Query 005117
Match_columns 713
No_of_seqs 188 out of 1218
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 18:19:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005117.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005117hhsearch_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 9E-199 2E-203 1612.4 48.1 684 1-713 1-705 (705)
2 PLN03119 putative ADP-ribosyla 100.0 4E-179 9E-184 1448.7 44.9 640 1-713 1-648 (648)
3 KOG0702 Predicted GTPase-activ 100.0 8.3E-47 1.8E-51 407.8 32.3 505 4-713 5-524 (524)
4 KOG0703 Predicted GTPase-activ 100.0 2.3E-35 5E-40 305.2 9.1 118 5-125 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 9E-35 2E-39 266.2 8.4 112 12-124 2-116 (116)
6 smart00105 ArfGap Putative GTP 100.0 5.6E-33 1.2E-37 253.2 10.7 106 21-126 1-109 (112)
7 COG5347 GTPase-activating prot 100.0 2.7E-30 5.8E-35 272.6 10.2 117 8-124 5-125 (319)
8 KOG0704 ADP-ribosylation facto 99.9 7.4E-28 1.6E-32 253.0 13.1 86 7-92 3-91 (386)
9 PLN03114 ADP-ribosylation fact 99.9 2.2E-25 4.8E-30 235.7 11.5 116 11-126 10-130 (395)
10 KOG0706 Predicted GTPase-activ 99.9 2E-24 4.3E-29 233.0 8.6 83 9-91 9-94 (454)
11 KOG0705 GTPase-activating prot 99.9 2.6E-23 5.6E-28 229.0 8.2 115 11-126 501-618 (749)
12 KOG0521 Putative GTPase activa 99.8 1.7E-20 3.6E-25 217.6 3.1 114 14-127 417-534 (785)
13 KOG0818 GTPase-activating prot 99.6 6.5E-17 1.4E-21 176.7 0.8 133 18-150 3-146 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.6 2.5E-16 5.4E-21 179.6 4.2 108 16-124 291-403 (1186)
15 PLN03131 hypothetical protein; 96.9 0.051 1.1E-06 63.2 18.3 90 330-427 359-469 (705)
16 PLN03119 putative ADP-ribosyla 94.4 2.1 4.5E-05 50.1 17.8 39 358-396 318-357 (648)
17 KOG0702 Predicted GTPase-activ 93.0 0.16 3.5E-06 57.8 5.9 142 150-301 1-144 (524)
18 KOG0521 Putative GTPase activa 87.1 0.13 2.8E-06 62.0 -1.3 67 20-88 627-697 (785)
19 PF00643 zf-B_box: B-box zinc 80.4 1.6 3.5E-05 33.2 2.7 40 22-63 2-42 (42)
20 PRK12495 hypothetical protein; 79.1 1.7 3.7E-05 45.5 3.2 38 12-53 29-68 (226)
21 TIGR00613 reco DNA repair prot 54.0 10 0.00022 38.7 2.7 33 20-52 144-177 (241)
22 PRK00085 recO DNA repair prote 50.0 8.3 0.00018 39.4 1.4 32 20-51 146-178 (247)
23 TIGR02419 C4_traR_proteo phage 46.1 12 0.00025 32.0 1.4 33 20-53 28-62 (63)
24 PF08271 TF_Zn_Ribbon: TFIIB z 45.1 11 0.00023 29.5 1.0 27 25-52 2-28 (43)
25 PF11781 RRN7: RNA polymerase 43.1 18 0.0004 27.8 1.9 28 21-51 6-33 (36)
26 PRK11019 hypothetical protein; 42.0 14 0.00031 33.7 1.5 33 22-55 35-69 (88)
27 COG1734 DksA DnaK suppressor p 39.1 23 0.00049 34.1 2.4 30 24-53 81-111 (120)
28 PRK13715 conjugal transfer pro 39.1 14 0.0003 32.5 0.8 31 23-53 34-65 (73)
29 KOG3362 Predicted BBOX Zn-fing 36.5 13 0.00029 36.9 0.4 34 21-55 116-150 (156)
30 PHA00080 DksA-like zinc finger 35.3 19 0.00041 31.6 1.1 45 8-53 13-62 (72)
31 COG1381 RecO Recombinational D 35.1 20 0.00044 37.7 1.5 30 21-50 152-182 (251)
32 TIGR02890 spore_yteA sporulati 32.8 28 0.00061 34.8 2.0 41 11-53 75-117 (159)
33 PRK10778 dksA RNA polymerase-b 28.9 68 0.0015 31.8 3.9 35 20-54 108-143 (151)
34 COG1997 RPL43A Ribosomal prote 28.3 58 0.0013 30.1 3.0 30 21-52 33-62 (89)
35 smart00401 ZnF_GATA zinc finge 27.8 44 0.00096 27.4 2.0 36 22-57 2-39 (52)
36 PF01286 XPA_N: XPA protein N- 27.5 18 0.0004 27.8 -0.2 27 24-50 4-31 (34)
37 TIGR00100 hypA hydrogenase nic 27.1 24 0.00051 33.2 0.3 44 19-66 66-113 (115)
38 PRK03681 hypA hydrogenase nick 25.4 25 0.00054 33.1 0.2 44 19-65 66-113 (114)
39 PRK00423 tfb transcription ini 24.7 43 0.00092 36.4 1.8 34 20-54 8-41 (310)
40 PRK00420 hypothetical protein; 24.3 1.6E+02 0.0035 28.2 5.3 45 5-52 3-49 (112)
41 cd07171 NR_DBD_ER DNA-binding 24.2 48 0.0011 29.6 1.8 31 22-55 2-32 (82)
42 COG5145 RAD14 DNA excision rep 24.0 26 0.00057 37.2 0.1 32 21-53 114-147 (292)
43 KOG2057 Predicted equilibrativ 24.0 1E+02 0.0023 34.6 4.5 69 349-420 327-406 (499)
44 PRK00564 hypA hydrogenase nick 23.8 30 0.00066 32.6 0.4 44 20-66 68-115 (117)
45 PF00320 GATA: GATA zinc finge 22.8 67 0.0015 24.4 2.0 30 26-55 1-32 (36)
46 cd06968 NR_DBD_ROR DNA-binding 22.3 55 0.0012 30.0 1.8 31 22-55 4-34 (95)
47 PF10764 Gin: Inhibitor of sig 21.9 55 0.0012 26.6 1.5 26 25-51 1-26 (46)
48 COG2174 RPL34A Ribosomal prote 21.6 58 0.0013 30.3 1.7 35 17-51 28-79 (93)
49 PRK12380 hydrogenase nickel in 20.7 39 0.00085 31.7 0.5 43 19-65 66-112 (113)
50 cd07173 NR_DBD_AR DNA-binding 20.6 60 0.0013 29.0 1.6 31 22-55 2-32 (82)
51 cd07170 NR_DBD_ERR DNA-binding 20.2 61 0.0013 29.9 1.6 30 23-55 4-33 (97)
52 PF04189 Gcd10p: Gcd10p family 20.1 92 0.002 34.2 3.2 47 66-120 106-152 (299)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=9.4e-199 Score=1612.38 Aligned_cols=684 Identities=61% Similarity=0.992 Sum_probs=658.8
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCCCceeeeecCCCCHHHHHHHHhcC
Q 005117 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (713)
Q Consensus 1 M~srke~ErnekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSItLDkWT~eEVe~Lq~gG 80 (713)
|++||++|+++++|++|+++|+|++|||||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
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 005117 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (713)
Q Consensus 81 N~rANeiwea~~d~~r~~~P~~sd~~~rreFIraKY~eKrF~~~k~~D~Ppr~~q~l~~~~~e~rR~ssy~S~SQSPp~d 160 (713)
|++||+|||++|+..+.++|...+.+++|+|||.||++|||+.....|+|+++.+.++.++.++||.++||+++|||||+
