Query 005699
Match_columns 682
No_of_seqs 194 out of 1216
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 12:24:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005699.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005699hhsearch_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 2E-188 4E-193 1527.8 45.2 653 1-682 1-705 (705)
2 PLN03119 putative ADP-ribosyla 100.0 1E-168 3E-173 1363.7 42.0 621 1-682 1-648 (648)
3 KOG0702 Predicted GTPase-activ 100.0 1.2E-45 2.5E-50 397.9 31.8 510 3-682 4-524 (524)
4 KOG0703 Predicted GTPase-activ 100.0 7.3E-36 1.6E-40 308.2 7.4 118 5-125 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 5.5E-35 1.2E-39 267.4 7.9 111 12-123 2-115 (116)
6 smart00105 ArfGap Putative GTP 100.0 3.3E-33 7.1E-38 254.4 10.0 106 21-126 1-109 (112)
7 COG5347 GTPase-activating prot 100.0 1.1E-30 2.4E-35 275.1 9.0 118 7-124 4-125 (319)
8 KOG0704 ADP-ribosylation facto 100.0 2.7E-28 5.8E-33 255.4 11.7 86 7-92 3-91 (386)
9 PLN03114 ADP-ribosylation fact 99.9 4.3E-26 9.2E-31 240.3 17.5 116 11-126 10-130 (395)
10 KOG0706 Predicted GTPase-activ 99.9 6.3E-25 1.4E-29 236.2 7.3 84 8-91 8-94 (454)
11 KOG0705 GTPase-activating prot 99.9 7.4E-24 1.6E-28 232.4 7.0 114 11-125 501-617 (749)
12 KOG0521 Putative GTPase activa 99.8 2.2E-20 4.8E-25 216.5 3.9 115 13-127 416-534 (785)
13 KOG1117 Rho- and Arf-GTPase ac 99.6 1.3E-16 2.8E-21 181.4 4.0 110 15-125 290-404 (1186)
14 KOG0818 GTPase-activating prot 99.6 6.9E-17 1.5E-21 175.8 -0.3 132 18-149 3-145 (669)
15 PLN03131 hypothetical protein; 97.1 0.14 3E-06 59.6 24.1 65 330-396 373-459 (705)
16 KOG0702 Predicted GTPase-activ 96.6 0.012 2.7E-07 66.2 10.7 143 150-302 1-145 (524)
17 KOG0521 Putative GTPase activa 89.7 0.083 1.8E-06 63.4 -0.6 68 20-89 627-698 (785)
18 PRK12495 hypothetical protein; 77.4 1.6 3.6E-05 45.3 2.5 38 12-53 29-68 (226)
19 PF00643 zf-B_box: B-box zinc 75.7 1.7 3.7E-05 32.8 1.6 40 22-63 2-42 (42)
20 PLN03119 putative ADP-ribosyla 74.6 1.7E+02 0.0037 34.9 17.5 27 329-355 336-371 (648)
21 TIGR00613 reco DNA repair prot 65.5 9.6 0.00021 38.8 4.9 33 20-52 144-177 (241)
22 PRK00085 recO DNA repair prote 59.0 7.6 0.00016 39.7 2.8 32 20-51 146-178 (247)
23 TIGR02419 C4_traR_proteo phage 51.2 8.6 0.00019 32.5 1.4 33 20-53 28-62 (63)
24 PRK11019 hypothetical protein; 47.5 10 0.00022 34.4 1.4 33 22-55 35-69 (88)
25 COG1734 DksA DnaK suppressor p 47.5 18 0.00039 34.5 3.1 30 24-53 81-111 (120)
26 PRK13715 conjugal transfer pro 43.2 11 0.00023 32.9 0.8 31 23-53 34-65 (73)
27 COG1381 RecO Recombinational D 42.2 13 0.00029 38.9 1.5 30 21-50 152-182 (251)
28 TIGR02890 spore_yteA sporulati 40.8 18 0.0004 35.9 2.1 42 10-53 74-117 (159)
29 PHA00080 DksA-like zinc finger 40.3 14 0.0003 32.1 1.1 45 8-53 13-62 (72)
30 PF11781 RRN7: RNA polymerase 36.9 19 0.00041 27.5 1.2 28 21-51 6-33 (36)
31 PF08271 TF_Zn_Ribbon: TFIIB z 35.6 12 0.00026 28.9 -0.1 27 25-52 2-28 (43)
32 PRK10778 dksA RNA polymerase-b 34.9 46 0.00099 32.9 3.8 36 20-55 108-144 (151)
33 smart00401 ZnF_GATA zinc finge 34.9 24 0.00053 28.7 1.6 36 22-57 2-39 (52)
34 PF01286 XPA_N: XPA protein N- 32.8 13 0.00028 28.3 -0.3 27 24-50 4-31 (34)
35 COG1997 RPL43A Ribosomal prote 29.0 41 0.00088 30.8 2.1 30 21-52 33-62 (89)
36 KOG3362 Predicted BBOX Zn-fing 26.9 22 0.00047 35.2 0.0 34 21-55 116-150 (156)
37 TIGR00100 hypA hydrogenase nic 25.6 24 0.00051 33.1 0.1 44 19-66 66-113 (115)
38 cd07173 NR_DBD_AR DNA-binding 25.6 47 0.001 29.5 1.9 31 22-55 2-32 (82)
39 PRK03681 hypA hydrogenase nick 24.7 24 0.00052 33.0 -0.1 44 19-65 66-113 (114)
40 COG5145 RAD14 DNA excision rep 23.8 41 0.00089 35.5 1.4 33 20-53 113-147 (292)
41 cd07171 NR_DBD_ER DNA-binding 23.1 48 0.001 29.4 1.5 31 22-55 2-32 (82)
42 PF10764 Gin: Inhibitor of sig 22.7 41 0.00088 27.1 0.9 26 25-51 1-26 (46)
43 PRK00564 hypA hydrogenase nick 22.7 29 0.00062 32.6 0.0 44 20-66 68-115 (117)
44 PF00320 GATA: GATA zinc finge 22.4 53 0.0011 24.8 1.4 30 26-55 1-32 (36)
45 COG5114 Histone acetyltransfer 21.5 1.3E+02 0.0029 33.5 4.7 32 187-224 159-190 (432)
46 TIGR02420 dksA RNA polymerase- 21.0 1.1E+02 0.0023 28.3 3.4 30 21-50 78-108 (110)
47 cd06968 NR_DBD_ROR DNA-binding 20.9 56 0.0012 29.8 1.5 31 22-55 4-34 (95)
48 COG2174 RPL34A Ribosomal prote 20.6 54 0.0012 30.2 1.3 35 17-51 28-79 (93)
49 PF04189 Gcd10p: Gcd10p family 20.5 89 0.0019 34.1 3.2 47 66-120 106-152 (299)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.8e-188 Score=1527.84 Aligned_cols=653 Identities=62% Similarity=1.013 Sum_probs=628.5
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCCCceeecccCCCCHHHHHHHHhcC
Q 005699 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (682)
Q Consensus 1 M~srk~~Er~ekiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSltLD~Wt~eEV~~Lq~gG 80 (682)
|++||++||++++|++|+++|+|++|||||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
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 005699 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (682)
Q Consensus 81 N~raN~iyea~~d~~~~~~P~~sd~~~rreFIraKY~eKrF~~~k~~D~Pp~~~q~l~~~~~e~rr~ss~~s~sqsPp~d 160 (682)
|++||+|||++|+..+.++|...+.+++|+|||+||++|||+.....|+|+++.+.++.++.++||.++||+++|+|||+
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 005699 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (682)
Q Consensus 161 ~~yedrr~~k~~~~l~Rkpgsd~~~~~Gk~ss~~~sP~r~s~~~~~Dr~a~~~s~~r~sd~s~s~~g~~~k~~~~sp~~~ 240 (682)
|+||||||||+...++|+||+|+++|.|||++|++||+|+.++|+||||+||++++|++||+++++|+++|.+.+|||++
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 005699 241 KDAGFNSPPVQLSRDVSSLKANFK-----------RDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQ 309 (682)
Q Consensus 241 K~~~~ssp~v~~~~~~~~~~~~~~-----------~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~ 309 (682)
|++. +||||+++|+|||+.++.. ++++|++++|||+|+|||||+||+++++|++||+|||||.+|+++
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 5789988999999765544 668999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCcccCCCCCCCCCCCCccccCCCCCCCCCCCCCCCccccCCCCCCccc-------------------------
