Query 005622
Match_columns 687
No_of_seqs 190 out of 1216
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 11:12:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005622.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005622hhsearch_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-201 2E-206 1630.7 48.1 683 1-687 1-705 (705)
2 PLN03119 putative ADP-ribosyla 100.0 3E-182 7E-187 1468.5 44.9 638 1-687 1-648 (648)
3 KOG0702 Predicted GTPase-activ 100.0 1.9E-47 4.2E-52 411.4 31.7 506 3-687 4-524 (524)
4 KOG0703 Predicted GTPase-activ 100.0 2.2E-35 4.7E-40 304.4 8.7 118 5-125 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 6.1E-35 1.3E-39 266.4 8.4 111 12-123 2-115 (116)
6 smart00105 ArfGap Putative GTP 100.0 3.7E-33 8E-38 253.5 10.5 106 21-126 1-109 (112)
7 COG5347 GTPase-activating prot 100.0 2.7E-30 5.8E-35 271.7 12.8 117 8-124 5-125 (319)
8 KOG0704 ADP-ribosylation facto 99.9 3.2E-27 7E-32 247.3 12.6 114 8-121 4-124 (386)
9 PLN03114 ADP-ribosylation fact 99.9 1.8E-25 3.9E-30 235.7 11.4 116 11-126 10-130 (395)
10 KOG0706 Predicted GTPase-activ 99.9 1.4E-24 3E-29 233.4 8.8 85 8-92 8-95 (454)
11 KOG0705 GTPase-activating prot 99.9 1.7E-23 3.8E-28 229.5 8.2 115 11-126 501-618 (749)
12 KOG0521 Putative GTPase activa 99.8 2E-20 4.4E-25 216.2 3.3 114 14-127 417-534 (785)
13 KOG1117 Rho- and Arf-GTPase ac 99.6 1.5E-16 3.3E-21 180.7 4.9 109 15-124 290-403 (1186)
14 KOG0818 GTPase-activating prot 99.6 9.8E-17 2.1E-21 174.7 0.5 133 18-150 3-146 (669)
15 PLN03131 hypothetical protein; 96.9 0.036 7.9E-07 64.1 17.0 89 330-426 359-468 (705)
16 PLN03119 putative ADP-ribosyla 93.5 2.2 4.7E-05 49.8 15.8 39 358-396 318-357 (648)
17 KOG0702 Predicted GTPase-activ 92.7 0.18 3.8E-06 57.3 5.7 142 150-301 1-144 (524)
18 KOG0521 Putative GTPase activa 89.6 0.07 1.5E-06 63.9 -1.3 68 20-89 627-698 (785)
19 PF00643 zf-B_box: B-box zinc 79.6 1.7 3.6E-05 32.9 2.5 40 22-63 2-42 (42)
20 PRK12495 hypothetical protein; 79.5 1.7 3.7E-05 45.3 3.3 38 12-53 29-68 (226)
21 TIGR00613 reco DNA repair prot 53.8 10 0.00023 38.4 2.7 33 20-52 144-177 (241)
22 PRK00085 recO DNA repair prote 49.9 13 0.00029 37.8 2.8 32 20-51 146-178 (247)
23 TIGR02419 C4_traR_proteo phage 44.6 12 0.00027 31.7 1.4 33 20-53 28-62 (63)
24 PF08271 TF_Zn_Ribbon: TFIIB z 43.4 12 0.00027 28.9 1.1 27 25-52 2-28 (43)
25 PF11781 RRN7: RNA polymerase 42.8 18 0.0004 27.6 1.9 28 21-51 6-33 (36)
26 PRK11019 hypothetical protein; 40.1 16 0.00034 33.3 1.4 33 22-55 35-69 (88)
27 COG1734 DksA DnaK suppressor p 39.1 13 0.00027 35.6 0.7 44 10-53 65-111 (120)
28 KOG3362 Predicted BBOX Zn-fing 39.0 12 0.00025 37.2 0.4 34 21-55 116-150 (156)
29 PRK13715 conjugal transfer pro 37.6 15 0.00031 32.2 0.8 31 23-53 34-65 (73)
30 COG1381 RecO Recombinational D 37.3 18 0.00039 37.9 1.6 30 21-50 152-182 (251)
31 PHA00080 DksA-like zinc finger 36.8 17 0.00037 31.7 1.0 45 8-53 13-62 (72)
32 smart00401 ZnF_GATA zinc finge 33.2 33 0.00072 28.0 2.1 36 22-57 2-39 (52)
33 PF01286 XPA_N: XPA protein N- 30.7 16 0.00035 28.0 -0.1 27 24-50 4-31 (34)
34 TIGR02890 spore_yteA sporulati 29.9 32 0.0007 34.2 1.9 32 21-53 84-117 (159)
35 COG1997 RPL43A Ribosomal prote 29.7 55 0.0012 30.1 3.1 30 21-52 33-62 (89)
36 cd00021 BBOX B-Box-type zinc f 26.8 45 0.00097 24.3 1.7 36 25-62 2-38 (39)
37 TIGR00100 hypA hydrogenase nic 25.8 32 0.00069 32.2 1.0 44 19-66 66-113 (115)
38 PRK10778 dksA RNA polymerase-b 25.6 82 0.0018 31.1 3.8 35 20-54 108-143 (151)
39 PF00320 GATA: GATA zinc finge 25.5 52 0.0011 24.9 1.9 30 26-55 1-32 (36)
40 KOG2057 Predicted equilibrativ 24.6 1E+02 0.0022 34.6 4.5 78 349-429 327-419 (499)
41 PRK03681 hypA hydrogenase nick 24.5 27 0.00058 32.7 0.2 44 19-65 66-113 (114)
42 COG5145 RAD14 DNA excision rep 23.8 27 0.00058 37.0 0.1 32 21-53 114-147 (292)
43 PRK00564 hypA hydrogenase nick 23.0 31 0.00067 32.5 0.3 44 20-66 68-115 (117)
44 cd07171 NR_DBD_ER DNA-binding 22.4 54 0.0012 29.1 1.7 31 22-55 2-32 (82)
45 PRK00423 tfb transcription ini 22.0 54 0.0012 35.4 1.9 33 20-53 8-40 (310)
46 PF14803 Nudix_N_2: Nudix N-te 21.7 39 0.00085 25.7 0.6 30 24-54 1-33 (34)
47 COG2174 RPL34A Ribosomal prote 21.6 56 0.0012 30.2 1.6 34 18-51 29-79 (93)
48 cd06968 NR_DBD_ROR DNA-binding 21.4 58 0.0012 29.7 1.7 31 22-55 4-34 (95)
49 PRK00420 hypothetical protein; 21.0 2.1E+02 0.0046 27.2 5.4 44 6-52 4-49 (112)
50 PF12760 Zn_Tnp_IS1595: Transp 20.6 1.2E+02 0.0026 23.9 3.1 42 7-50 3-44 (46)
51 COG2719 SpoVR Uncharacterized 20.4 29 0.00062 39.9 -0.5 8 418-425 270-277 (495)
52 PRK11767 SpoVR family protein; 20.4 29 0.00062 40.4 -0.6 8 418-425 273-280 (498)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1e-201 Score=1630.74 Aligned_cols=683 Identities=61% Similarity=1.000 Sum_probs=661.1
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCCCceeeeccCCCCHHHHHHHHhcC
Q 005622 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (687)
Q Consensus 1 M~srke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSItLDkWt~eEV~~Lq~gG 80 (687)
|++||++||++++|++|+++|+|++|||||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
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 cHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhcccccCCCCCCCCCCCccCCCCCccccccCCCCCCCCCCCCcc
Q 005622 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (687)
Q Consensus 81 N~rANeiwea~~d~~r~~~P~~sd~~krreFIraKY~eKrF~~~k~~D~Pp~~~q~l~~~~~e~rRsssy~s~sQsPp~d 160 (687)
|++||+|||++|+..+.++|...+.+++|+|||.|||+|||+.....++|+++.+.++.++.++||.++||+++|||||+
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 005622 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (687)
Q Consensus 161 ~~yEdrr~~k~~~~ltRkpgsd~~~~~gk~ss~~~sP~r~s~~~~~DRfa~e~s~~r~sd~~~s~~g~~~~~~~~sp~~~ 240 (687)
|+||||||||+...++|+||+++++|.|||++|++||+|+.++|+||||+||++++|++||+++++|+++|.+.+|||||
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------------cCCCCCCCCCcccccCCccccCCCccccccccCCCCccCCCCCc
Q 005622 241 KDAGFNSPPVQLSRDVSSLKANFK------------RDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDD 308 (687)