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 005117 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (713)
Q Consensus 161 ~qyEdrr~~k~~~~ltRkpgsd~~~~~gk~ss~~~sP~r~s~~~~~Drfa~e~s~~r~sdfs~s~~g~~~k~~~~sp~~~ 240 (713)
|+||||||||+...++|+||+++++|.|||++|++||+|+.+||+||||+||++++|++||+++++|+++|.+.+||+++
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 005117 241 KDAGFNSPPVQLSRDVSSLKANFK-----------RDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQ 309 (713)
Q Consensus 241 kd~~~ssp~v~~~~~i~~~~~~~~-----------~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~ 309 (713)
|++. +||||+++|+|||++++.+ .+++|++++|||+|+||+||+||+++++|+++|+|||||.+|+++
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 005117 310 AAGAPLDKISTFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTS 388 (713)
Q Consensus 310 ~~~~~q~~~~~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~s~~~~~~s~~~~q~~q~~ 388 (713)
+++++|.|+.++++..+...++++|+|++||+|+++..++++|||||+|+|+.| +|||||-+++..++++|.+|+.||+
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 005117 389 SPSSLNFF-QITEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQW 467 (713)
Q Consensus 389 ~~~~~d~f-~~~~~~~~~~~~~~~~~~~~p~n~GWAtfD~p~~~~s~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 467 (713)
++++|||| +|+||++++|+|++++||++||||||||||+++.++|++|++||+..+||.....+.+||.++++.++|||
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 99999999999999999999999999999988888999999999888999776557899999999999999
Q ss_pred CcccCCCCCCCCCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccc--cccCCCcCCCC
Q 005117 468 PAFQNSGANGPSPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFD--DFTSHLPSEGF 545 (713)
Q Consensus 468 ~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~--ds~~~~~~~~~ 545 (713)
|+|+++.++... .||++|.+++||||+|.. +++|+||||+ |+++++||+++
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 CCCCCCCccCCCCCCCCCccccc-cccccCCCCCCcccCCCC--CCCCCCCCCCCcCCCCCCCCC--ccccccccccCCC
Q 005117 546 KPNSEPHVDAYMPSPTPDQYLAI-VSQETNDDGNPRVASHDG--PPNMTVPSQADMGPSYNPSMF--PLMMRTHATEHKS 620 (713)
Q Consensus 546 ~~~~~~~~~~~~~~~t~~~~~~~-~~q~~~~d~~~~~ap~~~--~~~~~~ps~~~~gp~~~~~~~--~g~~~~~~~~~ks 620 (713)
++++++||+++++++. +||+++ ++||+++||+||+||+|+ +++|++|+.+|+||+|+++++ ||++++|+++|||
T Consensus 533 ~~~s~~q~~~~~~~t~-~q~~~~~~~~d~~~d~~~r~~p~~~~~~~g~~~~~~~~~~ps~~~~~~~~~~~~~s~~~~~ks 611 (705)
T PLN03131 533 KQSSEPQTAANMPPTA-DQLIGCKALEDFNKDGIKRTAPHGQGELPGLDEPSDILAEPSYTPPAHPIMEHAQSHANDHKS 611 (705)
T ss_pred cccccccccccCCCCc-ccccccccccccccccccccCCCCCcCCCCCCCCCccccCCCCCccccccccccccccCccCC
Confidence 9999999976655554 599999 999999999999999999 999999999999999999999 9999999999999
Q ss_pred CCCCCCCCCCCCCCCCcccchhhhhhhCCCCCCCCCccC-CCCcCCCCCCCCCcccccCCCCCccccccCCCCccccCCC
Q 005117 621 TNPFDFPCDSDLEQNNMFLDMSSLQAALPNAELPSPFLG-GATQSWFPQNPVSPFVQAAAQGGLAYMSGQSPSAQLANIP 699 (713)
Q Consensus 621 ~NPFDlp~dsd~e~~~mFmDmsSLQaaLP~~~lp~~f~g-g~~e~W~~qn~~~~yipsa~qGGl~~ma~q~p~s~l~ni~ 699 (713)
+||||||||+|+|++|||||||||||||||+|||++||| |||||||+||++|+|||+|+||||+|||||+|++||.|++
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 005117 700 TQEPVASVGGNPFA 713 (713)
Q Consensus 700 ~~~~~a~~~gNPFa 713 (713)
+|+||||+||||||
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=4.4e-179 Score=1448.67 Aligned_cols=640 Identities=51% Similarity=0.803 Sum_probs=594.3
Q ss_pred CCChhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCCCceeeeecCCCCHHHHHHHHhcC
Q 005117 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (713)
Q Consensus 1 M~srke~ErnekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSItLDkWT~eEVe~Lq~gG 80 (713)
|++||++||++++|++|+++|+|++|||||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
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 005117 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (713)
Q Consensus 81 N~rANeiwea~~d~~r~~~P~~sd~~~rreFIraKY~eKrF~~~k~~D~Ppr~~q~l~~~~~e~rR~ssy~S~SQSPp~d 160 (713)
|++||+|||++|+..+.++|...+.+++|+|||+||++|||+.....|+|+++.+..+.+++++||.++||+++|+|||+
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 99999999999998777788888888999999999999999999999999999999888889999999999999999999
Q ss_pred cchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCCcccccccccCCCCCCCCCCCCCCcc
Q 005117 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (713)
Q Consensus 161 ~qyEdrr~~k~~~~ltRkpgsd~~~~~gk~ss~~~sP~r~s~~~~~Drfa~e~s~~r~sdfs~s~~g~~~k~~~~sp~~~ 240 (713)
++|||||||||...|+||||+||+++ ||+++|+|+|+|+.++|+||||+||++++|++||+++++||++|.+.+||+|+
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 005117 241 KDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDKIST 320 (713)
Q Consensus 241 kd~~~ssp~v~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~~~~ 320 (713)
|.++++|+|++.++++..+... + ++++|||+|+||+||+|++++++|+++|++|.|+.+|.+++++++|.|+..
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 005117 321 FPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF-QI 398 (713)
Q Consensus 321 ~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~s~~~~~~s~~~~q~~q~~~~~~~d~f-~~ 398 (713)
. +|++++.++++|||||+|+|+.| +|||||.+.++.++++|.+|+.||+++++||+| +|
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 005117 399 TEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQWPAFQNSGANGP 478 (713)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~p~n~GWAtfD~p~~~~s~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 478 (713)
+||+++. +++||++||||||||||+|. +++++++||.. +..-..+.+||.++++.++||||+|+.+.+..
