Query 005151
Match_columns 711
No_of_seqs 200 out of 1190
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 18:54:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005151.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005151hhsearch_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 1.5E-99 3E-104 831.2 39.5 608 1-683 1-685 (705)
2 PLN03119 putative ADP-ribosyla 100.0 4.3E-81 9.4E-86 681.7 36.2 564 1-679 1-628 (648)
3 KOG0702 Predicted GTPase-activ 100.0 1.3E-48 2.9E-53 421.8 29.7 504 1-631 1-523 (524)
4 KOG0703 Predicted GTPase-activ 100.0 1.2E-36 2.7E-41 314.7 9.1 118 6-126 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 5.1E-35 1.1E-39 267.9 7.9 112 13-125 2-116 (116)
6 smart00105 ArfGap Putative GTP 100.0 1.5E-33 3.3E-38 257.0 9.6 107 22-128 1-110 (112)
7 COG5347 GTPase-activating prot 100.0 9.6E-31 2.1E-35 276.1 12.3 119 9-127 5-127 (319)
8 PLN03114 ADP-ribosylation fact 99.9 2.5E-25 5.5E-30 235.3 16.5 116 12-127 10-130 (395)
9 KOG0704 ADP-ribosylation facto 99.9 1.5E-25 3.3E-30 235.6 6.4 113 8-122 3-124 (386)
10 KOG0705 GTPase-activating prot 99.9 1.5E-24 3.4E-29 238.5 7.4 116 12-128 501-619 (749)
11 KOG0706 Predicted GTPase-activ 99.9 2.1E-23 4.5E-28 225.2 5.9 83 10-92 9-94 (454)
12 KOG0521 Putative GTPase activa 99.8 7.6E-21 1.7E-25 220.5 4.3 115 14-129 416-535 (785)
13 KOG0818 GTPase-activating prot 99.7 2.3E-17 4.9E-22 180.2 3.0 106 20-125 4-119 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 4.6E-17 1E-21 185.4 4.0 110 16-126 290-404 (1186)
15 KOG0702 Predicted GTPase-activ 97.5 0.019 4.1E-07 65.0 22.8 41 517-560 392-432 (524)
16 PLN03131 hypothetical protein; 94.4 0.92 2E-05 53.3 15.0 21 355-375 431-451 (705)
17 KOG0521 Putative GTPase activa 89.6 0.093 2E-06 63.1 -0.4 68 21-90 627-698 (785)
18 PF00643 zf-B_box: B-box zinc 81.2 0.89 1.9E-05 34.6 1.5 39 24-64 3-42 (42)
19 PRK00085 recO DNA repair prote 72.8 4.3 9.3E-05 41.6 4.1 38 16-53 137-179 (247)
20 PRK12495 hypothetical protein; 71.8 2.5 5.4E-05 44.3 2.1 29 21-53 39-67 (226)
21 COG1734 DksA DnaK suppressor p 64.2 3 6.5E-05 39.9 0.9 44 11-54 65-111 (120)
22 TIGR00613 reco DNA repair prot 60.7 4.9 0.00011 41.0 1.8 32 22-53 145-177 (241)
23 COG1381 RecO Recombinational D 56.0 5.5 0.00012 41.9 1.2 37 15-51 141-182 (251)
24 TIGR02419 C4_traR_proteo phage 48.1 8.8 0.00019 32.7 1.0 33 21-54 28-62 (63)
25 KOG0119 Splicing factor 1/bran 47.5 5.6E+02 0.012 30.5 18.6 39 605-648 482-520 (554)
26 PF01286 XPA_N: XPA protein N- 46.6 6 0.00013 30.3 -0.2 27 25-51 4-31 (34)
27 TIGR02890 spore_yteA sporulati 43.2 14 0.00031 36.8 1.8 42 12-54 75-117 (159)
28 PLN03119 putative ADP-ribosyla 43.0 3E+02 0.0065 33.2 12.3 8 355-362 391-398 (648)
29 PF11781 RRN7: RNA polymerase 42.3 13 0.00027 28.6 1.0 28 22-52 6-33 (36)
30 PRK11019 hypothetical protein; 41.2 16 0.00035 33.4 1.7 32 24-56 36-69 (88)
31 PF08271 TF_Zn_Ribbon: TFIIB z 40.1 9.6 0.00021 29.7 0.0 27 26-53 2-28 (43)
32 PHA00080 DksA-like zinc finger 36.9 16 0.00036 31.9 1.0 32 22-54 29-62 (72)
33 PRK10778 dksA RNA polymerase-b 36.8 20 0.00042 35.6 1.6 36 21-56 108-144 (151)
34 PF14376 Haem_bd: Haem-binding 32.6 25 0.00054 34.0 1.5 25 10-38 31-55 (137)
35 PRK13715 conjugal transfer pro 32.5 18 0.00038 31.9 0.5 30 25-54 35-65 (73)
36 cd00194 UBA Ubiquitin Associat 31.6 5.2 0.00011 29.7 -2.6 27 178-205 5-31 (38)
37 PRK03681 hypA hydrogenase nick 30.6 16 0.00035 34.3 -0.1 43 21-66 67-113 (114)
38 KOG4368 Predicted RNA binding 29.9 2.6E+02 0.0055 33.8 9.1 16 172-187 643-658 (757)
39 TIGR00100 hypA hydrogenase nic 29.6 23 0.00051 33.2 0.8 43 21-67 67-113 (115)
40 KOG2236 Uncharacterized conser 29.3 1.3E+02 0.0029 35.0 6.6 29 300-328 211-239 (483)
41 smart00401 ZnF_GATA zinc finge 28.7 28 0.00061 28.5 1.0 36 23-58 2-39 (52)
42 KOG2199 Signal transducing ada 28.6 1.5E+02 0.0032 34.2 6.7 15 657-671 437-451 (462)
43 PRK00564 hypA hydrogenase nick 26.4 23 0.00051 33.4 0.2 44 21-67 68-115 (117)
44 KOG3362 Predicted BBOX Zn-fing 26.0 22 0.00048 35.4 -0.0 33 23-56 117-150 (156)
45 PF01258 zf-dskA_traR: Prokary 25.4 11 0.00023 28.5 -1.8 30 25-54 4-34 (36)
46 COG1997 RPL43A Ribosomal prote 25.3 50 0.0011 30.5 2.0 30 22-53 33-62 (89)
47 cd07173 NR_DBD_AR DNA-binding 25.1 42 0.00092 30.0 1.5 31 23-56 2-32 (82)
48 PRK00420 hypothetical protein; 24.3 97 0.0021 29.6 3.8 46 6-54 3-50 (112)
49 COG2158 Uncharacterized protei 23.4 32 0.0007 32.7 0.5 23 36-58 52-76 (112)
50 PRK12380 hydrogenase nickel in 23.2 38 0.00082 31.8 0.9 42 21-66 67-112 (113)
51 PRK00762 hypA hydrogenase nick 22.6 35 0.00075 32.6 0.6 46 21-67 67-119 (124)
52 KOG2057 Predicted equilibrativ 22.1 1.2E+03 0.026 26.6 13.0 19 350-368 369-389 (499)
53 PRK11295 hypothetical protein; 21.6 85 0.0018 30.1 2.9 32 2-33 2-33 (113)
54 cd06968 NR_DBD_ROR DNA-binding 21.4 46 0.001 30.5 1.1 31 23-56 4-34 (95)
55 TIGR02420 dksA RNA polymerase- 21.3 48 0.001 30.8 1.2 31 22-52 78-109 (110)
56 cd07171 NR_DBD_ER DNA-binding 21.2 49 0.0011 29.5 1.2 31 23-56 2-32 (82)
57 PRK03824 hypA hydrogenase nick 20.8 50 0.0011 31.9 1.3 25 43-67 106-134 (135)
58 PRK13844 recombination protein 20.8 68 0.0015 33.4 2.3 42 7-56 39-81 (200)
59 PF12156 ATPase-cat_bd: Putati 20.8 1.5E+02 0.0032 26.8 4.1 31 26-56 2-38 (88)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.5e-99 Score=831.23 Aligned_cols=608 Identities=34% Similarity=0.516 Sum_probs=490.6
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCCcceeecccccCCHHHHHHHHhc
Q 005151 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (711)
Q Consensus 1 m~sr~keder~ekiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LGHrVKSLsLD~Wt~eEVe~m~~g 80 (711)
|++| |++|+++++|++|++.++|++|+||++++|+|||+|||||||++|+||||+|+||||||+||+|+++||++|+.+
T Consensus 1 m~Sk-kqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSGIHRsLghRVKSVTLD~WtdeEV~~Mk~g 79 (705)
T PLN03131 1 MGSR-KEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSGIHREFTHRVKSVSMSKFTSQDVEALQNG 79 (705)
T ss_pred Ccch-HHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchhhhcccCcccccccCCCCCHHHHHHHHHh
Confidence 8999 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHHHhhcCCCCCCCCCCCchHHHHHHHHHHHhhhcccccCCCCCCCCCCCCCCCcccccccc-cCCCCCCCCCCC