Q Consensus 241 k~~~~ssp~~~~~~~i~~~~~~~~------------~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~ 308 (687)
||.. +||||+++|||| |+|++. +.++|++++|||+|+|||||+||+++++|+++|+|||||.+|++
T Consensus 241 k~~~-~Sp~v~p~r~il-g~n~~~~~v~~~s~~~~~~~~~~~~~~Qrt~Ssgs~gS~dg~s~s~Ks~~s~sL~D~~~e~~ 318 (705)
T PLN03131 241 KDIA-FSPPIQPPKDIL-GEDVQQRRIDLFSAALCKQGAEGCPHIQRSASLGSIGSFDSLSVSIKSFNSGSLADIVAEAE 318 (705)
T ss_pred cccC-CCCCcccchhhc-cccccccccCCCcccccccccccccccccccccCcccccCCCccceeecccccccccccCcc
Confidence 9975 578998899999 666543 35789999999999999999999999999999999999999999
Q ss_pred cCcCCCCCcccccCCCCCCCCcCcccccCCCCCCCCCCCCCCCCCccCCCccccc-cccccccccCCCCCCCCCCCCCCC
Q 005622 309 QAAGAPLDKISTFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQT 387 (687)
Q Consensus 309 ~~~~~~q~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~~~~~~~~s~~~~q~~q~ 387 (687)
++++++|.|+.++++..+.+.+.++|+|++||+|++++.++++|||||+|+|+.| +|||||-+++..++++|.+|+.||
T Consensus 319 ~~~~~~q~k~~~~~~~~~~~~~~s~d~f~~~v~p~~~~~~a~pIDLFqlp~ts~a~~vdlf~~s~l~~~p~~n~~q~~qt 398 (705)
T PLN03131 319 QAAGNHQDKMPAFPRMAGSGSHASLDHFKAPVAPEAAAPMAPPIDLFQLPATSPAPPVDLFEIPPLDPAPAINAYQPPQT 398 (705)
T ss_pred ccccccccccCCccccccccccccccccccccccccccccCCchhhhhccCCCCCCcccccccCcccCCCccccCCCCcc
Confidence 9999999999999999999999999999999999999999999999999999988 999999999999999999999999
Q ss_pred CCCCCcccc-cccCCCccccccCCCcCCCCCCCCCcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCCC
Q 005622 388 SSPSSLNFF-QITEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQ 466 (687)
Q Consensus 388 ~~~~~~d~f-~~~~~~~~~~~~~~~~~~~~p~n~gwatfd~p~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~ 466 (687)
+.+++|||| +|+||++++|+|++++||++||||||||||+++.++|++|++||+..+||....-+.+||.+.++.++||
T Consensus 399 s~p~~~dlfag~~qqq~~~s~~~~~~~~s~pknegwa~fd~~~p~~s~~~~~n~t~~~v~~~~~~~~~~d~v~~~~~~~q 478 (705)
T PLN03131 399 SLPSSIDLFGGITQQQSINSLDEKSPELSIPKNEGWATFDGIQPIASTPGNENLTPFSIGPSMAGSANFDQVPSLDKGMQ 478 (705)
T ss_pred cCCccccccccccccCccccccccCcccCCccccCcccccCCCcccccCCcccccccccccccccCcchhhccccccccc
Confidence 999999999 9999999999999999999999999999998888899999999988899966644679999999999999
Q ss_pred CCcccCCCCCCCCCCCCCCCCCccccccCcccCC--Cccccc--cccCCCCCCCCCCCCCCcccCCCCCCCCCccccc-c
Q 005622 467 WPAFQNSGANGPSPSSDPWSGNLHIVQAPAVATS--SWNAFD--DFTSHLPSEGFKPNSEPHVDAYMPSPTPDQYLAI-V 541 (687)
Q Consensus 467 ~~~~~~s~~~~~~~~~d~w~~~~~~~~~~~~~~~--~WnaF~--ds~~~~~~~~~~~~~~~~~~~~~~~~t~~~~~~~-~ 541 (687)
||+|+++++++++++|++|++++||||+|.+ |+ +||||+ |+++++||+++++++++|++++++++. +||+++ +
T Consensus 479 ~Pp~~~~~~~~s~s~~~pW~~~~~~V~~~~~-~~~q~WnAF~~~ds~~~~~l~~~~~~s~~q~~~~~~~t~-~q~~~~~~ 556 (705)
T PLN03131 479 WPPFQNSSDEESASGPAPWLGDLHNVEAPDN-TSAQNWNAFEFDDSVAGIPLEGIKQSSEPQTAANMPPTA-DQLIGCKA 556 (705)
T ss_pred cCCCcccccccccccCCcccccchhcccCCc-cCccccccccccccccccccccccccccccccccCCCCc-cccccccc
Confidence 9999999999999999999999999999986 77 999999 999999999999999988876665555 599999 9
Q ss_pred ccccCCCCCCcccCCCC--CCCCCCCCCCccCCCCCCCCCCccccccccccccCCCCCCCCCCCccccccccchhhhhHH
Q 005622 542 SQETNDDGNPRVASHDG--PPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFDFPCDSDLEQNNMFLDMSSLQ 619 (687)
Q Consensus 542 ~q~~~~d~~~~~ap~~~--~~~~~~~~~~~~g~~~~~~~~~~~g~~~~~~~~~ks~NPFDlp~dsd~e~~~mFmDmsSLQ 619 (687)
+||+++||+||+||+++ +++|++|+.+|+||+|+|+++|+||++++|+++|||+||||||||||+|++||||||||||
T Consensus 557 ~~d~~~d~~~r~~p~~~~~~~g~~~~~~~~~~ps~~~~~~~~~~~~~s~~~~~ks~npfdl~~dsd~~~~~mf~d~sslq 636 (705)
T PLN03131 557 LEDFNKDGIKRTAPHGQGELPGLDEPSDILAEPSYTPPAHPIMEHAQSHANDHKSINPFDLPYDSDLEPGNMFLDMSSLE 636 (705)
T ss_pred ccccccccccccCCCCCcCCCCCCCCCccccCCCCCccccccccccccccCccCCCCCcCCccccccCcccceeehHHHH
Confidence 99999999999999999 9999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCCCCCCCCCccC-CCCcCCCCCCCCCcccccCCCCCccccccCCCCccccCCCCCCCcccCCCCCCC
Q 005622 620 AALPNAELPSPFLG-GATQSWFPQNPVSPFVQAAAQGGLAYMSGQSPSAQLANIPTQEPVASVGGNPFA 687 (687)
Q Consensus 620 aaLP~~~lp~~f~g-g~~e~W~~qn~~~~yips~~qGGl~~ma~q~p~s~l~ni~~~~~~a~~~gNPFa 687 (687)
|||||+|||++||| |||||||+||++|+|||+|+||||+|||||+|++||.|+++||||||+||||||
T Consensus 637 ~~lp~~~~~~~f~g~~~tepw~~~~~~~~yip~~pqggl~y~agq~~~~~~~~~~~~~~~af~~~npf~ 705 (705)
T PLN03131 637 AALPDAHLPSAFLGSGMTEPWFPQDLAMTYIPAAPQGGLAYMAGQAPNPQLGNVQTQGPVAFVGGNPFA 705 (705)
T ss_pred hhcCCCCCchhhhcCCCCCccccCCCcccccCCCCCCCchhhcccCCcchhhhhhccCccccCCCCCCC
Confidence 99999999999999 999999999999999999999999999999999999999999999999999997
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=3.4e-182 Score=1468.48 Aligned_cols=638 Identities=51% Similarity=0.793 Sum_probs=599.7
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCCCceeeeccCCCCHHHHHHHHhcC
Q 005622 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (687)
Q Consensus 1 M~srke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSItLDkWt~eEV~~Lq~gG 80 (687)
|++||++||++++|++|+++|+|++|||||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
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 cHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhcccccCCCCCCCCCCCccCCCCCccccccCCCCCCCCCCCCcc
Q 005622 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (687)
Q Consensus 81 N~rANeiwea~~d~~r~~~P~~sd~~krreFIraKY~eKrF~~~k~~D~Pp~~~q~l~~~~~e~rRsssy~s~sQsPp~d 160 (687)
|++||+|||++|+..+.++|...+.+++|+|||.||++|||+.....++|+++.+..+.+++++||.++||+++|+|||+
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 99999999999998777788888889999999999999999999999999999999898889999999999999999999
Q ss_pred cchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCcchhhhhcccccCCCCcccccccccCCCCCCCCCCCCCCcc
Q 005622 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (687)
Q Consensus 161 ~~yEdrr~~k~~~~ltRkpgsd~~~~~gk~ss~~~sP~r~s~~~~~DRfa~e~s~~r~sd~~~s~~g~~~~~~~~sp~~~ 240 (687)
++||||||||+...|+||||+||+++ ||+++|+++|+|+.++|+||||+||++++|++||+++++|+++|++.+||||+
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 005622 241 KDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDKIST 320 (687)
Q Consensus 241 k~~~~ssp~~~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~~~~ 320 (687)
|.++++|||++.++++..++... ++++|||+|+|||||+|++++++|+++|++|.|+.+|.+++++++|.|+..