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 21113456999999999999999988776554
Q ss_pred CCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccccccCCCcCCCCC--CCCCCCccCC
Q 005117 479 SPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFDDFTSHLPSEGFK--PNSEPHVDAY 556 (713)
Q Consensus 479 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~ds~~~~~~~~~~--~~~~~~~~~~ 556 (713)
++.||++|++++||||+++ ++++|+||||+|+++++||++++ +++++++.++
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 CCCCCCCccccc-cccccCCCCCCccc-CCCCCCCCCCCCCCCcCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCC
Q 005117 557 MPSPTPDQYLAI-VSQETNDDGNPRVA-SHDGPPNMTVPSQADMGPSYNPSMFPLMMRTHATEHKSTNPFDFPCDSDLEQ 634 (713)
Q Consensus 557 ~~~~t~~~~~~~-~~q~~~~d~~~~~a-p~~~~~~~~~ps~~~~gp~~~~~~~~g~~~~~~~~~ks~NPFDlp~dsd~e~ 634 (713)
.++|++||+++ ++||+++||+||+| |+|. ++|++|+++++||+|+++++ .|-+++||+||||||||+|+|+
T Consensus 499 -~~~t~~q~~~~r~~ed~~~dg~qr~~~p~g~-~g~~~~~~~~~~Ps~~~~~~-----~~~~~~ks~npfdl~~~sd~~~ 571 (648)
T PLN03119 499 -SYNTDHQHLESQVLEELSNDGTQTTRIPAGS-SAFGFPGNIGMAPSYSEEAW-----QHVNEQKSANPFDLPYDSEFDS 571 (648)
T ss_pred -CCCCcccccccccccccccccccccccCCCC-CCCCCCCccccCCCCCchhc-----cccccccCCCCcCCccccccCc
Confidence 45555599999 99999999999999 6665 99999999999999999866 2333699999999999999999
Q ss_pred CCcccchhhhhhhCCCCCCCCCccCCCCcCCCCCCCCCcccccCC--CCCccccccCCCCccccCCCCCCCcccCCCCCC
Q 005117 635 NNMFLDMSSLQAALPNAELPSPFLGGATQSWFPQNPVSPFVQAAA--QGGLAYMSGQSPSAQLANIPTQEPVASVGGNPF 712 (713)
Q Consensus 635 ~~mFmDmsSLQaaLP~~~lp~~f~gg~~e~W~~qn~~~~yipsa~--qGGl~~ma~q~p~s~l~ni~~~~~~a~~~gNPF 712 (713)
+|||||||||||||||+|||++|+|||||+||+||++|+|||+|+ ||||+|||||+|+ |+++++||||+|||||
T Consensus 572 ~~mf~d~tslq~~lp~~~~~~~~~~~~t~~w~~~~~~~~yip~~~~~qggl~y~~~q~~~----~~~~~~~~a~~~~npf 647 (648)
T PLN03119 572 NDMFLDMSSLQGALPDIQTPQAFLNGVSQPWLAADSVPSYLPAPAVAQGGLAYMAGQAST----NSAAQGPVAFTGGNPF 647 (648)
T ss_pred ccceeehHHHHhhcCCCCCchhhhcCCCcccccCCCcccccCCCccccCCchhhhcccch----hhhhcCccccCCCCCC
Confidence 999999999999999999999999999999999999999999977 9999999999999 6778899999999999
Q ss_pred C
Q 005117 713 A 713 (713)
Q Consensus 713 a 713 (713)
|
T Consensus 648 ~ 648 (648)
T PLN03119 648 A 648 (648)
T ss_pred C
Confidence 7
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=8.3e-47 Score=407.85 Aligned_cols=505 Identities=30% Similarity=0.419 Sum_probs=380.6
Q ss_pred hhHHHHH-HHHHHHHhcCCCCCCCcCCCCCCC-CeeEecceeeeehhhhhhhhcCC--CceeeeecCCCCHHHHHHHHhc
Q 005117 4 RKEEERN-EKIIRGLMKLPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGIHREFT--HRVKSVSMSKFTSQEVEALQNG 79 (713)
Q Consensus 4 rke~Ern-ekiLr~Llk~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSGIHR~LG--hrVKSItLDkWT~eEVe~Lq~g 79 (713)
+||+|++ |++||.|+++|+|++|++|+.... +|+++.-|-|||+.|+|..|.|. ||||+|+|.+|++.||..|+.+
T Consensus 5 ~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~qevs~lQsh 84 (524)
T KOG0702|consen 5 KKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQEVSFLQSH 84 (524)
T ss_pred cccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCCccccceeeeeeccccchHHHhhc
Confidence 3788887 999999999999999999999988 99999999999999999999995 9999999999999999999999
Q ss_pred CcHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhhccccCCCCCCCCCCCccCCCCCccccccCCCCCCCCCCCCc
Q 005117 80 GNQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPY 159 (713)
Q Consensus 80 GN~rANeiwea~~d~~r~~~P~~sd~~~rreFIraKY~eKrF~~~k~~D~Ppr~~q~l~~~~~e~rR~ssy~S~SQSPp~ 159 (713)
||+.+++||++.++..+-..|+..+.++.|+||+.||+.|||+..+..++-+.- +| ..++.. ++++
T Consensus 85 gNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~----------tr---~s~s~~-s~~~ 150 (524)
T KOG0702|consen 85 GNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSY----------TR---GSLSED-SRPV 150 (524)
T ss_pred chhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCccccccccc----------cc---cccccc-CCcc
Confidence 999999999999999988999999999999999999999999987554333210 00 001100 1111
Q ss_pred ccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCCcccccccccCCCCCCCCCCCCCCc
Q 005117 160 DYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNF 239 (713)
Q Consensus 160 d~qyEdrr~~k~~~~ltRkpgsd~~~~~gk~ss~~~sP~r~s~~~~~Drfa~e~s~~r~sdfs~s~~g~~~k~~~~sp~~ 239 (713)
...+ |++ +-+|+-- || +.|-
T Consensus 151 ~~s~---------------------------------~~~-----~~lrs~~---------------gd------~~P~- 170 (524)
T KOG0702|consen 151 SESR---------------------------------PET-----KSLRSLL---------------GD------HAPL- 170 (524)
T ss_pred cccC---------------------------------CCc-----ccccccc---------------CC------CCcc-
Confidence 0000 011 1112100 00 0010
Q ss_pred ccccCCCCCCccccccccccccCcccCCCCCCCCcccccCCCccccCCCccccccccCCCCccCCCCCCcCcCCCCCccc
Q 005117 240 QKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDKIS 319 (713)
Q Consensus 240 ~kd~~~ssp~v~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~~~ 319 (713)
+.+..++..+. + -.++-|-|-
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 ccCCCCCCCCcCcccccCCCCCCCCCCCCCCCCCccCCCCcccc-cccccccccCCCCCCCCCCCCCCCCCCCCcccccc
Q 005117 320 TFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFFQI 398 (713)
Q Consensus 320 ~~p~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~s~~~~~~s~~~~q~~q~~~~~~~d~f~~ 398 (713)
...--+|||+++.++.+ .++.||.+.+.+.+.++..+-.|+..++.+|+|.+
T Consensus 192 ---------------------------~~~~rfdlfg~~k~sd~~s~s~~qss~~~~ssp~~~~~~~~~~~~s~an~~~g 244 (524)
T KOG0702|consen 192 ---------------------------IVDDRFDLFGLPKASDAQSQSTFQSSIAPSSSPPNHQSVPQAYSDSPANIFAG 244 (524)
T ss_pred ---------------------------hhhhhhhhhcCcCcccccccCcccccccccCCCCccccchhhccccccccccc
Confidence 12245789999999888 99999998888888888888889999999999922
Q ss_pred --cCCCccccccCCCcCCCCCCCCCccc-ccCCCCCCCCCCccCcccccccCCC--CCCCCCCCCCCCCCCCCCCcccCC
Q 005117 399 --TEQPSTAILNRNPQELSIPKNEGWAT-FDTPPSAASIPGTESLSHAMVPANE--GSSVKSDQFPSSNTSMQWPAFQNS 473 (713)
Q Consensus 399 --~~~~~~~~~~~~~~~~~~p~n~GWAt-fD~p~~~~s~~~~~~~~~~~~p~~~--~~~~~~~~~~~~~~~~~~~~~~~s 473 (713)
-.||. ..+.+++.||||||+. +|+|..+.... .+|...- ...+||...+..+..|+.|...+.