Q 005151 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPPY 159 (711)
Q Consensus 81 GN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIr~KYveKrF~~e~~~DkPpRl~~gd~eds~e~Rr-~~~qs~SRSppy 159 (711)
||+++|+|||++|+..+++.|+.++.+++|+|||.|||+|+|+.....++|++....-+.+..|+|| ++|++|+|||+|
T Consensus 80 GN~~AN~iyeanwd~~r~~lP~~sd~ekrr~FIR~KYVeKRFa~~~s~d~pprd~q~~r~~e~e~rr~~syh~~SqSPpY 159 (705)
T PLN03131 80 GNQRAREIYLKDWDQQRQRLPDNSKVDKIREFIKDIYVDKKYAGGKTHDKPPRDLQRIRSHEDETRRACSYHSYSQSPPY 159 (705)
T ss_pred ccHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhhhcCCCCCCCchhhhhhhcccccccccccccCCCcCCCc
Confidence 9999999999999987777888888888999999999999999999999999887666777779999 999999999999
Q ss_pred cchhh-cccccCCCCCCCCccccccCCCCCCCCCchhhh--cccCCCccCCCCCCccccccccccccCCCC---CCCCcc
Q 005151 160 EDTYE-RRYNEQSSPGGRSDDKNSRYGYDERSPGNEQEN--RQFGDYRRTSPTRPEVINDWRRDDRFGNGR---KFEDRR 233 (711)
Q Consensus 160 ~d~~e-rRy~~rss~~~R~~dkl~rmgy~d~~~~~d~l~--~~~Gd~~r~sP~r~e~v~d~~~~Dr~~~~~---~~~~~r 233 (711)
+++|| ||||++..+++|+ +++|+.. +++|+|+| ||+|+ +|||+||||+++. +++|++
T Consensus 160 ~~~yedrRygk~~~~~~R~-------------pg~d~~~~~~k~~~~~~-SP~r~---~d~~~eDrf~ne~~~~r~~d~s 222 (705)
T PLN03131 160 DFQYEDRRYGKQAGILTRK-------------PGSDRGLNVGKMASFIC-SPTRL---NDRMFEDRFANEGSVSGVSDYS 222 (705)
T ss_pred ccccccccccccccccccC-------------Ccccccccccccccccc-Cchhh---hhhhhhcccccCCCCccccccc
Confidence 99998 6899988888877 7777764 99999999 99996 9999999999996 677777
Q ss_pred cCCCC--CCcCCCCCCCCCCCCCCCCCccCchhhhcCCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCChh
Q 005151 234 ISDGD--SKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQA 311 (711)
Q Consensus 234 ~s~~~--~~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~~ 311 (711)
+|+++ .+.+.+|||++||+.. || +|||+|+||||||++|||++|+|++..++++|.+++|||+|+|+++|++|+++
T Consensus 223 ~ss~~~~~r~~~~SP~~~k~~~~-Sp-~v~p~r~ilg~n~~~~~v~~~s~~~~~~~~~~~~~~Qrt~Ssgs~gS~dg~s~ 300 (705)
T PLN03131 223 VSSGGDLVRSGAESPNFQKDIAF-SP-PIQPPKDILGEDVQQRRIDLFSAALCKQGAEGCPHIQRSASLGSIGSFDSLSV 300 (705)
T ss_pred ccccccccccCCCCCCcccccCC-CC-CcccchhhccccccccccCCCcccccccccccccccccccccCcccccCCCcc
Confidence 77655 4557799999999874 45 66999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCccccCCCCCCCChhhhhhhhhhhcccccccCCCCCCCCCccccCCcCcccccCCCCCChhHHHhhccCCCCC
Q 005151 312 EVKLETTGSLIDFDADPKPSPAVAQAQQKTVAQSVVQPASSANDNNWASFDLAPQVKVSQTSSNLNTLETVFSQLSVPAS 391 (711)
Q Consensus 312 ~~k~~~s~sLiDf~~~~e~~~~~~~~~qt~~~~~~~~~~~s~~~~~wAsfd~~~~~~~~~~~~~~n~le~~l~qls~~~s 391 (711)
++|+++++|||||++|+|+..+. .|.++..... .......|+-|.+-..-++.+..+. .--.-|+||+..+.
T Consensus 301 s~Ks~~s~sL~D~~~e~~~~~~~---~q~k~~~~~~----~~~~~~~~s~d~f~~~v~p~~~~~~-a~pIDLFqlp~ts~ 372 (705)
T PLN03131 301 SIKSFNSGSLADIVAEAEQAAGN---HQDKMPAFPR----MAGSGSHASLDHFKAPVAPEAAAPM-APPIDLFQLPATSP 372 (705)
T ss_pred ceeecccccccccccCccccccc---cccccCCccc----ccccccccccccccccccccccccc-CCchhhhhccCCCC
Confidence 99999999999999999987653 3333222211 1334555565555444333333221 12456899999999
Q ss_pred CCCCCcCCCCCCCCCcccCCCcccccCCCCCCCcccCCCccccccccCCCCCccccccccCCCCCCCCCCCCCCCCcccc
Q 005151 392 VPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLPVSV 471 (711)
Q Consensus 392 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~f~~s~~s~~s~~~~~~~~~~~ 471 (711)
+|.++.+.++ + +- ...++.++.+++.|++ ....++.-+
T Consensus 373 a~~vdlf~~s--------~----------------l~---------------~~p~~n~~q~~qts~p---~~~dlfag~ 410 (705)
T PLN03131 373 APPVDLFEIP--------P----------------LD---------------PAPAINAYQPPQTSLP---SSIDLFGGI 410 (705)
T ss_pred CCcccccccC--------c----------------cc---------------CCCccccCCCCcccCC---ccccccccc
Confidence 9998888773 0 00 0112234445555554 455667788
Q ss_pred CCCCCCcccCCC---CCcCCCCCCccccccCCCCc--cCCCC------------------------Ccc---ccccccC-
Q 005151 472 NAGNSFSMQHQP---PLFPTAGGQFTASQFTPPVA--GSSNN------------------------QQW---NTSLAQN- 518 (711)
Q Consensus 472 ~~~q~~~~q~qq---~~f~~~~~~~~~q~~t~~~~--~~~nn------------------------Q~w---~~~~~q~- 518 (711)
++||..+..||. .-.|+++||.++...++++. +..|= ..| +..+.|+
T Consensus 411 ~qqq~~~s~~~~~~~~s~pknegwa~fd~~~p~~s~~~~~n~t~~~v~~~~~~~~~~d~v~~~~~~~q~Pp~~~~~~~~s 490 (705)
T PLN03131 411 TQQQSINSLDEKSPELSIPKNEGWATFDGIQPIASTPGNENLTPFSIGPSMAGSANFDQVPSLDKGMQWPPFQNSSDEES 490 (705)
T ss_pred cccCccccccccCcccCCccccCcccccCCCcccccCCcccccccccccccccCcchhhccccccccccCCCcccccccc
Confidence 888877755555 77899999999864444442 22222 234 3333344
Q ss_pred -CCCCCCCCCCCCCCCcccccCC--------------CCCCCCCCccccccCCccCcccccccccCCCCCCCCCCccCCC
Q 005151 519 -AQGPPAAQPAQSVPKPALESAS--------------GGLSQPSPVEVKSTGRTALPEDLFTANYSSFPASVPGWQTVPP 583 (711)
Q Consensus 519 -~~~~p~~~~~~~~~~~~~~~~~--------------~~~s~~~~~e~k~sgrkeLP~DlFt~~y~~~p~~vpGwq~~pp 583 (711)
++..||....+.|-++.+++.- .+.+....+|....--+.-.+|.|.....+......|.|+..|
T Consensus 491 ~s~~~pW~~~~~~V~~~~~~~~q~WnAF~~~ds~~~~~l~~~~~~s~~q~~~~~~~t~~q~~~~~~~~d~~~d~~~r~~p 570 (705)
T PLN03131 491 ASGPAPWLGDLHNVEAPDNTSAQNWNAFEFDDSVAGIPLEGIKQSSEPQTAANMPPTADQLIGCKALEDFNKDGIKRTAP 570 (705)
T ss_pred cccCCcccccchhcccCCccCccccccccccccccccccccccccccccccccCCCCcccccccccccccccccccccCC
Confidence 4556788888999998875421 2345556677777777888888999999999999999999999
Q ss_pred CCc----eeceeccCCC-------------CCCCcccccCCCCCCCCCCCCCCccccCCCCcccccccCCCCCCCCCCCC
Q 005151 584 HGM----VYAMQYNTAA-------------PMPNFVHSKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLR 646 (711)
Q Consensus 584 ~gm----g~~mqy~~~~-------------p~~~~~~~~ks~NPFD~~~~~~~~Q~~~fPsm~~lqgalp~~~~~~~~~~ 646 (711)
+|| ||+.+-...+ .|++--+..||+|||||.+|....+.-||-.|.+||+|||+. .++
T Consensus 571 ~~~~~~~g~~~~~~~~~~ps~~~~~~~~~~~~~s~~~~~ks~npfdl~~dsd~~~~~mf~d~sslq~~lp~~-----~~~ 645 (705)
T PLN03131 571 HGQGELPGLDEPSDILAEPSYTPPAHPIMEHAQSHANDHKSINPFDLPYDSDLEPGNMFLDMSSLEAALPDA-----HLP 645 (705)
T ss_pred CCCcCCCCCCCCCccccCCCCCccccccccccccccCccCCCCCcCCccccccCcccceeehHHHHhhcCCC-----CCc
Confidence 999 5555532222 344445678999999999999999999999999999999965 344
Q ss_pred CC-CC-CCCCCCCCCCCC-CCCCCCCCCCccccccCCCCC
Q 005151 647 TS-SL-TPSPAWMPPQAS-PYPSAMPSQMPTYAAAIPSQM 683 (711)
Q Consensus 647 ss-~~-~~s~~~~~~~~~-~y~~~~~~~~~~~~~~~~~~~ 683 (711)
+. +| +.+..|++.-+. +|+++.|+++++|||+..+..