T Consensus 240 -~~~~~~~~~~~~~~~~~~~~~~~-----~~~sqRT~SsGs~gSfDs~s~S~ks~~Sg~l~d~~~E~~~~~~~~q~~~~~ 313 (648)
T PLN03119 240 -QEAEFRSPQFQHSNAPPSENLFP-----GRQHQRTTSSGSVRSVDSNFMSIKSYTSGGLGEAVSESRQNTGSQQGKTSN 313 (648)
T ss_pred -cccccCCcccccccCcchhhccc-----ccccccccccccccccccccccccccccCCcccccccccccccccccccCC
Confidence 77899999999999986665542 689999999999999999999999999999999999999999999998765
Q ss_pred cCCCCCCCCcCcccccCCCCCCCCCCCCCCCCCccCCCccccc-cccccccccCCCCCCCCCCCCCCCCCCCCcccc-cc
Q 005622 321 FPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF-QI 398 (687)
Q Consensus 321 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~~~~~~~~s~~~~q~~q~~~~~~~d~f-~~ 398 (687)
. +|+++++++++|||||+|+|+.| +|||||.+.++.++++|.+|+.||+++++||+| +|
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 56788899999999999999888 999999999999999999999999999999999 99
Q ss_pred cCCCccccccCCCcCCCCCCCCCcccccCCCCCCCCCCccccccccccCCCCCCCCCCCCCCCCcCCCCCcccCCCCCCC
Q 005622 399 TEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQWPAFQNSGANGP 478 (687)
Q Consensus 399 ~~~~~~~~~~~~~~~~~~p~n~gwatfd~p~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 478 (687)
+||+++. +++||++||||||||||+|. +++++++||.. -.+. ..+.+||.+.++.++||||+|+++.+.++
T Consensus 375 ~qqq~~~----~~~~~s~pkneGWA~fd~p~--~s~~~~~ni~~--~~~~-~~~~~~d~v~~~~~~mq~Pp~~~~~~~~s 445 (648)
T PLN03119 375 LGQQPTS----RPSELSAPKNEGWASFDNPM--PAAKSTNVITS--PGDF-QLELKIEEILQPSTSMQLPPYPSTVDQHA 445 (648)
T ss_pred cccCccc----CccccccccccCcccccccc--cccCCcccccC--cccc-ccCcchhhhcccccccccCCCcccccccc
Confidence 9998774 99999999999999999555 78888988744 1122 23469999999999999999999999999
Q ss_pred CCCCCCCCCCccccccCcccCC--CccccccccCCCCCCCCC--CCCCCcccCCCCCCCCCccccc-cccccCCCCCCcc
Q 005622 479 SPSSDPWSGNLHIVQAPAVATS--SWNAFDDFTSHLPSEGFK--PNSEPHVDAYMPSPTPDQYLAI-VSQETNDDGNPRV 553 (687)
Q Consensus 479 ~~~~d~w~~~~~~~~~~~~~~~--~WnaF~ds~~~~~~~~~~--~~~~~~~~~~~~~~t~~~~~~~-~~q~~~~d~~~~~ 553 (687)
++|||+|++++||||+++ +|+ +||||+|+++++||++++ +++++++.++. ++|++||+++ ++||+++||+||+
T Consensus 446 ~s~~~pW~~~~~~V~~~~-~~~~q~WnAF~ds~~~~~l~~~~~~~~~~~~~~~~~-~~t~~q~~~~r~~ed~~~dg~qr~ 523 (648)
T PLN03119 446 LSIPSPWQEDLSNVLKDV-VDNPQPWNAFPDSIEANPLDSSRNIHQQVDGASTSS-YNTDHQHLESQVLEELSNDGTQTT 523 (648)
T ss_pred cccCCchhccchhcccCc-ccCccccccchhhhccCccccccccccccccccccC-CCCccccccccccccccccccccc
Confidence 999999999999999998 477 999999999999999999 88887776554 5555599999 9999999999999
Q ss_pred c-CCCCCCCCCCCCCCccCCCCCCCCCCccccccccccccCCCCCCCCCCCccccccccchhhhhHHhhCCCCCCCCCcc
Q 005622 554 A-SHDGPPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFDFPCDSDLEQNNMFLDMSSLQAALPNAELPSPFL 632 (687)
Q Consensus 554 a-p~~~~~~~~~~~~~~~g~~~~~~~~~~~g~~~~~~~~~ks~NPFDlp~dsd~e~~~mFmDmsSLQaaLP~~~lp~~f~ 632 (687)
| |+|+ ++|++|+++++||+|+++++|+|+ ++||+||||||||+|+|++|||||||||||||||+|||++|+
T Consensus 524 ~~p~g~-~g~~~~~~~~~~Ps~~~~~~~~~~-------~~ks~npfdl~~~sd~~~~~mf~d~tslq~~lp~~~~~~~~~ 595 (648)
T PLN03119 524 RIPAGS-SAFGFPGNIGMAPSYSEEAWQHVN-------EQKSANPFDLPYDSEFDSNDMFLDMSSLQGALPDIQTPQAFL 595 (648)
T ss_pred ccCCCC-CCCCCCCccccCCCCCchhccccc-------cccCCCCcCCccccccCcccceeehHHHHhhcCCCCCchhhh
Confidence 9 6665 999999999999999999999998 499999999999999999999999999999999999999999
Q ss_pred CCCCcCCCCCCCCCcccccCC--CCCccccccCCCCccccCCCCCCCcccCCCCCCC
Q 005622 633 GGATQSWFPQNPVSPFVQAAA--QGGLAYMSGQSPSAQLANIPTQEPVASVGGNPFA 687 (687)
Q Consensus 633 gg~~e~W~~qn~~~~yips~~--qGGl~~ma~q~p~s~l~ni~~~~~~a~~~gNPFa 687 (687)
||||||||+||++|+|||+|+ ||||+|||||+|+ |.++++||||+||||||
T Consensus 596 ~~~t~~w~~~~~~~~yip~~~~~qggl~y~~~q~~~----~~~~~~~~a~~~~npf~ 648 (648)
T PLN03119 596 NGVSQPWLAADSVPSYLPAPAVAQGGLAYMAGQAST----NSAAQGPVAFTGGNPFA 648 (648)
T ss_pred cCCCcccccCCCcccccCCCccccCCchhhhcccch----hhhhcCccccCCCCCCC
Confidence 999999999999999999977 9999999999999 67788999999999997
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.9e-47 Score=411.44 Aligned_cols=506 Identities=30% Similarity=0.420 Sum_probs=388.3
Q ss_pred chhHHHHH-HHHHHHHhcCCCCCCCcCCCCCCC-CeeEecceeeeehhhhhhhhcCC--CceeeeccCCCCHHHHHHHHh
Q 005622 3 SRKEEERN-EKIIRGLMKLPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGIHREFT--HRVKSVSMSKFTSQEVEALQN 78 (687)
Q Consensus 3 srke~Er~-ekiLr~Llk~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSGIHR~LG--hrVKSItLDkWt~eEV~~Lq~ 78 (687)
.+||+|++ |++||.|+++|+|++|++|+...+ +|+++.-|-|||+.|+|.-|.|. ||||+|+|.+|++.|+..|+.