T Consensus 245 e~~k~P~-----~~~~~asapk~eg~~s~sd~pvne~~~e-------~~i~s~~~~~~f~k~~e~paps~a~qlp~~ss~ 312 (524)
T KOG0702|consen 245 EPFKQPV-----SRPSFASAPKNEGWASLSDNPVNEAKSE-------NVITSPGSFADFLKFEEIPAPSVAMQLPPYSST 312 (524)
T ss_pred CCCCCCc-----cCccccccccccCCcccccCcccccccc-------ccccCcccchhhcccccccCcchhhhcCCcCCC
Confidence 23343 5778999999999999 89998755443 2233221 123688888889999999988877
Q ss_pred CCCCCCCCCCCCCCCcccccccccccccccccccCCCCCCCCCCCcccccccccccccccccccCCCcCCCCCCCCCCCc
Q 005117 474 GANGPSPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFDDFTSHLPSEGFKPNSEPHV 553 (713)
Q Consensus 474 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~~~~~~~~~~~~q~WnAF~ds~~~~~~~~~~~~~~~~~ 553 (713)
++......+.+|. ++|..-...+++|. +|+++-++++...+++..+-.+.+.
T Consensus 313 ~~~~q~t~~~~~n----------------------d~~ssf~~~~~Ap~------~~~~s~p~i~s~~~s~~~~l~~~~s 364 (524)
T KOG0702|consen 313 VDQHQPTIPSPWN----------------------DQGSSFGATPVAPP------LWVASPPSIGSNLLSSSRALAVQSS 364 (524)
T ss_pred ccccCCCCCCccc----------------------ccCcccccccccCC------ccccCCCCccccccccccccccccc
Confidence 7776654333111 33444334554444 7999999999999999998887764
Q ss_pred cCCCC-CCCCCccccc-cccccCCCCCCcccCCCCCCCCCCCCCCCcCCCCCCCCCccccccccccCCCCCCCCCCCCCC
Q 005117 554 DAYMP-SPTPDQYLAI-VSQETNDDGNPRVASHDGPPNMTVPSQADMGPSYNPSMFPLMMRTHATEHKSTNPFDFPCDSD 631 (713)
Q Consensus 554 ~~~~~-~~t~~~~~~~-~~q~~~~d~~~~~ap~~~~~~~~~ps~~~~gp~~~~~~~~g~~~~~~~~~ks~NPFDlp~dsd 631 (713)
+.-+. ++++++.+.+ ++++.-.+..|..++-.+..-+.+|..+-++|++..-.-+-....+...++.+++++|||+..
T Consensus 365 ~~gsa~~~~~~~~~n~~~~e~~~~s~~q~~s~ft~~~ts~~p~~~~~~pssn~~~~~~~Q~~~~~~~~g~~~~sl~~~~~ 444 (524)
T KOG0702|consen 365 VFGSAGYVPPHQPVNLGVLEELSNSTTQTFSAFTNESTSGFPAPIGMAPSSNHHQDDEFQPNHRNPQPGAAMSSLPYGFE 444 (524)
T ss_pred cccccccCCCCcccccccccccccccccccccccCcccccCccccccCCcccccccccccccccCCCCccccccCCCCCC
Confidence 34444 7889999999 999999999999988888888899999999999985322444445555678899999999999
Q ss_pred CCCC-CcccchhhhhhhCCCCCCCCCccCCCCcCCCCCCCCCccccc--CCCCCccccccCCCCccccCCCCCCCcccCC
Q 005117 632 LEQN-NMFLDMSSLQAALPNAELPSPFLGGATQSWFPQNPVSPFVQA--AAQGGLAYMSGQSPSAQLANIPTQEPVASVG 708 (713)
Q Consensus 632 ~e~~-~mFmDmsSLQaaLP~~~lp~~f~gg~~e~W~~qn~~~~yips--a~qGGl~~ma~q~p~s~l~ni~~~~~~a~~~ 708 (713)
.+.+ +||++|+.+|-++| .+.+..+.+|+...|..+.....|.|. -+|+|++||..++-- |.++|.||+|++
T Consensus 445 ~~~P~~~~fa~s~~qp~fP-~qt~~~q~~~~~~~~~~~~~~p~~~P~~~v~~~G~S~nPF~as~----~S~aq~~~~~p~ 519 (524)
T KOG0702|consen 445 FASPFDMFFAMSFPQPAFP-IQTPQVQQPGGSHFGLAGDSKPSYLPAPAVAQAGLSYNPFMASP----NSAAQFPVAFPG 519 (524)
T ss_pred cCCCccccccccCcCcCCC-CccccccCCCCCCccccccCCcccCccccccccccccCccccCC----CCcccccccCCC
Confidence 9999 99999999999999 888999999999999999999999998 559999999888531 277999999999
Q ss_pred CCCCC
Q 005117 709 GNPFA 713 (713)
Q Consensus 709 gNPFa 713 (713)
+|||+
T Consensus 520 ~nPF~ 524 (524)
T KOG0702|consen 520 TNPFL 524 (524)
T ss_pred CCCCC
Confidence 99995
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=2.3e-35 Score=305.25 Aligned_cols=118 Identities=31% Similarity=0.660 Sum_probs=107.3
Q ss_pred hHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCc
Q 005117 5 KEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGN 81 (713)
Q Consensus 5 ke~ErnekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN 81 (713)
...++++++|++|++.|+|++|||||+++|+|||+|+|||||++|+||||+|| | |||||+||.|++|+|+.|+..||
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 44678999999999999999999999999999999999999999999999999 5 99999999999999999999999
Q ss_pred HHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhhccccCCC
Q 005117 82 QRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGK 125 (713)
Q Consensus 82 ~rANeiwea~~d~~r~~~P~~sd~~~rreFIraKY~eKrF~~~k 125 (713)
.+||.+||++++.. ...|... +.++.|||+|||+|+|+...
T Consensus 87 ~~an~~~ea~~p~~-~~~p~~d--~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 87 AKANSYYEAKLPDP-FRRPGPD--DLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hhhhhhccccCCcc-ccCCChH--HHHHHHHHHHHhhhhhccch
Confidence 99999999998765 4445433 37888999999999999864
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=9e-35 Score=266.18 Aligned_cols=112 Identities=34% Similarity=0.740 Sum_probs=93.0
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC---CceeeeecCCCCHHHHHHHHhcCcHHHHHHH
Q 005117 12 KIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (713)
Q Consensus 12 kiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLDkWT~eEVe~Lq~gGN~rANeiw 88 (713)
++|++|++.|+|++|||||+++|+|||++||||||++|+|+||+|| ++||||+||+|+.+||++|+.+||.++|++|
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 005117 89 LKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (713)
Q Consensus 89 ea~~d~~r~~~P~~sd~~~rreFIraKY~eKrF~~~ 124 (713)
|++.+ ...+++..++.+.+++||++||++|+|+.+
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 234556677888899999999999999853
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=5.6e-33 Score=253.16 Aligned_cols=106 Identities=31% Similarity=0.701 Sum_probs=97.2
Q ss_pred CCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCcHHHHHHHhhcCccccC
Q 005117 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDWDFQRQ 97 (713)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN~rANeiwea~~d~~r~ 97 (713)
|+|++|||||+++|+||+++||||||++|+||||+|| | +||||+||+|++++|++|+.+||.++|++||++++....
