKR~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLGhRVKSLSLDkWT~EEVe~Mk~gG 80 (648)
T PLN03119 1 MGSKREEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFTHRVKSVSMSKFTSKEVEVLQNGG 80 (648)
T ss_pred CcchHHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCCceeeccccCCCCHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhhcCCcccCCCCCCCchHHHHHHHHHHHhhccccCCCCCCCCCCCccCCCCCcccccccCCCCCCCCCCCcc
Q 006400 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (647)
Q Consensus 81 N~rAN~iyea~~d~~~~~~P~~sd~~~~reFIraKYveKrF~~~k~~DkPpr~~q~l~~~~~e~rr~ssy~S~SQsPp~d 160 (647)
|++||+|||++|+..+.++|...+.+++|+|||.||++|+|+.....|+|+++.++.+.+++++||.++||+++|+|||+
T Consensus 81 N~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~~~~s~h~~s~sp~y~ 160 (648)
T PLN03119 81 NQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTRRANSYHSYSQSPPYD 160 (648)
T ss_pred hHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCcccccccccccccccccccCCCCCCCCCcc
Confidence 99999999999998777788888888999999999999999999999999999999999899999999999999999999
Q ss_pred cchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCccccccccccCCCCCCCCCCCCCCcc
Q 006400 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (647)
Q Consensus 161 ~~~Edrr~~k~~~~l~Rkpgsd~~~~~gk~s~~~~sP~r~s~~~~~DRfa~e~s~~r~sdfs~s~~g~~~k~~~~sp~~~ 240 (647)
++|||||||||...|+||||+||+++ ||+++|+|+|+|+.++|+||||+||++++|++||+++++||++|.+.+||||+
T Consensus 161 ~~ye~rr~~~~~~~~~~~~~s~r~~~-~k~~~~~~s~~~~~~~m~ed~f~~e~~~~r~sd~s~ss~g~~~~~~~~sp~~~ 239 (648)
T PLN03119 161 YQYEERRYGKIPLGFTGKSASVKGLH-AKASSFVYSPGRFSDHMFEDQFSNEDSAPRASDYSVSSAGDPFRSDIQSPNFQ 239 (648)
T ss_pred cchhhhhccccccccccCCCcccccc-ccccceeeccchHHHHhhhhhcccCCCCCcccccccccCCcccccCcCCCCcc
Confidence 99999999999999999999999998 99999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCCcccccccccccccCCCCCCCCCCCCccccCCCccccCCCccccccccCCCCccCCCCCccCcCCCCCcccc
Q 006400 241 KDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDKIST 320 (647)
Q Consensus 241 Kd~~~ssp~v~~~~~~~~~~~~~~~~~~~~~~~qrt~ss~S~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~~~~ 320 (647)
|.++++|||++.++++...... + ++++|||+|+||+||+|++++++|+++|++|.|+.+|.+++++++|.|+..
T Consensus 240 -~~~~~~~~~~~~~~~~~~~~~~----~-~~~sqRT~SsGs~gSfDs~s~S~ks~~Sg~l~d~~~E~~~~~~~~q~~~~~ 313 (648)
T PLN03119 240 -QEAEFRSPQFQHSNAPPSENLF----P-GRQHQRTTSSGSVRSVDSNFMSIKSYTSGGLGEAVSESRQNTGSQQGKTSN 313 (648)
T ss_pred -cccccCCcccccccCcchhhcc----c-ccccccccccccccccccccccccccccCCcccccccccccccccccccCC
Confidence 7789999999999988644432 2 689999999999999999999999999999999999999999999998765
Q ss_pred cCCCCCCCCcCccccCCCCCCCCCCCCCCCCCCccCCCccccc-cccccccccCCCCCCCCCCCCCCCCCCCCcccc-cc
Q 006400 321 FPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF-QI 398 (647)
Q Consensus 321 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlf~~p~~~~~-~v~~f~~~~~~~~~s~~~~q~~q~~~~~~~d~f-~~ 398 (647)
. +|++++.++++|||||+|+|+.| +|||||.|.++.++++|.+|+.||+++++||+| +|
T Consensus 314 ~-------------------~P~~~~~~aapIDLFqlp~ts~a~~vdlf~~~~~p~~p~~n~~q~~qts~p~~~~~f~~~ 374 (648)
T PLN03119 314 H-------------------VPLVAESTKAPIDLFQLPGAPVAQSVDTFQPSIAPRSPPVNLQQAPQTYSFTPANSFAGN 374 (648)
T ss_pred C-------------------CcccccccCCchhhhhccCCCCCccccccccccCCCCCccccCCCccccCCcchhhhhcc
Confidence 4 67788889999999999999888 999999999999999999999999999999999 99
Q ss_pred cCCCccccccCCCCCCCCCCCCCcccccCCCCCCCCCCccCcccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCC
Q 006400 399 TEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQWPAFQNSGANGP 478 (647)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~~~n~gwatfd~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 478 (647)
.||+++. +++||++||||||||||+|. +++++++||.. +.....+.+||.++++.++||||+|+.+.+..
T Consensus 375 ~qqq~~~----~~~~~s~pkneGWA~fd~p~--~s~~~~~ni~~---~~~~~~~~~~d~v~~~~~~mq~Pp~~~~~~~~- 444 (648)
T PLN03119 375 LGQQPTS----RPSELSAPKNEGWASFDNPM--PAAKSTNVITS---PGDFQLELKIEEILQPSTSMQLPPYPSTVDQH- 444 (648)
T ss_pred cccCccc----CccccccccccCcccccccc--cccCCcccccC---ccccccCcchhhhcccccccccCCCccccccc-
Confidence 9997774 99999999999999999554 78888888744 32223456999999999999999988776643
Q ss_pred CCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccccccCCCCCCCCC--CCCCCcccCC
Q 006400 479 SPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFDDFTSHLPSEGFK--PNSEPHVDAY 556 (647)
Q Consensus 479 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~ds~~~~~~~~~~--~~~~~~~~~~ 556 (647)
++.||++|.+++||||+++ ++++|+||||+|+++++||++++ +++++++.++
T Consensus 445 -------------------------s~s~~~pW~~~~~~V~~~~-~~~~q~WnAF~ds~~~~~l~~~~~~~~~~~~~~~~ 498 (648)
T PLN03119 445 -------------------------ALSIPSPWQEDLSNVLKDV-VDNPQPWNAFPDSIEANPLDSSRNIHQQVDGASTS 498 (648)
T ss_pred -------------------------ccccCCchhccchhcccCc-ccCccccccchhhhccCcccccccccccccccccc
Confidence 4457889999999999998 69999999999999999999999 8888777655
Q ss_pred CCCCCCCccccc-cccccCCCCCCccc-CCCCCCCCCCCCCCccCCCCCCCCCCcccccccccccCCCCCCCCCCCCCCC
Q 006400 557 MPSPTPDQYLAI-VSQETNDDGNPRVA-SHDGPPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFDFPCDSDL 634 (647)
Q Consensus 557 ~~~~t~~~~~~~-~~q~s~~dg~qr~a-p~~~f~~~~~ps~~v~gps~~p~~~~~mG~~~~~~~~~kstNPFDlPfdsD~ 634 (647)
+ ++|++||+++ ++||+++||+||+| |+|. ++|++|+++++||+|+++++|+|+ ++||+||||||||+|+
T Consensus 499 ~-~~t~~q~~~~r~~ed~~~dg~qr~~~p~g~-~g~~~~~~~~~~Ps~~~~~~~~~~-------~~ks~npfdl~~~sd~ 569 (648)
T PLN03119 499 S-YNTDHQHLESQVLEELSNDGTQTTRIPAGS-SAFGFPGNIGMAPSYSEEAWQHVN-------EQKSANPFDLPYDSEF 569 (648)
T ss_pred C-CCCcccccccccccccccccccccccCCCC-CCCCCCCccccCCCCCchhccccc-------cccCCCCcCCcccccc
Confidence 4 5555599999 99999999999999 6666 999999999999999999999998 4999999999999999
Q ss_pred CCCCcccccc
Q 006400 635 EQNNMVWPRF 644 (647)
Q Consensus 635 e~~nMFm~~~ 644 (647)
|++|||||+-
T Consensus 570 ~~~~mf~d~t 579 (648)
T PLN03119 570 DSNDMFLDMS 579 (648)
T ss_pred CcccceeehH
Confidence 9999999973
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=3.9e-36 Score=322.48 Aligned_cols=440 Identities=30% Similarity=0.409 Sum_probs=316.1
Q ss_pred CCch-hHHHHH-HHHHHHHhcCCCCCCCcCCCCCCC-CeeEccchhhhhhhhhhhhhcCC--CceeecccCCCCHHHHHH
Q 006400 1 MGSR-KEEERN-EKIIRGLMKLPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGIHREFT--HRVKSVSMSKFTSQEVEA 75 (647)
Q Consensus 1 M~sr-ke~Er~-ekiLr~Llk~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSGIHR~LG--hrVKSItLD~Wt~eEVe~ 75 (647)
|.++ ||+|++ |++||.|+++|+|++|++|+...+ +|+++.-|-|||+.|+|..|.|. ||||+|+|.+|++.||..