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 34788887 999999999999999999999988 99999999999999999999996 999999999999999999999
Q ss_pred cCcHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhcccccCCCCCCCCCCCccCCCCCccccccCCCCCCCCCCCC
Q 005622 79 GGNQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPP 158 (687)
Q Consensus 79 gGN~rANeiwea~~d~~r~~~P~~sd~~krreFIraKY~eKrF~~~k~~D~Pp~~~q~l~~~~~e~rRsssy~s~sQsPp 158 (687)
+||+.+++||++-++..+--.|+..+.++.|+||+.||+.|+|+..+..++-+. .+| ..++.. +++
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 HGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPS----------YTR---GSLSED-SRP 149 (524)
T ss_pred cchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCcccccccc----------ccc---cccccc-CCc
Confidence 999999999999999988889999999999999999999999998765443321 000 001100 111
Q ss_pred cccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCcchhhhhcccccCCCCcccccccccCCCCCCCCCCCCCC
Q 005622 159 YDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPN 238 (687)
Q Consensus 159 ~d~~yEdrr~~k~~~~ltRkpgsd~~~~~gk~ss~~~sP~r~s~~~~~DRfa~e~s~~r~sd~~~s~~g~~~~~~~~sp~ 238 (687)
+...+ |++ +-+|+-- |+ +.|-
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 000 0012100 01 0111
Q ss_pred cccccCCCCCCcccccccccccCCcccCCCCCCCCCcccccCCccccCCCccccccccCCCCccCCCCCccCcCCCCCcc
Q 005622 239 FQKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDKI 318 (687)
Q Consensus 239 ~~k~~~~ssp~~~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~~ 318 (687)
++ +..++..+.-+ .++-|-|-
T Consensus 171 ~~-------------------------------~~t~np~~~~~--------------~~~~~~~~-------------- 191 (524)
T KOG0702|consen 171 LA-------------------------------ESTKNPRSRGL--------------PKSPIRFE-------------- 191 (524)
T ss_pred hh-------------------------------hcccCccccCC--------------CCCCchhh--------------
Confidence 00 00111110000 00000000
Q ss_pred cccCCCCCCCCcCcccccCCCCCCCCCCCCCCCCCccCCCccccc-cccccccccCCCCCCCCCCCCCCCCCCCCcccc-
Q 005622 319 STFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAA-SVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF- 396 (687)
Q Consensus 319 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlf~~p~~~~a-~vd~f~~~~~~~~~s~~~~q~~q~~~~~~~d~f- 396 (687)
...--+|||+++.++.+ +++.||.+.+.+.+.++..+..|+..++.+|+|
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 11245788999988777 999999888888888888888899999999999
Q ss_pred -cccCCCccccccCCCcCCCCCCCCCccc-ccCCCCCCCCCCccccccccccCCCCC--CCCCCCCCCCCcCCCCCcccC
Q 005622 397 -QITEQPSTAILNRNPQELSIPKNEGWAT-FDTPPSAASIPGTESLSHAMVPANEGS--SVKSDQFPSSNTSMQWPAFQN 472 (687)
Q Consensus 397 -~~~~~~~~~~~~~~~~~~~~p~n~gwat-fd~p~~~~~~~~~~~~~~~~~p~~~~~--~~~~~~~~~~~~~~~~~~~~~ 472 (687)
+--+||. ..+.+++.||||||+. +|+|..+... ..+|...-.+ -.||....+.+..|+.|...+
T Consensus 244 ge~~k~P~-----~~~~~asapk~eg~~s~sd~pvne~~~-------e~~i~s~~~~~~f~k~~e~paps~a~qlp~~ss 311 (524)
T KOG0702|consen 244 GEPFKQPV-----SRPSFASAPKNEGWASLSDNPVNEAKS-------ENVITSPGSFADFLKFEEIPAPSVAMQLPPYSS 311 (524)
T ss_pred cCCCCCCc-----cCccccccccccCCcccccCccccccc-------cccccCcccchhhcccccccCcchhhhcCCcCC
Confidence 3223343 5778999999999999 7999865322 2333322211 268888999999999999999
Q ss_pred CCCCCCCCCCCCCCCCccccccCcccCCCccccccccCCCCCCCCCCCCCCcccCCCC-CCCCCccccc-cccccCCCCC
Q 005622 473 SGANGPSPSSDPWSGNLHIVQAPAVATSSWNAFDDFTSHLPSEGFKPNSEPHVDAYMP-SPTPDQYLAI-VSQETNDDGN 550 (687)
Q Consensus 473 s~~~~~~~~~d~w~~~~~~~~~~~~~~~~WnaF~ds~~~~~~~~~~~~~~~~~~~~~~-~~t~~~~~~~-~~q~~~~d~~ 550 (687)
.++..+.+....|.++...+-+...+-++|+++-++++...+++..+-.+.+.+.-+. ++++++.+.+ ++++.-.+..
T Consensus 312 ~~~~~q~t~~~~~nd~~ssf~~~~~Ap~~~~~s~p~i~s~~~s~~~~l~~~~s~~gsa~~~~~~~~~n~~~~e~~~~s~~ 391 (524)
T KOG0702|consen 312 TVDQHQPTIPSPWNDQGSSFGATPVAPPLWVASPPSIGSNLLSSSRALAVQSSVFGSAGYVPPHQPVNLGVLEELSNSTT 391 (524)
T ss_pred CccccCCCCCCcccccCcccccccccCCccccCCCCccccccccccccccccccccccccCCCCcccccccccccccccc
Confidence 9999999998889988887755444344999999999999999999988876444444 8889999999 9999999999
Q ss_pred CcccCCCCCCCCCCCCCCccCCCCCCCCCCccccccccccccCCCCCCCCCCCcccccc-ccchhhhhHHhhCCCCCCCC
Q 005622 551 PRVASHDGPPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFDFPCDSDLEQN-NMFLDMSSLQAALPNAELPS 629 (687)
Q Consensus 551 ~~~ap~~~~~~~~~~~~~~~g~~~~~~~~~~~g~~~~~~~~~ks~NPFDlp~dsd~e~~-~mFmDmsSLQaaLP~~~lp~ 629 (687)
+..++-.+..-+.+|..+-++|++..- .-|-....+...++.+++++|||+...+.+ +||++|+.+|-++| .|.+.
T Consensus 392 q~~s~ft~~~ts~~p~~~~~~pssn~~--~~~~~Q~~~~~~~~g~~~~sl~~~~~~~~P~~~~fa~s~~qp~fP-~qt~~ 468 (524)
T KOG0702|consen 392 QTFSAFTNESTSGFPAPIGMAPSSNHH--QDDEFQPNHRNPQPGAAMSSLPYGFEFASPFDMFFAMSFPQPAFP-IQTPQ 468 (524)
T ss_pred cccccccCcccccCccccccCCccccc--ccccccccccCCCCccccccCCCCCCcCCCccccccccCcCcCCC-Ccccc
Confidence 999998888889999999999998732 222233334444678999999999999999 99999999999999 88999
Q ss_pred CccCCCCcCCCCCCCCCccccc--CCCCCccccccCCCCccccCCCCCCCcccCCCCCCC
Q 005622 630 PFLGGATQSWFPQNPVSPFVQA--AAQGGLAYMSGQSPSAQLANIPTQEPVASVGGNPFA 687 (687)
Q Consensus 630 ~f~gg~~e~W~~qn~~~~yips--~~qGGl~~ma~q~p~s~l~ni~~~~~~a~~~gNPFa 687 (687)
.+++|+...|..+.....|.|. -+|+|++||..++-- |.++|.||+|+++|||+
T Consensus 469 ~q~~~~~~~~~~~~~~p~~~P~~~v~~~G~S~nPF~as~----~S~aq~~~~~p~~nPF~ 524 (524)
T KOG0702|consen 469 VQQPGGSHFGLAGDSKPSYLPAPAVAQAGLSYNPFMASP----NSAAQFPVAFPGTNPFL 524 (524)
T ss_pred ccCCCCCCccccccCCcccCccccccccccccCccccCC----CCcccccccCCCCCCCC
Confidence 9999999999999999999998 559999999988531 27799999999999995
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=2.2e-35 Score=304.44 Aligned_cols=118 Identities=31% Similarity=0.660 Sum_probs=107.2
Q ss_pred hHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCc
Q 005622 5 KEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGN 81 (687)
Q Consensus 5 ke~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWt~eEV~~Lq~gGN 81 (687)
...++++++|++||+.|+|++|||||+++|+|||+|+|||||++|+||||.|| | |||||+||.|++|+|+.|+..||
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 45688999999999999999999999999999999999999999999999999 5 99999999999999999999999
Q ss_pred HHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHhcccccCCC
Q 005622 82 QRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGK 125 (687)
Q Consensus 82 ~rANeiwea~~d~~r~~~P~~sd~~krreFIraKY~eKrF~~~k 125 (687)
.+||.+||+.++.. .+.|... ..++.|||+|||+|+|....
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 3444432 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=6.1e-35 Score=266.36 Aligned_cols=111 Identities=34% Similarity=0.750 Sum_probs=92.9
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC---CceeeeccCCCCHHHHHHHHhcCcHHHHHHH
Q 005622 12 KIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (687)
Q Consensus 12 kiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLDkWt~eEV~~Lq~gGN~rANeiw 88 (687)
++|++|++.|+|++|||||+++|+|||++||||||+.|+|+||+|| ++||||+||+|+.+||++|+.+||.++|++|
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 hhcCccccCCCCCCCchHHHHHHHHHHHhcccccC
Q 005622 89 LKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAG 123 (687)
Q Consensus 89 ea~~d~~r~~~P~~sd~~krreFIraKY~eKrF~~ 123 (687)
|++.+ ...+++..++.+++++||++||++|+|+.
T Consensus 82 e~~~~-~~~~~~~~~~~~~~~~fI~~KY~~k~f~~ 115 (116)
T PF01412_consen 82 EANSP-PPKKPPPSSDQEKREQFIRAKYVEKAFIS 115 (116)
T ss_dssp TTTST-TTTTHCTTSHHHHHHHHHHHHHTTHTTS-
T ss_pred HcCCC-CCCCCCCCCcHHHHHHHHHHHHHhhhhcc
Confidence 99932 33456667888899999999999999985
No 6
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=100.00 E-value=3.7e-33 Score=253.45 Aligned_cols=106 Identities=31% Similarity=0.701 Sum_probs=97.4
Q ss_pred CCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCcHHHHHHHhhcCccccC
Q 005622 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDWDFQRQ 97 (687)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWt~eEV~~Lq~gGN~rANeiwea~~d~~r~ 97 (687)
|+|++|||||+++|+||+++||||||++|+||||+|| | +||||+||+|++++|++|+.+||.++|++||++++....