T Consensus 646 ~~f~g~~~tepw~~~~~~~~yip~~pqggl~y~agq~~~~ 685 (705)
T PLN03131 646 SAFLGSGMTEPWFPQDLAMTYIPAAPQGGLAYMAGQAPNP 685 (705)
T ss_pred hhhhcCCCCCccccCCCcccccCCCCCCCchhhcccCCcc
Confidence 45 56 788999999876 999999999999999775554
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=4.3e-81 Score=681.69 Aligned_cols=564 Identities=31% Similarity=0.444 Sum_probs=423.0
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCCcceeecccccCCHHHHHHHHhc
Q 005151 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (711)
Q Consensus 1 m~sr~keder~ekiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LGHrVKSLsLD~Wt~eEVe~m~~g 80 (711)
|++| |++||++++|++|+++++|++|+||+..+|+|||+|||||||++|+||||+|+||||||+||+|+++||++|+.+
T Consensus 1 M~SK-R~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSGIHRsLGhRVKSLSLDkWT~EEVe~Mk~g 79 (648)
T PLN03119 1 MGSK-REEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSGIHREFTHRVKSVSMSKFTSKEVEVLQNG 79 (648)
T ss_pred Ccch-HHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchhhhccCCceeeccccCCCCHHHHHHHHHh
Confidence 8999 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChHHHHHHHhhcCCCCCCCCCCCchHHHHHHHHHHHhhhcccccCCCCCCCCCCCCCCCcccccccc-cCCCCCCCCCCC
Q 005151 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPPY 159 (711)
Q Consensus 81 GN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIr~KYveKrF~~e~~~DkPpRl~~gd~eds~e~Rr-~~~qs~SRSppy 159 (711)
||+++|+|||++|+..+++.|...+.+++|+|||.|||+|+|+.....+++++.....+....+.|+ ++|+++++|++|
T Consensus 80 GN~~AN~iyeanw~~~~~~~P~~sD~e~lr~FIR~KYVeKRF~~~~~~d~p~~~~~~~~~~~~~~~~~~s~h~~s~sp~y 159 (648)
T PLN03119 80 GNQRAREIYLKNWDHQRQRLPENSNAERVREFIKNVYVQKKYAGANDADKPSKDSQDHVSSEDMTRRANSYHSYSQSPPY 159 (648)
T ss_pred chHHHHHHHHhhcccccCCCCCCccHHHHHHHHHHHHhhhhccCcCCCCCCcccccccccccccccccccCCCCCCCCCc
Confidence 9999999999999887677788778888999999999999999999999988754344444446788 999999999999
Q ss_pred cchhh-cccccCCCCCCCCccccccCCCCCCCCCchhh-hcccCCCccCCCCCCccccccccccccCCCCCCCCcccCCC
Q 005151 160 EDTYE-RRYNEQSSPGGRSDDKNSRYGYDERSPGNEQE-NRQFGDYRRTSPTRPEVINDWRRDDRFGNGRKFEDRRISDG 237 (711)
Q Consensus 160 ~d~~e-rRy~~rss~~~R~~dkl~rmgy~d~~~~~d~l-~~~~Gd~~r~sP~r~e~v~d~~~~Dr~~~~~~~~~~r~s~~ 237 (711)
++.|| ||||++...+.|| ++.|+. .+++++|.+ ||+|+ +|||+||||.||.... |+||.
T Consensus 160 ~~~ye~rr~~~~~~~~~~~-------------~~s~r~~~~k~~~~~~-s~~~~---~~~m~ed~f~~e~~~~--r~sd~ 220 (648)
T PLN03119 160 DYQYEERRYGKIPLGFTGK-------------SASVKGLHAKASSFVY-SPGRF---SDHMFEDQFSNEDSAP--RASDY 220 (648)
T ss_pred ccchhhhhccccccccccC-------------CCccccccccccceee-ccchH---HHHhhhhhcccCCCCC--ccccc
Confidence 99998 9999999999998 777776 599999999 99999 8999999999998544 99873
Q ss_pred ------C-CCcCCCCCCCCCCCCCCCCCccCchhhhcCCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCCh
Q 005151 238 ------D-SKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQ 310 (711)
Q Consensus 238 ------~-~~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~ 310 (711)
+ .+.+.+||+++ |.++++||+.+ .++++.. ..--..++.|||+|+|+++|+|++.
T Consensus 221 s~ss~g~~~~~~~~sp~~~-~~~~~~~~~~~-~~~~~~~----------------~~~~~~~~sqRT~SsGs~gSfDs~s 282 (648)
T PLN03119 221 SVSSAGDPFRSDIQSPNFQ-QEAEFRSPQFQ-HSNAPPS----------------ENLFPGRQHQRTTSSGSVRSVDSNF 282 (648)
T ss_pred ccccCCcccccCcCCCCcc-cccccCCcccc-cccCcch----------------hhccccccccccccccccccccccc
Confidence 3 56677999999 55566665555 5554310 0001146789999999999999999
Q ss_pred hhhhhhccCccccCCCCCCCChhhhhhhhhhhcccccccCCCCCCCCCccccCCcCcccccCCCCCChhHHHhhccCCCC
Q 005151 311 AEVKLETTGSLIDFDADPKPSPAVAQAQQKTVAQSVVQPASSANDNNWASFDLAPQVKVSQTSSNLNTLETVFSQLSVPA 390 (711)
Q Consensus 311 ~~~k~~~s~sLiDf~~~~e~~~~~~~~~qt~~~~~~~~~~~s~~~~~wAsfd~~~~~~~~~~~~~~n~le~~l~qls~~~ 390 (711)
+++|++++++|.|+..|.+..-+. .|.++.. | +..+.++ ..- -..|+||+..+
T Consensus 283 ~S~ks~~Sg~l~d~~~E~~~~~~~---~q~~~~~----------------~-----~P~~~~~-~aa--pIDLFqlp~ts 335 (648)
T PLN03119 283 MSIKSYTSGGLGEAVSESRQNTGS---QQGKTSN----------------H-----VPLVAES-TKA--PIDLFQLPGAP 335 (648)
T ss_pred ccccccccCCcccccccccccccc---cccccCC----------------C-----Ccccccc-cCC--chhhhhccCCC
Confidence 999999999999999999876553 2322221 2 1112111 111 35689999999
Q ss_pred CCCCCCcCCCCCCCCCcccCCCcccccCCCCCCCcccCCCccccccccCCCCCccccccccCCCCCCCCCCCCCCCCccc
Q 005151 391 SVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLPVS 470 (711)
Q Consensus 391 s~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~f~~s~~s~~s~~~~~~~~~~ 470 (711)
.+|+++.+.++ ++ |...++..+.+++.+++++-. + +.-
T Consensus 336 ~a~~vdlf~~~-------------------~~--------------------p~~p~~n~~q~~qts~p~~~~--~-f~~ 373 (648)
T PLN03119 336 VAQSVDTFQPS-------------------IA--------------------PRSPPVNLQQAPQTYSFTPAN--S-FAG 373 (648)
T ss_pred CCccccccccc-------------------cC--------------------CCCCccccCCCccccCCcchh--h-hhc
Confidence 99999998874 00 112223445566666554221 2 223
Q ss_pred cCCCCCCcccCCC-CCcCCCCCCccccccCCCCccCCCC---------------------Ccc---cccccc--CCCCCC
Q 005151 471 VNAGNSFSMQHQP-PLFPTAGGQFTASQFTPPVAGSSNN---------------------QQW---NTSLAQ--NAQGPP 523 (711)
Q Consensus 471 ~~~~q~~~~q~qq-~~f~~~~~~~~~q~~t~~~~~~~nn---------------------Q~w---~~~~~q--~~~~~p 523 (711)
+++||-. +-++ .-.|+++||.++.+.++++-+..|= ..| +....| .++..|
T Consensus 374 ~~qqq~~--~~~~~~s~pkneGWA~fd~p~~s~~~~~ni~~~~~~~~~~~~d~v~~~~~~mq~Pp~~~~~~~~s~s~~~p 451 (648)
T PLN03119 374 NLGQQPT--SRPSELSAPKNEGWASFDNPMPAAKSTNVITSPGDFQLELKIEEILQPSTSMQLPPYPSTVDQHALSIPSP 451 (648)
T ss_pred ccccCcc--cCccccccccccCcccccccccccCCcccccCccccccCcchhhhcccccccccCCCcccccccccccCCc
Confidence 3333322 2333 6788999999987655555443221 233 122222 345567
Q ss_pred CCCCCCCCCCcccccCC-----CCCCCC---------CCccccccCCccCcccccccccCCCCCCCCCCccCC-CCCc-e
Q 005151 524 AAQPAQSVPKPALESAS-----GGLSQP---------SPVEVKSTGRTALPEDLFTANYSSFPASVPGWQTVP-PHGM-V 587 (711)
Q Consensus 524 ~~~~~~~~~~~~~~~~~-----~~~s~~---------~~~e~k~sgrkeLP~DlFt~~y~~~p~~vpGwq~~p-p~gm-g 587 (711)
|....+.|.++.+++.- +-.-.+ ...+....--+--.+|.|.....+...+..|.|+.. |+|| |
T Consensus 452 W~~~~~~V~~~~~~~~q~WnAF~ds~~~~~l~~~~~~~~~~~~~~~~~~~t~~q~~~~r~~ed~~~dg~qr~~~p~g~~g 531 (648)
T PLN03119 452 WQEDLSNVLKDVVDNPQPWNAFPDSIEANPLDSSRNIHQQVDGASTSSYNTDHQHLESQVLEELSNDGTQTTRIPAGSSA 531 (648)
T ss_pred hhccchhcccCcccCccccccchhhhccCccccccccccccccccccCCCCcccccccccccccccccccccccCCCCCC
Confidence 77788888888755421 000001 111112222244445666677777778899999999 8888 4
Q ss_pred eceeccCCCCCCCccc-------ccCCCCCCCCCCCCCCccccCCCCcccccccCCCCCCCCCCCCCC-CCCCCCCCCCC
Q 005151 588 YAMQYNTAAPMPNFVH-------SKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS-SLTPSPAWMPP 659 (711)
Q Consensus 588 ~~mqy~~~~p~~~~~~-------~~ks~NPFD~~~~~~~~Q~~~fPsm~~lqgalp~~~~~~~~~~ss-~~~~s~~~~~~ 659 (711)
|+.+-...++ |+|.- ..||+|||||.+|....+.-||-.|.+||++||+. .++++ +|+.+..|++.