T Consensus 1 ~a~~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~qevs~ 80 (524)
T KOG0702|consen 1 YAGYKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQEVSF 80 (524)
T ss_pred CCcccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCCccccceeeeeeccccchHH
Confidence 3344 777776 999999999999999999999988 99999999999999999999995 999999999999999999
Q ss_pred HHhcCcHHHHHHHhhcCCcccCCCCCCCchHHHHHHHHHHHhhccccCCCCCCCCCCCccCCCCCcccccccCCCCCCCC
Q 006400 76 LQNGGNQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQ 155 (647)
Q Consensus 76 Lq~gGN~rAN~iyea~~d~~~~~~P~~sd~~~~reFIraKYveKrF~~~k~~DkPpr~~q~l~~~~~e~rr~ssy~S~SQ 155 (647)
|+.+||+.+++||++-++..+--.|+..+.++.|+||+.||+.|+|+..+..++-+.- +| ..++..
T Consensus 81 lQshgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~----------tr---~s~s~~- 146 (524)
T KOG0702|consen 81 LQSHGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSY----------TR---GSLSED- 146 (524)
T ss_pred HhhcchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCccccccccc----------cc---cccccc-
Confidence 9999999999999999999988899999999999999999999999987554433211 00 001100
Q ss_pred CCCcccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCccccccccccCCCCCCCCCCC
Q 006400 156 SPPYDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQ 235 (647)
Q Consensus 156 sPp~d~~~Edrr~~k~~~~l~Rkpgsd~~~~~gk~s~~~~sP~r~s~~~~~DRfa~e~s~~r~sdfs~s~~g~~~k~~~~ 235 (647)
++++...+ |++ +-+|+-- || +
T Consensus 147 s~~~~~s~---------------------------------~~~-----~~lrs~~---------------gd------~ 167 (524)
T KOG0702|consen 147 SRPVSESR---------------------------------PET-----KSLRSLL---------------GD------H 167 (524)
T ss_pred CCcccccC---------------------------------CCc-----ccccccc---------------CC------C
Confidence 11111000 011 1122100 00 1
Q ss_pred CCCcccccCCCCCCcccccccccccccCCCCCCCCCCCCccccCCCccccCCCccccccccCCCCccCCCCCccCcCCCC
Q 006400 236 SPNFQKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPL 315 (647)
Q Consensus 236 sp~~~Kd~~~ssp~v~~~~~~~~~~~~~~~~~~~~~~~qrt~ss~S~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q 315 (647)
.|-.+ +..++..+. + -.++-|-|-
T Consensus 168 ~P~~~-------------------------------~~t~np~~~------~--------~~~~~~~~~----------- 191 (524)
T KOG0702|consen 168 APLLA-------------------------------ESTKNPRSR------G--------LPKSPIRFE----------- 191 (524)
T ss_pred Ccchh-------------------------------hcccCcccc------C--------CCCCCchhh-----------
Confidence 11100 001111100 0 000001000
Q ss_pred CcccccCCCCCCCCcCccccCCCCCCCCCCCCCCCCCCccCCCccccc-cccccccccCCCCCCCCCCCCCCCCCCCCcc
Q 006400 316 DKISTFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLN 394 (647)
Q Consensus 316 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlf~~p~~~~~-~v~~f~~~~~~~~~s~~~~q~~q~~~~~~~d 394 (647)
...-.+|||+++.++.+ +++.||.+++.+.+.++..+..|+..++.+|
T Consensus 192 -------------------------------~~~~rfdlfg~~k~sd~~s~s~~qss~~~~ssp~~~~~~~~~~~~s~an 240 (524)
T KOG0702|consen 192 -------------------------------IVDDRFDLFGLPKASDAQSQSTFQSSIAPSSSPPNHQSVPQAYSDSPAN 240 (524)
T ss_pred -------------------------------hhhhhhhhhcCcCcccccccCcccccccccCCCCccccchhhccccccc
Confidence 12246799999998888 9999999999888888888889999999999
Q ss_pred ccccc--CCCccccccCCCCCCCCCCCCCccc-ccCCCCCCCCCCccCcccccccCCC--CCCCCCCCCCCCCCCCCCCc
Q 006400 395 FFQIT--EQPSTAILNRNPQELSIPKNEGWAT-FDTPPSAASIPGTESLSHAMVPANE--GSSVKSDQFPSSNTSMQWPA 469 (647)
Q Consensus 395 ~f~~~--~~~~~~~~~~~~~~~~~~~n~gwat-fd~p~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 469 (647)
+|.++ .||. ..+..++.||||||+. +|+|..+.... .+|.+.- -...||+..+..+..|+.|.
