Query 005051
Match_columns 716
No_of_seqs 185 out of 1210
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 17:15:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005051.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005051hhsearch_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-200 2E-205 1627.9 47.9 687 1-716 1-705 (705)
2 PLN03119 putative ADP-ribosyla 100.0 1E-180 2E-185 1461.8 44.7 641 1-716 1-648 (648)
3 KOG0702 Predicted GTPase-activ 100.0 2.1E-46 4.6E-51 404.8 31.9 509 3-716 4-524 (524)
4 KOG0703 Predicted GTPase-activ 100.0 3.3E-35 7.2E-40 304.1 8.2 118 5-125 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 7.8E-35 1.7E-39 266.6 8.8 112 12-124 2-116 (116)
6 smart00105 ArfGap Putative GTP 100.0 5.1E-33 1.1E-37 253.4 10.7 106 21-126 1-109 (112)
7 COG5347 GTPase-activating prot 100.0 2E-30 4.2E-35 273.7 9.8 117 8-124 5-125 (319)
8 KOG0704 ADP-ribosylation facto 99.9 8.1E-28 1.8E-32 252.7 12.4 85 7-91 3-90 (386)
9 PLN03114 ADP-ribosylation fact 99.9 2.3E-25 5.1E-30 235.6 11.3 116 11-126 10-130 (395)
10 KOG0706 Predicted GTPase-activ 99.9 3E-24 6.4E-29 231.7 8.2 83 9-91 9-94 (454)
11 KOG0705 GTPase-activating prot 99.9 2.3E-23 5E-28 229.4 8.2 115 12-127 502-619 (749)
12 KOG0521 Putative GTPase activa 99.8 1.4E-20 3.1E-25 218.2 3.2 114 14-127 417-534 (785)
13 KOG1117 Rho- and Arf-GTPase ac 99.6 3.2E-16 6.8E-21 178.8 4.3 110 15-125 290-404 (1186)
14 KOG0818 GTPase-activating prot 99.6 1.4E-16 3.1E-21 174.1 0.8 131 18-148 3-144 (669)
15 PLN03131 hypothetical protein; 97.1 0.026 5.6E-07 65.5 18.5 90 330-427 359-469 (705)
16 PLN03119 putative ADP-ribosyla 93.6 4 8.6E-05 48.0 17.9 39 358-396 318-357 (648)
17 KOG0702 Predicted GTPase-activ 93.1 0.16 3.4E-06 58.0 5.9 142 150-301 1-144 (524)
18 KOG0521 Putative GTPase activa 88.4 0.11 2.4E-06 62.5 -0.8 67 20-88 627-697 (785)
19 PF00643 zf-B_box: B-box zinc 79.3 1.6 3.5E-05 33.2 2.4 40 22-63 2-42 (42)
20 PRK12495 hypothetical protein; 79.1 1.5 3.3E-05 45.9 2.7 38 12-53 29-68 (226)
21 PRK00085 recO DNA repair prote 61.0 12 0.00025 38.4 4.5 32 20-51 146-178 (247)
22 TIGR00613 reco DNA repair prot 52.8 9.9 0.00021 38.8 2.4 33 20-52 144-177 (241)
23 TIGR02419 C4_traR_proteo phage 46.4 12 0.00026 32.0 1.5 33 20-53 28-62 (63)
24 COG1734 DksA DnaK suppressor p 43.0 21 0.00045 34.4 2.7 44 10-53 65-111 (120)
25 PF08271 TF_Zn_Ribbon: TFIIB z 41.7 10 0.00022 29.5 0.4 27 25-52 2-28 (43)
26 PF11781 RRN7: RNA polymerase 40.5 18 0.0004 27.8 1.6 27 21-50 6-32 (36)
27 PRK11019 hypothetical protein; 40.2 16 0.00034 33.5 1.4 33 22-55 35-69 (88)
28 PRK13715 conjugal transfer pro 39.7 14 0.00031 32.5 1.0 31 23-53 34-65 (73)
29 COG1381 RecO Recombinational D 36.5 19 0.0004 38.0 1.5 30 21-50 152-182 (251)
30 PHA00080 DksA-like zinc finger 35.3 20 0.00044 31.4 1.3 45 8-53 13-62 (72)
31 KOG3362 Predicted BBOX Zn-fing 33.4 16 0.00034 36.4 0.3 34 21-55 116-150 (156)
32 PF01286 XPA_N: XPA protein N- 31.8 14 0.0003 28.5 -0.3 27 24-50 4-31 (34)
33 TIGR02890 spore_yteA sporulati 30.4 33 0.00073 34.2 2.1 32 21-53 84-117 (159)
34 smart00401 ZnF_GATA zinc finge 28.6 42 0.00091 27.5 2.0 36 22-57 2-39 (52)
35 cd00021 BBOX B-Box-type zinc f 27.9 45 0.00097 24.4 1.9 36 25-62 2-38 (39)
36 PRK10778 dksA RNA polymerase-b 26.9 80 0.0017 31.4 4.0 35 20-54 108-143 (151)
37 COG1997 RPL43A Ribosomal prote 26.1 59 0.0013 30.1 2.6 30 21-52 33-62 (89)
38 TIGR00100 hypA hydrogenase nic 25.6 23 0.0005 33.3 0.0 44 19-66 66-113 (115)
39 COG5145 RAD14 DNA excision rep 24.8 26 0.00057 37.2 0.2 32 21-53 114-147 (292)
40 cd07171 NR_DBD_ER DNA-binding 24.6 45 0.00098 29.8 1.7 31 22-55 2-32 (82)
41 KOG2057 Predicted equilibrativ 23.8 1.1E+02 0.0023 34.6 4.5 69 349-420 327-406 (499)
42 PRK03681 hypA hydrogenase nick 23.5 26 0.00056 33.0 -0.1 44 19-65 66-113 (114)
43 PRK00423 tfb transcription ini 22.5 43 0.00094 36.3 1.3 34 20-54 8-41 (310)
44 cd06968 NR_DBD_ROR DNA-binding 22.5 52 0.0011 30.2 1.7 31 22-55 4-34 (95)
45 cd07173 NR_DBD_AR DNA-binding 21.8 56 0.0012 29.2 1.7 31 22-55 2-32 (82)
46 PRK00564 hypA hydrogenase nick 21.7 32 0.00069 32.5 0.1 44 20-66 68-115 (117)
47 PRK00420 hypothetical protein; 21.4 1.9E+02 0.0041 27.7 5.1 44 6-52 4-49 (112)
48 COG2174 RPL34A Ribosomal prote 21.1 57 0.0012 30.4 1.6 35 17-51 28-79 (93)
49 PF00320 GATA: GATA zinc finge 20.6 91 0.002 23.7 2.4 30 26-55 1-32 (36)
50 cd07170 NR_DBD_ERR DNA-binding 20.4 57 0.0012 30.1 1.5 30 23-55 4-33 (97)
51 PF10764 Gin: Inhibitor of sig 20.2 56 0.0012 26.6 1.2 26 25-51 1-26 (46)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.1e-200 Score=1627.88 Aligned_cols=687 Identities=61% Similarity=0.998 Sum_probs=662.3
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCCCceeeeccCCCCHHHHHHHHhcC
Q 005051 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (716)
Q Consensus 1 M~srke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSItmDkWt~eEVe~Lq~gG 80 (716)
|++||++|+++++|++|+++|+|++|||||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
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 hHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhhccccCCCCCCCCCCCccCCCCCccccccCCCCCCCCCCCCcc
Q 005051 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (716)
Q Consensus 81 N~rAN~iyea~~d~~r~~~P~~sd~~~~reFIraKY~eKrF~~~k~~DkPpr~~q~l~~~~~e~rr~ssy~s~sqsPp~d 160 (716)
|++||+|||++|+..+.++|...+.+++|+|||.|||+|||+.....++|+++.+.++.++.++||.++||+++|||||+
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 99999999999998877888888889999999999999999999999999999999999999999999999999999999
Q ss_pred cchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCccccccccccCCCCCCCCCCCCCCcc
Q 005051 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (716)
Q Consensus 161 ~q~Edrr~~k~~~~l~R~pgsd~~~~~gk~ss~~~sP~r~s~~~~~DRfa~e~s~~r~sdfs~ss~g~~~k~~~~sp~~~ 240 (716)
++||||||||+...++|+||+++++|.|||++|++||+|+.+||+||||+||++++|++||+++++|+++|.+.+||+++
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 005051 241 KDAGFNSPPVQLSRDVSSLKANFK-----------RDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQ 309 (716)
Q Consensus 241 kd~~~ssp~v~~~~~i~~~~~~~~-----------~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~ 309 (716)
|++. +||||+++|+|||++++.+ .+++|++++|||+|+||+||+||+++++|+++|+|||||.+|+++
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 9976 5789988999999765533 457999999999999999999999999999999999999999999