T Consensus 532 ~~~~~~~~~~-Ps~~~~~~~~~~~~ks~npfdl~~~sd~~~~~mf~d~tslq~~lp~~-----~~~~~~~~~~t~~w~~~ 605 (648)
T PLN03119 532 FGFPGNIGMA-PSYSEEAWQHVNEQKSANPFDLPYDSEFDSNDMFLDMSSLQGALPDI-----QTPQAFLNGVSQPWLAA 605 (648)
T ss_pred CCCCCccccC-CCCCchhccccccccCCCCcCCccccccCcccceeehHHHHhhcCCC-----CCchhhhcCCCcccccC
Confidence 5555444332 56644 44999999999999999999999999999999963 34555 78999999999
Q ss_pred CCC-CCCCCCC--CCCccccccC
Q 005151 660 QAS-PYPSAMP--SQMPTYAAAI 679 (711)
Q Consensus 660 ~~~-~y~~~~~--~~~~~~~~~~ 679 (711)
-+. .|+++.| ++++.|+++.
T Consensus 606 ~~~~~yip~~~~~qggl~y~~~q 628 (648)
T PLN03119 606 DSVPSYLPAPAVAQGGLAYMAGQ 628 (648)
T ss_pred CCcccccCCCccccCCchhhhcc
Confidence 866 9999955 8888888854
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.3e-48 Score=421.77 Aligned_cols=504 Identities=29% Similarity=0.367 Sum_probs=363.9
Q ss_pred CcchhhhhHHH-HHHHHHHHcCCCCCCCcCCCCCCC-CeeEccchhhhhhhhhhhhccCC--cceeecccccCCHHHHHH
Q 005151 1 MANRLKEDEKN-ERIIRGLLKLQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIHREFT--HRVKSVSMAKFTSQEVKA 76 (711)
Q Consensus 1 m~sr~keder~-ekiLr~Llk~PgNk~CADCGs~~P-~WaSiNfGVFVCi~CSGIHR~LG--HrVKSLsLD~Wt~eEVe~ 76 (711)
|++++||+|+. |++||+|+++|+|++|++|+...+ +|+++.-|-|||+.|+|+-|.|. ||||+|+|.+|++.||..
T Consensus 1 ~a~~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~qevs~ 80 (524)
T KOG0702|consen 1 YAGYKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQEVSF 80 (524)
T ss_pred CCcccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCCccccceeeeeeccccchHH
Confidence 78999999998 999999999999999999999988 99999999999999999999996 999999999999999999
Q ss_pred HHhcChHHHHHHHhhcCCCCCCCCCCCchHHHHHHHHHHHhhhcccccCCCCCCCCCCCCCCCcccccccccCCCCCCCC
Q 005151 77 LQEGGNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRRDTYQGGSRS 156 (711)
Q Consensus 77 m~~gGN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIr~KYveKrF~~e~~~DkPpRl~~gd~eds~e~Rr~~~qs~SRS 156 (711)
|+.+||+.+++||++-.+.++--.||+.|.+++|+||+.|||.|+|+.+....+-+... | ...+.++
T Consensus 81 lQshgNq~~k~i~fkl~D~q~S~vPD~rn~~~~kef~q~~y~~kr~~v~~n~~k~~s~t----------r---~s~s~~s 147 (524)
T KOG0702|consen 81 LQSHGNQVCKEIWFKLFDFQRSNVPDSRNPQKVKEFQQEKYVKKRYYVPKNQMKIPSYT----------R---GSLSEDS 147 (524)
T ss_pred HhhcchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCcccccccccc----------c---ccccccC
Confidence 99999999999999999988888899999999999999999999999776544422211 1 0112223
Q ss_pred CCCcchhhcccccCCCCCCCCccccccCCCCCCCCCchhhh--cccCCCccCCCCCCccccccccccccCCCCCCCCccc
Q 005151 157 PPYEDTYERRYNEQSSPGGRSDDKNSRYGYDERSPGNEQEN--RQFGDYRRTSPTRPEVINDWRRDDRFGNGRKFEDRRI 234 (711)
Q Consensus 157 ppy~d~~erRy~~rss~~~R~~dkl~rmgy~d~~~~~d~l~--~~~Gd~~r~sP~r~e~v~d~~~~Dr~~~~~~~~~~r~ 234 (711)
+++.+. |...+-+|..++|+.+...... -+...+-+ +|.|||+|+||+ |+|+.-+.
T Consensus 148 ~~~~~s-------------~~~~~~lrs~~gd~~P~~~~~t~np~~~~~~~-~~~~~~~~~~rf--dlfg~~k~------ 205 (524)
T KOG0702|consen 148 RPVSES-------------RPETKSLRSLLGDHAPLLAESTKNPRSRGLPK-SPIRFEIVDDRF--DLFGLPKA------ 205 (524)
T ss_pred Cccccc-------------CCCccccccccCCCCcchhhcccCccccCCCC-CCchhhhhhhhh--hhhcCcCc------
Confidence 444433 3333444455566556554333 44567888 999999876655 56654332
Q ss_pred CCCCCCcCCCCCCCCCCCCCCCCCccCchhhhcCCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCChhhhh
Q 005151 235 SDGDSKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQAEVK 314 (711)
Q Consensus 235 s~~~~~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~~~~k 314 (711)
+| -..++...-|+++.++|+..+++++|+++-+-.|+++|+.|....+...+++..---..+.+..+.+.++.+.+
T Consensus 206 sd----~~s~s~~qss~~~~ssp~~~~~~~~~~~~s~an~~~ge~~k~P~~~~~~asapk~eg~~s~sd~pvne~~~e~~ 281 (524)
T KOG0702|consen 206 SD----AQSQSTFQSSIAPSSSPPNHQSVPQAYSDSPANIFAGEPFKQPVSRPSFASAPKNEGWASLSDNPVNEAKSENV 281 (524)
T ss_pred cc----ccccCcccccccccCCCCccccchhhcccccccccccCCCCCCccCccccccccccCCcccccCcccccccccc
Confidence 22 23457778899999999999999999999999999999999999999999888765555557889999999999
Q ss_pred hhccCccccCCCCCCCCh--hhhhhhhhhhcccccccCC-CCCCCCCccccCCcCcccccC---CCCCChhHHHhhccCC
Q 005151 315 LETTGSLIDFDADPKPSP--AVAQAQQKTVAQSVVQPAS-SANDNNWASFDLAPQVKVSQT---SSNLNTLETVFSQLSV 388 (711)
Q Consensus 315 ~~~s~sLiDf~~~~e~~~--~~~~~~qt~~~~~~~~~~~-s~~~~~wAsfd~~~~~~~~~~---~~~~n~le~~l~qls~ 388 (711)
..+..+++||+...|-++ ++.+.+--+..+.+.|+.+ +..+++|++|+.++....... ++..+.|.+.+.+|.|
T Consensus 282 i~s~~~~~~f~k~~e~paps~a~qlp~~ss~~~~~q~t~~~~~nd~~ssf~~~~~Ap~~~~~s~p~i~s~~~s~~~~l~~ 361 (524)
T KOG0702|consen 282 ITSPGSFADFLKFEEIPAPSVAMQLPPYSSTVDQHQPTIPSPWNDQGSSFGATPVAPPLWVASPPSIGSNLLSSSRALAV 361 (524)
T ss_pred ccCcccchhhcccccccCcchhhhcCCcCCCccccCCCCCCcccccCcccccccccCCccccCCCCcccccccccccccc
Confidence 999999999998887652 2212221111122223333 456899999999887755433 3566777788888888
Q ss_pred CCCCCCCCcCCCCCCCCCcccCCCcccccCCCCCCCcccCCCccccccccCCCCCccccccccCCCCCCCCCCCCCCCCc
Q 005151 389 PASVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLP 468 (711)
Q Consensus 389 ~~s~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~s~f~~s~~s~~s~~~~~~~~ 468 (711)
.++++|+. +.+.+++++-.+++- -
T Consensus 362 ~~s~~gsa-------------------------~~~~~~~~~n~~~~e-------------------------------~ 385 (524)
T KOG0702|consen 362 QSSVFGSA-------------------------GYVPPHQPVNLGVLE-------------------------------E 385 (524)
T ss_pred cccccccc-------------------------ccCCCCccccccccc-------------------------------c
Confidence 87776521 122223322211100 0
Q ss_pred cccCCCCCCcccCCC--CCcCCCCCCccccccCCCCccCCCCCccccccccCCCCCCCCCCCCCCCCcccccCCCCCCCC
Q 005151 469 VSVNAGNSFSMQHQP--PLFPTAGGQFTASQFTPPVAGSSNNQQWNTSLAQNAQGPPAAQPAQSVPKPALESASGGLSQP 546 (711)
Q Consensus 469 ~~~~~~q~~~~q~qq--~~f~~~~~~~~~q~~t~~~~~~~nnQ~w~~~~~q~~~~~p~~~~~~~~~~~~~~~~~~~~s~~ 546 (711)
..+...|.++-+.+. .+||++-|. +.+. ++|-.+ -.+..+.+.-+ + .
T Consensus 386 ~~~s~~q~~s~ft~~~ts~~p~~~~~-----------~pss-------n~~~~~---~~Q~~~~~~~~--g--------~ 434 (524)
T KOG0702|consen 386 LSNSTTQTFSAFTNESTSGFPAPIGM-----------APSS-------NHHQDD---EFQPNHRNPQP--G--------A 434 (524)
T ss_pred cccccccccccccCcccccCcccccc-----------CCcc-------cccccc---cccccccCCCC--c--------c
Confidence 112223333333332 555554443 1111 112222 12222222211 1 2
Q ss_pred CCccccccCCccCc-ccccccccCCCCCCCCCCccCCCCCceecee-ccCCCCCCC--cccccCCCCCCCCCCCCCCccc
Q 005151 547 SPVEVKSTGRTALP-EDLFTANYSSFPASVPGWQTVPPHGMVYAMQ-YNTAAPMPN--FVHSKSTTNPFDVNNDSHPVQA 622 (711)
Q Consensus 547 ~~~e~k~sgrkeLP-~DlFt~~y~~~p~~vpGwq~~pp~gmg~~mq-y~~~~p~~~--~~~~~ks~NPFD~~~~~~~~Q~ 622 (711)
...+.+..++.++| .++|++.|.-...|+++||...++||+|+|+ |.+....|+ .++.-+|+|||+.+-. .+.|.