T Consensus 241 ~~~ge~~k~P~-----~~~~~asapk~eg~~s~sd~pvne~~~e-------~~i~s~~~~~~f~k~~e~paps~a~qlp~ 308 (524)
T KOG0702|consen 241 IFAGEPFKQPV-----SRPSFASAPKNEGWASLSDNPVNEAKSE-------NVITSPGSFADFLKFEEIPAPSVAMQLPP 308 (524)
T ss_pred ccccCCCCCCc-----cCccccccccccCCcccccCcccccccc-------ccccCcccchhhcccccccCcchhhhcCC
Confidence 99322 3343 5788999999999999 89998765432 2222111 11258888889999999998
Q ss_pred ccCCCCCCCCCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCC
Q 006400 470 FQNSGANGPSPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFDDFTSHLPSEGFKPNS 549 (647)
Q Consensus 470 ~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~ds~~~~~~~~~~~~~ 549 (647)
..+.++......+.+|. ++|..-...+.+|. +|+++-++++...+++..+-.
T Consensus 309 ~ss~~~~~q~t~~~~~n----------------------d~~ssf~~~~~Ap~------~~~~s~p~i~s~~~s~~~~l~ 360 (524)
T KOG0702|consen 309 YSSTVDQHQPTIPSPWN----------------------DQGSSFGATPVAPP------LWVASPPSIGSNLLSSSRALA 360 (524)
T ss_pred cCCCccccCCCCCCccc----------------------ccCcccccccccCC------ccccCCCCccccccccccccc
Confidence 88777766554333221 23443334554444 799999999999999999988
Q ss_pred CCcccCCCC-CCCCCccccc-cccccCCCCCCcccCCCCCCCCCCCCCCccCCCCCCCCCCcccccccccccCCCCCCCC
Q 006400 550 EPHVDAYMP-SPTPDQYLAI-VSQETNDDGNPRVASHDGPPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFD 627 (647)
Q Consensus 550 ~~~~~~~~~-~~t~~~~~~~-~~q~s~~dg~qr~ap~~~f~~~~~ps~~v~gps~~p~~~~~mG~~~~~~~~~kstNPFD 627 (647)
+.+.+.-+. ++++++.+.+ ++++.-.+..|.+++-.+-.-+.+|..+-++|++.+- .-|-....+-..++.+++++
T Consensus 361 ~~~s~~gsa~~~~~~~~~n~~~~e~~~~s~~q~~s~ft~~~ts~~p~~~~~~pssn~~--~~~~~Q~~~~~~~~g~~~~s 438 (524)
T KOG0702|consen 361 VQSSVFGSAGYVPPHQPVNLGVLEELSNSTTQTFSAFTNESTSGFPAPIGMAPSSNHH--QDDEFQPNHRNPQPGAAMSS 438 (524)
T ss_pred cccccccccccCCCCcccccccccccccccccccccccCcccccCccccccCCccccc--ccccccccccCCCCcccccc
Confidence 876444444 8889999999 9999999999999998888889999999999998842 11222223333366899999
Q ss_pred CCCCCCCCCC-Ccccc
Q 006400 628 FPCDSDLEQN-NMVWP 642 (647)
Q Consensus 628 lPfdsD~e~~-nMFm~ 642 (647)
|||+...+.+ +||.+
T Consensus 439 l~~~~~~~~P~~~~fa 454 (524)
T KOG0702|consen 439 LPYGFEFASPFDMFFA 454 (524)
T ss_pred CCCCCCcCCCcccccc
Confidence 9999999999 88765
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.4e-35 Score=303.96 Aligned_cols=118 Identities=31% Similarity=0.660 Sum_probs=107.4
Q ss_pred hHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCc
Q 006400 5 KEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGN 81 (647)
Q Consensus 5 ke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN 81 (647)
...++++++|++||+.|+|++|||||+++|+|||+|+|||||++|+||||.|| | |||||+||.|++|+|+.|+..||
T Consensus 7 ~~~~~~~~~l~~Ll~~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkVkSv~LD~W~~eqv~~m~~~GN 86 (287)
T KOG0703|consen 7 GSNERNKRRLRELLREPDNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKVKSVTLDEWTDEQVDFMISMGN 86 (287)
T ss_pred cccchHHHHHHHHHcCcccCcccccCCCCCCeEEeecCeEEEeecccccccccchhheeeeeeccccCHHHHHHHHHHcc
Confidence 44688999999999999999999999999999999999999999999999999 5 99999999999999999999999
Q ss_pred HHHHHHHhhcCCcccCCCCCCCchHHHHHHHHHHHhhccccCCC
Q 006400 82 QRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGK 125 (647)
Q Consensus 82 ~rAN~iyea~~d~~~~~~P~~sd~~~~reFIraKYveKrF~~~k 125 (647)
.+||.+||+.++.. .+.|...+ .++.|||+|||+|+|....
T Consensus 87 ~~an~~~ea~~p~~-~~~p~~d~--~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 87 AKANSYYEAKLPDP-FRRPGPDD--LVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hhhhhhccccCCcc-ccCCChHH--HHHHHHHHHHhhhhhccch
Confidence 99999999998765 44454333 6888999999999999864
No 5
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=100.00 E-value=2.9e-35 Score=266.67 Aligned_cols=111 Identities=34% Similarity=0.750 Sum_probs=92.9
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC---CceeecccCCCCHHHHHHHHhcCcHHHHHHH
Q 006400 12 KIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (647)
Q Consensus 12 kiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLD~Wt~eEVe~Lq~gGN~rAN~iy 88 (647)
++|++|++.|+|++|||||+++|+|||++||||||+.|+|+||+|| ++||||+||+|+.+||++|+.+||.++|++|
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~ 81 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIW 81 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHH
Confidence 6899999999999999999999999999999999999999999999 6999999999999999999999999999999
Q ss_pred hhcCCcccCCCCCCCchHHHHHHHHHHHhhccccC
Q 006400 89 LKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAG 123 (647)
Q Consensus 89 ea~~d~~~~~~P~~sd~~~~reFIraKYveKrF~~ 123 (647)
|++.+ ...+++..++.+.+++||++||++|+|+.
T Consensus 82 e~~~~-~~~~~~~~~~~~~~~~fI~~KY~~k~f~~ 115 (116)
T PF01412_consen 82 EANSP-PPKKPPPSSDQEKREQFIRAKYVEKAFIS 115 (116)
T ss_dssp TTTST-TTTTHCTTSHHHHHHHHHHHHHTTHTTS-
T ss_pred HcCCC-CCCCCCCCCcHHHHHHHHHHHHHhhhhcc
Confidence 99932 33456667888899999999999999985
No 6
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=100.00 E-value=2.1e-33 Score=253.33 Aligned_cols=106 Identities=31% Similarity=0.701 Sum_probs=97.4
Q ss_pred CCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHHHhhcCCcccC
Q 006400 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDWDFQRQ 97 (647)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN~rAN~iyea~~d~~~~ 97 (647)
|+|++|||||+++|+|||++||||||++|+||||+|| | +||||+||+|++++|++|+.+||.++|++||++++....
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~ 80 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSL 80 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCcccc
Confidence 5899999999999999999999999999999999998 4 699999999999999999999999999999999987655
Q ss_pred CCCCCCchHHHHHHHHHHHhhccccCCCC
Q 006400 98 RLPDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (647)
Q Consensus 98 ~~P~~sd~~~~reFIraKYveKrF~~~k~ 126 (647)
+.|...+.+.+++||++||++|+|+....