Q ss_pred CcCCCCCcccccCCCCCCCCcCcccccCCCCCCCCCCCCCCCCCccCCCCcccc-cccccccccCCCCCCCCCCCCCCCC
Q 005051 310 AAGAPLDKISTFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTS 388 (716)
Q Consensus 310 ~~~~~q~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~s~~~~~~s~~~~q~~q~~ 388 (716)
+++++|.|+.++++..+...++++|+|++||+|+++..++++|||||+|+|+.| +|||||-+++..++++|.+|+.||+
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 999999999999999999999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred CCCCcccc-cccCCCccccccCCCcCCCCCCCCCcccccCCCCCCCCCCccCcccccccCCCCCCCCCCCCCCCCCCCCC
Q 005051 389 SPSSLNFF-QITEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQW 467 (716)
Q Consensus 389 ~~~~~d~f-~~~~~~~~~~~~~~~~~~~~p~neGWAtfD~p~~~~s~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 467 (716)
.+++|||| +|+||++++|+|++++||++||||||||||+++.++|++|++||+..+|+.....+.+||.++++.++|||
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 99999999999999999999999999999988888999999999888999777557899999999999999
Q ss_pred CcccCCCCCCCCCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccc--cccCCCcCCCC
Q 005051 468 PAFQNSGANGPSPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFD--DFTSHLPSEGF 545 (716)
Q Consensus 468 ~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~--ds~~~~~~~~~ 545 (716)
|+|+++.++... .||++|.+++||||+|.. +++|+||||+ |+++++||+++
T Consensus 480 Pp~~~~~~~~s~--------------------------s~~~pW~~~~~~V~~~~~-~~~q~WnAF~~~ds~~~~~l~~~ 532 (705)
T PLN03131 480 PPFQNSSDEESA--------------------------SGPAPWLGDLHNVEAPDN-TSAQNWNAFEFDDSVAGIPLEGI 532 (705)
T ss_pred CCCccccccccc--------------------------ccCCcccccchhcccCCc-cCccccccccccccccccccccc
Confidence 999988776543 577899999999999986 9999999999 99999999999
Q ss_pred CCCCCCCccCCCCCCCCCcchhhccccccCCCCCCcccCCCC--CCCCCCCCCCccCCCCCCCCCCcccccccccccCCC
Q 005051 546 KPNSEPHVDAYMPSPTPDQYLAIVSQQETNDDGNPRVASHDG--PPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKS 623 (716)
Q Consensus 546 ~~~~~~~~~~~~~~~t~~~~~~~~~~q~~~~d~~~~~ap~~~--~~~~~~ps~~~~g~~~~~~~~~~~g~~~~~~~~~ks 623 (716)
++++++||+++++++ .+||++++++||+++||++|+||+++ +++|++|+.+|+||+|+|+++|+||++++|+++|||
T Consensus 533 ~~~s~~q~~~~~~~t-~~q~~~~~~~~d~~~d~~~r~~p~~~~~~~g~~~~~~~~~~ps~~~~~~~~~~~~~s~~~~~ks 611 (705)
T PLN03131 533 KQSSEPQTAANMPPT-ADQLIGCKALEDFNKDGIKRTAPHGQGELPGLDEPSDILAEPSYTPPAHPIMEHAQSHANDHKS 611 (705)
T ss_pred cccccccccccCCCC-cccccccccccccccccccccCCCCCcCCCCCCCCCccccCCCCCccccccccccccccCccCC
Confidence 999999997665555 45999999999999999999999999 999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCCCcccchhhhhhhCCCCCCCCCccC-CCCcCCCCCCCCCcccccCCCCCccccccCCCCccccCCC
Q 005051 624 TNPFDFPCDSDLEQNNMFLDMSSLQAALPNAELPSPFLG-GATQSWFPQNPVSPFVQAAAQGGLAYMSGQSPSAQLANIP 702 (716)
Q Consensus 624 ~NPFDlp~dsd~e~~~mFmDmsSLQaaLP~~~lp~~f~g-g~~e~W~~qn~~~~yipsa~qGGl~~ma~q~p~s~l~ni~ 702 (716)
+||||||||+|+|++|||||||||||||||+|||++||| |||||||+||++|+|||+|+||||+|||||+|++||.|++
T Consensus 612 ~npfdl~~dsd~~~~~mf~d~sslq~~lp~~~~~~~f~g~~~tepw~~~~~~~~yip~~pqggl~y~agq~~~~~~~~~~ 691 (705)
T PLN03131 612 INPFDLPYDSDLEPGNMFLDMSSLEAALPDAHLPSAFLGSGMTEPWFPQDLAMTYIPAAPQGGLAYMAGQAPNPQLGNVQ 691 (705)
T ss_pred CCCcCCccccccCcccceeehHHHHhhcCCCCCchhhhcCCCCCccccCCCcccccCCCCCCCchhhcccCCcchhhhhh
Confidence 999999999999999999999999999999999999999 9999999999999999999999999999999999999999
Q ss_pred CCCCcccCCCCCCC
Q 005051 703 TQEPVASVGGNPFA 716 (716)
Q Consensus 703 ~~~~~a~~~gNPFa 716 (716)
+|+||||+||||||
T Consensus 692 ~~~~~af~~~npf~ 705 (705)
T PLN03131 692 TQGPVAFVGGNPFA 705 (705)
T ss_pred ccCccccCCCCCCC
Confidence 99999999999997
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=9.8e-181 Score=1461.83 Aligned_cols=641 Identities=51% Similarity=0.796 Sum_probs=598.6
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCCCceeeeccCCCCHHHHHHHHhcC
Q 005051 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (716)
Q Consensus 1 M~srke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSItmDkWt~eEVe~Lq~gG 80 (716)
|++||++||++++|++|+++|+|++|||||.++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
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 hHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhhccccCCCCCCCCCCCccCCCCCccccccCCCCCCCCCCCCcc
Q 005051 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (716)
Q Consensus 81 N~rAN~iyea~~d~~r~~~P~~sd~~~~reFIraKY~eKrF~~~k~~DkPpr~~q~l~~~~~e~rr~ssy~s~sqsPp~d 160 (716)
|++||+|||++|+..+.++|...+.+++|+|||.||++|||+..+..|+|+++.+..+.+++++||.++||+++|+|||+
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 99999999999998777788888888999999999999999999999999999988888888999999999999999999
Q ss_pred cchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCccccccccccCCCCCCCCCCCCCCcc
Q 005051 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (716)
Q Consensus 161 ~q~Edrr~~k~~~~l~R~pgsd~~~~~gk~ss~~~sP~r~s~~~~~DRfa~e~s~~r~sdfs~ss~g~~~k~~~~sp~~~ 240 (716)
++|||||||||...|+||||+||+++ ||+++|+|+|+|+.++|+||||+||++++|++||+++++||++|.+.+||+|+
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 005051 241 KDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDKIST 320 (716)
Q Consensus 241 kd~~~ssp~v~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~~~~ 320 (716)
|.++++|+|++.++++..+... + ++++|||+|+||+||+|++++++|+++|++|.|+.+|.+++++++|.|+..
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 7788999999999988754443 2 689999999999999999999999999999999999999999999998765
Q ss_pred cCCCCCCCCcCcccccCCCCCCCCCCCCCCCCCccCCCCcccc-cccccccccCCCCCCCCCCCCCCCCCCCCcccc-cc
Q 005051 321 FPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF-QI 398 (716)
Q Consensus 321 ~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~s~~~~~~s~~~~q~~q~~~~~~~d~f-~~ 398 (716)
. +|++++.++++|||||+|+|+.| +|||||.+.++.++++|.+|+.||+++++||+| +|
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 5 56788889999999999999999 999999999999999999999999999999999 99
Q ss_pred cCCCccccccCCCcCCCCCCCCCcccccCCCCCCCCCCccCcccccccCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCC
Q 005051 399 TEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQWPAFQNSGANGP 478 (716)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~p~neGWAtfD~p~~~~s~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 478 (716)
+||+++. +++||++||||||||||+|. +++++++||.. +..-..+.+||.++++.++||||+|+.+.+..