Q 005699 310 AAGAPLDKISTFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAAS------------------------- 364 (682)
Q Consensus 310 ~~~~~q~~~~~~p~~~~~~~~~~~dl~~~~~~~~~~~~~~~~idlfq~p~~~~~~------------------------- 364 (682)
+++++|.|+..+++.++.+.++++|+|++||+|++++++|+||||||+|+||.|+
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 9999999999999999999999999999999999999999999999999998754
Q ss_pred ----------ccCCCcccccCCCCcCCCCCCCCCcccccCCCCCCCCCCccCcccccccCCCCCCcCCCCCCCCCCCCCC
Q 005699 365 ----------ITEQPSTAILNRNPQELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQW 434 (682)
Q Consensus 365 ----------~~~q~~~~~~~~~~~~~~~~~n~gWAtfD~p~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~ 434 (682)
|+||++++|||++++||++||||||||||+++.++|++|++||+..+||.....+.+||.+.++.++|||
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 8999999999999999999999999999988877999999999999999877557899999999999999
Q ss_pred CccCCCCCCCCCCCCCCCCCCcccccccccccccccccccCCCCCCCCccccccccccccccccccc--cccCCccCCCC
Q 005699 435 PAFQNSGANGPSPSSDPWSGNLHIVQAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFD--DFTSHLPSEGF 512 (682)
Q Consensus 435 ~~~~~s~~~~~~~~~~~~~~~~~~~qw~~~~~s~~~~~~~~~~w~~~~~~~~~~~~~~~~q~Wnaf~--d~~~~~~~~~~ 512 (682)
|.|+.+.++... .+|++|.+++||||++.. ++.|+||||+ |+++++||+++
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 999988877644 356899999999999986 9999999999 99999999999
Q ss_pred CCCCCCcccCCCCCCCCccchhh-cccccCCCCCCcccCCCC--CCCCCCCCCCccCCCCCCCCCCcccccccccCCCCC
Q 005699 513 KPNSEPHVDAYMPSPTPDQYLAI-VSQETNDDGNPRVASHDG--PPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKS 589 (682)
Q Consensus 513 ~~~~~~~~~~~~~~~t~~~~~~s-~~qe~~~d~~~~~ap~~~--~~~~~~p~~~~~~psy~~~~~~~~g~~~~~~~~~ks 589 (682)
++++++||.++.++++ +||+++ ++||+++||++|+||+++ +++|++|+.+++||+|.++++|+||+|++|.+++||
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 9999999987777555 599999 999999999999999999 999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCcccccccccchhhHHhhCCCCCCCCCcCC-CCCCCCCCCCCCCccccccccCCccccccCCCCcccCCCC
Q 005699 590 TNPFDFPCDSDLEQNNMFLDMSSLQAALPNAELPSPFLG-GATQSWFPQNPVSPFVQAAAQGGLAYMSGQSPSAQLANIP 668 (682)
Q Consensus 590 ~NPFDlp~dsd~e~~~mF~DmsSLQaaLP~~~~p~~f~g-g~te~W~pqns~~~yips~~qGgl~yma~Q~p~~~~~n~~ 668 (682)
+||||||||+|+|++|||||||||||||||+|||++||| ||||+|||||++|+|||+|+||||+|||||+|++||.|.+
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 005699 669 TQEPVASVGGNPFA 682 (682)
Q Consensus 669 ~~~~~a~~~gNPFa 682 (682)
+++||||+||||||
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=1.2e-168 Score=1363.71 Aligned_cols=621 Identities=50% Similarity=0.800 Sum_probs=562.8
Q ss_pred CCchhHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCCCceeecccCCCCHHHHHHHHhcC
Q 005699 1 MGSRKEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFTHRVKSVSMSKFTSQEVEALQNGG 80 (682)
Q Consensus 1 M~srk~~Er~ekiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LGhrVKSltLD~Wt~eEV~~Lq~gG 80 (682)
|++||++||++++|++|+++|+|++|+|||+++|+|||+|||||||++|+||||+||||||||+||+|+++||++|+.+|
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 005699 81 NQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPPYD 160 (682)
Q Consensus 81 N~raN~iyea~~d~~~~~~P~~sd~~~rreFIraKY~eKrF~~~k~~D~Pp~~~q~l~~~~~e~rr~ss~~s~sqsPp~d 160 (682)
|++||+|||++|+..+.++|...+.+++|+|||+||++|||+.....|+|+++.+..+.+++++||.++||+++|+|+|+
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 99999999999998777788888888999999999999999999999999999999898889999999999999999999
Q ss_pred cchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCCcccccccccCCCCCCCCCCCCCCcc
Q 005699 161 YQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPNFQ 240 (682)
Q Consensus 161 ~~yedrr~~k~~~~l~Rkpgsd~~~~~Gk~ss~~~sP~r~s~~~~~Dr~a~~~s~~r~sd~s~s~~g~~~k~~~~sp~~~ 240 (682)
++|||||||||...|+||||+||+++ ||+++|+|+|+|+.++|+||||+||++++|++||+++++|+++|.+.+||||+
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 005699 241 KDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDKIST 320 (682)
Q Consensus 241 K~~~~ssp~v~~~~~~~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~~~~ 320 (682)
+.++++|+|++.++++...... + ++++|||+|+|||||+|++++++|+++|++|.|+.+|.+++++++|.|+..
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 6778899999999988855443 2 689999999999999999999999999999999999999999999999976
Q ss_pred CCCCCCCCCCCCccccCCCCCCCCCCCCCCCccccC------CCCCCc---------------ccccCCCcccccCCCCc
Q 005699 321 FPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQ------LPETSA---------------ASITEQPSTAILNRNPQ 379 (682)
Q Consensus 321 ~p~~~~~~~~~~~dl~~~~~~~~~~~~~~~~idlfq------~p~~~~---------------~~~~~q~~~~~~~~~~~ 379 (682)
.---........+|||+.| +|+.|.+||||| .|+..+ +.++||++++ +++
T Consensus 314 ~~P~~~~~~aapIDLFqlp-----~ts~a~~vdlf~~~~~p~~p~~n~~q~~qts~p~~~~~f~~~~qqq~~~----~~~ 384 (648)
T PLN03119 314 HVPLVAESTKAPIDLFQLP-----GAPVAQSVDTFQPSIAPRSPPVNLQQAPQTYSFTPANSFAGNLGQQPTS----RPS 384 (648)
T ss_pred CCcccccccCCchhhhhcc-----CCCCCccccccccccCCCCCccccCCCccccCCcchhhhhcccccCccc----Ccc
Confidence 6211122224678888655 567777888887 222211 1177887654 999
Q ss_pred CCCCCCCCCcccccCCCCCCCCCCccCcccccccCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCcccc
Q 005699 380 ELSIPKNEGWATFDTPPSAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQWPAFQNSGANGPSPSSDPWSGNLHIV 459 (682)
Q Consensus 380 ~~~~~~n~gWAtfD~p~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~ 459 (682)
|+++||||||||||+|. ++.++++||.. +..-..+.+||.++++.++|+||.|+.+.+...+
T Consensus 385 ~~s~pkneGWA~fd~p~--~s~~~~~ni~~---~~~~~~~~~~d~v~~~~~~mq~Pp~~~~~~~~s~------------- 446 (648)
T PLN03119 385 ELSAPKNEGWASFDNPM--PAAKSTNVITS---PGDFQLELKIEEILQPSTSMQLPPYPSTVDQHAL------------- 446 (648)
T ss_pred ccccccccCcccccccc--cccCCcccccC---ccccccCcchhhhcccccccccCCCccccccccc-------------
Confidence 99999999999999554 88888888744 2222446799999999999999999887655533
Q ss_pred cccccccccccccccCCCCCCCCccccccccccccccccccccccCCccCCCCC--CCCCCcccCCCCCCCCccchhh-c
Q 005699 460 QAPAVATSAQVVSAASDPWPGNLHNGEAPAIATNMQSWNAFDDFTSHLPSEGFK--PNSEPHVDAYMPSPTPDQYLAI-V 536 (682)