T Consensus 435 ~~~sl~~~~~~~~P~~~~fa~s~~qp~fP~qt~~~q~~~~~~~~~~~~~~p~~~P~~~v~~~G~S~nPF~as~~-S~aq~ 513 (524)
T KOG0702|consen 435 AMSSLPYGFEFASPFDMFFAMSFPQPAFPIQTPQVQQPGGSHFGLAGDSKPSYLPAPAVAQAGLSYNPFMASPN-SAAQF 513 (524)
T ss_pred ccccCCCCCCcCCCccccccccCcCcCCCCccccccCCCCCCccccccCCcccCccccccccccccCccccCCC-Ccccc
Confidence 34678889999999 9999999999889999999999999999999 888887666 9999999999999754 34455
Q ss_pred cC-CCCcccc
Q 005151 623 QT-FPSMASL 631 (711)
Q Consensus 623 ~~-fPsm~~l 631 (711)
+. ||+|.++
T Consensus 514 ~~~~p~~nPF 523 (524)
T KOG0702|consen 514 PVAFPGTNPF 523 (524)
T ss_pred cccCCCCCCC
Confidence 43 7888765
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.2e-36 Score=314.69 Aligned_cols=118 Identities=28% Similarity=0.588 Sum_probs=107.4
Q ss_pred hhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcCh
Q 005151 6 KEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGN 82 (711)
Q Consensus 6 keder~ekiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN 82 (711)
...++++++|++||+.++|+.|||||+++|+|||+|+|||||++|+||||.|| | |||||+||.|++|+|+.|+..||
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 45678999999999999999999999999999999999999999999999998 5 99999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCCCCCCchHHHHHHHHHHHhhhcccccCC
Q 005151 83 QRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (711)
Q Consensus 83 ~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIr~KYveKrF~~e~ 126 (711)
.+||++||++++.. ...|..+ +.++.|||+|||.|+|+.+.
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 99999999997664 4445432 36789999999999999865
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=5.1e-35 Score=267.92 Aligned_cols=112 Identities=34% Similarity=0.706 Sum_probs=92.1
Q ss_pred HHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC---cceeecccccCCHHHHHHHHhcChHHHHHHH
Q 005151 13 RIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEVL 89 (711)
Q Consensus 13 kiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG---HrVKSLsLD~Wt~eEVe~m~~gGN~~aN~i~ 89 (711)
++|+.|++.++|++|||||+.+|+|||++||||||++|+|+||+|| |+||||+||+|+++||++|+.+||.++|++|
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 hhcCCCCCCCCCCCchHHHHHHHHHHHhhhcccccC
Q 005151 90 LKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (711)
Q Consensus 90 Ea~~~~~~~p~Pdssd~~~lreFIr~KYveKrF~~e 125 (711)
|++.... .+.+..++.+.+++||++||++++|+.+
T Consensus 82 e~~~~~~-~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 82 EANSPPP-KKPPPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp TTTSTTT-TTHCTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred HcCCCCC-CCCCCCCcHHHHHHHHHHHHHhhhhccC
Confidence 9983333 3445567778889999999999999853
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=1.5e-33 Score=257.01 Aligned_cols=107 Identities=28% Similarity=0.631 Sum_probs=98.1
Q ss_pred CCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcChHHHHHHHhhcCCCCCC
Q 005151 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEWDPQRQ 98 (711)
Q Consensus 22 PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~i~Ea~~~~~~~ 98 (711)
|+|++||||++.+|+|||++||||||++|+||||+|| | +||||+||+|++++|++|+.+||.++|++||++++....
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 5 699999999999999999999999999999999987655
Q ss_pred CCCCCchHHHHHHHHHHHhhhcccccCCCC
Q 005151 99 SFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (711)
Q Consensus 99 p~Pdssd~~~lreFIr~KYveKrF~~e~~~ 128 (711)
+.|..++.+.+++||+.||++|+|+.++..
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 556666677888999999999999987654
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=9.6e-31 Score=276.09 Aligned_cols=119 Identities=21% Similarity=0.531 Sum_probs=103.0
Q ss_pred HHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcChHHH
Q 005151 9 EKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRA 85 (711)
Q Consensus 9 er~ekiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN~~a 85 (711)
...+++|..|.+.++|+.|||||+.+|+|||+|||||||++||||||+|| | +||||+||+|+++||++|+.+||.+|
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 34567788888899999999999999999999999999999999999999 4 99999999999999999999999999
Q ss_pred HHHHhhcCCCC-CCCCCCCchHHHHHHHHHHHhhhcccccCCC
Q 005151 86 KEVLLKEWDPQ-RQSFPDSSNVERLRNFIKHVYVDRRYTGERN 127 (711)
Q Consensus 86 N~i~Ea~~~~~-~~p~Pdssd~~~lreFIr~KYveKrF~~e~~ 127 (711)
|+|||++.-.. ..+.-...|...+++||++||++++|.....
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~ 127 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSS 127 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccccc
Confidence 99999876442 1222234456678899999999999998744
No 8
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.93 E-value=2.5e-25 Score=235.29 Aligned_cols=116 Identities=23% Similarity=0.400 Sum_probs=97.0
Q ss_pred HHHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcChHHHHHH
Q 005151 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (711)
Q Consensus 12 ekiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~i 88 (711)
.++|++|++.++|++|+||++.+|+||++|||||||++|+||||.|| | +||||+||+|++++|++|+.+||.++|+|
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 55799999999999999999999999999999999999999999998 4 89999999999999999999999999999
Q ss_pred HhhcCCCCC--CCCCCCchHHHHHHHHHHHhhhcccccCCC
Q 005151 89 LLKEWDPQR--QSFPDSSNVERLRNFIKHVYVDRRYTGERN 127 (711)
Q Consensus 89 ~Ea~~~~~~--~p~Pdssd~~~lreFIr~KYveKrF~~e~~ 127 (711)
|+.+.-... ...-..+....+-+.+.+|++++.+..+..
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 987532111 111123455555556889999999986654
No 9
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.91 E-value=1.5e-25 Score=235.59 Aligned_cols=113 Identities=28% Similarity=0.548 Sum_probs=92.3
Q ss_pred hHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcChHH
Q 005151 8 DEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQR 84 (711)
Q Consensus 8 der~ekiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN~~ 84 (711)
+-++++.|+.|....+|+.|+||++.+|+|||++||||||++|+|+||.|| | +|||||||+|.+.||++|+.+||++
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 346778888888888999999999999999999999999999999999999 5 9999999999999999999999999
Q ss_pred HHHHHhhcCC------CCCCCCCCCchHHHHHHHHHHHhhhccc
Q 005151 85 AKEVLLKEWD------PQRQSFPDSSNVERLRNFIKHVYVDRRY 122 (711)
Q Consensus 85 aN~i~Ea~~~------~~~~p~Pdssd~~~lreFIr~KYveKrF 122 (711)
+++|++..-. .+.++ ++.-....|+-|.+.-+.+.|
T Consensus 83 ~~eFL~s~~~~~e~~~i~eKY--ns~aAa~yRdki~~laegr~w 124 (386)
T KOG0704|consen 83 FREFLSSQGIYKETWPIREKY--NSRAAALYRDKIAALAEGREW 124 (386)
T ss_pred HHHHHhhCccccccccHHHhh--ccHHHHHHHHHHHHHhcCCcc
Confidence 9999986421 11111 122234456667776666666
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.90 E-value=1.5e-24 Score=238.46 Aligned_cols=116 Identities=23% Similarity=0.472 Sum_probs=106.9
Q ss_pred HHHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC---cceeecccccCCHHHHHHHHhcChHHHHHH
Q 005151 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (711)
Q Consensus 12 ekiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG---HrVKSLsLD~Wt~eEVe~m~~gGN~~aN~i 88 (711)
...|+.|.+.+||..|+||+.++|.|+++|+|+++|++|+||||.|| +||++|.||.|..|.+.+|..+||+.||++
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 45678888899999999999999999999999999999999999998 399999999999999999999999999999
Q ss_pred HhhcCCCCCCCCCCCchHHHHHHHHHHHhhhcccccCCCC
Q 005151 89 LLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (711)
Q Consensus 89 ~Ea~~~~~~~p~Pdssd~~~lreFIr~KYveKrF~~e~~~ 128 (711)
||.....+.+|.|+++.++ +|+||++||++|.|......
T Consensus 581 WE~~~~G~~KPs~~s~REE-kErwIr~KYeqklFLaPl~~ 619 (749)
T KOG0705|consen 581 WEGSSQGQTKPSPDSSREE-KERWIRAKYEQKLFLAPLPC 619 (749)
T ss_pred hhhhccCCcCCCccccHHH-HHHHHHHHHHHHhhcCCCCC
Confidence 9998888888888887755 58899999999999987665
No 11
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.88 E-value=2.1e-23 Score=225.18 Aligned_cols=83 Identities=22% Similarity=0.584 Sum_probs=79.2
Q ss_pred HHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcChHHHH
Q 005151 10 KNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAK 86 (711)
Q Consensus 10 r~ekiLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN~~aN 86 (711)
....+++.|...++|+.|+|||+++|+|++|+|||||||+|+++||+|| | +|||..||+|+.+||..|+.+||.+|+
T Consensus 9 d~~~vfkkLRs~~~NKvCFDCgAknPtWaSVTYGIFLCiDCSAvHRnLGVHiSFVRSTnLDsWs~~qLR~M~~GGN~nA~ 88 (454)
T KOG0706|consen 9 DIQTVFKKLRSQSENKVCFDCGAKNPTWASVTYGIFLCIDCSAVHRNLGVHISFVRSTNLDSWSWEQLRRMQVGGNANAR 88 (454)
T ss_pred hHHHHHHHHhcCCCCceecccCCCCCCceeecceEEEEEecchhhhccccceEEEeecccccCCHHHHhHhhhcCchhHH
Confidence 3467899999999999999999999999999999999999999999999 5 999999999999999999999999999
Q ss_pred HHHhhc
Q 005151 87 EVLLKE 92 (711)
Q Consensus 87 ~i~Ea~ 92 (711)
.|+..+
T Consensus 89 ~FFkqh 94 (454)
T KOG0706|consen 89 VFFKQH 94 (454)
T ss_pred HHHHHc
Confidence 999865
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.81 E-value=7.6e-21 Score=220.50 Aligned_cols=115 Identities=22% Similarity=0.451 Sum_probs=101.4
Q ss_pred HHHHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcChHHHHHHHh
Q 005151 14 IIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLL 90 (711)
Q Consensus 14 iLr~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~i~E 90 (711)
.+..+...++|..|+|||++.|+|+++|+||.+||+|+||||+|| | ||+||+||.|..+.+.+|+++||..+|.|||
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 4 9999999999999999999999999999999
Q ss_pred hcCCCCC--CCCCCCchHHHHHHHHHHHhhhcccccCCCCC
Q 005151 91 KEWDPQR--QSFPDSSNVERLRNFIKHVYVDRRYTGERNYD 129 (711)
Q Consensus 91 a~~~~~~--~p~Pdssd~~~lreFIr~KYveKrF~~e~~~D 129 (711)
+.+.... ++.+.++ ...++.||++||++++|..+....