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 9998774 99999999999999999554 78888888744 21224467999999999999999988776554
Q ss_pred CCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccccccCCCcCCCCC--CCCCCCccCC
Q 005051 479 SPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFDDFTSHLPSEGFK--PNSEPHVDAY 556 (716)
Q Consensus 479 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~ds~~~~~~~~~~--~~~~~~~~~~ 556 (716)
++.||++|++++||||+++ ++++|+||||+|+++++||++++ +++++++.++
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 3457789999999999998 69999999999999999999999 8888788655
Q ss_pred CCCCCCCcchhhccccccCCCCCCccc-CCCCCCCCCCCCCCccCCCCCCCCCCcccccccccccCCCCCCCCCCCCCCC
Q 005051 557 MPSPTPDQYLAIVSQQETNDDGNPRVA-SHDGPPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFDFPCDSDL 635 (716)
Q Consensus 557 ~~~~t~~~~~~~~~~q~~~~d~~~~~a-p~~~~~~~~~ps~~~~g~~~~~~~~~~~g~~~~~~~~~ks~NPFDlp~dsd~ 635 (716)
.++|++||+++|++||+++||+||+| |+|. ++|++|+++++||+|+++++|+|+ ++||+||||||||+|+
T Consensus 499 -~~~t~~q~~~~r~~ed~~~dg~qr~~~p~g~-~g~~~~~~~~~~Ps~~~~~~~~~~-------~~ks~npfdl~~~sd~ 569 (648)
T PLN03119 499 -SYNTDHQHLESQVLEELSNDGTQTTRIPAGS-SAFGFPGNIGMAPSYSEEAWQHVN-------EQKSANPFDLPYDSEF 569 (648)
T ss_pred -CCCCcccccccccccccccccccccccCCCC-CCCCCCCccccCCCCCchhccccc-------cccCCCCcCCcccccc
Confidence 45555599999999999999999999 6665 999999999999999999999988 4999999999999999
Q ss_pred CCCCcccchhhhhhhCCCCCCCCCccCCCCcCCCCCCCCCcccccCC--CCCccccccCCCCccccCCCCCCCcccCCCC
Q 005051 636 EQNNMFLDMSSLQAALPNAELPSPFLGGATQSWFPQNPVSPFVQAAA--QGGLAYMSGQSPSAQLANIPTQEPVASVGGN 713 (716)
Q Consensus 636 e~~~mFmDmsSLQaaLP~~~lp~~f~gg~~e~W~~qn~~~~yipsa~--qGGl~~ma~q~p~s~l~ni~~~~~~a~~~gN 713 (716)
|++|||||||||||||||+|||++|+|||||+||+||++|+|||+|+ ||||+|||||+|+ |+++++||||+|||
T Consensus 570 ~~~~mf~d~tslq~~lp~~~~~~~~~~~~t~~w~~~~~~~~yip~~~~~qggl~y~~~q~~~----~~~~~~~~a~~~~n 645 (648)
T PLN03119 570 DSNDMFLDMSSLQGALPDIQTPQAFLNGVSQPWLAADSVPSYLPAPAVAQGGLAYMAGQAST----NSAAQGPVAFTGGN 645 (648)
T ss_pred CcccceeehHHHHhhcCCCCCchhhhcCCCcccccCCCcccccCCCccccCCchhhhcccch----hhhhcCccccCCCC
Confidence 99999999999999999999999999999999999999999999977 9999999999999 67788999999999
Q ss_pred CCC
Q 005051 714 PFA 716 (716)
Q Consensus 714 PFa 716 (716)
|||
T Consensus 646 pf~ 648 (648)
T PLN03119 646 PFA 648 (648)
T ss_pred CCC
Confidence 997
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=2.1e-46 Score=404.78 Aligned_cols=509 Identities=30% Similarity=0.404 Sum_probs=378.5
Q ss_pred chhHHHHH-HHHHHHHhcCCCCCCCcCCCCCCC-CeeEecceeheehhhhhhhhcCC--CceeeeccCCCCHHHHHHHHh
Q 005051 3 SRKEEERN-EKIIRGLMKLPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGIHREFT--HRVKSVSMSKFTSQEVEALQN 78 (716)
Q Consensus 3 srke~Er~-ekiLr~Llk~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSGIHR~LG--hrVKSItmDkWt~eEVe~Lq~ 78 (716)
.+||+|++ |++||.|+++|+|++|++|+.... +|+++.-|-|||+.|+|..|.|. ||||+|+|.+|++.||..|+.
T Consensus 4 ~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~qevs~lQs 83 (524)
T KOG0702|consen 4 YKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQEVSFLQS 83 (524)
T ss_pred ccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCCccccceeeeeeccccchHHHhh
Confidence 34888887 999999999999999999999988 99999999999999999999995 999999999999999999999
Q ss_pred cChHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhhccccCCCCCCCCCCCccCCCCCccccccCCCCCCCCCCCC
Q 005051 79 GGNQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPP 158 (716)
Q Consensus 79 gGN~rAN~iyea~~d~~r~~~P~~sd~~~~reFIraKY~eKrF~~~k~~DkPpr~~q~l~~~~~e~rr~ssy~s~sqsPp 158 (716)
+||+.+++||++.++..+--.|+..+.++.|+||+.||+.|+|+..+..++-+.- +|. .++. .+++
T Consensus 84 hgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~----------tr~---s~s~-~s~~ 149 (524)
T KOG0702|consen 84 HGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSY----------TRG---SLSE-DSRP 149 (524)
T ss_pred cchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCccccccccc----------ccc---cccc-cCCc
Confidence 9999999999999999988899999999999999999999999987554333210 110 0110 0111
Q ss_pred cccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCccccccccccCCCCCCCCCCCCCC
Q 005051 159 YDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPN 238 (716)
Q Consensus 159 ~d~q~Edrr~~k~~~~l~R~pgsd~~~~~gk~ss~~~sP~r~s~~~~~DRfa~e~s~~r~sdfs~ss~g~~~k~~~~sp~ 238 (716)
+...+ |++ +-+|+-- || +.|-
T Consensus 150 ~~~s~---------------------------------~~~-----~~lrs~~---------------gd------~~P~ 170 (524)
T KOG0702|consen 150 VSESR---------------------------------PET-----KSLRSLL---------------GD------HAPL 170 (524)
T ss_pred ccccC---------------------------------CCc-----ccccccc---------------CC------CCcc
Confidence 11100 011 1112100 00 0010
Q ss_pred cccccCCCCCCccccccccccccCcccCCCCCCCCcccccCCCccccCCCccccccccCCCCccCCCCCCcCcCCCCCcc
Q 005051 239 FQKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDKI 318 (716)
Q Consensus 239 ~~kd~~~ssp~v~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~~ 318 (716)
+.+..++..+. + -.++-|-|-
T Consensus 171 -------------------------------~~~~t~np~~~------~--------~~~~~~~~~-------------- 191 (524)
T KOG0702|consen 171 -------------------------------LAESTKNPRSR------G--------LPKSPIRFE-------------- 191 (524)
T ss_pred -------------------------------hhhcccCcccc------C--------CCCCCchhh--------------
Confidence 00111111100 0 000001110
Q ss_pred cccCCCCCCCCcCcccccCCCCCCCCCCCCCCCCCccCCCCcccc-cccccccccCCCCCCCCCCCCCCCCCCCCccccc
Q 005051 319 STFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFFQ 397 (716)
Q Consensus 319 ~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~s~~~~~~s~~~~q~~q~~~~~~~d~f~ 397 (716)
...--+|||+++.++.+ +++.||.+.+.+.+.++..+..|+..++.+|+|.