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 005117 98 RLPDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (713)
Q Consensus 98 ~~P~~sd~~~rreFIraKY~eKrF~~~k~ 126 (713)
+.+...+...+++||++||++|+|+....
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhcccccc
Confidence 55555667888899999999999987744
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=2.7e-30 Score=272.62 Aligned_cols=117 Identities=24% Similarity=0.576 Sum_probs=103.4
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCcHHH
Q 005117 8 ERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRA 84 (713)
Q Consensus 8 ErnekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN~rA 84 (713)
...++++..|++.++|++|||||+.+|+||++|||||||++||||||+|| | +||||+||+|+.+||++|+.+||.+|
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 45677788888999999999999999999999999999999999999999 4 99999999999999999999999999
Q ss_pred HHHHhhcCccc-cCCCCCCCchHHHHHHHHHHHhhccccCC
Q 005117 85 REIYLKDWDFQ-RQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (713)
Q Consensus 85 Neiwea~~d~~-r~~~P~~sd~~~rreFIraKY~eKrF~~~ 124 (713)
|+||+++.-.. ..+.-...+...+++||+.||++++|...
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 99999886432 12222456778889999999999999876
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=7.4e-28 Score=252.96 Aligned_cols=86 Identities=33% Similarity=0.690 Sum_probs=80.9
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCcHH
Q 005117 7 EERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQR 83 (713)
Q Consensus 7 ~ErnekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN~r 83 (713)
..|+++.|++|+...+|+.|+||++++|+||+++||||||++|+|+||.|| | +|||||||+|.+.||++|++|||++
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 4 9999999999999999999999999
Q ss_pred HHHHHhhcC
Q 005117 84 AREIYLKDW 92 (713)
Q Consensus 84 ANeiwea~~ 92 (713)
++++++..-
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=2.2e-25 Score=235.73 Aligned_cols=116 Identities=22% Similarity=0.422 Sum_probs=95.8
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCcHHHHHH
Q 005117 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (713)
Q Consensus 11 ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN~rANei 87 (713)
.++|++|+++++|++|+|||+++|+|++++||||||++|+||||.|| | +||||+||+|++++|++|+.+||.++|++
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 HhhcCccccCCCCC--CCchHHHHHHHHHHHhhccccCCCC
Q 005117 88 YLKDWDFQRQRLPD--NSNVNKVRDFIKNVYVDRRYAGGKT 126 (713)
Q Consensus 88 wea~~d~~r~~~P~--~sd~~~rreFIraKY~eKrF~~~k~ 126 (713)
|+.+.-.....+.. .+....+..-+.+|++++.++.+..
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 98753111111112 2344455556888899998876653
No 10
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.90 E-value=2e-24 Score=232.99 Aligned_cols=83 Identities=24% Similarity=0.622 Sum_probs=79.5
Q ss_pred HHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCcHHHH
Q 005117 9 RNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAR 85 (713)
Q Consensus 9 rnekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN~rAN 85 (713)
..+.+++.|+..+.||+|||||+++|+|++|+|||||||+|+++||+|| | +|||..||+|+.+||+.|+.|||.+|+
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 005117 86 EIYLKD 91 (713)
Q Consensus 86 eiwea~ 91 (713)
.++..+
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=2.6e-23 Score=228.96 Aligned_cols=115 Identities=19% Similarity=0.452 Sum_probs=102.3
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC---CceeeeecCCCCHHHHHHHHhcCcHHHHHH
Q 005117 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (713)
Q Consensus 11 ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLDkWT~eEVe~Lq~gGN~rANei 87 (713)
.-.|+.|...+||.+|+||+.++|.|+++|+|++||++|+||||.|| +|||+|.||.|..|.+..|..+||+.||++
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 34588999999999999999999999999999999999999999998 399999999999999999999999999999
Q ss_pred HhhcCccccCCCCCCCchHHHHHHHHHHHhhccccCCCC
Q 005117 88 YLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (713)
Q Consensus 88 wea~~d~~r~~~P~~sd~~~rreFIraKY~eKrF~~~k~ 126 (713)
||......+.+- ..+..++++.||++||++|.|.....
T Consensus 581 WE~~~~G~~KPs-~~s~REEkErwIr~KYeqklFLaPl~ 618 (749)
T KOG0705|consen 581 WEGSSQGQTKPS-PDSSREEKERWIRAKYEQKLFLAPLP 618 (749)
T ss_pred hhhhccCCcCCC-ccccHHHHHHHHHHHHHHHhhcCCCC
Confidence 998665543332 34567888999999999999987643
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.79 E-value=1.7e-20 Score=217.59 Aligned_cols=114 Identities=26% Similarity=0.539 Sum_probs=101.5
Q ss_pred HHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCcHHHHHHHhh
Q 005117 14 IRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLK 90 (713)
Q Consensus 14 Lr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN~rANeiwea 90 (713)
+..+.+.++|.+|+|||++.|+|+++|+||.+||+|+||||+|| | ||+|++||.|..+.+.+++++||..+|.|||+
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 3 99999999999999999999999999999999
Q ss_pred cCccccCCCC-CCCchHHHHHHHHHHHhhccccCCCCC
Q 005117 91 DWDFQRQRLP-DNSNVNKVRDFIKNVYVDRRYAGGKTP 127 (713)
Q Consensus 91 ~~d~~r~~~P-~~sd~~~rreFIraKY~eKrF~~~k~~ 127 (713)
.+.....++| ..++...++.||++||++++|..+...
T Consensus 497 ~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~ 534 (785)
T KOG0521|consen 497 LLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQ 534 (785)
T ss_pred ccccccccCCCCccchhhhhHhhhcccceeeEeecccc
Confidence 9865433333 334577888999999999999887544
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.62 E-value=6.5e-17 Score=176.67 Aligned_cols=133 Identities=20% Similarity=0.382 Sum_probs=100.4
Q ss_pred hcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCcHHHHHHHhhcC-c
Q 005117 18 MKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDW-D 93 (713)
Q Consensus 18 lk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN~rANeiwea~~-d 93 (713)
++...-+.|+|||+++|.|+||+-|||||.+|..+||.|| | .||+|....|.++.|+++....|..+|.|||..+ +
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 8999999999999999999999999999999875 3
Q ss_pred c----ccCCCCCCCchH--HHHHHHHHHHhhccccCCC-CCCCCCCCccCCCCCccccccCCCC
Q 005117 94 F----QRQRLPDNSNVN--KVRDFIKNVYVDRRYAGGK-TPDKPPKDTQGLGSHLDESRRASSY 150 (713)
Q Consensus 94 ~----~r~~~P~~sd~~--~rreFIraKY~eKrF~~~k-~~D~Ppr~~q~l~~~~~e~rR~ssy 150 (713)
+ .+.++|...|.. .+.+|||+||+...|+.+. +.|.-......+..+....+|+..+
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 222344444432 3567999999999999843 3443322222333444555555433
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.61 E-value=2.5e-16 Score=179.59 Aligned_cols=108 Identities=26% Similarity=0.517 Sum_probs=96.5
Q ss_pred HHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC---CceeeeecC--CCCHHHHHHHHhcCcHHHHHHHhh
Q 005117 16 GLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMS--KFTSQEVEALQNGGNQRAREIYLK 90 (713)
Q Consensus 16 ~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLD--kWT~eEVe~Lq~gGN~rANeiwea 90 (713)
++.....|+.|+|||++.|.||++|++|.||-.|+|-||.|| ++|+|++|| .|+.+-|+++...||.++|.||-.