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhcccccc
Confidence 55666667888999999999999987644
No 7
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.96 E-value=1.7e-30 Score=271.39 Aligned_cols=117 Identities=24% Similarity=0.576 Sum_probs=103.4
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHH
Q 006400 8 ERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRA 84 (647)
Q Consensus 8 Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN~rA 84 (647)
...++++..|++.++|++|||||+++|+||++|||||||++||||||+|| | +||||+||+|+.+||++|+.+||.+|
T Consensus 5 ~~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~a 84 (319)
T COG5347 5 SEDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSNA 84 (319)
T ss_pred hHHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchhh
Confidence 45677888889999999999999999999999999999999999999999 4 99999999999999999999999999
Q ss_pred HHHHhhcCCccc-CCCCCCCchHHHHHHHHHHHhhccccCC
Q 006400 85 REIYLKDWDFQR-QRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (647)
Q Consensus 85 N~iyea~~d~~~-~~~P~~sd~~~~reFIraKYveKrF~~~ 124 (647)
|.||+++.-... .++-...+...+++||+.||++++|...
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 999998864321 2222456777889999999999999876
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=4.5e-28 Score=252.30 Aligned_cols=86 Identities=33% Similarity=0.690 Sum_probs=80.8
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHH
Q 006400 7 EERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQR 83 (647)
Q Consensus 7 ~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN~r 83 (647)
..|+++.|++|+...+|+.|+||++++|+|||++||||||++|+|+||.|| | +|||||||+|.+.||++|++|||.+
T Consensus 3 sprtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~ 82 (386)
T KOG0704|consen 3 SPRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNER 82 (386)
T ss_pred ChHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchh
Confidence 357888899998888999999999999999999999999999999999999 5 9999999999999999999999999
Q ss_pred HHHHHhhcC
Q 006400 84 AREIYLKDW 92 (647)
Q Consensus 84 AN~iyea~~ 92 (647)
++++++..-
T Consensus 83 ~~eFL~s~~ 91 (386)
T KOG0704|consen 83 FREFLSSQG 91 (386)
T ss_pred HHHHHhhCc
Confidence 999987653
No 9
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.92 E-value=1.5e-25 Score=234.89 Aligned_cols=116 Identities=22% Similarity=0.414 Sum_probs=96.0
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHH
Q 006400 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (647)
Q Consensus 11 ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN~rAN~i 87 (647)
.++|++|+++|+|++|+|||+++|+|++++||||||++|+||||.|| | +|||++||+|+.++|++|+.+||.++|++
T Consensus 10 ~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~f 89 (395)
T PLN03114 10 ISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVF 89 (395)
T ss_pred HHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHH
Confidence 45699999999999999999999999999999999999999999999 4 89999999999999999999999999999
Q ss_pred HhhcCCcccCCCC--CCCchHHHHHHHHHHHhhccccCCCC
Q 006400 88 YLKDWDFQRQRLP--DNSNVNKVRDFIKNVYVDRRYAGGKT 126 (647)
Q Consensus 88 yea~~d~~~~~~P--~~sd~~~~reFIraKYveKrF~~~k~ 126 (647)
|+.+.-.....+. ..+....+.+-+.+|++++.+..+..
T Consensus 90 F~qhG~~~~~~~~~KY~S~aA~~Yre~L~keVa~~~a~~~~ 130 (395)
T PLN03114 90 FKQYGWSDGGKTEAKYTSRAADLYKQILAKEVAKSKAEEEL 130 (395)
T ss_pred HHHcCCCCCCCcccccCCHHHHHHHHHHHHHHHHhhhcccc
Confidence 9875311111111 22444555566888899998876643
No 10
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.91 E-value=5.7e-25 Score=235.00 Aligned_cols=85 Identities=24% Similarity=0.598 Sum_probs=80.6
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHH
Q 006400 8 ERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRA 84 (647)
Q Consensus 8 Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN~rA 84 (647)
...+.+++.|+..+.||+|||||+++|+|++|+|||||||+|+++||+|| | +|||..||+|+.+||++|+.|||.+|
T Consensus 8 ~d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA 87 (454)
T KOG0706|consen 8 QDIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANA 87 (454)
T ss_pred hhHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhH
Confidence 34678899999999999999999999999999999999999999999999 5 99999999999999999999999999
Q ss_pred HHHHhhcC
Q 006400 85 REIYLKDW 92 (647)
Q Consensus 85 N~iyea~~ 92 (647)
+.|+..+-
T Consensus 88 ~~FFkqhg 95 (454)
T KOG0706|consen 88 RVFFKQHG 95 (454)
T ss_pred HHHHHHcC
Confidence 99998763
No 11
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.89 E-value=7.6e-24 Score=231.06 Aligned_cols=116 Identities=19% Similarity=0.446 Sum_probs=103.3
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC---CceeecccCCCCHHHHHHHHhcCcHHHHHH
Q 006400 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (647)
Q Consensus 11 ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLD~Wt~eEVe~Lq~gGN~rAN~i 87 (647)
.-.|+.|+..+||.+|+||+.++|.||++|+|+++|++|+||||.|| +|||+|.||.|..|.+..|..+||+.||.+
T Consensus 501 a~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~v 580 (749)
T KOG0705|consen 501 AMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSV 580 (749)
T ss_pred HHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHH
Confidence 34688999999999999999999999999999999999999999999 399999999999999999999999999999
Q ss_pred HhhcCCcccCCCCCCCchHHHHHHHHHHHhhccccCCCCC
Q 006400 88 YLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTP 127 (647)
Q Consensus 88 yea~~d~~~~~~P~~sd~~~~reFIraKYveKrF~~~k~~ 127 (647)
||......+ ++...+..++++.||++||++|.|......
T Consensus 581 WE~~~~G~~-KPs~~s~REEkErwIr~KYeqklFLaPl~~ 619 (749)
T KOG0705|consen 581 WEGSSQGQT-KPSPDSSREEKERWIRAKYEQKLFLAPLPC 619 (749)
T ss_pred hhhhccCCc-CCCccccHHHHHHHHHHHHHHHhhcCCCCC
Confidence 998665443 333456788899999999999999876543
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.81 E-value=7.1e-21 Score=218.51 Aligned_cols=115 Identities=26% Similarity=0.544 Sum_probs=102.0
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHHHh
Q 006400 13 IIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYL 89 (647)
Q Consensus 13 iLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN~rAN~iye 89 (647)
.+..+.+.|+|.+|+|||++.|+|+++|+||.+||+|+||||+|| | ||+|++||.|..+.+.+++++||..+|.|||
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e 495 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYE 495 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhh
Confidence 367888999999999999999999999999999999999999999 4 9999999999999999999999999999999
Q ss_pred hcCCcccCCCCC-CCchHHHHHHHHHHHhhccccCCCCC
Q 006400 90 KDWDFQRQRLPD-NSNVNKVRDFIKNVYVDRRYAGGKTP 127 (647)
Q Consensus 90 a~~d~~~~~~P~-~sd~~~~reFIraKYveKrF~~~k~~ 127 (647)
+.+.....++|. .++...++.||++||++++|......