Q Consensus 460 qw~~~~~s~~~~~~~~~~w~~~~~~~~~~~~~~~~q~Wnaf~d~~~~~~~~~~~--~~~~~~~~~~~~~~t~~~~~~s-~ 536 (682)
.+|++|.+++||||+++ ++++|+||||+|++++++|++++ ++.++++.++.+ .|++||+++ +
T Consensus 447 -------------s~~~pW~~~~~~V~~~~-~~~~q~WnAF~ds~~~~~l~~~~~~~~~~~~~~~~~~-~t~~q~~~~r~ 511 (648)
T PLN03119 447 -------------SIPSPWQEDLSNVLKDV-VDNPQPWNAFPDSIEANPLDSSRNIHQQVDGASTSSY-NTDHQHLESQV 511 (648)
T ss_pred -------------ccCCchhccchhcccCc-ccCccccccchhhhccCccccccccccccccccccCC-CCccccccccc
Confidence 46689999999999998 69999999999999999999999 888888876666 555599999 9
Q ss_pred ccccCCCCCCccc-CCCCCCCCCCCCCCccCCCCCCCCCCcccccccccCCCCCCCCCCCCCCCcccccccccchhhHHh
Q 005699 537 SQETNDDGNPRVA-SHDGPPNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFDFPCDSDLEQNNMFLDMSSLQA 615 (682)
Q Consensus 537 ~qe~~~d~~~~~a-p~~~~~~~~~p~~~~~~psy~~~~~~~~g~~~~~~~~~ks~NPFDlp~dsd~e~~~mF~DmsSLQa 615 (682)
+||+++||++|+| |++. ++|++|+++++||+|.++++|+|+ ++||+||||||||+|+|++||||||+||||
T Consensus 512 ~ed~~~dg~qr~~~p~g~-~g~~~~~~~~~~Ps~~~~~~~~~~-------~~ks~npfdl~~~sd~~~~~mf~d~tslq~ 583 (648)
T PLN03119 512 LEELSNDGTQTTRIPAGS-SAFGFPGNIGMAPSYSEEAWQHVN-------EQKSANPFDLPYDSEFDSNDMFLDMSSLQG 583 (648)
T ss_pred ccccccccccccccCCCC-CCCCCCCccccCCCCCchhccccc-------cccCCCCcCCccccccCcccceeehHHHHh
Confidence 9999999999999 6666 999999999999999999999988 599999999999999999999999999999
Q ss_pred hCCCCCCCCCcCCCCCCCCCCCCCCCccccccc--cCCccccccCCCCcccCCCCCCCCcccCCCCCCC
Q 005699 616 ALPNAELPSPFLGGATQSWFPQNPVSPFVQAAA--QGGLAYMSGQSPSAQLANIPTQEPVASVGGNPFA 682 (682)
Q Consensus 616 aLP~~~~p~~f~gg~te~W~pqns~~~yips~~--qGgl~yma~Q~p~~~~~n~~~~~~~a~~~gNPFa 682 (682)
||||+|+|++|+|||||+||+||++|+|||+++ ||||+|||||+|+ |.++++||||+||||||
T Consensus 584 ~lp~~~~~~~~~~~~t~~w~~~~~~~~yip~~~~~qggl~y~~~q~~~----~~~~~~~~a~~~~npf~ 648 (648)
T PLN03119 584 ALPDIQTPQAFLNGVSQPWLAADSVPSYLPAPAVAQGGLAYMAGQAST----NSAAQGPVAFTGGNPFA 648 (648)
T ss_pred hcCCCCCchhhhcCCCcccccCCCcccccCCCccccCCchhhhcccch----hhhhcCccccCCCCCCC
Confidence 999999999999999999999999999999977 9999999999999 56678889999999997
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.2e-45 Score=397.94 Aligned_cols=510 Identities=29% Similarity=0.390 Sum_probs=362.8
Q ss_pred chhHHHHH-HHHHHHHhcCCCCCCCcCCCCCCC-CeeEecchhhhhhhhhhhhhcCC--CceeecccCCCCHHHHHHHHh
Q 005699 3 SRKEEERN-EKIIRGLMKLPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGIHREFT--HRVKSVSMSKFTSQEVEALQN 78 (682)
Q Consensus 3 srk~~Er~-ekiLr~Llk~PgNk~CaDCGa~~P-~WaSvnfGVFVCi~CSGIHR~LG--hrVKSltLD~Wt~eEV~~Lq~ 78 (682)
.+||+|++ |++||.|+++|+|++|++|+.+.+ +|++++-|-|+|+.|+|..|.|. ||||+|+|.++++.||..|+.
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 35888887 999999999999999999999988 99999999999999999999995 999999999999999999999
Q ss_pred cCcHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHHhccccCCCCCCCCCCCcCCCCCCcccccccCCCCCCCCCCC
Q 005699 79 GGNQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGKTPDKPPKDTQGLGSHLDESRRASSYHSYSQSPP 158 (682)
Q Consensus 79 gGN~raN~iyea~~d~~~~~~P~~sd~~~rreFIraKY~eKrF~~~k~~D~Pp~~~q~l~~~~~e~rr~ss~~s~sqsPp 158 (682)
+||+.+++||++-++..+-..|+..+.++.|+|||.||+.|+|+..+..++-+.-. + ..++. .+++
T Consensus 84 hgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~t---r----------~s~s~-~s~~ 149 (524)
T KOG0702|consen 84 HGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSYT---R----------GSLSE-DSRP 149 (524)
T ss_pred cchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCcccccccccc---c----------ccccc-cCCc
Confidence 99999999999999999889999999999999999999999999876554432211 1 01111 0222
Q ss_pred cccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCCcccccccccCCCCCCCCCCCCCC
Q 005699 159 YDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDPFRPGAQSPN 238 (682)
Q Consensus 159 ~d~~yedrr~~k~~~~l~Rkpgsd~~~~~Gk~ss~~~sP~r~s~~~~~Dr~a~~~s~~r~sd~s~s~~g~~~k~~~~sp~ 238 (682)
+...+.+ ++..|.--..+.|.-.-+...-.-.+...+|.|+ +..+|||.+-+..- -+| --.++..
T Consensus 150 ~~~s~~~-~~~lrs~~gd~~P~~~~~t~np~~~~~~~~~~~~--~~~~~rfdlfg~~k-~sd-----------~~s~s~~ 214 (524)
T KOG0702|consen 150 VSESRPE-TKSLRSLLGDHAPLLAESTKNPRSRGLPKSPIRF--EIVDDRFDLFGLPK-ASD-----------AQSQSTF 214 (524)
T ss_pred ccccCCC-ccccccccCCCCcchhhcccCccccCCCCCCchh--hhhhhhhhhhcCcC-ccc-----------ccccCcc
Confidence 2221211 1111110111112111110000011223556666 46777776543322 111 1113455
Q ss_pred ccccCCCCCCCccc-cccccccccccccCCCCCCCCccccccCCccccCCCccccccccCCCCccCCCCCCcccCCCCCC
Q 005699 239 FQKDAGFNSPPVQL-SRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTDVSEHDDQAAGAPLDK 317 (682)
Q Consensus 239 ~~K~~~~ssp~v~~-~~~~~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d~~~~~~~~~~~~q~~ 317 (682)
.-|.++.++|++.+ +..+++ | +++||.
T Consensus 215 qss~~~~ssp~~~~~~~~~~~---------------------------~------------s~an~~------------- 242 (524)
T KOG0702|consen 215 QSSIAPSSSPPNHQSVPQAYS---------------------------D------------SPANIF------------- 242 (524)
T ss_pred cccccccCCCCccccchhhcc---------------------------c------------cccccc-------------
Confidence 55666666666654 444444 1 344443
Q ss_pred cccCCCCCCCCCCCCccccCCCCCCCCCCCCCCCccccCCCCCCcccccCCCcccccCCCCcCCCCCCCCCccc-ccCCC
Q 005699 318 ISTFPQSHGPVNYGGLDLFEAPVVPETVPSTAPPIDLFQLPETSAASITEQPSTAILNRNPQELSIPKNEGWAT-FDTPP 396 (682)
Q Consensus 318 ~~~~p~~~~~~~~~~~dl~~~~~~~~~~~~~~~~idlfq~p~~~~~~~~~q~~~~~~~~~~~~~~~~~n~gWAt-fD~p~ 396 (682)
.-|+|++|+ ..+..++.||||||+. +|+|.
T Consensus 243 --------------~ge~~k~P~-----------------------------------~~~~~asapk~eg~~s~sd~pv 273 (524)
T KOG0702|consen 243 --------------AGEPFKQPV-----------------------------------SRPSFASAPKNEGWASLSDNPV 273 (524)
T ss_pred --------------ccCCCCCCc-----------------------------------cCccccccccccCCcccccCcc
Confidence 223344442 4566889999999999 78888
Q ss_pred CCCCCCCccCcccccccCCCCCCcCCCCCCCCCCCCCCCccCCCCCCCCCCCCCCCCCCcccccccccccccccccccCC
Q 005699 397 SAASIPGTESLSHAMVPANEGSSVKSDQFPSSNTSMQWPAFQNSGANGPSPSSDPWSGNLHIVQAPAVATSAQVVSAASD 476 (682)
Q Consensus 397 ~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~qw~~~~~s~~~~~~~~~ 476 (682)
.+-..+.. +-++..++. ..||...+..+..|+-|...+.++.+.-... .