T Consensus 496 ~~l~~~~~~~~~~~~~-~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 496 ALLPSYDSSKPTASSS-RQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred cccccccccCCCCccc-hhhhhHhhhcccceeeEeecccch
Confidence 9887543 4444443 556788999999999998776543
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.66 E-value=2.3e-17 Score=180.16 Aligned_cols=106 Identities=20% Similarity=0.443 Sum_probs=90.6
Q ss_pred cCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcChHHHHHHHhhcC-CC
Q 005151 20 KLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEW-DP 95 (711)
Q Consensus 20 k~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~i~Ea~~-~~ 95 (711)
+...-+.|+|||.++|.|+|+|-|+|||.+|..+||.|| | .||+|....|.++.|++...+.|..+|.|||..+ ++
T Consensus 4 ~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld~ 83 (669)
T KOG0818|consen 4 RLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLDP 83 (669)
T ss_pred cchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccCc
Confidence 445567999999999999999999999999999999999 4 8999999999999999999999999999999765 22
Q ss_pred ------CCCCCCCCchHHHHHHHHHHHhhhcccccC
Q 005151 96 ------QRQSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (711)
Q Consensus 96 ------~~~p~Pdssd~~~lreFIr~KYveKrF~~e 125 (711)
.+++.|...-.....+|||+||+...|+.+
T Consensus 84 st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~ 119 (669)
T KOG0818|consen 84 ATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHR 119 (669)
T ss_pred hhhhcccCCCCCcCCCCccHHHHHHHHHHheeeecc
Confidence 245555543333457899999999999984
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.65 E-value=4.6e-17 Score=185.44 Aligned_cols=110 Identities=26% Similarity=0.534 Sum_probs=99.4
Q ss_pred HHHHcCCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccCC---cceeecccc--cCCHHHHHHHHhcChHHHHHHHh
Q 005151 16 RGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMA--KFTSQEVKALQEGGNQRAKEVLL 90 (711)
Q Consensus 16 r~Llk~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~LG---HrVKSLsLD--~Wt~eEVe~m~~gGN~~aN~i~E 90 (711)
.++.....|+.|+||++..|.||++|++|.||-.|+|-||.|| ++|+|++|| .|+.+.|+++..+||.++|.||-
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 5567788999999999999999999999999999999999998 699999999 69999999999999999999999
Q ss_pred hcCCCCCCCCCCCchHHHHHHHHHHHhhhcccccCC
Q 005151 91 KEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (711)
Q Consensus 91 a~~~~~~~p~Pdssd~~~lreFIr~KYveKrF~~e~ 126 (711)
.++++...-.|+++- ..+++||+.||.+.+|..+.
T Consensus 370 ~nl~~~e~lh~dssp-~~r~~fi~~Kykeg~fRk~~ 404 (1186)
T KOG1117|consen 370 GNLPPNEHLHPDSSP-STRRQFIKEKYKEGKFRKEH 404 (1186)
T ss_pred cCCCCccccCCCCCc-chhhhHHHHHhhcccccccc
Confidence 999887777777654 45688999999999998653
No 15
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=97.51 E-value=0.019 Score=65.01 Aligned_cols=41 Identities=10% Similarity=0.054 Sum_probs=24.1
Q ss_pred cCCCCCCCCCCCCCCCCcccccCCCCCCCCCCccccccCCccCc
Q 005151 517 QNAQGPPAAQPAQSVPKPALESASGGLSQPSPVEVKSTGRTALP 560 (711)
Q Consensus 517 q~~~~~p~~~~~~~~~~~~~~~~~~~~s~~~~~e~k~sgrkeLP 560 (711)
|+...+-+++++.....-+... ..+.+..+|....+|+++|
T Consensus 392 q~~s~ft~~~ts~~p~~~~~~p---ssn~~~~~~~Q~~~~~~~~ 432 (524)
T KOG0702|consen 392 QTFSAFTNESTSGFPAPIGMAP---SSNHHQDDEFQPNHRNPQP 432 (524)
T ss_pred cccccccCcccccCccccccCC---cccccccccccccccCCCC
Confidence 6665665555553332222222 2456677788888888887
No 16
>PLN03131 hypothetical protein; Provisional
Probab=94.38 E-value=0.92 Score=53.31 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=14.2
Q ss_pred CCCCccccCCcCcccccCCCC
Q 005151 355 DNNWASFDLAPQVKVSQTSSN 375 (711)
Q Consensus 355 ~~~wAsfd~~~~~~~~~~~~~ 375 (711)
+.+||+||...+-..++...|
T Consensus 431 negwa~fd~~~p~~s~~~~~n 451 (705)
T PLN03131 431 NEGWATFDGIQPIASTPGNEN 451 (705)
T ss_pred ccCcccccCCCcccccCCccc
Confidence 789999997665544444444
No 17
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=89.56 E-value=0.093 Score=63.13 Aligned_cols=68 Identities=16% Similarity=0.266 Sum_probs=54.4
Q ss_pred CCCCCCCcCCCCC-CCCeeEccchhhhhhhhhhhhccCC-c--ceeecccccCCHHHHHHHHhcChHHHHHHHh
Q 005151 21 LQDNRRCINCNSL-GTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLL 90 (711)
Q Consensus 21 ~PgNk~CADCGs~-~P~WaSiNfGVFVCi~CSGIHR~LG-H--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~i~E 90 (711)
...+..|++|++. .-.|+|+|+.+-+|+.|+++|+.++ | .+.++.|++..+ |..+...||..++..|.
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 4457899999984 7899999999999999999999996 4 667777777666 77777667666665554
No 18
>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=81.19 E-value=0.89 Score=34.58 Aligned_cols=39 Identities=15% Similarity=0.475 Sum_probs=33.3
Q ss_pred CCCCcCCCCCCCCeeEccchhhhhhhhhhh-hccCCcceeec
Q 005151 24 NRRCINCNSLGTQYVCTNFWTFVCTNCSGI-HREFTHRVKSV 64 (711)
Q Consensus 24 Nk~CADCGs~~P~WaSiNfGVFVCi~CSGI-HR~LGHrVKSL 64 (711)
+..|..|......|.+.+=.++||..|... |+. |+|..|
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~--H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG--HKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT--SEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCCC--CEEeEC
Confidence 578999999889999999999999999998 877 877664
No 19
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=72.85 E-value=4.3 Score=41.56 Aligned_cols=38 Identities=26% Similarity=0.471 Sum_probs=29.2
Q ss_pred HHHHcC----CCCCCCcCCCCCCC-CeeEccchhhhhhhhhhh
Q 005151 16 RGLLKL----QDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGI 53 (711)
Q Consensus 16 r~Llk~----PgNk~CADCGs~~P-~WaSiNfGVFVCi~CSGI 53 (711)
.+|++. |.-..|+-||.... .|.+..-|.|+|..|...
T Consensus 137 ~~lL~~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~~ 179 (247)
T PRK00085 137 LRLLAELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGDP 179 (247)
T ss_pred HHHHHHcCCccchhhHhcCCCCCCceEEecccCCcccccccCc
Confidence 355553 44569999998754 789999999999999733
No 20
>PRK12495 hypothetical protein; Provisional
Probab=71.83 E-value=2.5 Score=44.29 Aligned_cols=29 Identities=17% Similarity=0.239 Sum_probs=23.8
Q ss_pred CCCCCCCcCCCCCCCCeeEccchhhhhhhhhhh
Q 005151 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (711)
Q Consensus 21 ~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGI 53 (711)
...+..|-+||.+-|.+ -|+.+|..|..+
T Consensus 39 tmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred ccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 45678999999998832 599999999865
No 21
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=64.19 E-value=3 Score=39.89 Aligned_cols=44 Identities=14% Similarity=0.250 Sum_probs=26.3
Q ss_pred HHHHHHHHHcCCCC--CCCcCCCCCCC-CeeEccchhhhhhhhhhhh
Q 005151 11 NERIIRGLLKLQDN--RRCINCNSLGT-QYVCTNFWTFVCTNCSGIH 54 (711)
Q Consensus 11 ~ekiLr~Llk~PgN--k~CADCGs~~P-~WaSiNfGVFVCi~CSGIH 54 (711)
..++-..|.+.... .+|.+||.+=| .=.-..-+..+|+.|.-.|
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 38999999622 1222334678999999876
No 22
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=60.66 E-value=4.9 Score=40.96 Aligned_cols=32 Identities=22% Similarity=0.508 Sum_probs=26.3
Q ss_pred CCCCCCcCCCCCCC-CeeEccchhhhhhhhhhh
Q 005151 22 QDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGI 53 (711)
Q Consensus 22 PgNk~CADCGs~~P-~WaSiNfGVFVCi~CSGI 53 (711)
|.-..|+.||..++ .|.+...|.|+|.+|...