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~ 534 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQ 534 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccc
Confidence 998754333333 44577788999999999999887543
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.62 E-value=1.6e-16 Score=179.63 Aligned_cols=109 Identities=25% Similarity=0.506 Sum_probs=97.0
Q ss_pred HHHhcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC---CceeecccC--CCCHHHHHHHHhcCcHHHHHHHh
Q 006400 15 RGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMS--KFTSQEVEALQNGGNQRAREIYL 89 (647)
Q Consensus 15 r~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLD--~Wt~eEVe~Lq~gGN~rAN~iye 89 (647)
.++.....|+.|||||++.|.||++|++|.||-.|+|-||.|| ++|+|++|| .|+.+.|+++...||.++|.||-
T Consensus 290 eriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa 369 (1186)
T KOG1117|consen 290 ERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWA 369 (1186)
T ss_pred HHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccc
Confidence 3566778999999999999999999999999999999999998 599999998 79999999999999999999999
Q ss_pred hcCCcccCCCCCCCchHHHHHHHHHHHhhccccCC
Q 006400 90 KDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (647)
Q Consensus 90 a~~d~~~~~~P~~sd~~~~reFIraKYveKrF~~~ 124 (647)
.++++...-.| .+.+..|++||++||.+.+|...
T Consensus 370 ~nl~~~e~lh~-dssp~~r~~fi~~Kykeg~fRk~ 403 (1186)
T KOG1117|consen 370 GNLPPNEHLHP-DSSPSTRRQFIKEKYKEGKFRKE 403 (1186)
T ss_pred cCCCCccccCC-CCCcchhhhHHHHHhhccccccc
Confidence 99876544344 35677899999999999988654
No 14
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.61 E-value=8.1e-17 Score=174.40 Aligned_cols=133 Identities=20% Similarity=0.382 Sum_probs=100.8
Q ss_pred hcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHHHhhcC-C
Q 006400 18 MKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDW-D 93 (647)
Q Consensus 18 lk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN~rAN~iyea~~-d 93 (647)
++...-+.|+|||+++|.||||+-|+|||.+|..+||.|| | .||+|....|.++.|++.....|..+|.|||..+ +
T Consensus 3 k~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld 82 (669)
T KOG0818|consen 3 KRLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLD 82 (669)
T ss_pred ccchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccC
Confidence 3445678999999999999999999999999999999999 4 8999999999999999999999999999999775 3
Q ss_pred c----ccCCCCCCCchH--HHHHHHHHHHhhccccCCC-CCCCCCCCccCCCCCcccccccCCC
Q 006400 94 F----QRQRLPDNSNVN--KVRDFIKNVYVDRRYAGGK-TPDKPPKDTQGLGSHLDESRRASSY 150 (647)
Q Consensus 94 ~----~~~~~P~~sd~~--~~reFIraKYveKrF~~~k-~~DkPpr~~q~l~~~~~e~rr~ssy 150 (647)
+ .+.++|...|.. .+.+|||+||+...|+.+. +.|.-....+++..+.....|+..+
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~~~~rDdD~~~~~~LsrQLhasvRt~nl 146 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHRLPCRDDDSVTAKDLSKQLHSSVRTGNL 146 (669)
T ss_pred chhhhcccCCCCCcCCCCccHHHHHHHHHHheeeeccCCCCCcchhhHHHHHHHHHHHhhcccH
Confidence 2 223444444432 3567999999999998743 3443333333444444555555533
No 15
>PLN03131 hypothetical protein; Provisional
Probab=96.77 E-value=0.094 Score=60.53 Aligned_cols=39 Identities=38% Similarity=0.701 Sum_probs=24.8
Q ss_pred cCccccCCCCCCCCCCCCCCCCCCccCCCccccc-cccccccccC
Q 006400 330 YGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQA 373 (647)
Q Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~dlf~~p~~~~~-~v~~f~~~~~ 373 (647)
.-.+|||.+| +++.+.++|||+++-..++ +|.+.|.++.
T Consensus 359 a~pIDLFqlp-----~ts~a~~vdlf~~s~l~~~p~~n~~q~~qt 398 (705)
T PLN03131 359 APPIDLFQLP-----ATSPAPPVDLFEIPPLDPAPAINAYQPPQT 398 (705)
T ss_pred CCchhhhhcc-----CCCCCCcccccccCcccCCCccccCCCCcc
Confidence 4567899874 4567788999997654333 5555444333
No 16
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=95.83 E-value=0.51 Score=54.38 Aligned_cols=39 Identities=21% Similarity=0.361 Sum_probs=23.8
Q ss_pred Cccc-cccccccccccCCCCCCCCCCCCCCCCCCCCcccc
Q 006400 358 PETS-AASVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF 396 (647)
Q Consensus 358 p~~~-~~~v~~f~~~~~~~~~s~~~~q~~q~~~~~~~d~f 396 (647)
.+++ ++||||||-.+.|.++++++.|+.=.++-++|+++
T Consensus 318 ~~~~~aapIDLFqlp~ts~a~~vdlf~~~~~p~~p~~n~~ 357 (648)
T PLN03119 318 VAESTKAPIDLFQLPGAPVAQSVDTFQPSIAPRSPPVNLQ 357 (648)
T ss_pred cccccCCchhhhhccCCCCCccccccccccCCCCCccccC
Confidence 3344 44999998666666666666664444444555555
No 17
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=94.58 E-value=0.058 Score=60.67 Aligned_cols=142 Identities=20% Similarity=0.161 Sum_probs=104.9
Q ss_pred CCCCCCCCCcccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCccccccccccCCCCC
Q 006400 150 YHSYSQSPPYDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDP 229 (647)
Q Consensus 150 y~S~SQsPp~d~~~Edrr~~k~~~~l~Rkpgsd~~~~~gk~s~~~~sP~r~s~~~~~DRfa~e~s~~r~sdfs~s~~g~~ 229 (647)
|+++.+.+.|+|.|+.||++|..++ |+=-.=..+ +...-+.+.++++-.++.++-+.+....+|..++++..-+++
T Consensus 1 ~a~~~ke~E~~~ek~iR~l~kLP~N--rrC~nCnsl--~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~q 76 (524)
T KOG0702|consen 1 YAGYKKEDEYDYEKEIRRLLKLPEN--RRCINCNSL--VAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQ 76 (524)
T ss_pred CCcccccchhHHHHHHHHHhcCCCC--Cceeecccc--ccceEEEeeccceeeeccchhhccCCCccccceeeeeecccc
Confidence 5778888999999999999998633 332121122 223446688999999999999999999999999999999998
Q ss_pred CCCCCCC-CC-cccccCCCCCCcccccccccccccCCCCCCCCCCCCccccCCCccccCCCccccccccCCCCc
Q 006400 230 FRPGAQS-PN-FQKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLT 301 (647)
Q Consensus 230 ~k~~~~s-p~-~~Kd~~~ssp~v~~~~~~~~~~~~~~~~~~~~~~~qrt~ss~S~~s~~~~~~~~k~~~s~sl~ 301 (647)
.....|+ +| ..|++.+-.+-.++ +..+..++.--....||+.....--.++.|.+.+++|+.++|-
T Consensus 77 evs~lQshgNq~~k~i~fkl~D~q~------S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~tr~s~s 144 (524)
T KOG0702|consen 77 EVSFLQSHGNQVCKEIWFKLFDFQR------SNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSYTRGSLS 144 (524)