T Consensus 274 ne~~~e~~-i~s~~~~~~----f~k~~e~paps~a~qlp~~ss~~~~~q~t~~--------------------------~ 322 (524)
T KOG0702|consen 274 NEAKSENV-ITSPGSFAD----FLKFEEIPAPSVAMQLPPYSSTVDQHQPTIP--------------------------S 322 (524)
T ss_pred cccccccc-ccCcccchh----hcccccccCcchhhhcCCcCCCccccCCCCC--------------------------C
Confidence 64332211 001122222 2677777778888888877766665554221 2
Q ss_pred CCCCCCccccccccccccccccccccccCCccCCCCCCCCCCcccCC-CCCCCCccchhh-cccccCCCCCCcccCCCCC
Q 005699 477 PWPGNLHNGEAPAIATNMQSWNAFDDFTSHLPSEGFKPNSEPHVDAY-MPSPTPDQYLAI-VSQETNDDGNPRVASHDGP 554 (682)
Q Consensus 477 ~w~~~~~~~~~~~~~~~~q~Wnaf~d~~~~~~~~~~~~~~~~~~~~~-~~~~t~~~~~~s-~~qe~~~d~~~~~ap~~~~ 554 (682)
+|.++...+-+.. .-.-+|+++-++++...+++..+-.+++.+.- ..+.++++.+.+ +.+|+-.+..+..++-.+-
T Consensus 323 ~~nd~~ssf~~~~--~Ap~~~~~s~p~i~s~~~s~~~~l~~~~s~~gsa~~~~~~~~~n~~~~e~~~~s~~q~~s~ft~~ 400 (524)
T KOG0702|consen 323 PWNDQGSSFGATP--VAPPLWVASPPSIGSNLLSSSRALAVQSSVFGSAGYVPPHQPVNLGVLEELSNSTTQTFSAFTNE 400 (524)
T ss_pred cccccCccccccc--ccCCccccCCCCccccccccccccccccccccccccCCCCcccccccccccccccccccccccCc
Confidence 4544443331111 22347999999999999999999988873333 337889999999 9999999999988888888
Q ss_pred CCCCCCCCCccCCCCCCCCCCcccccccccCCCCCCCCCCCCCCCccccc-ccccchhhHHhhCCCCCCCCCcCCCCCCC
Q 005699 555 PNMTVPSQADMGPSYNPSMFPLMGQMRTHATEHKSTNPFDFPCDSDLEQN-NMFLDMSSLQAALPNAELPSPFLGGATQS 633 (682)
Q Consensus 555 ~~~~~p~~~~~~psy~~~~~~~~g~~~~~~~~~ks~NPFDlp~dsd~e~~-~mF~DmsSLQaaLP~~~~p~~f~gg~te~ 633 (682)
.-+.+|..+.++|+|+.- .-|-..+.+-.+++.+++|+|||+...+.+ +||.+|+.+|-++| .+++-.+.+|+.+.
T Consensus 401 ~ts~~p~~~~~~pssn~~--~~~~~Q~~~~~~~~g~~~~sl~~~~~~~~P~~~~fa~s~~qp~fP-~qt~~~q~~~~~~~ 477 (524)
T KOG0702|consen 401 STSGFPAPIGMAPSSNHH--QDDEFQPNHRNPQPGAAMSSLPYGFEFASPFDMFFAMSFPQPAFP-IQTPQVQQPGGSHF 477 (524)
T ss_pred ccccCccccccCCccccc--ccccccccccCCCCccccccCCCCCCcCCCccccccccCcCcCCC-CccccccCCCCCCc
Confidence 879999999999999841 223333445555778999999999999999 99999999999999 78888899999999
Q ss_pred CCCCCCCCccccc--cccCCccccccCCCCcccCCCCCCCCcccCCCCCCC
Q 005699 634 WFPQNPVSPFVQA--AAQGGLAYMSGQSPSAQLANIPTQEPVASVGGNPFA 682 (682)
Q Consensus 634 W~pqns~~~yips--~~qGgl~yma~Q~p~~~~~n~~~~~~~a~~~gNPFa 682 (682)
|+.+.....|.|+ -.|+|++||..++-- |.++|.|++|+|+|||.
T Consensus 478 ~~~~~~~p~~~P~~~v~~~G~S~nPF~as~----~S~aq~~~~~p~~nPF~ 524 (524)
T KOG0702|consen 478 GLAGDSKPSYLPAPAVAQAGLSYNPFMASP----NSAAQFPVAFPGTNPFL 524 (524)
T ss_pred cccccCCcccCccccccccccccCccccCC----CCcccccccCCCCCCCC
Confidence 9999999999998 569999999888643 27799999999999995
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=7.3e-36 Score=308.20 Aligned_cols=118 Identities=31% Similarity=0.660 Sum_probs=107.8
Q ss_pred hHHHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCc
Q 005699 5 KEEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGN 81 (682)
Q Consensus 5 k~~Er~ekiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSltLD~Wt~eEV~~Lq~gGN 81 (682)
...++++++|++||+.|+|++|||||+++|+|||+|+|||||++|+||||.|| | |||||+||.|++|+|+.|+.+||
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 45788999999999999999999999999999999999999999999999999 5 99999999999999999999999
Q ss_pred HHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHHhccccCCC
Q 005699 82 QRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGK 125 (682)
Q Consensus 82 ~raN~iyea~~d~~~~~~P~~sd~~~rreFIraKY~eKrF~~~k 125 (682)
.+||++||+.++.. .+.|... +.++.|||+|||+|+|....
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 37889999999999999864
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=5.5e-35 Score=267.40 Aligned_cols=111 Identities=34% Similarity=0.750 Sum_probs=93.0
Q ss_pred HHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC---CceeecccCCCCHHHHHHHHhcCcHHHHHHH
Q 005699 12 KIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREIY 88 (682)
Q Consensus 12 kiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSltLD~Wt~eEV~~Lq~gGN~raN~iy 88 (682)
++|++|++.|+|++|||||+.+|+|||++||||||++|+|+||+|| ++||||+||+|+.+||++|+.+||.++|++|
T Consensus 2 ~~l~~l~~~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~VkSi~~d~w~~~ev~~~~~~GN~~~n~~~ 81 (116)
T PF01412_consen 2 KILRELLKKPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRVKSITMDNWSPEEVQRMREGGNKRANSIW 81 (116)
T ss_dssp HHHHHHHCSTTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--EEETTTS---HHHHHHHHHSHHHHHHHHH
T ss_pred HHHHHHHcCcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhccccccCCCCHHHHHHHHHHChHHHHHHH
Confidence 6899999999999999999999999999999999999999999999 6999999999999999999999999999999
Q ss_pred hhcCccccCCCCCCCchHHHHHHHHHHHHhccccC
Q 005699 89 LKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAG 123 (682)
Q Consensus 89 ea~~d~~~~~~P~~sd~~~rreFIraKY~eKrF~~ 123 (682)
|++.+ ...+++..++.+++++||++||++|+|+.
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 23456667888899999999999999985
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=3.3e-33 Score=254.44 Aligned_cols=106 Identities=31% Similarity=0.701 Sum_probs=97.3
Q ss_pred CCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHHHhhcCccccC
Q 005699 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDWDFQRQ 97 (682)
Q Consensus 21 PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSltLD~Wt~eEV~~Lq~gGN~raN~iyea~~d~~~~ 97 (682)
|+|++|||||+++|+|||++||||||++|+||||+|| | +||||+||+|+++||++|+.+||.++|++||++++....
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 005699 98 RLPDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (682)
Q Consensus 98 ~~P~~sd~~~rreFIraKY~eKrF~~~k~ 126 (682)
+.+...+..++++||++||++|+|+....
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~ 109 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPES 109 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhcccccc
Confidence 55555667889999999999999987644
No 7
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.96 E-value=1.1e-30 Score=275.12 Aligned_cols=118 Identities=24% Similarity=0.575 Sum_probs=104.6
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHH
Q 005699 7 EERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQR 83 (682)
Q Consensus 7 ~Er~ekiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSltLD~Wt~eEV~~Lq~gGN~r 83 (682)
+...++++..|++.++|++|||||+.+|+||++|||||||++||||||+|| | +||||+||.|+.+||++|+.+||.+
T Consensus 4 ~~~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~ 83 (319)
T COG5347 4 KSEDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSN 83 (319)
T ss_pred chHHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchh
Confidence 345677888889999999999999999999999999999999999999999 4 9999999999999999999999999
Q ss_pred HHHHHhhcCccc-cCCCCCCCchHHHHHHHHHHHHhccccCC
Q 005699 84 AREIYLKDWDFQ-RQRLPDNSNVNKVRDFIKNVYVDRRYAGG 124 (682)
Q Consensus 84 aN~iyea~~d~~-~~~~P~~sd~~~rreFIraKY~eKrF~~~ 124 (682)
||+||+++.-.. ..++-...+...+++||+.||++++|...