T Consensus 291 riW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa~ 370 (1186)
T KOG1117|consen 291 RIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWAG 370 (1186)
T ss_pred HHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCccccccccc
Confidence 456678999999999999999999999999999999999998 599999998 699999999999999999999999
Q ss_pred cCccccCCCCCCCchHHHHHHHHHHHhhccccCC
Q 005117 91 DWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (713)
Q Consensus 91 ~~d~~r~~~P~~sd~~~rreFIraKY~eKrF~~~ 124 (713)
++++...-.|+ +.+..|++||++||.+.+|...
T Consensus 371 nl~~~e~lh~d-ssp~~r~~fi~~Kykeg~fRk~ 403 (1186)
T KOG1117|consen 371 NLPPNEHLHPD-SSPSTRRQFIKEKYKEGKFRKE 403 (1186)
T ss_pred CCCCccccCCC-CCcchhhhHHHHHhhccccccc
Confidence 98766554443 4677899999999999988654
No 15
>PLN03131 hypothetical protein; Provisional
Probab=96.89 E-value=0.051 Score=63.20 Aligned_cols=90 Identities=31% Similarity=0.393 Sum_probs=46.8
Q ss_pred cCcccccCCCCCCCCCCCCCCCCCccCCCCcccc---------------cccccccccCCCCCCCC-CCCCCCCCCCC--
Q 005117 330 YGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA---------------SVNMSEMSQASSVPSTN-TYQPAQTSSPS-- 391 (713)
Q Consensus 330 ~~~~~~~~~p~~~~~~~~~~~~~dlf~~p~~~~a---------------~vd~f~~s~~~~~~s~~-~~q~~q~~~~~-- 391 (713)
...+|||.+|.. +.+.++||||++-..++ +||||++.--- .+++ ++|.+++.+..
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 005117 392 -SLNFFQITEQ-PSTAILNRNPQELSIP-KNEGWATFDT 427 (713)
Q Consensus 392 -~~d~f~~~~~-~~~~~~~~~~~~~~~p-~n~GWAtfD~ 427 (713)
---+|+-.+| .++++ ..+.+.+.|| .+.|-+-||.
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 5555555553
No 16
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=94.41 E-value=2.1 Score=50.11 Aligned_cols=39 Identities=18% Similarity=0.346 Sum_probs=22.2
Q ss_pred CCcccc-cccccccccCCCCCCCCCCCCCCCCCCCCcccc
Q 005117 358 PETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF 396 (713)
Q Consensus 358 p~~~~a-~vd~f~~s~~~~~~s~~~~q~~q~~~~~~~d~f 396 (713)
.+++.| ||||||-...|.++++++.|+.=.++-++|+++
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=93.00 E-value=0.16 Score=57.79 Aligned_cols=142 Identities=20% Similarity=0.160 Sum_probs=102.3
Q ss_pred CCCCCCCCCcccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCCcccccccccCCCCC
Q 005117 150 YHSYSQSPPYDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDP 229 (713)
Q Consensus 150 y~S~SQSPp~d~qyEdrr~~k~~~~ltRkpgsd~~~~~gk~ss~~~sP~r~s~~~~~Drfa~e~s~~r~sdfs~s~~g~~ 229 (713)
|+++.+.+.|+|.|+.||++|.. ..|+=-.=..+ +...-+.+.++++-.++.++-+.++...+|..++++..-+++
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 57788889999999999999986 23331121222 223446688999999999999999999999999999999988
Q ss_pred CCCCCCC-CC-cccccCCCCCCccccccccccccCcccCCCCCCCCcccccCCCccccCCCccccccccCCCCc
Q 005117 230 FRPGAQS-PN-FQKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLT 301 (713)
Q Consensus 230 ~k~~~~s-p~-~~kd~~~ssp~v~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~ 301 (713)
.....|+ .| ..|++.+-..-.++ ...+..++..-.+..||+.....--.++.+.+.+++|+.++|-
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 8888777 66 66666554443332 1222333444445667888888888888999999999987764
No 18
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=87.14 E-value=0.13 Score=61.95 Aligned_cols=67 Identities=16% Similarity=0.282 Sum_probs=50.7
Q ss_pred CCCCCCCcCCCC-CCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeecCCCCHHHHHHHHhcCcHHHHHHH
Q 005117 20 LPPNRRCINCNS-LGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (713)
Q Consensus 20 ~PgNk~CADCGa-~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWT~eEVe~Lq~gGN~rANeiw 88 (713)
...+..|++|++ ..-.|+|+++.+.+|+.|+++|+.++ + .++++.|+...+ |..+...||..++..|
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 57899999999999999999999996 4 556666666555 5556555555555444
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=80.43 E-value=1.6 Score=33.18 Aligned_cols=40 Identities=15% Similarity=0.421 Sum_probs=33.4
Q ss_pred CCCCCcCCCCCCCCeeEecceeeeehhhhhh-hhcCCCceeee
Q 005117 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGI-HREFTHRVKSV 63 (713)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGI-HR~LGhrVKSI 63 (713)
.+..|..|+.....+.+.+=.++||..|... |+. |+|.+|
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=79.09 E-value=1.7 Score=45.47 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=27.8
Q ss_pred HHHHHHhc--CCCCCCCcCCCCCCCCeeEecceeeeehhhhhhh
Q 005117 12 KIIRGLMK--LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIH 53 (713)
Q Consensus 12 kiLr~Llk--~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIH 53 (713)
++-..|++ ...++.|-+||.+=|.+ -|+.+|..|..+-
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 33334444 45889999999988832 5999999998653
No 21
>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=53.95 E-value=10 Score=38.67 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=27.0
Q ss_pred CCCCCCCcCCCCCCC-CeeEecceeeeehhhhhh
Q 005117 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGI 52 (713)
Q Consensus 20 ~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSGI 52 (713)
.|.-..|+.||..++ .|.+...|.++|.+|...
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 22
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=50.00 E-value=8.3 Score=39.44 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=26.5
Q ss_pred CCCCCCCcCCCCCCC-CeeEecceeeeehhhhh
Q 005117 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSG 51 (713)
Q Consensus 20 ~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSG 51 (713)
.|.-..|+-||.... .|.+...|.++|..|..
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 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=46.08 E-value=12 Score=31.99 Aligned_cols=33 Identities=24% Similarity=0.411 Sum_probs=22.5
Q ss_pred CCCCCCCcCCCCCCC--CeeEecceeeeehhhhhhh
Q 005117 20 LPPNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIH 53 (713)
Q Consensus 20 ~PgNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIH 53 (713)
.++...|.+||..=| ++. ..-|+..|+.|...+
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 223788999998754
No 24
>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=45.07 E-value=11 Score=29.46 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=20.7
Q ss_pred CCcCCCCCCCCeeEecceeeeehhhhhh
Q 005117 25 RCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (713)
Q Consensus 25 ~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (713)
+|-.||+.. ....-.-|-+||..|.-|
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 25
>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=43.11 E-value=18 Score=27.80 Aligned_cols=28 Identities=25% Similarity=0.565 Sum_probs=23.5
Q ss_pred CCCCCCcCCCCCCCCeeEecceeeeehhhhh
Q 005117 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSG 51 (713)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSG 51 (713)
..|..|..|++. |....=|-++|.+|-.