T Consensus 145 p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 145 LDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred cccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 45579999998543 688999999999999864
No 23
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=55.96 E-value=5.5 Score=41.88 Aligned_cols=37 Identities=22% Similarity=0.454 Sum_probs=29.1
Q ss_pred HHHHHcC----CCCCCCcCCCCCC-CCeeEccchhhhhhhhh
Q 005151 15 IRGLLKL----QDNRRCINCNSLG-TQYVCTNFWTFVCTNCS 51 (711)
Q Consensus 15 Lr~Llk~----PgNk~CADCGs~~-P~WaSiNfGVFVCi~CS 51 (711)
..+||.. +.=..|+.||... +..+++-.|-+||.+|.
T Consensus 141 el~lL~~~G~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 141 ELKLLGELGIGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHHHHHcCCccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 3455553 2336999999985 57999999999999999
No 24
>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=48.08 E-value=8.8 Score=32.70 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=22.7
Q ss_pred CCCCCCCcCCCCCCC--CeeEccchhhhhhhhhhhh
Q 005151 21 LQDNRRCINCNSLGT--QYVCTNFWTFVCTNCSGIH 54 (711)
Q Consensus 21 ~PgNk~CADCGs~~P--~WaSiNfGVFVCi~CSGIH 54 (711)
.++...|.|||..=| .|. ..-|+..|+.|...+
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 455679999999633 222 234788999998754
No 25
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=47.46 E-value=5.6e+02 Score=30.52 Aligned_cols=39 Identities=28% Similarity=0.375 Sum_probs=24.7
Q ss_pred cCCCCCCCCCCCCCCccccCCCCcccccccCCCCCCCCCCCCCC
Q 005151 605 KSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS 648 (711)
Q Consensus 605 ~ks~NPFD~~~~~~~~Q~~~fPsm~~lqgalp~~~~~~~~~~ss 648 (711)
-.++-|||-. .|+.--|.+-.-.|+-..|+++.+|.+.+
T Consensus 482 ~~~~pp~~r~-----a~~~a~Pg~p~~~~~~~~vPpp~g~~p~~ 520 (554)
T KOG0119|consen 482 TTSIPPGDRQ-----AQAAAPPGAPFHGGNYNAVPPPPGLQPAN 520 (554)
T ss_pred cccCCccccc-----ccccCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence 3666777764 24444466666666766677777777765
No 26
>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=46.60 E-value=6 Score=30.34 Aligned_cols=27 Identities=30% Similarity=0.653 Sum_probs=16.8
Q ss_pred CCCcCCCCC-CCCeeEccchhhhhhhhh
Q 005151 25 RRCINCNSL-GTQYVCTNFWTFVCTNCS 51 (711)
Q Consensus 25 k~CADCGs~-~P~WaSiNfGVFVCi~CS 51 (711)
..|.+|+.. .=.|..-+|+.-||.+|.
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 479999996 578999999999999995
No 27
>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=43.25 E-value=14 Score=36.81 Aligned_cols=42 Identities=12% Similarity=0.177 Sum_probs=23.7
Q ss_pred HHHHHHHHcCCCCCCCcCCCCCC-CCeeEccchhhhhhhhhhhh
Q 005151 12 ERIIRGLLKLQDNRRCINCNSLG-TQYVCTNFWTFVCTNCSGIH 54 (711)
Q Consensus 12 ekiLr~Llk~PgNk~CADCGs~~-P~WaSiNfGVFVCi~CSGIH 54 (711)
+++|.+| ....=.+|.+||..= ..=.-+--++-.|+.|...+
T Consensus 75 e~AL~Ri-~~G~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 75 EHALQKI-ENGTYGICEVCGKPIPYERLEAIPTATTCVECQNRK 117 (159)
T ss_pred HHHHHHH-hCCCCCeecccCCcccHHHHhhCCCcchhHHHHHHh
Confidence 3344444 223335899999861 11111222556999999865
No 28
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=43.03 E-value=3e+02 Score=33.22 Aligned_cols=8 Identities=63% Similarity=1.415 Sum_probs=7.6
Q ss_pred CCCCcccc
Q 005151 355 DNNWASFD 362 (711)
Q Consensus 355 ~~~wAsfd 362 (711)
+.+||+||
T Consensus 391 neGWA~fd 398 (648)
T PLN03119 391 NEGWASFD 398 (648)
T ss_pred ccCccccc
Confidence 78999999
No 29
>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=42.34 E-value=13 Score=28.63 Aligned_cols=28 Identities=21% Similarity=0.515 Sum_probs=23.3
Q ss_pred CCCCCCcCCCCCCCCeeEccchhhhhhhhhh
Q 005151 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSG 52 (711)
Q Consensus 22 PgNk~CADCGs~~P~WaSiNfGVFVCi~CSG 52 (711)
..|..|..|++. |...+=|-++|.+|-.
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCce
Confidence 346679999998 8888899999999954
No 30
>PRK11019 hypothetical protein; Provisional
Probab=41.24 E-value=16 Score=33.37 Aligned_cols=32 Identities=13% Similarity=0.163 Sum_probs=22.5
Q ss_pred CCCCcCCCCCCC--CeeEccchhhhhhhhhhhhcc
Q 005151 24 NRRCINCNSLGT--QYVCTNFWTFVCTNCSGIHRE 56 (711)
Q Consensus 24 Nk~CADCGs~~P--~WaSiNfGVFVCi~CSGIHR~ 56 (711)
-..|.|||..=| .|.- --++-.|+.|...+-.
T Consensus 36 yg~C~~CG~~Ip~~Rl~A-~P~a~~Cv~Cq~~~E~ 69 (88)
T PRK11019 36 LTECEECGEPIPEARRKA-IPGVRLCVACQQEKDL 69 (88)
T ss_pred CCeeCcCCCcCcHHHHhh-cCCccccHHHHHHHHH
Confidence 469999999743 2322 2377899999987643
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=40.09 E-value=9.6 Score=29.69 Aligned_cols=27 Identities=30% Similarity=0.563 Sum_probs=20.9
Q ss_pred CCcCCCCCCCCeeEccchhhhhhhhhhh
Q 005151 26 RCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (711)
Q Consensus 26 ~CADCGs~~P~WaSiNfGVFVCi~CSGI 53 (711)
+|-.||+.. ......-|-+||..|--|
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 699999977 455667899999999544
No 32
>PHA00080 DksA-like zinc finger domain containing protein
Probab=36.93 E-value=16 Score=31.93 Aligned_cols=32 Identities=16% Similarity=0.270 Sum_probs=21.4
Q ss_pred CCCCCCcCCCCCCC--CeeEccchhhhhhhhhhhh
Q 005151 22 QDNRRCINCNSLGT--QYVCTNFWTFVCTNCSGIH 54 (711)
Q Consensus 22 PgNk~CADCGs~~P--~WaSiNfGVFVCi~CSGIH 54 (711)
.+...|.|||..=| .|.- .-++..|+.|...+
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a-~P~~~~Cv~Cq~~~ 62 (72)
T PHA00080 29 PSATHCEECGDPIPEARREA-VPGCRTCVSCQEIL 62 (72)
T ss_pred CCCCEecCCCCcCcHHHHHh-CCCccCcHHHHHHH
Confidence 34458999999632 2322 23667899999865
No 33
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=36.82 E-value=20 Score=35.57 Aligned_cols=36 Identities=14% Similarity=0.206 Sum_probs=22.0
Q ss_pred CCCCCCCcCCCCCCC-CeeEccchhhhhhhhhhhhcc
Q 005151 21 LQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIHRE 56 (711)
Q Consensus 21 ~PgNk~CADCGs~~P-~WaSiNfGVFVCi~CSGIHR~ 56 (711)
...-.+|-+||..=| .=.-.--++..|+.|...|-.