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 CCCCCCchHHHHHHHHHHHhcccccCCCC
Q 005622 98 RLPDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (687)
Q Consensus 98 ~~P~~sd~~krreFIraKY~eKrF~~~k~ 126 (687)
+.+...+.+++++||++||++|+|+....
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhcccccc
Confidence 55555667888999999999999987754
No 7
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.97 E-value=2.7e-30 Score=271.70 Aligned_cols=117 Identities=24% Similarity=0.576 Sum_probs=104.1
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCcHHH
Q 005622 8 ERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRA 84 (687)
Q Consensus 8 Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWt~eEV~~Lq~gGN~rA 84 (687)
...++++..|++.++|++|||||+.+|+||++|||||||++||||||+|| | +||||+||+|+.+||++|+.+||.+|
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-cCCCCCCCchHHHHHHHHHHHhcccccCC
Q 005622 85 REIYLKDWDFQ-RQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (687)
Q Consensus 85 Neiwea~~d~~-r~~~P~~sd~~krreFIraKY~eKrF~~~ 124 (687)
|.||+++.-.. ..++-...+...+++||+.||++++|...
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 99999886432 12333557778899999999999999876
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.94 E-value=3.2e-27 Score=247.33 Aligned_cols=114 Identities=29% Similarity=0.579 Sum_probs=91.4
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCcHHH
Q 005622 8 ERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRA 84 (687)
Q Consensus 8 Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWt~eEV~~Lq~gGN~rA 84 (687)
-|+++.|++|+...+|+.|+||++.+|+|||++||||||++|+|+||.|| | +|||||||+|.+.||++|++|||+++
T Consensus 4 prtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~ 83 (386)
T KOG0704|consen 4 PRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERF 83 (386)
T ss_pred hHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhH
Confidence 57788888888888999999999999999999999999999999999999 4 99999999999999999999999999
Q ss_pred HHHHhhcCcccc-CCCCCCCc---hHHHHHHHHHHHhcccc
Q 005622 85 REIYLKDWDFQR-QRLPDNSN---VNKVRDFIKNVYVDRRY 121 (687)
Q Consensus 85 Neiwea~~d~~r-~~~P~~sd---~~krreFIraKY~eKrF 121 (687)
++|++..-.... .++-..+| ...+|+-|++.-+.+.|
T Consensus 84 ~eFL~s~~~~~e~~~i~eKYns~aAa~yRdki~~laegr~w 124 (386)
T KOG0704|consen 84 REFLSSQGIYKETWPIREKYNSRAAALYRDKIAALAEGREW 124 (386)
T ss_pred HHHHhhCccccccccHHHhhccHHHHHHHHHHHHHhcCCcc
Confidence 999876532211 11111111 23445566665555666
No 9
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.92 E-value=1.8e-25 Score=235.66 Aligned_cols=116 Identities=22% Similarity=0.414 Sum_probs=95.9
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCcHHHHHH
Q 005622 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (687)
Q Consensus 11 ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWt~eEV~~Lq~gGN~rANei 87 (687)
.++|++|+++|+|++|+|||+++|+||+++||||||++|+||||.|| | +|||++||+|+.++|++|+.+||.++|+|
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 HhhcCccccCCC--CCCCchHHHHHHHHHHHhcccccCCCC
Q 005622 88 YLKDWDFQRQRL--PDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (687)
Q Consensus 88 wea~~d~~r~~~--P~~sd~~krreFIraKY~eKrF~~~k~ 126 (687)
|+.+.-.....+ -..+...++.+.+.+|++++.++.+..
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 987531111111 122444455556888899998876653
No 10
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.90 E-value=1.4e-24 Score=233.41 Aligned_cols=85 Identities=24% Similarity=0.598 Sum_probs=80.3
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCcHHH
Q 005622 8 ERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRA 84 (687)
Q Consensus 8 Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWt~eEV~~Lq~gGN~rA 84 (687)
...+.+++.|+..+.||+|||||+++|+|++|+|||||||+|+++||+|| | +|||..||+|+.+||+.|+.|||.+|
T Consensus 8 ~d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA 87 (454)
T KOG0706|consen 8 QDIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANA 87 (454)
T ss_pred hhHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhH
Confidence 34567899999999999999999999999999999999999999999999 5 99999999999999999999999999
Q ss_pred HHHHhhcC
Q 005622 85 REIYLKDW 92 (687)
Q Consensus 85 Neiwea~~ 92 (687)
+.|+..+-
T Consensus 88 ~~FFkqhg 95 (454)
T KOG0706|consen 88 RVFFKQHG 95 (454)
T ss_pred HHHHHHcC
Confidence 99998763
No 11
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.89 E-value=1.7e-23 Score=229.54 Aligned_cols=115 Identities=19% Similarity=0.455 Sum_probs=102.3
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC---CceeeeccCCCCHHHHHHHHhcCcHHHHHH
Q 005622 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (687)
Q Consensus 11 ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLDkWt~eEV~~Lq~gGN~rANei 87 (687)
...|+.|+..+||.+|+||+.++|.|+++|+|++||++|+||||.|| +|||+|.||.|..|.+..|..+||+.||++
T Consensus 501 a~a~qairn~rgn~~c~dc~~~n~~wAslnlg~l~cieCsgihr~lgt~lSrvr~LeLDdWPvEl~~Vm~aiGN~~AN~v 580 (749)
T KOG0705|consen 501 AMALQAIRNMRGNSHCVDCGTPNPKWASLNLGVLMCIECSGIHRNLGTHLSRVRSLELDDWPVELLKVMSAIGNDLANSV 580 (749)
T ss_pred HHHHHHHhcCcCCceeeecCCCCcccccccCCeEEEEEchhhhhhhhhhhhhhhccccccCcHHHHHHHHHhhhhHHHHH
Confidence 34688999999999999999999999999999999999999999999 499999999999999999999999999999
Q ss_pred HhhcCccccCCCCCCCchHHHHHHHHHHHhcccccCCCC
Q 005622 88 YLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (687)
Q Consensus 88 wea~~d~~r~~~P~~sd~~krreFIraKY~eKrF~~~k~ 126 (687)
||......+. +...+..++++.||++||++|.|...-.
T Consensus 581 WE~~~~G~~K-Ps~~s~REEkErwIr~KYeqklFLaPl~ 618 (749)
T KOG0705|consen 581 WEGSSQGQTK-PSPDSSREEKERWIRAKYEQKLFLAPLP 618 (749)
T ss_pred hhhhccCCcC-CCccccHHHHHHHHHHHHHHHhhcCCCC
Confidence 9986654433 3334678888999999999999987643
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.79 E-value=2e-20 Score=216.20 Aligned_cols=114 Identities=25% Similarity=0.521 Sum_probs=101.5
Q ss_pred HHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC---CceeeeccCCCCHHHHHHHHhcCcHHHHHHHhh
Q 005622 14 IRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREIYLK 90 (687)
Q Consensus 14 Lr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLDkWt~eEV~~Lq~gGN~rANeiwea 90 (687)
+..+.+.|+|.+|+|||++.|+|+++|+||.+||+|+||||+|| +||+|++||.|..+.+.+++++||..+|.|||+
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 499999999999999999999999999999999
Q ss_pred cCccccCCCC-CCCchHHHHHHHHHHHhcccccCCCCC
Q 005622 91 DWDFQRQRLP-DNSNVNKVRDFIKNVYVDRRYAGGKTP 127 (687)
Q Consensus 91 ~~d~~r~~~P-~~sd~~krreFIraKY~eKrF~~~k~~ 127 (687)
.+.....++| ..++...++.||++||++++|......
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
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.63 E-value=1.5e-16 Score=180.74 Aligned_cols=109 Identities=25% Similarity=0.506 Sum_probs=97.3
Q ss_pred HHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC---CceeeeccC--CCCHHHHHHHHhcCcHHHHHHHh
Q 005622 15 RGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMS--KFTSQEVEALQNGGNQRAREIYL 89 (687)
Q Consensus 15 r~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSItLD--kWt~eEV~~Lq~gGN~rANeiwe 89 (687)
.+++....|+.|||||+..|.|+++|++|.||-.|+|-||.|| ++|+|++|| .|+.+-++++...||.++|.||.