T Consensus 192 ----------------------------~~~~rfdlfg~~k~sd~~s~s~~qss~~~~ssp~~~~~~~~~~~~s~an~~~ 243 (524)
T KOG0702|consen 192 ----------------------------IVDDRFDLFGLPKASDAQSQSTFQSSIAPSSSPPNHQSVPQAYSDSPANIFA 243 (524)
T ss_pred ----------------------------hhhhhhhhhcCcCcccccccCcccccccccCCCCccccchhhcccccccccc
Confidence 11245788999998888 9999999888888888888888999999999992
Q ss_pred c--cCCCccccccCCCcCCCCCCCCCccc-ccCCCCCCCCCCccCcccccccCCCCCCCCCCCCCCCCCCCCCCcccCCC
Q 005051 398 I--TEQPSTAILNRNPQELSIPKNEGWAT-FDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQWPAFQNSG 474 (716)
Q Consensus 398 ~--~~~~~~~~~~~~~~~~~~p~neGWAt-fD~p~~~~s~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~s~ 474 (716)
+ -.||. ..+.+++.||||||+. +|+|..+........ +...++ ...||...+..+..|+.|...+.+
T Consensus 244 ge~~k~P~-----~~~~~asapk~eg~~s~sd~pvne~~~e~~i~-s~~~~~----~f~k~~e~paps~a~qlp~~ss~~ 313 (524)
T KOG0702|consen 244 GEPFKQPV-----SRPSFASAPKNEGWASLSDNPVNEAKSENVIT-SPGSFA----DFLKFEEIPAPSVAMQLPPYSSTV 313 (524)
T ss_pred cCCCCCCc-----cCccccccccccCCcccccCcccccccccccc-Ccccch----hhcccccccCcchhhhcCCcCCCc
Confidence 2 23343 5778999999999999 899987554431111 112222 236788888899999999888777
Q ss_pred CCCCCCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccccccCCCcCCCCCCCCCCCcc
Q 005051 475 ANGPSPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFDDFTSHLPSEGFKPNSEPHVD 554 (716)
Q Consensus 475 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~ds~~~~~~~~~~~~~~~~~~ 554 (716)
+......+.+|. ++|..-...+++|. +|+++-++++...+++..+-.+.+.+
T Consensus 314 ~~~q~t~~~~~n----------------------d~~ssf~~~~~Ap~------~~~~s~p~i~s~~~s~~~~l~~~~s~ 365 (524)
T KOG0702|consen 314 DQHQPTIPSPWN----------------------DQGSSFGATPVAPP------LWVASPPSIGSNLLSSSRALAVQSSV 365 (524)
T ss_pred cccCCCCCCccc----------------------ccCcccccccccCC------ccccCCCCcccccccccccccccccc
Confidence 766654333111 33444334554444 79999999999999999988877643
Q ss_pred CCCC-CCCCCcchhhccccccCCCCCCcccCCCCCCCCCCCCCCccCCCCCCCCCCcccccccccccCCCCCCCCCCCCC
Q 005051 555 AYMP-SPTPDQYLAIVSQQETNDDGNPRVASHDGPPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFDFPCDS 633 (716)
Q Consensus 555 ~~~~-~~t~~~~~~~~~~q~~~~d~~~~~ap~~~~~~~~~ps~~~~g~~~~~~~~~~~g~~~~~~~~~ks~NPFDlp~ds 633 (716)
.-+. ++++++.+.+-+.++.-.+..+..++-.+..-+.+|..+-++|++.+- .-|-....+...++.+++++|||+.
T Consensus 366 ~gsa~~~~~~~~~n~~~~e~~~~s~~q~~s~ft~~~ts~~p~~~~~~pssn~~--~~~~~Q~~~~~~~~g~~~~sl~~~~ 443 (524)
T KOG0702|consen 366 FGSAGYVPPHQPVNLGVLEELSNSTTQTFSAFTNESTSGFPAPIGMAPSSNHH--QDDEFQPNHRNPQPGAAMSSLPYGF 443 (524)
T ss_pred ccccccCCCCcccccccccccccccccccccccCcccccCccccccCCccccc--ccccccccccCCCCccccccCCCCC
Confidence 4444 788999999987788889999999998888888899999999998742 2222233344446789999999999
Q ss_pred CCCCC-CcccchhhhhhhCCCCCCCCCccCCCCcCCCCCCCCCccccc--CCCCCccccccCCCCccccCCCCCCCcccC
Q 005051 634 DLEQN-NMFLDMSSLQAALPNAELPSPFLGGATQSWFPQNPVSPFVQA--AAQGGLAYMSGQSPSAQLANIPTQEPVASV 710 (716)
Q Consensus 634 d~e~~-~mFmDmsSLQaaLP~~~lp~~f~gg~~e~W~~qn~~~~yips--a~qGGl~~ma~q~p~s~l~ni~~~~~~a~~ 710 (716)
..+.+ +||++|+.+|-++| .+.+..+.+|+...|..+.....|.|. -+|+|++||..++-- |.++|.||+|+
T Consensus 444 ~~~~P~~~~fa~s~~qp~fP-~qt~~~q~~~~~~~~~~~~~~p~~~P~~~v~~~G~S~nPF~as~----~S~aq~~~~~p 518 (524)
T KOG0702|consen 444 EFASPFDMFFAMSFPQPAFP-IQTPQVQQPGGSHFGLAGDSKPSYLPAPAVAQAGLSYNPFMASP----NSAAQFPVAFP 518 (524)
T ss_pred CcCCCccccccccCcCcCCC-CccccccCCCCCCccccccCCcccCccccccccccccCccccCC----CCcccccccCC
Confidence 99999 99999999999999 888999999999999999999999998 559999999888531 27799999999
Q ss_pred CCCCCC
Q 005051 711 GGNPFA 716 (716)
Q Consensus 711 ~gNPFa 716 (716)
++|||+
T Consensus 519 ~~nPF~ 524 (524)
T KOG0702|consen 519 GTNPFL 524 (524)
T ss_pred CCCCCC
Confidence 999995
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=3.3e-35 Score=304.13 Aligned_cols=118 Identities=31% Similarity=0.651 Sum_probs=107.1
Q ss_pred hHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCh
Q 005051 5 KEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGN 81 (716)
Q Consensus 5 ke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN 81 (716)
...++++++|++|++.|+|++|||||+++|+|||+|+|||||++|+||||+|| | |||||+||.|++|+|+.|+..||
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 45678999999999999999999999999999999999999999999999999 5 99999999999999999999999
Q ss_pred HHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhhccccCCC
Q 005051 82 QRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGK 125 (716)
Q Consensus 82 ~rAN~iyea~~d~~r~~~P~~sd~~~~reFIraKY~eKrF~~~k 125 (716)
.+||++||+.++.. .+.|.. .+.++.|||+|||+|+|+...
T Consensus 87 ~~an~~~ea~~p~~-~~~p~~--d~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 87 AKANSYYEAKLPDP-FRRPGP--DDLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hhhhhhccccCCcc-ccCCCh--HHHHHHHHHHHHhhhhhccch
Confidence 99999999998765 344433 237888999999999999864
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=7.8e-35 Score=266.60 Aligned_cols=112 Identities=34% Similarity=0.740 Sum_probs=93.2
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC---CceeeeccCCCCHHHHHHHHhcChHHHHHHH
Q 005051 12 KIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (716)
Q Consensus 12 kiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItmDkWt~eEVe~Lq~gGN~rAN~iy 88 (716)
++|++|++.|+|++|||||+++|+|||++||||||++|+|+||+|| ++||||+||+|+.+||++|+.+||.++|++|
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 hhcCccccCCCCCCCchHHHHHHHHHHHhhccccCC
Q 005051 89 LKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (716)
Q Consensus 89 ea~~d~~r~~~P~~sd~~~~reFIraKY~eKrF~~~ 124 (716)
|++.+ ...+++...+.+.+++||++||++|+|+.+
T Consensus 82 e~~~~-~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 82 EANSP-PPKKPPPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp TTTST-TTTTHCTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred HcCCC-CCCCCCCCCcHHHHHHHHHHHHHhhhhccC
Confidence 99932 334566677888899999999999999853
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=5.1e-33 Score=253.44 Aligned_cols=106 Identities=31% Similarity=0.701 Sum_probs=97.5
Q ss_pred CCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcChHHHHHHHhhcCccccC
Q 005051 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDWDFQRQ 97 (716)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN~rAN~iyea~~d~~r~ 97 (716)
|+|++|||||+++|+||+++||||||++|+||||+|| | +||||+||+|++++|++|+.+||.++|++||++++....
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 005051 98 RLPDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (716)
Q Consensus 98 ~~P~~sd~~~~reFIraKY~eKrF~~~k~ 126 (716)
+.+...+...+++||++||++|+|+....