T Consensus 84 a~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~ 125 (319)
T COG5347 84 ANRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDD 125 (319)
T ss_pred hhhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccc
Confidence 999999986432 12233457788899999999999999876
No 8
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.95 E-value=2.7e-28 Score=255.35 Aligned_cols=86 Identities=33% Similarity=0.690 Sum_probs=81.3
Q ss_pred HHHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHH
Q 005699 7 EERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQR 83 (682)
Q Consensus 7 ~Er~ekiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSltLD~Wt~eEV~~Lq~gGN~r 83 (682)
..|+++.|++|+...+|+.|+||++.+|+|||++||||||++|+|+||.|| | +|||||||+|.+.||++|++|||++
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 457889999999999999999999999999999999999999999999999 4 9999999999999999999999999
Q ss_pred HHHHHhhcC
Q 005699 84 AREIYLKDW 92 (682)
Q Consensus 84 aN~iyea~~ 92 (682)
+++|++..-
T Consensus 83 ~~eFL~s~~ 91 (386)
T KOG0704|consen 83 FREFLSSQG 91 (386)
T ss_pred HHHHHhhCc
Confidence 999988653
No 9
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.94 E-value=4.3e-26 Score=240.32 Aligned_cols=116 Identities=22% Similarity=0.421 Sum_probs=96.6
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHH
Q 005699 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (682)
Q Consensus 11 ekiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSltLD~Wt~eEV~~Lq~gGN~raN~i 87 (682)
.++|++|+++++|++|+|||+++|+|++++||||||++|+||||.|| | +|||++||+|++++|++|+.+||.++|+|
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 HhhcCccc--cCCCCCCCchHHHHHHHHHHHHhccccCCCC
Q 005699 88 YLKDWDFQ--RQRLPDNSNVNKVRDFIKNVYVDRRYAGGKT 126 (682)
Q Consensus 88 yea~~d~~--~~~~P~~sd~~~rreFIraKY~eKrF~~~k~ 126 (682)
|+.+--.. ..+.-..+...++.+.+.+|++++.+..+..
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 98753111 1111123445556666888899998876654
No 10
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.91 E-value=6.3e-25 Score=236.18 Aligned_cols=84 Identities=24% Similarity=0.621 Sum_probs=80.1
Q ss_pred HHHHHHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHH
Q 005699 8 ERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRA 84 (682)
Q Consensus 8 Er~ekiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSltLD~Wt~eEV~~Lq~gGN~ra 84 (682)
...+++++.|+.++.||+|||||+++|+|++|+|||||||+|+++||+|| | +|||..||+|+.+||++|+.|||.+|
T Consensus 8 ~d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA 87 (454)
T KOG0706|consen 8 QDIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANA 87 (454)
T ss_pred hhHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhH
Confidence 44678899999999999999999999999999999999999999999999 5 99999999999999999999999999
Q ss_pred HHHHhhc
Q 005699 85 REIYLKD 91 (682)
Q Consensus 85 N~iyea~ 91 (682)
+.|+..+
T Consensus 88 ~~FFkqh 94 (454)
T KOG0706|consen 88 RVFFKQH 94 (454)
T ss_pred HHHHHHc
Confidence 9999876
No 11
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.89 E-value=7.4e-24 Score=232.43 Aligned_cols=114 Identities=19% Similarity=0.463 Sum_probs=102.5
Q ss_pred HHHHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC---CceeecccCCCCHHHHHHHHhcCcHHHHHH
Q 005699 11 EKIIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREI 87 (682)
Q Consensus 11 ekiLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSltLD~Wt~eEV~~Lq~gGN~raN~i 87 (682)
...|+.|+..+||.+|+||+..+|.||++|+|++||++|+||||.|| +|||+|.||.|..|.+..|..+||+.||++
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 35688999999999999999999999999999999999999999998 499999999999999999999999999999
Q ss_pred HhhcCccccCCCCCCCchHHHHHHHHHHHHhccccCCC
Q 005699 88 YLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGK 125 (682)
Q Consensus 88 yea~~d~~~~~~P~~sd~~~rreFIraKY~eKrF~~~k 125 (682)
||...... .++...+..+++++|||+||++|.|...-
T Consensus 581 WE~~~~G~-~KPs~~s~REEkErwIr~KYeqklFLaPl 617 (749)
T KOG0705|consen 581 WEGSSQGQ-TKPSPDSSREEKERWIRAKYEQKLFLAPL 617 (749)
T ss_pred hhhhccCC-cCCCccccHHHHHHHHHHHHHHHhhcCCC
Confidence 99866544 23334577889999999999999998763
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.79 E-value=2.2e-20 Score=216.51 Aligned_cols=115 Identities=25% Similarity=0.526 Sum_probs=102.3
Q ss_pred HHHHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC---CceeecccCCCCHHHHHHHHhcCcHHHHHHHh
Q 005699 13 IIRGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMSKFTSQEVEALQNGGNQRAREIYL 89 (682)
Q Consensus 13 iLr~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSltLD~Wt~eEV~~Lq~gGN~raN~iye 89 (682)
.+..+.+.++|.+|+|||++.|+|+++|+||.+||+|+||||+|| +||+|++||.|..+.+.+++++||..+|.|||
T Consensus 416 ~~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e 495 (785)
T KOG0521|consen 416 VIEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYE 495 (785)
T ss_pred hhhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhh
Confidence 367888899999999999999999999999999999999999999 49999999999999999999999999999999
Q ss_pred hcCccccCCCCC-CCchHHHHHHHHHHHHhccccCCCCC
Q 005699 90 KDWDFQRQRLPD-NSNVNKVRDFIKNVYVDRRYAGGKTP 127 (682)
Q Consensus 90 a~~d~~~~~~P~-~sd~~~rreFIraKY~eKrF~~~k~~ 127 (682)
+.+.....++|. .++...++.||++||++++|..+...
T Consensus 496 ~~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~ 534 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQ 534 (785)
T ss_pred cccccccccCCCCccchhhhhHhhhcccceeeEeecccc
Confidence 998654333443 45578899999999999999887543
No 13
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.62 E-value=1.3e-16 Score=181.37 Aligned_cols=110 Identities=25% Similarity=0.504 Sum_probs=96.9
Q ss_pred HHHhcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC---CceeecccC--CCCHHHHHHHHhcCcHHHHHHHh
Q 005699 15 RGLMKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT---HRVKSVSMS--KFTSQEVEALQNGGNQRAREIYL 89 (682)
Q Consensus 15 r~Llk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG---hrVKSltLD--~Wt~eEV~~Lq~gGN~raN~iye 89 (682)
.++.....|+.|+|||+..|.||++|++|.||-.|+|-||.|| ++|+|++|| .|+.+-|+++...||.++|.||.
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 3455677899999999999999999999999999999999998 699999998 69999999999999999999999
Q ss_pred hcCccccCCCCCCCchHHHHHHHHHHHHhccccCCC
Q 005699 90 KDWDFQRQRLPDNSNVNKVRDFIKNVYVDRRYAGGK 125 (682)
Q Consensus 90 a~~d~~~~~~P~~sd~~~rreFIraKY~eKrF~~~k 125 (682)
.++.+...-.| .+.+..|++||++||++.+|....
T Consensus 370 ~nl~~~e~lh~-dssp~~r~~fi~~Kykeg~fRk~~ 404 (1186)
T KOG1117|consen 370 GNLPPNEHLHP-DSSPSTRRQFIKEKYKEGKFRKEH 404 (1186)
T ss_pred cCCCCccccCC-CCCcchhhhHHHHHhhcccccccc
Confidence 99866544333 456788999999999999987653
No 14
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.61 E-value=6.9e-17 Score=175.84 Aligned_cols=132 Identities=20% Similarity=0.388 Sum_probs=100.4
Q ss_pred hcCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHHHhhcC-c
Q 005699 18 MKLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYLKDW-D 93 (682)
Q Consensus 18 lk~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSltLD~Wt~eEV~~Lq~gGN~raN~iyea~~-d 93 (682)
++...-+.|+|||+++|.||||+-|+|||.+|..+||.|| | .||+|....|.++.|++.....|..+|.|||..+ +
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 8999999999999999999999999999999886 3
Q ss_pred c----ccCCCCCCCch--HHHHHHHHHHHHhccccCCC-CCCCCCCCcCCCCCCcccccccCC
Q 005699 94 F----QRQRLPDNSNV--NKVRDFIKNVYVDRRYAGGK-TPDKPPKDTQGLGSHLDESRRASS 149 (682)
Q Consensus 94 ~----~~~~~P~~sd~--~~rreFIraKY~eKrF~~~k-~~D~Pp~~~q~l~~~~~e~rr~ss 149 (682)
+ .+.++|...|. -.+.+|||+||+...|+.++ +.|.-.+...++...+...+|+..