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 3566788999999999999999999999999999999999998 699999998 69999999999999999999999
Q ss_pred hcCccccCCCCCCCchHHHHHHHHHHHhcccccCC
Q 005622 90 KDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (687)
Q Consensus 90 a~~d~~r~~~P~~sd~~krreFIraKY~eKrF~~~ 124 (687)
.++.+...-.| .+.++.|++||++||.+.+|...
T Consensus 370 ~nl~~~e~lh~-dssp~~r~~fi~~Kykeg~fRk~ 403 (1186)
T KOG1117|consen 370 GNLPPNEHLHP-DSSPSTRRQFIKEKYKEGKFRKE 403 (1186)
T ss_pred cCCCCccccCC-CCCcchhhhHHHHHhhccccccc
Confidence 99876654333 45678899999999999988654
No 14
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.60 E-value=9.8e-17 Score=174.73 Aligned_cols=133 Identities=20% Similarity=0.381 Sum_probs=100.0
Q ss_pred hcCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCcHHHHHHHhhcC-c
Q 005622 18 MKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDW-D 93 (687)
Q Consensus 18 lk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWt~eEV~~Lq~gGN~rANeiwea~~-d 93 (687)
++...-+.|+|||+++|.|+||+-|||||.+|..+||.|| | .||+|....|.++.|++.....|..+|.|||..+ +
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 8999999999999999999999999999999876 3
Q ss_pred cc----cCCCCCCCchH--HHHHHHHHHHhcccccCCC-CCCCCCCCccCCCCCccccccCCCC
Q 005622 94 FQ----RQRLPDNSNVN--KVRDFIKNVYVDRRYAGGK-TPDKPPKDTQGLGSHLDESRRASSY 150 (687)
Q Consensus 94 ~~----r~~~P~~sd~~--krreFIraKY~eKrF~~~k-~~D~Pp~~~q~l~~~~~e~rRsssy 150 (687)
+. +.++|...|.. .+.+|||+||+...|+.+. +.|.-...-..+..+....+|+..+
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 21 22334333332 3567999999999998743 3443322222333445555565543
No 15
>PLN03131 hypothetical protein; Provisional
Probab=96.87 E-value=0.036 Score=64.13 Aligned_cols=89 Identities=29% Similarity=0.391 Sum_probs=45.9
Q ss_pred cCcccccCCCCCCCCCCCCCCCCCccCCCcccc---------------ccccccccccC-CCCCCCCCCCCCCCCCCCC-
Q 005622 330 YGGLDLFEAPVVPETVPSTAPPIDLFQLPETSA---------------ASVNMSEMSQA-SSVPSTNTYQPAQTSSPSS- 392 (687)
Q Consensus 330 ~~~~~~~~~~~~~~~~~~~~~~~dlf~~p~~~~---------------a~vd~f~~~~~-~~~~s~~~~q~~q~~~~~~- 392 (687)
...+|||.+|.. +.+.++||||++-..+ .+||||++.-- .++. .++|.+++.+...
T Consensus 359 a~pIDLFqlp~t-----s~a~~vdlf~~s~l~~~p~~n~~q~~qts~p~~~dlfag~~qqq~~~--s~~~~~~~~s~pkn 431 (705)
T PLN03131 359 APPIDLFQLPAT-----SPAPPVDLFEIPPLDPAPAINAYQPPQTSLPSSIDLFGGITQQQSIN--SLDEKSPELSIPKN 431 (705)
T ss_pred CCchhhhhccCC-----CCCCcccccccCcccCCCccccCCCCcccCCccccccccccccCccc--cccccCcccCCccc
Confidence 457899988654 7788899999664322 25666665221 1111 1233333332221
Q ss_pred --cccccccCC-CccccccCCCcCCCCC-CCCCccccc
Q 005622 393 --LNFFQITEQ-PSTAILNRNPQELSIP-KNEGWATFD 426 (687)
Q Consensus 393 --~d~f~~~~~-~~~~~~~~~~~~~~~p-~n~gwatfd 426 (687)
--+|+-.+| .++++ ..+...+.|| .+.|-+-||
T Consensus 432 egwa~fd~~~p~~s~~~-~~n~t~~~v~~~~~~~~~~d 468 (705)
T PLN03131 432 EGWATFDGIQPIASTPG-NENLTPFSIGPSMAGSANFD 468 (705)
T ss_pred cCcccccCCCcccccCC-cccccccccccccccCcchh
Confidence 346642344 54444 5555554554 445555554
No 16
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=93.54 E-value=2.2 Score=49.81 Aligned_cols=39 Identities=21% Similarity=0.361 Sum_probs=22.4
Q ss_pred Cccc-cccccccccccCCCCCCCCCCCCCCCCCCCCcccc
Q 005622 358 PETS-AASVNMSEMSQASSVPSTNTYQPAQTSSPSSLNFF 396 (687)
Q Consensus 358 p~~~-~a~vd~f~~~~~~~~~s~~~~q~~q~~~~~~~d~f 396 (687)
.+++ ++||||||-...|.++++++.|+.=.++-++|+++
T Consensus 318 ~~~~~aapIDLFqlp~ts~a~~vdlf~~~~~p~~p~~n~~ 357 (648)
T PLN03119 318 VAESTKAPIDLFQLPGAPVAQSVDTFQPSIAPRSPPVNLQ 357 (648)
T ss_pred cccccCCchhhhhccCCCCCccccccccccCCCCCccccC
Confidence 3444 44999998655555656555554433344445544
No 17
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=92.72 E-value=0.18 Score=57.34 Aligned_cols=142 Identities=20% Similarity=0.161 Sum_probs=104.4
Q ss_pred CCCCCCCCCcccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCcchhhhhcccccCCCCcccccccccCCCCC
Q 005622 150 YHSYSQSPPYDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDP 229 (687)
Q Consensus 150 y~s~sQsPp~d~~yEdrr~~k~~~~ltRkpgsd~~~~~gk~ss~~~sP~r~s~~~~~DRfa~e~s~~r~sd~~~s~~g~~ 229 (687)
|+++.+.++|+|.|+.||++|..++ ||=-.=..+ +....+.+.++++-.++.++-+.++...+|..+++|..-+++
T Consensus 1 ~a~~~ke~E~~~ek~iR~l~kLP~N--rrC~nCnsl--~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~q 76 (524)
T KOG0702|consen 1 YAGYKKEDEYDYEKEIRRLLKLPEN--RRCINCNSL--VAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQ 76 (524)
T ss_pred CCcccccchhHHHHHHHHHhcCCCC--Cceeecccc--ccceEEEeeccceeeeccchhhccCCCccccceeeeeecccc
Confidence 5778888999999999999998633 442121222 223446688999999999999999999999999999999999
Q ss_pred CCCCCCC-CC-cccccCCCCCCcccccccccccCCcccCCCCCCCCCcccccCCccccCCCccccccccCCCCc
Q 005622 230 FRPGAQS-PN-FQKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLT 301 (687)
Q Consensus 230 ~~~~~~s-p~-~~k~~~~ssp~~~~~~~i~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~ 301 (687)
.....|+ +| ++|++-+-.+-.+| ...+..++..-.+..||+.....--.++.+.+.+++|+.++|-
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 77 67776555544332 1112233444445667888888888889899999999987764
No 18
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=89.64 E-value=0.07 Score=63.92 Aligned_cols=68 Identities=16% Similarity=0.272 Sum_probs=52.7
Q ss_pred CCCCCCCcCCCC-CCCCeeEecceeeeehhhhhhhhcCC-C--ceeeeccCCCCHHHHHHHHhcCcHHHHHHHh
Q 005622 20 LPPNRRCINCNS-LGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYL 89 (687)
Q Consensus 20 ~PgNk~CADCGa-~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSItLDkWt~eEV~~Lq~gGN~rANeiwe 89 (687)
...+..|++|++ +.-.|+++++.+.+|+.|+++|+.++ + .++++.|+...+ |..+...||..++..|.
T Consensus 627 ~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~ 698 (785)
T KOG0521|consen 627 ASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATA 698 (785)
T ss_pred hccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhh
Confidence 445889999997 67899999999999999999999997 3 566666666665 66666666665555543
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=79.59 E-value=1.7 Score=32.91 Aligned_cols=40 Identities=15% Similarity=0.421 Sum_probs=33.4
Q ss_pred CCCCCcCCCCCCCCeeEecceeeeehhhhhh-hhcCCCceeee
Q 005622 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGI-HREFTHRVKSV 63 (687)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGI-HR~LGhrVKSI 63 (687)
.+..|..|+.....+.+.+=.++||..|... |+. |+|.+|
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=79.46 E-value=1.7 Score=45.30 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=27.9
Q ss_pred HHHHHHhc--CCCCCCCcCCCCCCCCeeEecceeeeehhhhhhh
Q 005622 12 KIIRGLMK--LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIH 53 (687)
Q Consensus 12 kiLr~Llk--~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIH 53 (687)
++-..|++ ...++.|-+||.+=|.+ -|+.+|..|..+-
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 34334444 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=53.80 E-value=10 Score=38.44 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=27.1
Q ss_pred CCCCCCCcCCCCCCC-CeeEecceeeeehhhhhh
Q 005622 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGI 52 (687)
Q Consensus 20 ~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSGI 52 (687)
.|.=..|+.||..++ .|.+...|.++|..|...