T ss_pred chHHHhhcchhhhhhhhhcchhhhh------ccCCCcccchhhHHHHhhhhccceeecCccccccccccccccc
Confidence 8888887 76 66666444433222 2334445555556678888888888899999999999997764
No 18
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=89.08 E-value=0.11 Score=61.78 Aligned_cols=67 Identities=16% Similarity=0.282 Sum_probs=49.8
Q ss_pred CCCCCCCcCCCC-CCCCeeEccchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHHH
Q 006400 20 LPPNRRCINCNS-LGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (647)
Q Consensus 20 ~PgNk~CADCGa-~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLD~Wt~eEVe~Lq~gGN~rAN~iy 88 (647)
...+..|++|++ +.-.|+++++.+.+|+.|+++|+.++ | .++++.|+...+ |..+...||..++..|
T Consensus 627 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~ 697 (785)
T KOG0521|consen 627 ASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHAT 697 (785)
T ss_pred hccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhh
Confidence 345889999997 67899999999999999999999997 4 555656665555 5555555555544444
No 19
>PRK12495 hypothetical protein; Provisional
Probab=76.30 E-value=1.7 Score=44.97 Aligned_cols=37 Identities=19% Similarity=0.227 Sum_probs=27.4
Q ss_pred HHHHHHhc--CCCCCCCcCCCCCCCCeeEccchhhhhhhhhhh
Q 006400 12 KIIRGLMK--LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (647)
Q Consensus 12 kiLr~Llk--~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (647)
++-..|++ ...++.|-+||.+=|.+ -|+.+|..|..+
T Consensus 29 ~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 29 RMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred HHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 33344444 45889999999988832 599999999865
No 20
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=75.85 E-value=1.7 Score=32.58 Aligned_cols=40 Identities=15% Similarity=0.421 Sum_probs=33.3
Q ss_pred CCCCCcCCCCCCCCeeEccchhhhhhhhhhh-hhcCCCceeec
Q 006400 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGI-HREFTHRVKSV 63 (647)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGI-HR~LGhrVKSI 63 (647)
.+..|..|+.....+.+.+=+++||..|... |+. |+|.+|
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~--H~~~~i 42 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG--HKIVPI 42 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT--SEEEEC
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC--CEEeEC
Confidence 3578999998878999999999999999987 887 877664
No 21
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=56.61 E-value=9.7 Score=38.48 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=26.2
Q ss_pred CCCCCCCcCCCCCCC-CeeEccchhhhhhhhh
Q 006400 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCS 50 (647)
Q Consensus 20 ~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CS 50 (647)
.|.-..|+-||.... .|.+...|.++|..|.
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCccccccc
Confidence 355679999998644 7889999999999997
No 22
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=56.60 E-value=6.9 Score=39.39 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=27.0
Q ss_pred CCCCCCCcCCCCCCC-CeeEccchhhhhhhhhhh
Q 006400 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGI 52 (647)
Q Consensus 20 ~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSGI 52 (647)
.|.-..|+.||..++ .|.++..|.++|.+|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 456689999998544 678899999999999864
No 23
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=51.05 E-value=9.1 Score=32.23 Aligned_cols=33 Identities=24% Similarity=0.411 Sum_probs=22.5
Q ss_pred CCCCCCCcCCCCCCC--CeeEccchhhhhhhhhhhh
Q 006400 20 LPPNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIH 53 (647)
Q Consensus 20 ~PgNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIH 53 (647)
.++...|.+||.+=| .+. ..-|+..|+.|...+
T Consensus 28 ~~s~g~C~~Cg~~Ip~~Rl~-a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 28 GPSLRECEDCGEPIPEARRE-ALPGVTRCVSCQEIL 62 (63)
T ss_pred CCCCCeeccCCCcChHHHHh-hcCCcCCcHHHHhhc
Confidence 456789999998633 222 223788899998754
No 24
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=49.19 E-value=10 Score=35.97 Aligned_cols=30 Identities=17% Similarity=0.360 Sum_probs=19.4
Q ss_pred CCCcCCCCCCCC-eeEccchhhhhhhhhhhh
Q 006400 24 RRCINCNSLGPQ-YVCTNFWTFVCMTCSGIH 53 (647)
Q Consensus 24 k~CADCGa~~P~-WaSvnfGVFVCi~CSGIH 53 (647)
.+|.+||.+=|. =.-.--+..+|++|.-.|
T Consensus 81 G~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~ 111 (120)
T COG1734 81 GICEECGEPIPEARLEARPTARLCIECQERA 111 (120)
T ss_pred cchhccCCcCCHHHHhhCcchHHHHHHHHHH
Confidence 489999986221 011122578999999876
No 25
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=43.88 E-value=11 Score=32.75 Aligned_cols=31 Identities=16% Similarity=0.270 Sum_probs=20.6
Q ss_pred CCCCcCCCCCCCCeeE-ccchhhhhhhhhhhh
Q 006400 23 NRRCINCNSLGPQYVC-TNFWTFVCMTCSGIH 53 (647)
Q Consensus 23 Nk~CADCGa~~P~WaS-vnfGVFVCi~CSGIH 53 (647)
...|.|||.+=|.==- .--|+..|+.|...+
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 3589999986432111 122788999998754
No 26
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=42.28 E-value=13 Score=38.62 Aligned_cols=30 Identities=27% Similarity=0.676 Sum_probs=26.0
Q ss_pred CCCCCCcCCCCCC-CCeeEccchhhhhhhhh
Q 006400 21 PPNRRCINCNSLG-PQYVCTNFWTFVCMTCS 50 (647)
Q Consensus 21 PgNk~CADCGa~~-P~WaSvnfGVFVCi~CS 50 (647)
+.=..|+.||... +...++-.|-++|.+|.
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3447999999975 57999999999999999
No 27
>PRK11019 hypothetical protein; Provisional
Probab=42.27 E-value=16 Score=32.96 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=23.0
Q ss_pred CCCCCcCCCCCCC--CeeEccchhhhhhhhhhhhhc
Q 006400 22 PNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIHRE 55 (647)
Q Consensus 22 gNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIHR~ 55 (647)
.-..|.+||.+=| .+.-+. ++-.|++|...+-.