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 8888899999999953
No 26
>PRK11019 hypothetical protein; Provisional
Probab=41.95 E-value=14 Score=33.69 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=22.8
Q ss_pred CCCCCcCCCCCCC--CeeEecceeeeehhhhhhhhc
Q 005117 22 PNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIHRE 55 (713)
Q Consensus 22 gNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIHR~ 55 (713)
.-..|.+||..=| .+.-+. ++-.|++|...+-.
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 4579999998533 333232 67889999987643
No 27
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=39.08 E-value=23 Score=34.06 Aligned_cols=30 Identities=17% Similarity=0.360 Sum_probs=19.2
Q ss_pred CCCcCCCCCCCC-eeEecceeeeehhhhhhh
Q 005117 24 RRCINCNSLGPQ-YVCTNFWTFVCMTCSGIH 53 (713)
Q Consensus 24 k~CADCGa~~P~-WaSvnfGVFVCi~CSGIH 53 (713)
.+|.+||.+=|. =.-.--+..+|++|.-.|
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 489999985221 011122577999999776
No 28
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=39.05 E-value=14 Score=32.54 Aligned_cols=31 Identities=16% Similarity=0.270 Sum_probs=20.5
Q ss_pred CCCCcCCCCCCCCeeE-ecceeeeehhhhhhh
Q 005117 23 NRRCINCNSLGPQYVC-TNFWTFVCMTCSGIH 53 (713)
Q Consensus 23 Nk~CADCGa~~P~WaS-vnfGVFVCi~CSGIH 53 (713)
...|.|||.+=|.==- .--|+..|+.|...+
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 29
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=36.46 E-value=13 Score=36.93 Aligned_cols=34 Identities=32% Similarity=0.690 Sum_probs=28.5
Q ss_pred CCCCCCcCCCCCCCCeeEecceeeeeh-hhhhhhhc
Q 005117 21 PPNRRCINCNSLGPQYVCTNFWTFVCM-TCSGIHRE 55 (713)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi-~CSGIHR~ 55 (713)
|--+.|+-|| -...|.|++-|.-+|. .|-++|.+
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 4557899999 6778999999998886 89999965
No 30
>PHA00080 DksA-like zinc finger domain containing protein
Probab=35.33 E-value=19 Score=31.59 Aligned_cols=45 Identities=18% Similarity=0.380 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhc---CCCCCCCcCCCCCCC--CeeEecceeeeehhhhhhh
Q 005117 8 ERNEKIIRGLMK---LPPNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIH 53 (713)
Q Consensus 8 ErnekiLr~Llk---~PgNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIH 53 (713)
...+..|...+. ..+...|.+||..=| .+.-+. |+..|+.|...+
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 334444444433 345568999998532 332222 667799998865
No 31
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=35.07 E-value=20 Score=37.67 Aligned_cols=30 Identities=27% Similarity=0.676 Sum_probs=25.9
Q ss_pred CCCCCCcCCCCCC-CCeeEecceeeeehhhh
Q 005117 21 PPNRRCINCNSLG-PQYVCTNFWTFVCMTCS 50 (713)
Q Consensus 21 PgNk~CADCGa~~-P~WaSvnfGVFVCi~CS 50 (713)
+.=..|+.||... +..++.-.|-++|.+|.
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3447999999975 57999999999999999
No 32
>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=32.78 E-value=28 Score=34.76 Aligned_cols=41 Identities=12% Similarity=0.246 Sum_probs=23.5
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCC--CCeeEecceeeeehhhhhhh
Q 005117 11 EKIIRGLMKLPPNRRCINCNSLG--PQYVCTNFWTFVCMTCSGIH 53 (713)
Q Consensus 11 ekiLr~Llk~PgNk~CADCGa~~--P~WaSvnfGVFVCi~CSGIH 53 (713)
+++|.+|.. ..=..|.+||..= -+.-.+. ++-.|+.|...+
T Consensus 75 e~AL~Ri~~-G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 75 EHALQKIEN-GTYGICEVCGKPIPYERLEAIP-TATTCVECQNRK 117 (159)
T ss_pred HHHHHHHhC-CCCCeecccCCcccHHHHhhCC-CcchhHHHHHHh
Confidence 334444432 3446899999841 1111122 467899999875
No 33
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=28.92 E-value=68 Score=31.85 Aligned_cols=35 Identities=11% Similarity=0.136 Sum_probs=21.7
Q ss_pred CCCCCCCcCCCCCCCC-eeEecceeeeehhhhhhhh
Q 005117 20 LPPNRRCINCNSLGPQ-YVCTNFWTFVCMTCSGIHR 54 (713)
Q Consensus 20 ~PgNk~CADCGa~~P~-WaSvnfGVFVCi~CSGIHR 54 (713)
.+.-..|-+||.+=|. =.-+-=++..|+.|...|-
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 0001114678999998764
No 34
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=28.25 E-value=58 Score=30.08 Aligned_cols=30 Identities=13% Similarity=0.273 Sum_probs=23.9
Q ss_pred CCCCCCcCCCCCCCCeeEecceeeeehhhhhh
Q 005117 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (713)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (713)
-.--.|-.|+.. .---+..|||.|..|--.
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 35
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=27.75 E-value=44 Score=27.39 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=29.2
Q ss_pred CCCCCcCCCCC-CCCeeEeccee-eeehhhhhhhhcCC
Q 005117 22 PNRRCINCNSL-GPQYVCTNFWT-FVCMTCSGIHREFT 57 (713)
Q Consensus 22 gNk~CADCGa~-~P~WaSvnfGV-FVCi~CSGIHR~LG 57 (713)
..+.|.+|+.. -|.|=.-..|- +||-.|.--.+..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 35789999984 68898888886 99999988777665
No 36
>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=27.53 E-value=18 Score=27.77 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=16.5
Q ss_pred CCCcCCCCC-CCCeeEecceeeeehhhh
Q 005117 24 RRCINCNSL-GPQYVCTNFWTFVCMTCS 50 (713)
Q Consensus 24 k~CADCGa~-~P~WaSvnfGVFVCi~CS 50 (713)
..|.+|+.. .-+|..-+|+.-||..|.
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 37
>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=27.09 E-value=24 Score=33.23 Aligned_cols=44 Identities=23% Similarity=0.509 Sum_probs=30.1
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcC--CC--ceeeeecC
Q 005117 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (713)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItLD 66 (713)
..|.--+|.+||. +..+..-.+.|-.|.+..-.+ |. +|++|.++
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 333332357899999876444 43 88888765
No 38
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=25.40 E-value=25 Score=33.06 Aligned_cols=44 Identities=11% Similarity=0.290 Sum_probs=30.4
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcC--CC--ceeeeec
Q 005117 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSM 65 (713)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItL 65 (713)
..|..-+|-+||. .+....+..+.|-.|.+....+ |. +|++|-+
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 2223344557899999876665 32 7888765
No 39
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=24.70 E-value=43 Score=36.37 Aligned_cols=34 Identities=18% Similarity=0.205 Sum_probs=23.9
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhh
Q 005117 20 LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHR 54 (713)
Q Consensus 20 ~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR 54 (713)
.....+|-+||... --....-|-.||.+|.-|..