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 688999999999999864
No 22
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=49.90 E-value=13 Score=37.79 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=26.6
Q ss_pred CCCCCCCcCCCCCCC-CeeEecceeeeehhhhh
Q 005622 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSG 51 (687)
Q Consensus 20 ~PgNk~CADCGa~~P-~WaSvnfGVFVCi~CSG 51 (687)
.|.-..|+-||.... .|.+...|.++|..|..
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 455679999998644 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=44.59 E-value=12 Score=31.67 Aligned_cols=33 Identities=24% Similarity=0.411 Sum_probs=22.2
Q ss_pred CCCCCCCcCCCCCCC--CeeEecceeeeehhhhhhh
Q 005622 20 LPPNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIH 53 (687)
Q Consensus 20 ~PgNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIH 53 (687)
.++...|.+||..=| ++. ..-|+..|+.|...+
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 223778899998654
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=43.36 E-value=12 Score=28.94 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=20.7
Q ss_pred CCcCCCCCCCCeeEecceeeeehhhhhh
Q 005622 25 RCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (687)
Q Consensus 25 ~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (687)
+|-.||+.. ....-.-|-+||..|.-|
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=42.80 E-value=18 Score=27.64 Aligned_cols=28 Identities=25% Similarity=0.565 Sum_probs=23.5
Q ss_pred CCCCCCcCCCCCCCCeeEecceeeeehhhhh
Q 005622 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSG 51 (687)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSG 51 (687)
..|..|..|++. |....=|-++|.+|-.
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCce
Confidence 456779999997 8888999999999953
No 26
>PRK11019 hypothetical protein; Provisional
Probab=40.05 E-value=16 Score=33.31 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=22.7
Q ss_pred CCCCCcCCCCCCC--CeeEecceeeeehhhhhhhhc
Q 005622 22 PNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIHRE 55 (687)
Q Consensus 22 gNk~CADCGa~~P--~WaSvnfGVFVCi~CSGIHR~ 55 (687)
.-..|.+||..=| .+.-+. ++-.|++|...+-.
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 3579999998533 333333 67789999987643
No 27
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=39.10 E-value=13 Score=35.59 Aligned_cols=44 Identities=18% Similarity=0.307 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCCC--CCCcCCCCCCCC-eeEecceeeeehhhhhhh
Q 005622 10 NEKIIRGLMKLPPN--RRCINCNSLGPQ-YVCTNFWTFVCMTCSGIH 53 (687)
Q Consensus 10 ~ekiLr~Llk~PgN--k~CADCGa~~P~-WaSvnfGVFVCi~CSGIH 53 (687)
.+++-..|.+.... .+|.+||.+=|. =.-.--+..+|+.|.-.|
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 489999985211 011112567899998776
No 28
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=39.05 E-value=12 Score=37.16 Aligned_cols=34 Identities=32% Similarity=0.690 Sum_probs=28.6
Q ss_pred CCCCCCcCCCCCCCCeeEecceeeeeh-hhhhhhhc
Q 005622 21 PPNRRCINCNSLGPQYVCTNFWTFVCM-TCSGIHRE 55 (687)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi-~CSGIHR~ 55 (687)
|--+.|+-|| -...|.|++-|.-+|. .|-++|.+
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 4456899999 6778999999998886 89999965
No 29
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=37.61 E-value=15 Score=32.24 Aligned_cols=31 Identities=16% Similarity=0.264 Sum_probs=20.2
Q ss_pred CCCCcCCCCCCCCee-Eecceeeeehhhhhhh
Q 005622 23 NRRCINCNSLGPQYV-CTNFWTFVCMTCSGIH 53 (687)
Q Consensus 23 Nk~CADCGa~~P~Wa-SvnfGVFVCi~CSGIH 53 (687)
...|.|||..=|.== -.--|+..|+.|...+
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 358999998533211 1122788999998754
No 30
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=37.34 E-value=18 Score=37.88 Aligned_cols=30 Identities=27% Similarity=0.676 Sum_probs=25.9
Q ss_pred CCCCCCcCCCCCC-CCeeEecceeeeehhhh
Q 005622 21 PPNRRCINCNSLG-PQYVCTNFWTFVCMTCS 50 (687)
Q Consensus 21 PgNk~CADCGa~~-P~WaSvnfGVFVCi~CS 50 (687)
+.=..|+.||... +..+++-.|-++|.+|.
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3447999999964 57999999999999999
No 31
>PHA00080 DksA-like zinc finger domain containing protein
Probab=36.81 E-value=17 Score=31.72 Aligned_cols=45 Identities=16% Similarity=0.326 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhc---CCCCCCCcCCCCCC--CCeeEecceeeeehhhhhhh
Q 005622 8 ERNEKIIRGLMK---LPPNRRCINCNSLG--PQYVCTNFWTFVCMTCSGIH 53 (687)
Q Consensus 8 Er~ekiLr~Llk---~PgNk~CADCGa~~--P~WaSvnfGVFVCi~CSGIH 53 (687)
...+..|...+. ..+...|.+||..= ..+.-+. |+..|+.|...+
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 34556899999853 2333223 567799998865
No 32
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=33.24 E-value=33 Score=27.97 Aligned_cols=36 Identities=19% Similarity=0.396 Sum_probs=29.3
Q ss_pred CCCCCcCCCC-CCCCeeEeccee-eeehhhhhhhhcCC
Q 005622 22 PNRRCINCNS-LGPQYVCTNFWT-FVCMTCSGIHREFT 57 (687)
Q Consensus 22 gNk~CADCGa-~~P~WaSvnfGV-FVCi~CSGIHR~LG 57 (687)
..+.|.+|+. .-|.|=.-..|- +||-.|.-..+..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 3579999997 468898888886 99999987777665
No 33
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=30.67 E-value=16 Score=27.95 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=16.6
Q ss_pred CCCcCCCCC-CCCeeEecceeeeehhhh
Q 005622 24 RRCINCNSL-GPQYVCTNFWTFVCMTCS 50 (687)
Q Consensus 24 k~CADCGa~-~P~WaSvnfGVFVCi~CS 50 (687)
..|.+|+.. .-+|..-+|+.-||..|.
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 479999984 678999999999999995
No 34
>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=29.89 E-value=32 Score=34.17 Aligned_cols=32 Identities=13% Similarity=0.229 Sum_probs=19.9
Q ss_pred CCCCCCcCCCCCC--CCeeEecceeeeehhhhhhh
Q 005622 21 PPNRRCINCNSLG--PQYVCTNFWTFVCMTCSGIH 53 (687)
Q Consensus 21 PgNk~CADCGa~~--P~WaSvnfGVFVCi~CSGIH 53 (687)
..=.+|.+||..= -++--+. ++-.|+.|...+
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 1111122 467899999875
No 35
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=29.70 E-value=55 Score=30.09 Aligned_cols=30 Identities=13% Similarity=0.273 Sum_probs=23.7
Q ss_pred CCCCCCcCCCCCCCCeeEecceeeeehhhhhh
Q 005622 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (687)
Q Consensus 21 PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (687)
-.--.|-.|+.. .---+..||+.|..|--.
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 345689999998 555688999999999643
No 36
>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=26.80 E-value=45 Score=24.32 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=24.5
Q ss_pred CCcCCCCCCCCeeEecceeeeehhhhh-hhhcCCCceee
Q 005622 25 RCINCNSLGPQYVCTNFWTFVCMTCSG-IHREFTHRVKS 62 (687)
Q Consensus 25 ~CADCGa~~P~WaSvnfGVFVCi~CSG-IHR~LGhrVKS 62 (687)
.|-.|+.....+.+.+=+..||..|.- .|+ +|.+..