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~ 69 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAIP-GVRLCVACQQEKDL 69 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHH
Confidence 4579999998633 333333 67889999987643
No 28
>PHA00080 DksA-like zinc finger domain containing protein
Probab=38.65 E-value=16 Score=31.65 Aligned_cols=32 Identities=22% Similarity=0.504 Sum_probs=21.6
Q ss_pred CCCCCCcCCCCCCC--CeeEccchhhhhhhhhhhh
Q 006400 21 PPNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIH 53 (647)
Q Consensus 21 PgNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIH 53 (647)
.+...|.+||..=| .+.-+. |+..|+.|...+
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~ 62 (72)
T PHA00080 29 PSATHCEECGDPIPEARREAVP-GCRTCVSCQEIL 62 (72)
T ss_pred CCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHH
Confidence 45568999998532 333233 667799998865
No 29
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=38.18 E-value=43 Score=37.08 Aligned_cols=81 Identities=22% Similarity=0.249 Sum_probs=45.2
Q ss_pred CCCCCccCCCccccc-cccccccc----cCCCCCCCCCCCCCCCCCCC-CcccccccCCCccccccC--CCCCCCCCCCC
Q 006400 349 APPIDLFQLPETSAA-SVNMSEMS----QASSVPSTNTYQPAQTSSPS-SLNFFQITEQPSTAILNR--NPQELSIPKNE 420 (647)
Q Consensus 349 ~~~~dlf~~p~~~~~-~v~~f~~~----~~~~~~s~~~~q~~q~~~~~-~~d~f~~~~~~~~~~~~~--~~~~~~~~~n~ 420 (647)
..-.|||+--+-+.+ .-|||..- .+-++++||.-|..-++--- =.|+|+|.+-|+-+.++. +...+..|.||
T Consensus 327 gdl~dLFDgsa~s~~gaadlfG~faDf~~aaaagsfn~a~atA~Sg~GdfgD~~AF~aAPsgpmAqSgef~g~aaaPa~e 406 (499)
T KOG2057|consen 327 GDLDDLFDGSAPSPAGAADLFGAFADFFGAAAAGSFNAAPATAPSGGGDFGDLFAFGAAPSGPMAQSGEFAGPAAAPANE 406 (499)
T ss_pred ccHHHHhcCcCCCCCCchhhcCchhhhhhhhccCccccccccccCCCCcchhhhhhcCCCCccccccccccCccccchhh
Confidence 345677874444443 44444431 13456788887776665543 378999999886554443 33444445544
Q ss_pred ----CcccccCCC
Q 006400 421 ----GWATFDTPP 429 (647)
Q Consensus 421 ----gwatfd~p~ 429 (647)
-..-||-|+
T Consensus 407 ~~nGS~na~~~~p 419 (499)
T KOG2057|consen 407 ASNGSFNAFDFGP 419 (499)
T ss_pred hccCccccCCCCc
Confidence 234455554
No 30
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=37.22 E-value=23 Score=34.88 Aligned_cols=42 Identities=12% Similarity=0.218 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCC--CCeeEccchhhhhhhhhhhh
Q 006400 10 NEKIIRGLMKLPPNRRCINCNSLG--PQYVCTNFWTFVCMTCSGIH 53 (647)
Q Consensus 10 ~ekiLr~Llk~PgNk~CADCGa~~--P~WaSvnfGVFVCi~CSGIH 53 (647)
.+++|.+|.. ..=-.|.+||..= -+.--+. ++-.|+.|...+
T Consensus 74 Ie~AL~Ri~~-G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 74 IEHALQKIEN-GTYGICEVCGKPIPYERLEAIP-TATTCVECQNRK 117 (159)
T ss_pred HHHHHHHHhC-CCCCeecccCCcccHHHHhhCC-CcchhHHHHHHh
Confidence 3344444433 3445899999851 1222222 466899999865
No 31
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=36.81 E-value=18 Score=27.44 Aligned_cols=28 Identities=25% Similarity=0.565 Sum_probs=23.3
Q ss_pred CCCCCCcCCCCCCCCeeEccchhhhhhhhhh
Q 006400 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSG 51 (647)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSG 51 (647)
..|..|..|++. |....=|-++|.+|-.
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCce
Confidence 456779999987 8888889999999853
No 32
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=36.16 E-value=11 Score=29.01 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=20.5
Q ss_pred CCcCCCCCCCCeeEccchhhhhhhhhhh
Q 006400 25 RCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (647)
Q Consensus 25 ~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (647)
+|-.||+.. ....-.-|-+||..|.-|
T Consensus 2 ~Cp~Cg~~~-~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE-IVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE-EEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCc-eEEcCCCCeEECCCCCCE
Confidence 699999976 455567899999999544
No 33
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=33.58 E-value=12 Score=28.49 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=16.5
Q ss_pred CCCcCCCCC-CCCeeEccchhhhhhhhh
Q 006400 24 RRCINCNSL-GPQYVCTNFWTFVCMTCS 50 (647)
Q Consensus 24 k~CADCGa~-~P~WaSvnfGVFVCi~CS 50 (647)
..|.+||.. .-+|..-+|+.-||..|.
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 479999985 668999999999999994
No 34
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=32.09 E-value=28 Score=28.17 Aligned_cols=36 Identities=19% Similarity=0.396 Sum_probs=29.6
Q ss_pred CCCCCcCCCC-CCCCeeEccchh-hhhhhhhhhhhcCC
Q 006400 22 PNRRCINCNS-LGPQYVCTNFWT-FVCMTCSGIHREFT 57 (647)
Q Consensus 22 gNk~CADCGa-~~P~WaSvnfGV-FVCi~CSGIHR~LG 57 (647)
..+.|..|+. ..|.|=.-..|- +||-.|.--.+..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 3578999997 468898888886 99999988777665
No 35
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=30.07 E-value=63 Score=31.67 Aligned_cols=35 Identities=11% Similarity=0.136 Sum_probs=21.6
Q ss_pred CCCCCCCcCCCCCCCCe-eEccchhhhhhhhhhhhh
Q 006400 20 LPPNRRCINCNSLGPQY-VCTNFWTFVCMTCSGIHR 54 (647)
Q Consensus 20 ~PgNk~CADCGa~~P~W-aSvnfGVFVCi~CSGIHR 54 (647)
.+.-..|-+||.+=|.= .-+-=++..|+.|...|-
T Consensus 108 ~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E 143 (151)
T PRK10778 108 DEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAE 143 (151)
T ss_pred CCCCceeccCCCcccHHHHhcCCCccccHHHHHHHH
Confidence 45668999999852100 001114578999998764
No 36
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=27.08 E-value=27 Score=36.75 Aligned_cols=32 Identities=22% Similarity=0.419 Sum_probs=24.9
Q ss_pred CCCCCCcCCCC--CCCCeeEccchhhhhhhhhhhh
Q 006400 21 PPNRRCINCNS--LGPQYVCTNFWTFVCMTCSGIH 53 (647)
Q Consensus 21 PgNk~CADCGa--~~P~WaSvnfGVFVCi~CSGIH 53 (647)
.-+.+|++|.. .++.+-+ .||+-||-.|+.-|
T Consensus 114 ~~apkC~eC~~IelD~~l~d-~F~~~VC~~Cr~~~ 147 (292)
T COG5145 114 ALAPKCKECLQIELDDELED-TFGISVCRSCRHSM 147 (292)
T ss_pred hhCccceeeeeeecchHHHh-hhcchhHHhhhhhc
Confidence 36899999997 3444433 58999999999888
No 37
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=25.28 E-value=45 Score=29.40 Aligned_cols=31 Identities=16% Similarity=0.613 Sum_probs=25.4
Q ss_pred CCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhc
Q 006400 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (647)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (647)
..+.|.=||...- ...||++.|..|.+..|.