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~~~~rDdD~~~~~~LsrQLhasvRt~n 145 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHRLPCRDDDSVTAKDLSKQLHSSVRTGN 145 (669)
T ss_pred chhhhcccCCCCCcCCCCccHHHHHHHHHHheeeeccCCCCCcchhhHHHHHHHHHHHhhccc
Confidence 2 22234444343 24677999999999998743 444333332333334444455543
No 15
>PLN03131 hypothetical protein; Provisional
Probab=97.10 E-value=0.14 Score=59.59 Aligned_cols=65 Identities=32% Similarity=0.393 Sum_probs=32.4
Q ss_pred CCCccccCCCCC-C--------CCCCCCCCCcccc-----CCCCCC--------cccccCCCcccccCCCCcCCCCCCCC
Q 005699 330 YGGLDLFEAPVV-P--------ETVPSTAPPIDLF-----QLPETS--------AASITEQPSTAILNRNPQELSIPKNE 387 (682)
Q Consensus 330 ~~~~dl~~~~~~-~--------~~~~~~~~~idlf-----q~p~~~--------~~~~~~q~~~~~~~~~~~~~~~~~n~ 387 (682)
.+..|||..+-+ | .+-|++-++|||| |.+.++ ++|-++. =++.|...+..+...++
T Consensus 373 a~~vdlf~~s~l~~~p~~n~~q~~qts~p~~~dlfag~~qqq~~~s~~~~~~~~s~pkneg--wa~fd~~~p~~s~~~~~ 450 (705)
T PLN03131 373 APPVDLFEIPPLDPAPAINAYQPPQTSLPSSIDLFGGITQQQSINSLDEKSPELSIPKNEG--WATFDGIQPIASTPGNE 450 (705)
T ss_pred CCcccccccCcccCCCccccCCCCcccCCccccccccccccCccccccccCcccCCccccC--cccccCCCcccccCCcc
Confidence 356677765532 2 3445666789998 333332 2222222 13344445555555555
Q ss_pred CcccccCCC
Q 005699 388 GWATFDTPP 396 (682)
Q Consensus 388 gWAtfD~p~ 396 (682)
.---|-.|.
T Consensus 451 n~t~~~v~~ 459 (705)
T PLN03131 451 NLTPFSIGP 459 (705)
T ss_pred ccccccccc
Confidence 555554444
No 16
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=96.61 E-value=0.012 Score=66.19 Aligned_cols=143 Identities=20% Similarity=0.166 Sum_probs=106.1
Q ss_pred CCCCCCCCCcccchhhhccccccccccCCCCCCCCCCCCCCCCcccCCCCCchhhhhcccccCCCCcccccccccCCCCC
Q 005699 150 YHSYSQSPPYDYQYEDRRYGKLGAVLTRKPGSDRGHYVGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVSSGGDP 229 (682)
Q Consensus 150 ~~s~sqsPp~d~~yedrr~~k~~~~l~Rkpgsd~~~~~Gk~ss~~~sP~r~s~~~~~Dr~a~~~s~~r~sd~s~s~~g~~ 229 (682)
|+++.+.+.|+|.|+.||++|..++ ||=-.=..+ +....+.+.++++-.++..+-+.+....||..+++|..-+++
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 5677888999999999999998633 332121122 224456789999999999999999999999999999988888
Q ss_pred CCCCCCC-CC-ccccCCCCCCCccccccccccccccccCCCCCCCCccccccCCccccCCCccccccccCCCCcc
Q 005699 230 FRPGAQS-PN-FQKDAGFNSPPVQLSRDVSSLKANFKRDVDGIPHPKRTTSLGSMGSFDSNSVSLKSCNSGGLTD 302 (682)
Q Consensus 230 ~k~~~~s-p~-~~K~~~~ssp~v~~~~~~~~~~~~~~~~~~~~~~~qrt~ss~s~~s~~~~~~~~k~~~s~sl~d 302 (682)
.....|+ .| ..|++.+-..-.++ +..+..|+.--.+..||+.....--.++.|.+.+++|+.++|--
T Consensus 77 evs~lQshgNq~~k~i~fkl~D~q~------S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~tr~s~s~ 145 (524)
T KOG0702|consen 77 EVSFLQSHGNQVCKEIWFKLFDFQR------SNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSYTRGSLSE 145 (524)
T ss_pred chHHHhhcchhhhhhhhhcchhhhh------ccCCCcccchhhHHHHhhhhccceeecCcccccccccccccccc
Confidence 8888776 66 66666544433322 23445566666677788888888888888889999999877654
No 17
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=89.75 E-value=0.083 Score=63.41 Aligned_cols=68 Identities=16% Similarity=0.272 Sum_probs=52.6
Q ss_pred CCCCCCCcCCCC-CCCCeeEecchhhhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCcHHHHHHHh
Q 005699 20 LPPNRRCINCNS-LGPQYVCTNFWTFVCMTCSGIHREFT-H--RVKSVSMSKFTSQEVEALQNGGNQRAREIYL 89 (682)
Q Consensus 20 ~PgNk~CaDCGa-~~P~WaSvnfGVFVCi~CSGIHR~LG-h--rVKSltLD~Wt~eEV~~Lq~gGN~raN~iye 89 (682)
...+..|++|++ ..-.|+++++.+.+|+.|+++|+.++ + .++++.|+...+ |..+...||..++..|.
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 445899999997 56899999999999999999999997 3 566666666665 66666666665555543
No 18
>PRK12495 hypothetical protein; Provisional
Probab=77.42 E-value=1.6 Score=45.33 Aligned_cols=38 Identities=18% Similarity=0.203 Sum_probs=28.1
Q ss_pred HHHHHHhc--CCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhh
Q 005699 12 KIIRGLMK--LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIH 53 (682)
Q Consensus 12 kiLr~Llk--~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIH 53 (682)
++-..|++ ...++.|-+||.+=|.+ -|+.+|..|..+-
T Consensus 29 ~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 29 RMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQPV 68 (226)
T ss_pred HHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCcc
Confidence 34344444 45889999999988833 5999999998663
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=75.74 E-value=1.7 Score=32.83 Aligned_cols=40 Identities=15% Similarity=0.421 Sum_probs=33.3
Q ss_pred CCCCCcCCCCCCCCeeEecchhhhhhhhhhh-hhcCCCceeec
Q 005699 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGI-HREFTHRVKSV 63 (682)
Q Consensus 22 gNk~CaDCGa~~P~WaSvnfGVFVCi~CSGI-HR~LGhrVKSl 63 (682)
.+..|..|+.....+.+.+=.++||..|... |+. |+|.+|
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 3678999998878999999999999999987 887 877664
No 20
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=74.64 E-value=1.7e+02 Score=34.93 Aligned_cols=27 Identities=19% Similarity=0.376 Sum_probs=19.8
Q ss_pred CCCCccccCCCCCC---------CCCCCCCCCcccc
Q 005699 329 NYGGLDLFEAPVVP---------ETVPSTAPPIDLF 355 (682)
Q Consensus 329 ~~~~~dl~~~~~~~---------~~~~~~~~~idlf 355 (682)
..+..|||...+.+ .+-|++-++||||
T Consensus 336 ~a~~vdlf~~~~~p~~p~~n~~q~~qts~p~~~~~f 371 (648)
T PLN03119 336 VAQSVDTFQPSIAPRSPPVNLQQAPQTYSFTPANSF 371 (648)
T ss_pred CCccccccccccCCCCCccccCCCccccCCcchhhh
Confidence 34678999966666 4455667899999
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=65.54 E-value=9.6 Score=38.81 Aligned_cols=33 Identities=18% Similarity=0.390 Sum_probs=27.2
Q ss_pred CCCCCCCcCCCCCCC-CeeEecchhhhhhhhhhh
Q 005699 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSGI 52 (682)
Q Consensus 20 ~PgNk~CaDCGa~~P-~WaSvnfGVFVCi~CSGI 52 (682)
.|.-..|+.||..++ .|.+...|.++|.+|...
T Consensus 144 ~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 144 ALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred CcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 466689999998544 678899999999999864
No 22
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=58.96 E-value=7.6 Score=39.70 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=26.8
Q ss_pred CCCCCCCcCCCCCCC-CeeEecchhhhhhhhhh
Q 005699 20 LPPNRRCINCNSLGP-QYVCTNFWTFVCMTCSG 51 (682)
Q Consensus 20 ~PgNk~CaDCGa~~P-~WaSvnfGVFVCi~CSG 51 (682)
.|.-..|+-||.... .|.+..-|.++|..|..