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhcccccc
Confidence 55666667888999999999999997644
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=2e-30 Score=273.68 Aligned_cols=117 Identities=24% Similarity=0.576 Sum_probs=103.8
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcChHHH
Q 005051 8 ERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRA 84 (716)
Q Consensus 8 Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN~rA 84 (716)
...++++..|++.++|++|||||+++|+||++|||||||++||||||+|| | +||||+||+|+.+||++|+.+||.+|
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 45677888888999999999999999999999999999999999999999 4 99999999999999999999999999
Q ss_pred HHHHhhcCccc-cCCCCCCCchHHHHHHHHHHHhhccccCC
Q 005051 85 REIYLKDWDFQ-RQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (716)
Q Consensus 85 N~iyea~~d~~-r~~~P~~sd~~~~reFIraKY~eKrF~~~ 124 (716)
|+||+++.-.. ..++-...+...+++||+.||++++|...
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 99999886432 12233456778899999999999999876
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=8.1e-28 Score=252.73 Aligned_cols=85 Identities=33% Similarity=0.714 Sum_probs=80.5
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcChHH
Q 005051 7 EERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQR 83 (716)
Q Consensus 7 ~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN~r 83 (716)
..|+++.|++|+...+|++|+||++++|+||+++||||||++|+|+||.|| | +|||||||+|.+.||++|++|||++
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 457888999998888999999999999999999999999999999999999 5 9999999999999999999999999
Q ss_pred HHHHHhhc
Q 005051 84 AREIYLKD 91 (716)
Q Consensus 84 AN~iyea~ 91 (716)
++++++..
T Consensus 83 ~~eFL~s~ 90 (386)
T KOG0704|consen 83 FREFLSSQ 90 (386)
T ss_pred HHHHHhhC
Confidence 99998765
No 9
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.92 E-value=2.3e-25 Score=235.62 Aligned_cols=116 Identities=22% Similarity=0.414 Sum_probs=95.7
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcChHHHHHH
Q 005051 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (716)
Q Consensus 11 ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN~rAN~i 87 (716)
.++|++|+++|+|++|+|||+++|+|++++||||||++|+||||.|| | +||||+||+|++++|++|+.+||.++|++
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 45599999999999999999999999999999999999999999999 4 89999999999999999999999999999
Q ss_pred HhhcCccccCCCC--CCCchHHHHHHHHHHHhhccccCCCC
Q 005051 88 YLKDWDFQRQRLP--DNSNVNKVRDFIKNVYVDRRYAGGKT 126 (716)
Q Consensus 88 yea~~d~~r~~~P--~~sd~~~~reFIraKY~eKrF~~~k~ 126 (716)
|+.+.-.....+. ..+...++.+.+.+|++++.+..+..
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 9865311111111 12344455556888899998876653
No 10
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.90 E-value=3e-24 Score=231.72 Aligned_cols=83 Identities=24% Similarity=0.622 Sum_probs=79.4
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcChHHHH
Q 005051 9 RNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAR 85 (716)
Q Consensus 9 r~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN~rAN 85 (716)
..+++++.|+..+.||+|||||+++|+|++|+|||||||+|+++||+|| | +|||..||+|+.+||+.|+.|||.+|+
T Consensus 9 d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~ 88 (454)
T KOG0706|consen 9 DIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANAR 88 (454)
T ss_pred hHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHH
Confidence 4567899999999999999999999999999999999999999999999 5 999999999999999999999999999
Q ss_pred HHHhhc
Q 005051 86 EIYLKD 91 (716)
Q Consensus 86 ~iyea~ 91 (716)
.|+..+
T Consensus 89 ~FFkqh 94 (454)
T KOG0706|consen 89 VFFKQH 94 (454)
T ss_pred HHHHHc
Confidence 999876
No 11
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.88 E-value=2.3e-23 Score=229.39 Aligned_cols=115 Identities=19% Similarity=0.451 Sum_probs=102.4
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC---CceeeeccCCCCHHHHHHHHhcChHHHHHHH
Q 005051 12 KIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (716)
Q Consensus 12 kiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItmDkWt~eEVe~Lq~gGN~rAN~iy 88 (716)
-.|+.|...+||.+|+||+.++|.|+++|+|++|||+|+||||.|| +|||+|.||.|..|.+..|..+||+.||++|
T Consensus 502 ~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~vW 581 (749)
T KOG0705|consen 502 MALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSVW 581 (749)
T ss_pred HHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHHh
Confidence 4588899999999999999999999999999999999999999998 3999999999999999999999999999999
Q ss_pred hhcCccccCCCCCCCchHHHHHHHHHHHhhccccCCCCC
Q 005051 89 LKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTP 127 (716)
Q Consensus 89 ea~~d~~r~~~P~~sd~~~~reFIraKY~eKrF~~~k~~ 127 (716)
|......+.+ ...+..++++.||++||++|.|......
T Consensus 582 E~~~~G~~KP-s~~s~REEkErwIr~KYeqklFLaPl~~ 619 (749)
T KOG0705|consen 582 EGSSQGQTKP-SPDSSREEKERWIRAKYEQKLFLAPLPC 619 (749)
T ss_pred hhhccCCcCC-CccccHHHHHHHHHHHHHHHhhcCCCCC
Confidence 9866554332 2346788889999999999999876543
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.80 E-value=1.4e-20 Score=218.15 Aligned_cols=114 Identities=26% Similarity=0.539 Sum_probs=101.6
Q ss_pred HHHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcChHHHHHHHhh
Q 005051 14 IRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLK 90 (716)
Q Consensus 14 Lr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN~rAN~iyea 90 (716)
+..+.+.|+|.+|+|||++.|+|+++|+||.+||+|+||||+|| | ||+|++||.|..+.+.+++++||..+|.|||+
T Consensus 417 ~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~ 496 (785)
T KOG0521|consen 417 IEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEA 496 (785)
T ss_pred hhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhc
Confidence 67888899999999999999999999999999999999999999 4 99999999999999999999999999999999
Q ss_pred cCccccCCCC-CCCchHHHHHHHHHHHhhccccCCCCC
Q 005051 91 DWDFQRQRLP-DNSNVNKVRDFIKNVYVDRRYAGGKTP 127 (716)
Q Consensus 91 ~~d~~r~~~P-~~sd~~~~reFIraKY~eKrF~~~k~~ 127 (716)
.+.....++| ..++...++.||++||++++|..+...
T Consensus 497 ~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~ 534 (785)
T KOG0521|consen 497 LLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQ 534 (785)
T ss_pred ccccccccCCCCccchhhhhHhhhcccceeeEeecccc
Confidence 9865433333 345577888999999999999887544
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.60 E-value=3.2e-16 Score=178.82 Aligned_cols=110 Identities=25% Similarity=0.504 Sum_probs=97.4
Q ss_pred HHHhcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC---CceeeeccC--CCCHHHHHHHHhcChHHHHHHHh
Q 005051 15 RGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMS--KFTSQEVEALQNGGNQRAREIYL 89 (716)
Q Consensus 15 r~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItmD--kWt~eEVe~Lq~gGN~rAN~iye 89 (716)
.++.....|+.|+|||++.|.||++|++|.||-.|+|-||.|| ++|+|++|| .|+.+-|+++...||.++|.||-
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 3556678999999999999999999999999999999999998 599999998 69999999999999999999999
Q ss_pred hcCccccCCCCCCCchHHHHHHHHHHHhhccccCCC
Q 005051 90 KDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGK 125 (716)
Q Consensus 90 a~~d~~r~~~P~~sd~~~~reFIraKY~eKrF~~~k 125 (716)
.++.+...-.| .+.+..|++||++||.+.+|....
T Consensus 370 ~nl~~~e~lh~-dssp~~r~~fi~~Kykeg~fRk~~ 404 (1186)
T KOG1117|consen 370 GNLPPNEHLHP-DSSPSTRRQFIKEKYKEGKFRKEH 404 (1186)
T ss_pred cCCCCccccCC-CCCcchhhhHHHHHhhcccccccc
Confidence 99876654444 356788999999999999886543
No 14
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.60 E-value=1.4e-16 Score=174.08 Aligned_cols=131 Identities=20% Similarity=0.385 Sum_probs=98.4
Q ss_pred hcCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcChHHHHHHHhhcC-c
Q 005051 18 MKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDW-D 93 (716)
Q Consensus 18 lk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN~rAN~iyea~~-d 93 (716)
++...-+.|+|||+++|.|+||+-|||||.+|..+||.|| | .||+|....|.++.|++.....|..+|.|||..+ +
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-CCCCCCCCccCCCCCccccccCC
Q 005051 94 F----QRQRLPDNSNVN--KVRDFIKNVYVDRRYAGGK-TPDKPPKDTQGLGSHLDESRRAS 148 (716)
Q Consensus 94 ~----~r~~~P~~sd~~--~~reFIraKY~eKrF~~~k-~~DkPpr~~q~l~~~~~e~rr~s 148 (716)
+ .+.++|...|.. .+.+|||+||+.-.|+.+. +.|.-....+.+..+.....|+.