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 466676656677777888899999963 265 565543
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=25.80 E-value=32 Score=32.22 Aligned_cols=44 Identities=23% Similarity=0.509 Sum_probs=29.8
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcC--CC--ceeeeccC
Q 005622 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (687)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItLD 66 (687)
..|.--+|.+||. +..+....+.|-.|.+..-.+ |. +|++|.++
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 42 88888764
No 38
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=25.58 E-value=82 Score=31.14 Aligned_cols=35 Identities=11% Similarity=0.136 Sum_probs=21.5
Q ss_pred CCCCCCCcCCCCCCCC-eeEecceeeeehhhhhhhh
Q 005622 20 LPPNRRCINCNSLGPQ-YVCTNFWTFVCMTCSGIHR 54 (687)
Q Consensus 20 ~PgNk~CADCGa~~P~-WaSvnfGVFVCi~CSGIHR 54 (687)
.+.-.+|-+||..=|. =.-+--++..|+.|...|-
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 4566899999984110 0011114578999998764
No 39
>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=25.48 E-value=52 Score=24.86 Aligned_cols=30 Identities=23% Similarity=0.463 Sum_probs=21.7
Q ss_pred CcCCCC-CCCCeeEecceee-eehhhhhhhhc
Q 005622 26 CINCNS-LGPQYVCTNFWTF-VCMTCSGIHRE 55 (687)
Q Consensus 26 CADCGa-~~P~WaSvnfGVF-VCi~CSGIHR~ 55 (687)
|.+|++ ..|.|=....|-. ||-.|.-.+|.
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 899997 4799998888877 99999876654
No 40
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=24.61 E-value=1e+02 Score=34.61 Aligned_cols=78 Identities=23% Similarity=0.258 Sum_probs=44.7
Q ss_pred CCCCCccCCCccccc--------cccccccccCCCCCCCCCCCCCCCCCCC-CcccccccCCCccccc--cCCCcCCCCC
Q 005622 349 APPIDLFQLPETSAA--------SVNMSEMSQASSVPSTNTYQPAQTSSPS-SLNFFQITEQPSTAIL--NRNPQELSIP 417 (687)
Q Consensus 349 ~~~~dlf~~p~~~~a--------~vd~f~~~~~~~~~s~~~~q~~q~~~~~-~~d~f~~~~~~~~~~~--~~~~~~~~~p 417 (687)
..-.|||+--+-+.+ ++|+|. +-++.+||.-|..-++--- =.|+|.|.+-|+-+.. -++...++.|
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 345677773333333 555554 3456788887776665543 3789999888764433 3444445555
Q ss_pred CCC----CcccccCCC
Q 005622 418 KNE----GWATFDTPP 429 (687)
Q Consensus 418 ~n~----gwatfd~p~ 429 (687)
.|| -.--||-|+
T Consensus 404 a~e~~nGS~na~~~~p 419 (499)
T KOG2057|consen 404 ANEASNGSFNAFDFGP 419 (499)
T ss_pred hhhhccCccccCCCCc
Confidence 554 234455555
No 41
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=24.46 E-value=27 Score=32.69 Aligned_cols=44 Identities=11% Similarity=0.290 Sum_probs=30.2
Q ss_pred cCCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcC--CC--ceeeecc
Q 005622 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSM 65 (687)
Q Consensus 19 k~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItL 65 (687)
..|..-+|.+||. .+....+..+.|-.|.+....+ |. +|++|-+
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 3567779999995 2333344557899999876665 32 7888754
No 42
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=23.77 E-value=27 Score=36.98 Aligned_cols=32 Identities=22% Similarity=0.419 Sum_probs=24.9
Q ss_pred CCCCCCcCCCC--CCCCeeEecceeeeehhhhhhh
Q 005622 21 PPNRRCINCNS--LGPQYVCTNFWTFVCMTCSGIH 53 (687)
Q Consensus 21 PgNk~CADCGa--~~P~WaSvnfGVFVCi~CSGIH 53 (687)
.-+.+|..|.. .++.+-+ .||+-||..|+.-|
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 3444443 58999999999888
No 43
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.01 E-value=31 Score=32.45 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=28.0
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeeeehhhhhhhhcC--CC--ceeeeccC
Q 005622 20 LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (687)
Q Consensus 20 ~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSItLD 66 (687)
.|.--+|.+||.. |....+..+.|-.|.+....+ |. +|++|.++
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 32 78887653
No 44
>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=22.37 E-value=54 Score=29.13 Aligned_cols=31 Identities=13% Similarity=0.470 Sum_probs=25.4
Q ss_pred CCCCCcCCCCCCCCeeEecceeeeehhhhhhhhc
Q 005622 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (687)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (687)
.|..|.=||... ....||++.|..|.+..|.
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 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.96 E-value=54 Score=35.43 Aligned_cols=33 Identities=18% Similarity=0.207 Sum_probs=23.4
Q ss_pred CCCCCCCcCCCCCCCCeeEecceeeeehhhhhhh
Q 005622 20 LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIH 53 (687)
Q Consensus 20 ~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGIH 53 (687)
.....+|-+||... --....-|-.||.+|.-|.
T Consensus 8 ~~~~~~Cp~Cg~~~-iv~d~~~Ge~vC~~CG~Vl 40 (310)
T PRK00423 8 EEEKLVCPECGSDK-LIYDYERGEIVCADCGLVI 40 (310)
T ss_pred cccCCcCcCCCCCC-eeEECCCCeEeecccCCcc
Confidence 34557899999732 2223566999999998764
No 46
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=21.68 E-value=39 Score=25.72 Aligned_cols=30 Identities=23% Similarity=0.425 Sum_probs=15.3
Q ss_pred CCCcCCCCCCCCeeEe---cceeeeehhhhhhhh
Q 005622 24 RRCINCNSLGPQYVCT---NFWTFVCMTCSGIHR 54 (687)
Q Consensus 24 k~CADCGa~~P~WaSv---nfGVFVCi~CSGIHR 54 (687)
|.|-.||.+ ..+... +.-=++|..|.-||-
T Consensus 1 kfC~~CG~~-l~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGP-LERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccCh-hhhhcCCCCCccceECCCCCCEEe
Confidence 578899986 223222 344678999999883
No 47
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=21.64 E-value=56 Score=30.22 Aligned_cols=34 Identities=18% Similarity=0.395 Sum_probs=23.7
Q ss_pred hcCCCCCCCcCCCCCC-----------------CCeeEecceeeeehhhhh
Q 005622 18 MKLPPNRRCINCNSLG-----------------PQYVCTNFWTFVCMTCSG 51 (687)
Q Consensus 18 lk~PgNk~CADCGa~~-----------------P~WaSvnfGVFVCi~CSG 51 (687)
.+.++--+|++||.+= -.=+.=.||-.+|.+|..
T Consensus 29 kK~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 29 KKKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred eccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 4567778999999741 112244689999999974
No 48
>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=21.38 E-value=58 Score=29.75 Aligned_cols=31 Identities=19% Similarity=0.470 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeEecceeeeehhhhhhhhc
Q 005622 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (687)
Q Consensus 22 gNk~CADCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (687)
.+..|.=||... ....||++.|..|.+..|.
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 3467999999999998875
No 49
>PRK00420 hypothetical protein; Validated
Probab=21.02 E-value=2.1e+02 Score=27.24 Aligned_cols=44 Identities=18% Similarity=0.156 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhc--CCCCCCCcCCCCCCCCeeEecceeeeehhhhhh
Q 005622 6 EEERNEKIIRGLMK--LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (687)
Q Consensus 6 e~Er~ekiLr~Llk--~PgNk~CADCGa~~P~WaSvnfGVFVCi~CSGI 52 (687)
+++..+++-+.|++ .=-+..|-.||.+-.. +.-|-.+|..|..+
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 2246999999975432 36688899999764
No 50
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.59 E-value=1.2e+02 Score=23.88 Aligned_cols=42 Identities=17% Similarity=0.258 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecceeeeehhhh
Q 005622 7 EERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCS 50 (687)
Q Consensus 7 ~Er~ekiLr~Llk~PgNk~CADCGa~~P~WaSvnfGVFVCi~CS 50 (687)
++.-.+.|..++=. ..-.|--||.....+.. +.+.|-|-.|.
T Consensus 3 e~~c~~~l~~~RW~-~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 3 EEACREYLEEIRWP-DGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred HHHHHHHHHHhcCC-CCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 34445555555444 33789999998443333 36899999885
No 51
>COG2719 SpoVR Uncharacterized conserved protein [Function unknown]
Probab=20.45 E-value=29 Score=39.89 Aligned_cols=8 Identities=88% Similarity=1.610 Sum_probs=7.2
Q ss_pred CCCCcccc
Q 005622 418 KNEGWATF 425 (687)
Q Consensus 418 ~n~gwatf 425 (687)
-|||||||
T Consensus 270 MNEGWAtf 277 (495)
T COG2719 270 MNEGWATF 277 (495)
T ss_pred hhhhHHHH
Confidence 39999999
No 52
>PRK11767 SpoVR family protein; Provisional
Probab=20.37 E-value=29 Score=40.38 Aligned_cols=8 Identities=88% Similarity=1.610 Sum_probs=7.2
Q ss_pred CCCCcccc
Q 005622 418 KNEGWATF 425 (687)
Q Consensus 418 ~n~gwatf 425 (687)
=|||||||
T Consensus 273 MNEGWAsy 280 (498)
T PRK11767 273 MNEGWATF 280 (498)
T ss_pred HhhHhHHH
Confidence 39999998
Done!