T Consensus 2 ~~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEAS---GCHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECcchhhhHHHHHHH
Confidence 4667999997653 468999999999998876
No 38
>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. 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 domain, a non-conserv
Probab=25.09 E-value=38 Score=29.84 Aligned_cols=31 Identities=13% Similarity=0.470 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhc
Q 006400 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (647)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (647)
.|..|.=||... ....||++.|..|.+..|-
T Consensus 2 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYA---SGYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcC---cceEECceeehhhHHhHHH
Confidence 467899999754 3478999999999998866
No 39
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=24.03 E-value=24 Score=32.79 Aligned_cols=44 Identities=23% Similarity=0.509 Sum_probs=29.6
Q ss_pred cCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcC--CC--ceeecccC
Q 006400 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (647)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItLD 66 (647)
..|.--+|.+||. +..+....+.|-.|.+..-.+ |. +|++|.++
T Consensus 66 ~~p~~~~C~~Cg~----~~~~~~~~~~CP~Cgs~~~~i~~G~El~I~~ie~~ 113 (115)
T TIGR00100 66 DEPVECECEDCSE----EVSPEIDLYRCPKCHGIMLQVRAGKELNLKSIEVE 113 (115)
T ss_pred eeCcEEEcccCCC----EEecCCcCccCcCCcCCCcEEecCCeEEEEEEEEE
Confidence 3567779999994 233322357899999876444 42 88888764
No 40
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=24.02 E-value=23 Score=32.90 Aligned_cols=44 Identities=11% Similarity=0.290 Sum_probs=30.2
Q ss_pred cCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcC--CC--ceeeccc
Q 006400 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSM 65 (647)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItL 65 (647)
..|..-+|-+||. .+....+..+.|-.|.+....+ |. +|++|-+
T Consensus 66 ~~p~~~~C~~Cg~---~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~iEv 113 (114)
T PRK03681 66 EQEAECWCETCQQ---YVTLLTQRVRRCPQCHGDMLRIVADDGLQIRRIEI 113 (114)
T ss_pred eeCcEEEcccCCC---eeecCCccCCcCcCcCCCCcEEccCCeEEEEEEEE
Confidence 3567789999995 2333344557899999876665 32 7887754
No 41
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which 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. RORbe
Probab=23.19 E-value=43 Score=30.32 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhc
Q 006400 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (647)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (647)
.+..|.=||... ....||++.|..|.+..|-
T Consensus 4 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKS---SGIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcC---cceEECceeehhhHHhhHH
Confidence 467899999865 3468999999999999876
No 42
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=23.04 E-value=29 Score=34.29 Aligned_cols=34 Identities=32% Similarity=0.720 Sum_probs=27.1
Q ss_pred CCCCCCcCCCCCCCCeeEccchhhhh-hhhhhhhhc
Q 006400 21 PPNRRCINCNSLGPQYVCTNFWTFVC-MTCSGIHRE 55 (647)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVC-i~CSGIHR~ 55 (647)
|--+.|+-|| -...|.|++-|.-+| ..|-++|.+
T Consensus 116 P~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 116 PLRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred CcchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 3446899999 667789999998877 478889865
No 43
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=22.71 E-value=56 Score=29.81 Aligned_cols=30 Identities=13% Similarity=0.273 Sum_probs=23.7
Q ss_pred CCCCCCcCCCCCCCCeeEccchhhhhhhhhhh
Q 006400 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (647)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (647)
-.--.|-.|+.+ .---+..|||.|..|--.
T Consensus 33 ~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~ 62 (89)
T COG1997 33 RAKHVCPFCGRT--TVKRIATGIWKCRKCGAK 62 (89)
T ss_pred hcCCcCCCCCCc--ceeeeccCeEEcCCCCCe
Confidence 345689999987 555688999999999643
No 44
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=22.09 E-value=49 Score=30.38 Aligned_cols=35 Identities=20% Similarity=0.435 Sum_probs=24.4
Q ss_pred HhcCCCCCCCcCCCCCC-------C----------CeeEccchhhhhhhhhh
Q 006400 17 LMKLPPNRRCINCNSLG-------P----------QYVCTNFWTFVCMTCSG 51 (647)
Q Consensus 17 Llk~PgNk~CADCGa~~-------P----------~WaSvnfGVFVCi~CSG 51 (647)
..+.++--+|++||.+= | .=+.=.||-.+|-+|..
T Consensus 28 ~kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 28 EKKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eeccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 34567778999999851 1 11245689999999974
No 45
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.21 E-value=29 Score=32.40 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=28.1
Q ss_pred CCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhhcC--CC--ceeecccC
Q 006400 20 LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (647)
Q Consensus 20 ~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItLD 66 (647)
.|.--+|.+||.. |....+..+.|-.|.+..-.+ |. +|++|.++
T Consensus 68 vp~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~~~i~~G~El~I~~iE~~ 115 (117)
T PRK00564 68 EKVELECKDCSHV---FKPNALDYGVCEKCHSKNVIITQGNEMRLLSLEML 115 (117)
T ss_pred cCCEEEhhhCCCc---cccCCccCCcCcCCCCCceEEecCCEEEEEEEEEE
Confidence 3455689999942 222234455699999875554 42 78887653
No 46
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=21.20 E-value=43 Score=25.10 Aligned_cols=30 Identities=23% Similarity=0.463 Sum_probs=21.6
Q ss_pred CcCCCC-CCCCeeEccchhh-hhhhhhhhhhc
Q 006400 26 CINCNS-LGPQYVCTNFWTF-VCMTCSGIHRE 55 (647)
Q Consensus 26 CADCGa-~~P~WaSvnfGVF-VCi~CSGIHR~ 55 (647)
|..|+. ..|.|-....|-. ||-.|.-.+|.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk 32 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKK 32 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHH
Confidence 889997 4799998888877 99999876665
No 47
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=21.17 E-value=47 Score=30.27 Aligned_cols=30 Identities=17% Similarity=0.587 Sum_probs=24.5
Q ss_pred CCCCcCCCCCCCCeeEccchhhhhhhhhhhhhc
Q 006400 23 NRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (647)
Q Consensus 23 Nk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (647)
+..|.=||...- ...||++.|..|.+..|.
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 457999997653 468999999999999876
No 48
>COG2719 SpoVR Uncharacterized conserved protein [Function unknown]
Probab=20.25 E-value=29 Score=39.58 Aligned_cols=8 Identities=88% Similarity=1.610 Sum_probs=7.3
Q ss_pred CCCCcccc
Q 006400 418 KNEGWATF 425 (647)
Q Consensus 418 ~n~gwatf 425 (647)
-|||||||
T Consensus 270 MNEGWAtf 277 (495)
T COG2719 270 MNEGWATF 277 (495)
T ss_pred hhhhHHHH
Confidence 49999999
No 49
>PRK11767 SpoVR family protein; Provisional
Probab=20.21 E-value=29 Score=40.06 Aligned_cols=8 Identities=88% Similarity=1.610 Sum_probs=7.3
Q ss_pred CCCCcccc
Q 006400 418 KNEGWATF 425 (647)
Q Consensus 418 ~n~gwatf 425 (647)
=|||||||
T Consensus 273 MNEGWAsy 280 (498)
T PRK11767 273 MNEGWATF 280 (498)
T ss_pred HhhHhHHH
Confidence 49999999
Done!