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~~~~rDdD~~~~~~LsrQLhasvRt~ 144 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHRLPCRDDDSVTAKDLSKQLHSSVRTG 144 (669)
T ss_pred chhhhcccCCCCCcCCCCccHHHHHHHHHHheeeeccCCCCCcchhhHHHHHHHHHHHhhcc
Confidence 2 222334333322 3567999999999999743 33333222223333444444544
No 15
>PLN03131 hypothetical protein; Provisional
Probab=97.11 E-value=0.026 Score=65.53 Aligned_cols=90 Identities=31% Similarity=0.393 Sum_probs=46.7
Q ss_pred cCcccccCCCCCCCCCCCCCCCCCccCCCCcccc---------------cccccccccCCCCCCCC-CCCCCCCCCCC--
Q 005051 330 YGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA---------------SVNMSEMSQASSVPSTN-TYQPAQTSSPS-- 391 (716)
Q Consensus 330 ~~~~~~~~~p~~~~~~~~~~~~~dlf~~p~~~~a---------------~vd~f~~s~~~~~~s~~-~~q~~q~~~~~-- 391 (716)
...+|||.+|.. +.+.++||||++-..++ +||||++.--- .+++ ++|.+++.+..
T Consensus 359 a~pIDLFqlp~t-----s~a~~vdlf~~s~l~~~p~~n~~q~~qts~p~~~dlfag~~qq--q~~~s~~~~~~~~s~pkn 431 (705)
T PLN03131 359 APPIDLFQLPAT-----SPAPPVDLFEIPPLDPAPAINAYQPPQTSLPSSIDLFGGITQQ--QSINSLDEKSPELSIPKN 431 (705)
T ss_pred CCchhhhhccCC-----CCCCcccccccCcccCCCccccCCCCcccCCcccccccccccc--CccccccccCcccCCccc
Confidence 457899988654 77888999996643222 56666542210 1111 22333332222
Q ss_pred -CcccccccCC-CccccccCCCcCCCCC-CCCCcccccC
Q 005051 392 -SLNFFQITEQ-PSTAILNRNPQELSIP-KNEGWATFDT 427 (716)
Q Consensus 392 -~~d~f~~~~~-~~~~~~~~~~~~~~~p-~neGWAtfD~ 427 (716)
---+|+-.+| .++++ ..+.+.+.|| .+.|-+-||.
T Consensus 432 egwa~fd~~~p~~s~~~-~~n~t~~~v~~~~~~~~~~d~ 469 (705)
T PLN03131 432 EGWATFDGIQPIASTPG-NENLTPFSIGPSMAGSANFDQ 469 (705)
T ss_pred cCcccccCCCcccccCC-cccccccccccccccCcchhh
Confidence 1346642344 44444 5566665555 4555555553
No 16
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=93.55 E-value=4 Score=47.98 Aligned_cols=39 Identities=18% Similarity=0.346 Sum_probs=22.1
Q ss_pred CCcccc-cccccccccCCCCCCCCCCCCCCCCCCCCcccc
Q 005051 358 PETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF 396 (716)
Q Consensus 358 p~~~~a-~vd~f~~s~~~~~~s~~~~q~~q~~~~~~~d~f 396 (716)
.+++.| ||||||-...|.++++++.|+.=.++-++|+++
T Consensus 318 ~~~~~aapIDLFqlp~ts~a~~vdlf~~~~~p~~p~~n~~ 357 (648)
T PLN03119 318 VAESTKAPIDLFQLPGAPVAQSVDTFQPSIAPRSPPVNLQ 357 (648)
T ss_pred cccccCCchhhhhccCCCCCccccccccccCCCCCccccC
Confidence 444555 999998555555555555554333344444444
No 17
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=93.08 E-value=0.16 Score=57.96 Aligned_cols=142 Identities=20% Similarity=0.160 Sum_probs=102.3
Q ss_pred CCCCCCCCCcccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCccccccccccCCCCC
Q 005051 150 YHSYSQSPPYDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDP 229 (716)
Q Consensus 150 y~s~sqsPp~d~q~Edrr~~k~~~~l~R~pgsd~~~~~gk~ss~~~sP~r~s~~~~~DRfa~e~s~~r~sdfs~ss~g~~ 229 (716)
|+++.+.+.|+|.|+.||++|.. ..|+=-.=..+ +...-+.+.++++-.++.++-+.+....+|..++++..-+++
T Consensus 1 ~a~~~ke~E~~~ek~iR~l~kLP--~NrrC~nCnsl--~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~q 76 (524)
T KOG0702|consen 1 YAGYKKEDEYDYEKEIRRLLKLP--ENRRCINCNSL--VAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQ 76 (524)
T ss_pred CCcccccchhHHHHHHHHHhcCC--CCCceeecccc--ccceEEEeeccceeeeccchhhccCCCccccceeeeeecccc
Confidence 57788889999999999999976 23331111112 223446688999999999999999999999999999999998
Q ss_pred CCCCCCC-CC-cccccCCCCCCccccccccccccCcccCCCCCCCCcccccCCCccccCCCccccccccCCCCc
Q 005051 230 FRPGAQS-PN-FQKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLT 301 (716)
Q Consensus 230 ~k~~~~s-p~-~~kd~~~ssp~v~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~ 301 (716)
+....|+ .| ..|++.+-..-.++ ...+..++..-.+..||+.....--.++.+.+.+++|+.++|-
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 66 66666554443332 1222333444445667888888888888999999999987764
No 18
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=88.43 E-value=0.11 Score=62.50 Aligned_cols=67 Identities=16% Similarity=0.282 Sum_probs=51.2
Q ss_pred CCCCCCCcCCCC-CCCCeeEecceeheehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcChHHHHHHH
Q 005051 20 LPPNRRCINCNS-LGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (716)
Q Consensus 20 ~PgNk~CADCGa-~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItmDkWt~eEVe~Lq~gGN~rAN~iy 88 (716)
...+..|++|++ ..-.|+|+++.+.+|+.|+++|+.++ | .++++.|+...+ |..+...||..++..|
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 455889999987 67899999999999999999999997 4 556666666555 6666555555555544
No 19
>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=79.28 E-value=1.6 Score=33.16 Aligned_cols=40 Identities=15% Similarity=0.421 Sum_probs=33.4
Q ss_pred CCCCCcCCCCCCCCeeEecceeheehhhhhh-hhcCCCceeee
Q 005051 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGI-HREFTHRVKSV 63 (716)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGI-HR~LGhrVKSI 63 (716)
.+..|..|+.....+.+.+=.++||..|... |+. |+|.+|
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 3578999998888999999999999999987 887 877764
No 20
>PRK12495 hypothetical protein; Provisional
Probab=79.08 E-value=1.5 Score=45.90 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=27.9
Q ss_pred HHHHHHhc--CCCCCCCcCCCCCCCCeeEecceeheehhhhhhh
Q 005051 12 KIIRGLMK--LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIH 53 (716)
Q Consensus 12 kiLr~Llk--~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIH 53 (716)
++-..|++ ...++.|-+||.+=|.+ -|+.+|..|..+-
T Consensus 29 ~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 29 RMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQPV 68 (226)
T ss_pred HHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCcc
Confidence 34344444 45889999999988832 5999999998653
No 21
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=61.02 E-value=12 Score=38.42 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=26.5
Q ss_pred CCCCCCCcCCCCCCC-CeeEecceeheehhhhh
Q 005051 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSG 51 (716)
Q Consensus 20 ~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSG 51 (716)
.|.-..|+-||.... .|.+...|.++|..|..