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 456689999998654 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=51.22 E-value=8.6 Score=32.55 Aligned_cols=33 Identities=24% Similarity=0.411 Sum_probs=22.5
Q ss_pred CCCCCCCcCCCCCCC--CeeEecchhhhhhhhhhhh
Q 005699 20 LPPNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIH 53 (682)
Q Consensus 20 ~PgNk~CaDCGa~~P--~WaSvnfGVFVCi~CSGIH 53 (682)
.++...|.+||..=| ++. ..-|+..|+.|...+
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 223778899998754
No 24
>PRK11019 hypothetical protein; Provisional
Probab=47.48 E-value=10 Score=34.37 Aligned_cols=33 Identities=15% Similarity=0.314 Sum_probs=22.9
Q ss_pred CCCCCcCCCCCCC--CeeEecchhhhhhhhhhhhhc
Q 005699 22 PNRRCINCNSLGP--QYVCTNFWTFVCMTCSGIHRE 55 (682)
Q Consensus 22 gNk~CaDCGa~~P--~WaSvnfGVFVCi~CSGIHR~ 55 (682)
.-..|.+||..=| ++.-+. ++-.|++|...+-.
T Consensus 35 syg~C~~CG~~Ip~~Rl~A~P-~a~~Cv~Cq~~~E~ 69 (88)
T PRK11019 35 SLTECEECGEPIPEARRKAIP-GVRLCVACQQEKDL 69 (88)
T ss_pred cCCeeCcCCCcCcHHHHhhcC-CccccHHHHHHHHH
Confidence 4579999998633 333222 67889999987643
No 25
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=47.47 E-value=18 Score=34.52 Aligned_cols=30 Identities=17% Similarity=0.360 Sum_probs=19.3
Q ss_pred CCCcCCCCCCCC-eeEecchhhhhhhhhhhh
Q 005699 24 RRCINCNSLGPQ-YVCTNFWTFVCMTCSGIH 53 (682)
Q Consensus 24 k~CaDCGa~~P~-WaSvnfGVFVCi~CSGIH 53 (682)
.+|.+||.+=|. =.-.--++.+|++|.-.|
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 011122578999999876
No 26
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=43.25 E-value=11 Score=32.95 Aligned_cols=31 Identities=16% Similarity=0.270 Sum_probs=20.4
Q ss_pred CCCCcCCCCCCCCeeE-ecchhhhhhhhhhhh
Q 005699 23 NRRCINCNSLGPQYVC-TNFWTFVCMTCSGIH 53 (682)
Q Consensus 23 Nk~CaDCGa~~P~WaS-vnfGVFVCi~CSGIH 53 (682)
...|.|||..=|.==- .--|+..|+.|...+
T Consensus 34 ~~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 34 VYLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred cccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 4689999986332111 122788999998764
No 27
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=42.22 E-value=13 Score=38.90 Aligned_cols=30 Identities=27% Similarity=0.676 Sum_probs=26.4
Q ss_pred CCCCCCcCCCCCC-CCeeEecchhhhhhhhh
Q 005699 21 PPNRRCINCNSLG-PQYVCTNFWTFVCMTCS 50 (682)
Q Consensus 21 PgNk~CaDCGa~~-P~WaSvnfGVFVCi~CS 50 (682)
+.=..|+.||... +...++-.|-++|.+|.
T Consensus 152 ~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 152 PNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred cchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 4558999999975 57999999999999999
No 28
>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=40.82 E-value=18 Score=35.88 Aligned_cols=42 Identities=12% Similarity=0.218 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCCCCCCcCCCCCC--CCeeEecchhhhhhhhhhhh
Q 005699 10 NEKIIRGLMKLPPNRRCINCNSLG--PQYVCTNFWTFVCMTCSGIH 53 (682)
Q Consensus 10 ~ekiLr~Llk~PgNk~CaDCGa~~--P~WaSvnfGVFVCi~CSGIH 53 (682)
.+++|++|.. ..=..|.+||..= -+.--+. ++-.|+.|...+
T Consensus 74 Ie~AL~Ri~~-G~YG~Ce~CGe~I~~~RL~a~P-~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 74 IEHALQKIEN-GTYGICEVCGKPIPYERLEAIP-TATTCVECQNRK 117 (159)
T ss_pred HHHHHHHHhC-CCCCeecccCCcccHHHHhhCC-CcchhHHHHHHh
Confidence 3444555533 3446899999841 1121122 466899999875
No 29
>PHA00080 DksA-like zinc finger domain containing protein
Probab=40.27 E-value=14 Score=32.15 Aligned_cols=45 Identities=16% Similarity=0.326 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhc---CCCCCCCcCCCCCC--CCeeEecchhhhhhhhhhhh
Q 005699 8 ERNEKIIRGLMK---LPPNRRCINCNSLG--PQYVCTNFWTFVCMTCSGIH 53 (682)
Q Consensus 8 Er~ekiLr~Llk---~PgNk~CaDCGa~~--P~WaSvnfGVFVCi~CSGIH 53 (682)
...+..|...+. ..+...|.+||..= .++.-+. |+..|+.|...+
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 34567899999853 2332222 567799999865
No 30
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=36.88 E-value=19 Score=27.46 Aligned_cols=28 Identities=25% Similarity=0.565 Sum_probs=23.3
Q ss_pred CCCCCCcCCCCCCCCeeEecchhhhhhhhhh
Q 005699 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSG 51 (682)
Q Consensus 21 PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSG 51 (682)
..|..|..|++. |....=|-++|.+|-.
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 8888889999999853
No 31
>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=35.61 E-value=12 Score=28.94 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=20.4
Q ss_pred CCcCCCCCCCCeeEecchhhhhhhhhhh
Q 005699 25 RCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (682)
Q Consensus 25 ~CaDCGa~~P~WaSvnfGVFVCi~CSGI 52 (682)
+|-.||+.. ....-.-|-+||..|.-|
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 445566799999999544
No 32
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=34.91 E-value=46 Score=32.87 Aligned_cols=36 Identities=11% Similarity=0.108 Sum_probs=22.2
Q ss_pred CCCCCCCcCCCCCCCC-eeEecchhhhhhhhhhhhhc
Q 005699 20 LPPNRRCINCNSLGPQ-YVCTNFWTFVCMTCSGIHRE 55 (682)
Q Consensus 20 ~PgNk~CaDCGa~~P~-WaSvnfGVFVCi~CSGIHR~ 55 (682)
.+.-..|-+||..=|. =.-+-=++..|+.|...|-.
T Consensus 108 ~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~ 144 (151)
T PRK10778 108 DEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEI 144 (151)
T ss_pred CCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHH
Confidence 4667999999985110 00011145789999987643
No 33
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=34.87 E-value=24 Score=28.68 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=29.6
Q ss_pred CCCCCcCCCCC-CCCeeEecchh-hhhhhhhhhhhcCC
Q 005699 22 PNRRCINCNSL-GPQYVCTNFWT-FVCMTCSGIHREFT 57 (682)
Q Consensus 22 gNk~CaDCGa~-~P~WaSvnfGV-FVCi~CSGIHR~LG 57 (682)
..+.|..|+.. -|.|=.-..|- +||-.|.-..|..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 35799999985 58898888886 99999998777765
No 34
>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=32.79 E-value=13 Score=28.28 Aligned_cols=27 Identities=30% Similarity=0.599 Sum_probs=16.6
Q ss_pred CCCcCCCCC-CCCeeEecchhhhhhhhh
Q 005699 24 RRCINCNSL-GPQYVCTNFWTFVCMTCS 50 (682)
Q Consensus 24 k~CaDCGa~-~P~WaSvnfGVFVCi~CS 50 (682)
..|.+|+.. .-+|..-+|+.-||..|.
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 578999999999999995
No 35
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=29.00 E-value=41 Score=30.77 Aligned_cols=30 Identities=13% Similarity=0.273 Sum_probs=24.0
Q ss_pred CCCCCCcCCCCCCCCeeEecchhhhhhhhhhh
Q 005699 21 PPNRRCINCNSLGPQYVCTNFWTFVCMTCSGI 52 (682)
Q Consensus 21 PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGI 52 (682)
-.--.|-.|+.. .---+..||+.|..|--.