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 40
>PRK00420 hypothetical protein; Validated
Probab=24.35 E-value=1.6e+02 Score=28.16 Aligned_cols=45 Identities=18% Similarity=0.162 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHHHhc--CCCCCCCcCCCCCCCCeeEecceeeeehhhhhh
Q 005117 5 KEEERNEKIIRGLMK--LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (713)
Q Consensus 5 ke~ErnekiLr~Llk--~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (713)
++++..+++-+.|++ .=-+..|-.||.+-.. +.-|-.+|..|..+
T Consensus 3 ~~~~~~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~---lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 3 ESEDIVKKAAELLLKGAKMLSKHCPVCGLPLFE---LKDGEVVCPVHGKV 49 (112)
T ss_pred ccHHHHHHHHHHHHhHHHHccCCCCCCCCccee---cCCCceECCCCCCe
Confidence 345555666555555 2246899999975432 36688899999764
No 41
>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=24.21 E-value=48 Score=29.56 Aligned_cols=31 Identities=13% Similarity=0.470 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEecceeeeehhhhhhhhc
Q 005117 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (713)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (713)
.|..|.=||... ....||++.|..|.+..|.
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 3578999999999998865
No 42
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=24.04 E-value=26 Score=37.19 Aligned_cols=32 Identities=22% Similarity=0.419 Sum_probs=24.7
Q ss_pred CCCCCCcCCCC--CCCCeeEecceeeeehhhhhhh
Q 005117 21 PPNRRCINCNS--LGPQYVCTNFWTFVCMTCSGIH 53 (713)
Q Consensus 21 PgNk~CADCGa--~~P~WaSvnfGVFVCi~CSGIH 53 (713)
.-+.+|++|.. .++.+-+ .||+-||..|+.-|
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 58999999999887
No 43
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=23.99 E-value=1e+02 Score=34.62 Aligned_cols=69 Identities=22% Similarity=0.197 Sum_probs=39.9
Q ss_pred CCCCCccCCCCcccc--------cccccccccCCCCCCCCCCCCCCCCCCC-CcccccccCCCcccccc--CCCcCCCCC
Q 005117 349 APPIDLFQLPETSAA--------SVNMSEMSQASSVPSTNTYQPAQTSSPS-SLNFFQITEQPSTAILN--RNPQELSIP 417 (713)
Q Consensus 349 ~~~~dlf~~p~~~~a--------~vd~f~~s~~~~~~s~~~~q~~q~~~~~-~~d~f~~~~~~~~~~~~--~~~~~~~~p 417 (713)
..-.|||+--+-+.+ ++|+|. +-++++||.-|..-++--- =.|+|.|.+-|+-+..+ ++...+..|
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 37889988887644333 344444445
Q ss_pred CCC
Q 005117 418 KNE 420 (713)
Q Consensus 418 ~n~ 420 (713)
.||
T Consensus 404 a~e 406 (499)
T KOG2057|consen 404 ANE 406 (499)
T ss_pred hhh
Confidence 544
No 44
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.76 E-value=30 Score=32.64 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=28.3
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcC--CC--ceeeeecC
Q 005117 20 LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (713)
Q Consensus 20 ~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItLD 66 (713)
.|.--+|.+||.. |....+..+.|-.|.+....+ |. +|++|.++
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 78888664
No 45
>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=22.82 E-value=67 Score=24.40 Aligned_cols=30 Identities=23% Similarity=0.480 Sum_probs=21.7
Q ss_pred CcCCCCC-CCCeeEecceee-eehhhhhhhhc
Q 005117 26 CINCNSL-GPQYVCTNFWTF-VCMTCSGIHRE 55 (713)
Q Consensus 26 CADCGa~-~P~WaSvnfGVF-VCi~CSGIHR~ 55 (713)
|.+|+.. -|.|-....|-. ||-.|.-.+|.
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 799998888877 99999876654
No 46
>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=22.29 E-value=55 Score=30.00 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeEecceeeeehhhhhhhhc
Q 005117 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (713)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (713)
.+..|.=||... ....||++.|..|.+..|.
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 3468999999999998875
No 47
>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=21.88 E-value=55 Score=26.57 Aligned_cols=26 Identities=23% Similarity=0.631 Sum_probs=19.4
Q ss_pred CCcCCCCCCCCeeEecceeeeehhhhh
Q 005117 25 RCINCNSLGPQYVCTNFWTFVCMTCSG 51 (713)
Q Consensus 25 ~CADCGa~~P~WaSvnfGVFVCi~CSG 51 (713)
.|+=|+..... .-.=+|-|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48889887666 334468999999964
No 48
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=21.63 E-value=58 Score=30.27 Aligned_cols=35 Identities=17% Similarity=0.357 Sum_probs=24.2
Q ss_pred HhcCCCCCCCcCCCCCC-----------------CCeeEecceeeeehhhhh
Q 005117 17 LMKLPPNRRCINCNSLG-----------------PQYVCTNFWTFVCMTCSG 51 (713)
Q Consensus 17 Llk~PgNk~CADCGa~~-----------------P~WaSvnfGVFVCi~CSG 51 (713)
.++.++--+|++||.+= -.=+.=.||-.+|-+|..
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 111244689999999974
No 49
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.71 E-value=39 Score=31.71 Aligned_cols=43 Identities=23% Similarity=0.411 Sum_probs=28.6
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcC--CC--ceeeeec
Q 005117 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSM 65 (713)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItL 65 (713)
..|..-+|-+||. ...+....+.|-.|.+....+ |. +|++|.+
T Consensus 66 ~vp~~~~C~~Cg~----~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~iEv 112 (113)
T PRK12380 66 YKPAQAWCWDCSQ----VVEIHQHDAQCPHCHGERLRVDTGDSLIVKSIEV 112 (113)
T ss_pred eeCcEEEcccCCC----EEecCCcCccCcCCCCCCcEEccCCeEEEEEEEE
Confidence 3567789999994 223333456699999765454 43 7888765
No 50
>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=20.56 E-value=60 Score=29.00 Aligned_cols=31 Identities=16% Similarity=0.613 Sum_probs=25.4
Q ss_pred CCCCCcCCCCCCCCeeEecceeeeehhhhhhhhc
Q 005117 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (713)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (713)
..+.|.=||...- ...||++.|..|.+..|.
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 468999999999998865
No 51
>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=20.17 E-value=61 Score=29.93 Aligned_cols=30 Identities=17% Similarity=0.587 Sum_probs=24.5
Q ss_pred CCCCcCCCCCCCCeeEecceeeeehhhhhhhhc
Q 005117 23 NRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (713)
Q Consensus 23 Nk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (713)
+..|.=||...- ...||++.|..|.+..|.
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 52
>PF04189 Gcd10p: Gcd10p family; InterPro: IPR007316 eIF-3 is a multisubunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit of eIF3 [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation
Probab=20.14 E-value=92 Score=34.16 Aligned_cols=47 Identities=30% Similarity=0.461 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHHhcCcHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhhcc
Q 005117 66 SKFTSQEVEALQNGGNQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRR 120 (713)
Q Consensus 66 DkWT~eEVe~Lq~gGN~rANeiwea~~d~~r~~~P~~sd~~~rreFIraKY~eKr 120 (713)
.+.|.+||+.|+..|-. +++|-++-.... ..=+.+-+|-++||++|+
T Consensus 106 QkLt~eeIe~LK~~g~s-g~eII~kLiens-------~tF~~KT~FSqeKYlkrK 152 (299)
T PF04189_consen 106 QKLTQEEIEELKKEGVS-GEEIIEKLIENS-------STFDKKTEFSQEKYLKRK 152 (299)
T ss_pred ccCCHHHHHHHHHcCCC-HHHHHHHHHHhc-------cchhhhhHHHHHHHHHHH
Confidence 46889999999866443 555554433211 122345579999998765
Done!