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 355679999998644 78899999999999973
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=52.79 E-value=9.9 Score=38.77 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=26.9
Q ss_pred CCCCCCCcCCCCCCC-CeeEecceeheehhhhhh
Q 005051 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGI 52 (716)
Q Consensus 20 ~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSGI 52 (716)
.|.=..|+.||..++ .|.+...|.++|.+|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 456679999998544 688899999999999864
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=46.39 E-value=12 Score=31.96 Aligned_cols=33 Identities=24% Similarity=0.411 Sum_probs=22.5
Q ss_pred CCCCCCCcCCCCCCC--CeeEecceeheehhhhhhh
Q 005051 20 LPPNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIH 53 (716)
Q Consensus 20 ~PgNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIH 53 (716)
.++...|.+||.+=| ++. ..-|+..|+.|...+
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 456789999998533 222 223788899998754
No 24
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=42.95 E-value=21 Score=34.35 Aligned_cols=44 Identities=18% Similarity=0.307 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCCC--CCCcCCCCCCCC-eeEecceeheehhhhhhh
Q 005051 10 NEKIIRGLMKLPPN--RRCINCNSLGPQ-YVCTNFWTFVCMTCSGIH 53 (716)
Q Consensus 10 ~ekiLr~Llk~PgN--k~CADCGa~~P~-WaSvnfGVFVCi~CSGIH 53 (716)
.+++-..|.++... .+|.+||.+=|. =.-.--+..+|+.|.-.|
T Consensus 65 l~~i~~al~rIe~gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~ 111 (120)
T COG1734 65 LRKIESALDRIEEGTYGICEECGEPIPEARLEARPTARLCIECQERA 111 (120)
T ss_pred HHHHHHHHHHHHcCCccchhccCCcCCHHHHhhCcchHHHHHHHHHH
Confidence 33333444443333 489999985221 011122578999999776
No 25
>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=41.66 E-value=10 Score=29.54 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=20.7
Q ss_pred CCcCCCCCCCCeeEecceeheehhhhhh
Q 005051 25 RCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (716)
Q Consensus 25 ~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (716)
+|-.||+.. ....-.-|-+||..|.-|
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 26
>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=40.54 E-value=18 Score=27.82 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=23.1
Q ss_pred CCCCCCcCCCCCCCCeeEecceeheehhhh
Q 005051 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCS 50 (716)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CS 50 (716)
..|..|..|++. |....=|-++|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 456779999987 888889999999985
No 27
>PRK11019 hypothetical protein; Provisional
Probab=40.16 E-value=16 Score=33.47 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=22.7
Q ss_pred CCCCCcCCCCCCC--CeeEecceeheehhhhhhhhc
Q 005051 22 PNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIHRE 55 (716)
Q Consensus 22 gNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIHR~ 55 (716)
.-..|.+||.+=| ++.-+. ++-.|++|...+-.
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 333222 67889999987643
No 28
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=39.65 E-value=14 Score=32.48 Aligned_cols=31 Identities=16% Similarity=0.264 Sum_probs=20.5
Q ss_pred CCCCcCCCCCCCCee-Eecceeheehhhhhhh
Q 005051 23 NRRCINCNSLGPQYV-CTNFWTFVCMTCSGIH 53 (716)
Q Consensus 23 Nk~CADCGa~~P~Wa-SvnfGVFVCi~CSGIH 53 (716)
...|.|||.+=|.== -.--|+..|+.|...+
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 458999998643211 1223788999998764
No 29
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=36.46 E-value=19 Score=37.98 Aligned_cols=30 Identities=27% Similarity=0.676 Sum_probs=25.9
Q ss_pred CCCCCCcCCCCCC-CCeeEecceeheehhhh
Q 005051 21 PPNRRCINCNSLG-PQYVCTNFWTFVCMTCS 50 (716)
Q Consensus 21 PgNk~CADCGa~~-P~WaSvnfGVFVCi~CS 50 (716)
+.=..|+.||... +..+++-.|-++|.+|.
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3447999999975 57999999999999999
No 30
>PHA00080 DksA-like zinc finger domain containing protein
Probab=35.26 E-value=20 Score=31.43 Aligned_cols=45 Identities=16% Similarity=0.326 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhc---CCCCCCCcCCCCCC--CCeeEecceeheehhhhhhh
Q 005051 8 ERNEKIIRGLMK---LPPNRRCINCNSLG--PQYVCTNFWTFVCMTCSGIH 53 (716)
Q Consensus 8 Er~ekiLr~Llk---~PgNk~CADCGa~~--P~WaSvnfGVFVCi~CSGIH 53 (716)
...+..|...+. ..+...|.+||..= .++.-+. |+..|+.|...+
T Consensus 13 ~~~~~al~~~~~~~~~~~~~~C~~Cg~~Ip~~Rl~a~P-~~~~Cv~Cq~~~ 62 (72)
T PHA00080 13 LQRERALANRRNKYQAPSATHCEECGDPIPEARREAVP-GCRTCVSCQEIL 62 (72)
T ss_pred HHHHHHHHHHHhcccCCCCCEecCCCCcCcHHHHHhCC-CccCcHHHHHHH
Confidence 334444444432 34556899999853 2332222 667799999865
No 31
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=33.35 E-value=16 Score=36.44 Aligned_cols=34 Identities=32% Similarity=0.690 Sum_probs=28.3
Q ss_pred CCCCCCcCCCCCCCCeeEecceeheeh-hhhhhhhc
Q 005051 21 PPNRRCINCNSLGPQYVCTNFWTFVCM-TCSGIHRE 55 (716)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi-~CSGIHR~ 55 (716)
|--+.|+-|| -...|.|++-|.-+|. .|-++|.+
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 4556899999 6778999999998886 89999965
No 32
>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=31.82 E-value=14 Score=28.50 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=16.5
Q ss_pred CCCcCCCCC-CCCeeEecceeheehhhh
Q 005051 24 RRCINCNSL-GPQYVCTNFWTFVCMTCS 50 (716)
Q Consensus 24 k~CADCGa~-~P~WaSvnfGVFVCi~CS 50 (716)
..|.+||.. .-+|..-+|+.-||..|.
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 568999999999999995
No 33
>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=30.44 E-value=33 Score=34.25 Aligned_cols=32 Identities=13% Similarity=0.229 Sum_probs=19.9
Q ss_pred CCCCCCcCCCCCC--CCeeEecceeheehhhhhhh
Q 005051 21 PPNRRCINCNSLG--PQYVCTNFWTFVCMTCSGIH 53 (716)
Q Consensus 21 PgNk~CADCGa~~--P~WaSvnfGVFVCi~CSGIH 53 (716)
..=.+|.+||..= -+.--+. ++-.|+.|...+
T Consensus 84 G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 84 GTYGICEVCGKPIPYERLEAIP-TATTCVECQNRK 117 (159)
T ss_pred CCCCeecccCCcccHHHHhhCC-CcchhHHHHHHh
Confidence 3445899999841 1111111 467899999875
No 34
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=28.56 E-value=42 Score=27.53 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=29.3
Q ss_pred CCCCCcCCCCC-CCCeeEeccee-heehhhhhhhhcCC
Q 005051 22 PNRRCINCNSL-GPQYVCTNFWT-FVCMTCSGIHREFT 57 (716)
Q Consensus 22 gNk~CADCGa~-~P~WaSvnfGV-FVCi~CSGIHR~LG 57 (716)
..+.|.+|+.. -|.|=.-..|- +||-.|.-..+..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 35799999984 68898888886 99999988777665
No 35
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=27.95 E-value=45 Score=24.45 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=24.8
Q ss_pred CCcCCCCCCCCeeEecceeheehhhhh-hhhcCCCceee
Q 005051 25 RCINCNSLGPQYVCTNFWTFVCMTCSG-IHREFTHRVKS 62 (716)
Q Consensus 25 ~CADCGa~~P~WaSvnfGVFVCi~CSG-IHR~LGhrVKS 62 (716)
.|-.|+.....+.+.+=+..||..|.- .|+ +|.+..
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~--~H~~~~ 38 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVHS--GHRRVP 38 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhcC--CCCEee
Confidence 466676656677788888899999963 265 565544
No 36
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=26.91 E-value=80 Score=31.38 Aligned_cols=35 Identities=11% Similarity=0.136 Sum_probs=21.7
Q ss_pred CCCCCCCcCCCCCCCC-eeEecceeheehhhhhhhh
Q 005051 20 LPPNRRCINCNSLGPQ-YVCTNFWTFVCMTCSGIHR 54 (716)
Q Consensus 20 ~PgNk~CADCGa~~P~-WaSvnfGVFVCi~CSGIHR 54 (716)
.+.-.+|-+||.+=|. =.-+-=++..|+.|...|-
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 4566899999985210 0011114678999998764
No 37
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=26.15 E-value=59 Score=30.07 Aligned_cols=30 Identities=13% Similarity=0.273 Sum_probs=23.8
Q ss_pred CCCCCCcCCCCCCCCeeEecceeheehhhhhh
Q 005051 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (716)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (716)
-.--.|-.|+.+ .---+..|||.|..|--.