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 344569999998611 111112245689999987643
No 34
>PF14376 Haem_bd: Haem-binding domain
Probab=32.58 E-value=25 Score=34.00 Aligned_cols=25 Identities=32% Similarity=0.624 Sum_probs=17.0
Q ss_pred HHHHHHHHHHcCCCCCCCcCCCCCCCCee
Q 005151 10 KNERIIRGLLKLQDNRRCINCNSLGTQYV 38 (711)
Q Consensus 10 r~ekiLr~Llk~PgNk~CADCGs~~P~Wa 38 (711)
...+.++.|++ +-|.||++.+..|-
T Consensus 31 ~~p~~v~~il~----~~CydCHSn~T~~P 55 (137)
T PF14376_consen 31 KAPEEVKIILK----NSCYDCHSNNTRYP 55 (137)
T ss_pred cchHHHHHHHH----ccccccCCCCCCCc
Confidence 34445566664 57999999876664
No 35
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=32.49 E-value=18 Score=31.85 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=20.3
Q ss_pred CCCcCCCCCCCC-eeEccchhhhhhhhhhhh
Q 005151 25 RRCINCNSLGTQ-YVCTNFWTFVCTNCSGIH 54 (711)
Q Consensus 25 k~CADCGs~~P~-WaSiNfGVFVCi~CSGIH 54 (711)
..|.|||..=|. =.-.--|+..|+.|...+
T Consensus 35 ~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 35 YLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred ccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 589999997431 111223778999998754
No 36
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=31.57 E-value=5.2 Score=29.73 Aligned_cols=27 Identities=11% Similarity=0.176 Sum_probs=22.8
Q ss_pred ccccccCCCCCCCCCchhhhcccCCCcc
Q 005151 178 DDKNSRYGYDERSPGNEQENRQFGDYRR 205 (711)
Q Consensus 178 ~dkl~rmgy~d~~~~~d~l~~~~Gd~~r 205 (711)
.+++.+|||+ ++....+|+..+||+++
T Consensus 5 v~~L~~mGf~-~~~~~~AL~~~~~d~~~ 31 (38)
T cd00194 5 LEQLLEMGFS-REEARKALRATNNNVER 31 (38)
T ss_pred HHHHHHcCCC-HHHHHHHHHHhCCCHHH
Confidence 3567899999 66788999999999887
No 37
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=30.56 E-value=16 Score=34.29 Aligned_cols=43 Identities=12% Similarity=0.338 Sum_probs=30.3
Q ss_pred CCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccC--Cc--ceeeccc
Q 005151 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSM 66 (711)
Q Consensus 21 ~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~L--GH--rVKSLsL 66 (711)
.|..-+|-+||.. |....+..|.|-.|-+..-.+ |. +|++|.+
T Consensus 67 ~p~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~iEv 113 (114)
T PRK03681 67 QEAECWCETCQQY---VTLLTQRVRRCPQCHGDMLRIVADDGLQIRRIEI 113 (114)
T ss_pred eCcEEEcccCCCe---eecCCccCCcCcCcCCCCcEEccCCeEEEEEEEE
Confidence 4677799999953 333345557899999987666 32 8888765
No 38
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=29.87 E-value=2.6e+02 Score=33.81 Aligned_cols=16 Identities=25% Similarity=0.420 Sum_probs=7.7
Q ss_pred CCCCCCccccccCCCC
Q 005151 172 SPGGRSDDKNSRYGYD 187 (711)
Q Consensus 172 s~~~R~~dkl~rmgy~ 187 (711)
++.+|+.++-+.|.|+
T Consensus 643 sSrSrs~SRsrS~srs 658 (757)
T KOG4368|consen 643 SSRSRSQSRSRSKSYS 658 (757)
T ss_pred ccccccCCcccccccC
Confidence 3444444554555555
No 39
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=29.58 E-value=23 Score=33.25 Aligned_cols=43 Identities=21% Similarity=0.451 Sum_probs=29.8
Q ss_pred CCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccC--C--cceeecccc
Q 005151 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--T--HRVKSVSMA 67 (711)
Q Consensus 21 ~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~L--G--HrVKSLsLD 67 (711)
.|.--+|.+||.. ..+..-.|.|-.|.+..-.+ | -+|++|.++
T Consensus 67 ~p~~~~C~~Cg~~----~~~~~~~~~CP~Cgs~~~~i~~G~El~I~~ie~~ 113 (115)
T TIGR00100 67 EPVECECEDCSEE----VSPEIDLYRCPKCHGIMLQVRAGKELNLKSIEVE 113 (115)
T ss_pred eCcEEEcccCCCE----EecCCcCccCcCCcCCCcEEecCCeEEEEEEEEE
Confidence 4667799999942 23332357899999976555 3 288888765
No 40
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.27 E-value=1.3e+02 Score=35.03 Aligned_cols=29 Identities=17% Similarity=0.212 Sum_probs=16.0
Q ss_pred CCCCCCCCCChhhhhhhccCccccCCCCC
Q 005151 300 SGNLGSANENQAEVKLETTGSLIDFDADP 328 (711)
Q Consensus 300 ~~~~~s~~~~~~~~k~~~s~sLiDf~~~~ 328 (711)
.|-+-++...-+-++.-..+.++|+++-.
T Consensus 211 lG~V~svv~~~VII~s~~~~~vlde~Svl 239 (483)
T KOG2236|consen 211 LGKVSSVVDQQVIIESTCNKEVLDEDSVL 239 (483)
T ss_pred hhHHHHHhhhceEEEeccCcccccccceE
Confidence 34444455555555555556777765543
No 41
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=28.73 E-value=28 Score=28.49 Aligned_cols=36 Identities=17% Similarity=0.359 Sum_probs=29.4
Q ss_pred CCCCCcCCCCC-CCCeeEccchh-hhhhhhhhhhccCC
Q 005151 23 DNRRCINCNSL-GTQYVCTNFWT-FVCTNCSGIHREFT 58 (711)
Q Consensus 23 gNk~CADCGs~-~P~WaSiNfGV-FVCi~CSGIHR~LG 58 (711)
....|.+|+.. -|.|=.-..|. +||-.|.--.+..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 35799999986 58898888886 99999988777655
No 42
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=28.56 E-value=1.5e+02 Score=34.22 Aligned_cols=15 Identities=40% Similarity=0.791 Sum_probs=7.5
Q ss_pred CCCCCCCCCCCCCCC
Q 005151 657 MPPQASPYPSAMPSQ 671 (711)
Q Consensus 657 ~~~~~~~y~~~~~~~ 671 (711)
+++|+++|+.-.+++
T Consensus 437 ~~~qs~p~~~Q~~q~ 451 (462)
T KOG2199|consen 437 VTPQSVPYPEQNQQQ 451 (462)
T ss_pred CCCCCCCchhhccCC
Confidence 445555665544433
No 43
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.36 E-value=23 Score=33.38 Aligned_cols=44 Identities=18% Similarity=0.344 Sum_probs=28.5
Q ss_pred CCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccC--Cc--ceeecccc
Q 005151 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSMA 67 (711)
Q Consensus 21 ~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~L--GH--rVKSLsLD 67 (711)
.|.--+|-+||.. |-...+..+.|-.|.+..-.+ |. +|++|.++
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 3445689999943 222234445699999876665 32 88888664
No 44
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=26.03 E-value=22 Score=35.38 Aligned_cols=33 Identities=30% Similarity=0.648 Sum_probs=26.8
Q ss_pred CCCCCcCCCCCCCCeeEccchhhhh-hhhhhhhcc
Q 005151 23 DNRRCINCNSLGTQYVCTNFWTFVC-TNCSGIHRE 56 (711)
Q Consensus 23 gNk~CADCGs~~P~WaSiNfGVFVC-i~CSGIHR~ 56 (711)
--+.|+-|| -.--|.|++-|.-.| ..|-.+|.+
T Consensus 117 ~r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 117 LRKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred cchhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 346899999 666799999999877 579999965
No 45
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=25.43 E-value=11 Score=28.46 Aligned_cols=30 Identities=13% Similarity=0.301 Sum_probs=17.0
Q ss_pred CCCcCCCCCCC-CeeEccchhhhhhhhhhhh
Q 005151 25 RRCINCNSLGT-QYVCTNFWTFVCTNCSGIH 54 (711)
Q Consensus 25 k~CADCGs~~P-~WaSiNfGVFVCi~CSGIH 54 (711)
.+|.+||..=+ .=.-+.-+..+|+.|+..|
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 35999998521 1112223777999998765
No 46
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.34 E-value=50 Score=30.46 Aligned_cols=30 Identities=13% Similarity=0.317 Sum_probs=23.6
Q ss_pred CCCCCCcCCCCCCCCeeEccchhhhhhhhhhh
Q 005151 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (711)
Q Consensus 22 PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGI 53 (711)
-.-..|-.|+.. .---+..||+.|..|-..
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 455678999999999754
No 47
>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=25.06 E-value=42 Score=29.96 Aligned_cols=31 Identities=13% Similarity=0.555 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEccchhhhhhhhhhhhcc
Q 005151 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (711)
Q Consensus 23 gNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~ 56 (711)
..+.|.=|+...- ...||++.|..|.+..|.
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 4567999997654 458999999999998876
No 48
>PRK00420 hypothetical protein; Validated
Probab=24.33 E-value=97 Score=29.62 Aligned_cols=46 Identities=15% Similarity=0.155 Sum_probs=31.1
Q ss_pred hhhHHHHHHHHHHHc--CCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhh
Q 005151 6 KEDEKNERIIRGLLK--LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIH 54 (711)
Q Consensus 6 keder~ekiLr~Llk--~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIH 54 (711)
++++..+++-+.|++ .--+..|-.||.+-.. ++-|-.+|-.|..+.
T Consensus 3 ~~~~~~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~---lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 3 ESEDIVKKAAELLLKGAKMLSKHCPVCGLPLFE---LKDGEVVCPVHGKVY 50 (112)
T ss_pred ccHHHHHHHHHHHHhHHHHccCCCCCCCCccee---cCCCceECCCCCCee
Confidence 345556666666666 3346899999976432 367888999998643
No 49
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=23.40 E-value=32 Score=32.69 Aligned_cols=23 Identities=22% Similarity=0.563 Sum_probs=20.8
Q ss_pred CeeEccch--hhhhhhhhhhhccCC
Q 005151 36 QYVCTNFW--TFVCTNCSGIHREFT 58 (711)
Q Consensus 36 ~WaSiNfG--VFVCi~CSGIHR~LG 58 (711)
.|++-.-| |+-|.+|--|||+-+
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~ 76 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEG 76 (112)
T ss_pred ceeEcCCCCEEeeccccceecccch
Confidence 89998889 999999999999854
No 50
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.19 E-value=38 Score=31.82 Aligned_cols=42 Identities=21% Similarity=0.426 Sum_probs=28.3
Q ss_pred CCCCCCCcCCCCCCCCeeEccchhhhhhhhhhhhccC--Cc--ceeeccc
Q 005151 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSM 66 (711)
Q Consensus 21 ~PgNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~L--GH--rVKSLsL 66 (711)
.|..-+|-+||.. ..+....|.|-.|-+....+ |. +|++|.+
T Consensus 67 vp~~~~C~~Cg~~----~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~iEv 112 (113)
T PRK12380 67 KPAQAWCWDCSQV----VEIHQHDAQCPHCHGERLRVDTGDSLIVKSIEV 112 (113)
T ss_pred eCcEEEcccCCCE----EecCCcCccCcCCCCCCcEEccCCeEEEEEEEE
Confidence 4667799999943 22333455699999876555 42 8888765
No 51
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.65 E-value=35 Score=32.57 Aligned_cols=46 Identities=15% Similarity=0.387 Sum_probs=29.6
Q ss_pred CCCCCCCcCCCCCC-CCeeEcc-ch-hhhhhhhhhhhccC--Cc--ceeecccc
Q 005151 21 LQDNRRCINCNSLG-TQYVCTN-FW-TFVCTNCSGIHREF--TH--RVKSVSMA 67 (711)
Q Consensus 21 ~PgNk~CADCGs~~-P~WaSiN-fG-VFVCi~CSGIHR~L--GH--rVKSLsLD 67 (711)
.|.--+| +||... ..+..+. +. .+.|-.|-+.+-.+ |. +|++|.++
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~Ieve 119 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGRECNVKNIKIE 119 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCCeEEEEEEEEe