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 345789999998 555788999999999743
No 36
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=26.87 E-value=22 Score=35.24 Aligned_cols=34 Identities=32% Similarity=0.720 Sum_probs=27.5
Q ss_pred CCCCCCcCCCCCCCCeeEecchhhhh-hhhhhhhhc
Q 005699 21 PPNRRCINCNSLGPQYVCTNFWTFVC-MTCSGIHRE 55 (682)
Q Consensus 21 PgNk~CaDCGa~~P~WaSvnfGVFVC-i~CSGIHR~ 55 (682)
|--+.|+-|| -...|.|++-|.-+| ..|-++|.+
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 677789999998877 579999965
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=25.60 E-value=24 Score=33.06 Aligned_cols=44 Identities=23% Similarity=0.490 Sum_probs=30.0
Q ss_pred cCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcC--C--CceeecccC
Q 005699 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--T--HRVKSVSMS 66 (682)
Q Consensus 19 k~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~L--G--hrVKSltLD 66 (682)
..|.--+|.+||. +..+....+.|-.|.+..-.+ | -+|++|.++
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 3577789999994 223322357899999876454 4 288888764
No 38
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=25.59 E-value=47 Score=29.49 Aligned_cols=31 Identities=16% Similarity=0.613 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhc
Q 005699 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (682)
Q Consensus 22 gNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (682)
..+.|.=||...- ...|||+.|..|.+..|.
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 4677999997654 468999999999998876
No 39
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=24.68 E-value=24 Score=33.01 Aligned_cols=44 Identities=11% Similarity=0.303 Sum_probs=30.5
Q ss_pred cCCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcC--CC--ceeeccc
Q 005699 19 KLPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSM 65 (682)
Q Consensus 19 k~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSltL 65 (682)
..|..-+|.+||.. +....+..+.|-.|.+....+ |. +|++|-+
T Consensus 66 ~~p~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~iEv 113 (114)
T PRK03681 66 EQEAECWCETCQQY---VTLLTQRVRRCPQCHGDMLRIVADDGLQIRRIEI 113 (114)
T ss_pred eeCcEEEcccCCCe---eecCCccCCcCcCcCCCCcEEccCCeEEEEEEEE
Confidence 35778899999962 323344557899999887665 32 7887754
No 40
>COG5145 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]
Probab=23.81 E-value=41 Score=35.53 Aligned_cols=33 Identities=21% Similarity=0.434 Sum_probs=25.5
Q ss_pred CCCCCCCcCCCC--CCCCeeEecchhhhhhhhhhhh
Q 005699 20 LPPNRRCINCNS--LGPQYVCTNFWTFVCMTCSGIH 53 (682)
Q Consensus 20 ~PgNk~CaDCGa--~~P~WaSvnfGVFVCi~CSGIH 53 (682)
..-+.+|++|.. .++.+-+ .||+-||..|+.-|
T Consensus 113 i~~apkC~eC~~IelD~~l~d-~F~~~VC~~Cr~~~ 147 (292)
T COG5145 113 IALAPKCKECLQIELDDELED-TFGISVCRSCRHSM 147 (292)
T ss_pred hhhCccceeeeeeecchHHHh-hhcchhHHhhhhhc
Confidence 347899999997 3444433 58999999999888
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=23.13 E-value=48 Score=29.39 Aligned_cols=31 Identities=13% Similarity=0.485 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhc
Q 005699 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (682)
Q Consensus 22 gNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (682)
.|..|.=||...- ...||++.|..|.+..|.
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997553 468999999999998866
No 42
>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=22.74 E-value=41 Score=27.09 Aligned_cols=26 Identities=23% Similarity=0.631 Sum_probs=19.7
Q ss_pred CCcCCCCCCCCeeEecchhhhhhhhhh
Q 005699 25 RCINCNSLGPQYVCTNFWTFVCMTCSG 51 (682)
Q Consensus 25 ~CaDCGa~~P~WaSvnfGVFVCi~CSG 51 (682)
.|+=|+..... .-.=+|-|||.+|-.
T Consensus 1 ~CiiC~~~~~~-GI~I~~~fIC~~CE~ 26 (46)
T PF10764_consen 1 KCIICGKEKEE-GIHIYGKFICSDCEK 26 (46)
T ss_pred CeEeCCCcCCC-CEEEECeEehHHHHH
Confidence 48889887665 444578999999974
No 43
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.65 E-value=29 Score=32.63 Aligned_cols=44 Identities=18% Similarity=0.310 Sum_probs=28.4
Q ss_pred CCCCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhcC--CC--ceeecccC
Q 005699 20 LPPNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHREF--TH--RVKSVSMS 66 (682)
Q Consensus 20 ~PgNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~L--Gh--rVKSltLD 66 (682)
.|.--+|.+||.. |....+..+.|-.|.+....+ |. +|++|.++
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 4556689999943 222234445699999876555 42 78887653
No 44
>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=22.41 E-value=53 Score=24.75 Aligned_cols=30 Identities=23% Similarity=0.480 Sum_probs=21.8
Q ss_pred CcCCCCC-CCCeeEecchhh-hhhhhhhhhhc
Q 005699 26 CINCNSL-GPQYVCTNFWTF-VCMTCSGIHRE 55 (682)
Q Consensus 26 CaDCGa~-~P~WaSvnfGVF-VCi~CSGIHR~ 55 (682)
|.+|++. -|.|-....|-. ||-.|.-.+|.
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 8999985 699998888877 99999877665
No 45
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=21.51 E-value=1.3e+02 Score=33.46 Aligned_cols=32 Identities=31% Similarity=0.565 Sum_probs=22.8
Q ss_pred CCCCCCcccCCCCCchhhhhcccccCCCCccccccccc
Q 005699 187 VGKISSLVHSPGRMSEQMFEDRFANEGSCSRISDYSVS 224 (682)
Q Consensus 187 ~Gk~ss~~~sP~r~s~~~~~Dr~a~~~s~~r~sd~s~s 224 (682)
-+-+++ |-|+|+. +|.-|-||.-++ |-|-++.
T Consensus 159 cheiqg--yMPgRle---Fd~EymnEaE~p-ikDm~fd 190 (432)
T COG5114 159 CHEIQG--YMPGRLE---FDVEYMNEAEVP-IKDMSFD 190 (432)
T ss_pred hhhhhc--cCCCccc---cchhhhhccccc-ccccccC
Confidence 344444 6799985 778888888888 7776664
No 46
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=21.02 E-value=1.1e+02 Score=28.31 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=17.3
Q ss_pred CCCCCCcCCCCCCCCee-Eecchhhhhhhhh
Q 005699 21 PPNRRCINCNSLGPQYV-CTNFWTFVCMTCS 50 (682)
Q Consensus 21 PgNk~CaDCGa~~P~Wa-SvnfGVFVCi~CS 50 (682)
+.-..|.+||..=|.== -.-=++..|+.|.
T Consensus 78 g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 78 GEYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 45589999998521100 0111456799985
No 47
>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=20.88 E-value=56 Score=29.76 Aligned_cols=31 Identities=19% Similarity=0.495 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEecchhhhhhhhhhhhhc
Q 005699 22 PNRRCINCNSLGPQYVCTNFWTFVCMTCSGIHRE 55 (682)
Q Consensus 22 gNk~CaDCGa~~P~WaSvnfGVFVCi~CSGIHR~ 55 (682)
.+..|.=||...-. ..||++.|..|.+..|.
T Consensus 4 ~~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSSG---IHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCcc---eEECceeehhhHHhhHH
Confidence 46789999986543 57999999999999876
No 48
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=20.57 E-value=54 Score=30.19 Aligned_cols=35 Identities=20% Similarity=0.467 Sum_probs=24.1
Q ss_pred HhcCCCCCCCcCCCCC-------CC----------CeeEecchhhhhhhhhh
Q 005699 17 LMKLPPNRRCINCNSL-------GP----------QYVCTNFWTFVCMTCSG 51 (682)
Q Consensus 17 Llk~PgNk~CaDCGa~-------~P----------~WaSvnfGVFVCi~CSG 51 (682)
..+.++--+|++||.. -| .=+.=.||-.+|.+|..
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 3456777899999974 01 11244689899999974
No 49
>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=20.46 E-value=89 Score=34.12 Aligned_cols=47 Identities=30% Similarity=0.466 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHHhcCcHHHHHHHhhcCccccCCCCCCCchHHHHHHHHHHHHhcc
Q 005699 66 SKFTSQEVEALQNGGNQRAREIYLKDWDFQRQRLPDNSNVNKVRDFIKNVYVDRR 120 (682)
Q Consensus 66 D~Wt~eEV~~Lq~gGN~raN~iyea~~d~~~~~~P~~sd~~~rreFIraKY~eKr 120 (682)
.+.+.+||+.|+.-|-. +++|-++-... .+.=+.+.+|-++||++|+
T Consensus 106 QkLt~eeIe~LK~~g~s-g~eII~kLien-------s~tF~~KT~FSqeKYlkrK 152 (299)
T PF04189_consen 106 QKLTQEEIEELKKEGVS-GEEIIEKLIEN-------SSTFDKKTEFSQEKYLKRK 152 (299)
T ss_pred ccCCHHHHHHHHHcCCC-HHHHHHHHHHh-------ccchhhhhHHHHHHHHHHH
Confidence 46889999999865433 44554432211 1122355679999998865
Done!