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 345689999988 555688999999999643
No 38
>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=25.57 E-value=23 Score=33.28 Aligned_cols=44 Identities=23% Similarity=0.509 Sum_probs=30.1
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcC--CC--ceeeeccC
Q 005051 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (716)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItmD 66 (716)
..|.--+|.+||. +..+..-.+.|-.|.+..-.+ |. +|++|.++
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 3567789999994 333332357899999876444 43 88888764
No 39
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=24.75 E-value=26 Score=37.23 Aligned_cols=32 Identities=22% Similarity=0.419 Sum_probs=24.7
Q ss_pred CCCCCCcCCCC--CCCCeeEecceeheehhhhhhh
Q 005051 21 PPNRRCINCNS--LGPQYVCTNFWTFVCMTCSGIH 53 (716)
Q Consensus 21 PgNk~CADCGa--~~P~WaSvnfGVFVCi~CSGIH 53 (716)
.-+.+|..|.. .++.+-+ .||+-||..|+.-|
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 46899999997 3444433 58999999999888
No 40
>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=24.65 E-value=45 Score=29.76 Aligned_cols=31 Identities=13% Similarity=0.470 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEecceeheehhhhhhhhc
Q 005051 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (716)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (716)
.|..|.=||... ....||++.|..|.+..|.
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 467899999755 3478999999999998866
No 41
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=23.77 E-value=1.1e+02 Score=34.60 Aligned_cols=69 Identities=22% Similarity=0.196 Sum_probs=40.0
Q ss_pred CCCCCccCCCCcccc--------cccccccccCCCCCCCCCCCCCCCCCCC-CcccccccCCCccccc--cCCCcCCCCC
Q 005051 349 APPIDLFQLPETSAA--------SVNMSEMSQASSVPSTNTYQPAQTSSPS-SLNFFQITEQPSTAIL--NRNPQELSIP 417 (716)
Q Consensus 349 ~~~~dlf~~p~~~~a--------~vd~f~~s~~~~~~s~~~~q~~q~~~~~-~~d~f~~~~~~~~~~~--~~~~~~~~~p 417 (716)
..-.|||+--+-+.+ ++|+|. +-++++||.-|..-++--- =.|+|.|.+-|+-+.. -++...+..|
T Consensus 327 gdl~dLFDgsa~s~~gaadlfG~faDf~~---aaaagsfn~a~atA~Sg~GdfgD~~AF~aAPsgpmAqSgef~g~aaaP 403 (499)
T KOG2057|consen 327 GDLDDLFDGSAPSPAGAADLFGAFADFFG---AAAAGSFNAAPATAPSGGGDFGDLFAFGAAPSGPMAQSGEFAGPAAAP 403 (499)
T ss_pred ccHHHHhcCcCCCCCCchhhcCchhhhhh---hhccCccccccccccCCCCcchhhhhhcCCCCccccccccccCccccc
Confidence 345677874333333 455554 3456788887776665543 3788999888764433 3344444445
Q ss_pred CCC
Q 005051 418 KNE 420 (716)
Q Consensus 418 ~ne 420 (716)
.||
T Consensus 404 a~e 406 (499)
T KOG2057|consen 404 ANE 406 (499)
T ss_pred hhh
Confidence 544
No 42
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.54 E-value=26 Score=32.97 Aligned_cols=44 Identities=11% Similarity=0.290 Sum_probs=30.3
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcC--CC--ceeeecc
Q 005051 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSM 65 (716)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItm 65 (716)
..|..-+|-+||. .+....+..+.|-.|.+....+ |. +|++|-+
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 4577789999995 2223344557899999876665 32 7887754
No 43
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.54 E-value=43 Score=36.32 Aligned_cols=34 Identities=18% Similarity=0.205 Sum_probs=23.7
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeheehhhhhhhh
Q 005051 20 LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHR 54 (716)
Q Consensus 20 ~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR 54 (716)
.....+|-+||... --....-|-.||.+|.-|..
T Consensus 8 ~~~~~~Cp~Cg~~~-iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 8 EEEKLVCPECGSDK-LIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred cccCCcCcCCCCCC-eeEECCCCeEeecccCCccc
Confidence 34557899999742 22235669999999998643
No 44
>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=22.48 E-value=52 Score=30.18 Aligned_cols=31 Identities=19% Similarity=0.485 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeEecceeheehhhhhhhhc
Q 005051 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (716)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (716)
.+..|.=||...- ...||++.|..|.+..|.
T Consensus 4 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSS---GIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCc---ceEECceeehhhHHhhHH
Confidence 4678999998653 467999999999999875
No 45
>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=21.81 E-value=56 Score=29.21 Aligned_cols=31 Identities=16% Similarity=0.613 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeEecceeheehhhhhhhhc
Q 005051 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (716)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (716)
..+.|.=||...- ...||++.|..|.+..|.
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 4677999997653 468999999999998866
No 46
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.67 E-value=32 Score=32.53 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=28.2
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeheehhhhhhhhcC--CC--ceeeeccC
Q 005051 20 LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (716)
Q Consensus 20 ~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItmD 66 (716)
.|.--+|.+||.. |....+..+.|-.|.+....+ |. +|++|-++
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 222234455699999876554 43 78887653
No 47
>PRK00420 hypothetical protein; Validated
Probab=21.39 E-value=1.9e+02 Score=27.74 Aligned_cols=44 Identities=18% Similarity=0.156 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhc--CCCCCCCcCCCCCCCCeeEecceeheehhhhhh
Q 005051 6 EEERNEKIIRGLMK--LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (716)
Q Consensus 6 e~Er~ekiLr~Llk--~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (716)
+++..+++-+.|++ .=-+..|-.||.+-.. +.-|-.+|..|...
T Consensus 4 ~~~~~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~---lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 4 SEDIVKKAAELLLKGAKMLSKHCPVCGLPLFE---LKDGEVVCPVHGKV 49 (112)
T ss_pred cHHHHHHHHHHHHhHHHHccCCCCCCCCccee---cCCCceECCCCCCe
Confidence 44555555555555 2246899999975432 36688899999754
No 48
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=21.07 E-value=57 Score=30.36 Aligned_cols=35 Identities=17% Similarity=0.357 Sum_probs=24.1
Q ss_pred HhcCCCCCCCcCCCCCC-----------------CCeeEecceeheehhhhh
Q 005051 17 LMKLPPNRRCINCNSLG-----------------PQYVCTNFWTFVCMTCSG 51 (716)
Q Consensus 17 Llk~PgNk~CADCGa~~-----------------P~WaSvnfGVFVCi~CSG 51 (716)
..++++--+|++||.+= -.=+.=.||-.+|.+|..
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 111244689899999974
No 49
>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=20.64 E-value=91 Score=23.73 Aligned_cols=30 Identities=23% Similarity=0.480 Sum_probs=21.6
Q ss_pred CcCCCCC-CCCeeEecceeh-eehhhhhhhhc
Q 005051 26 CINCNSL-GPQYVCTNFWTF-VCMTCSGIHRE 55 (716)
Q Consensus 26 CADCGa~-~P~WaSvnfGVF-VCi~CSGIHR~ 55 (716)
|.+|+.. .|.|=....|-. ||-.|.-.+|.
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 8899984 799998888876 99999877665
No 50
>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=20.45 E-value=57 Score=30.11 Aligned_cols=30 Identities=17% Similarity=0.587 Sum_probs=24.5
Q ss_pred CCCCcCCCCCCCCeeEecceeheehhhhhhhhc
Q 005051 23 NRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (716)
Q Consensus 23 Nk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (716)
+..|.=||...- ...||++.|..|.+..|.
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 468999999999998875
No 51
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=20.16 E-value=56 Score=26.57 Aligned_cols=26 Identities=23% Similarity=0.631 Sum_probs=19.5
Q ss_pred CCcCCCCCCCCeeEecceeheehhhhh
Q 005051 25 RCINCNSLGPQYVCTNFWTFVCMTCSG 51 (716)
Q Consensus 25 ~CADCGa~~P~WaSvnfGVFVCi~CSG 51 (716)
+|+=|+..... .-.=+|-|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48889887665 334468999999974
Done!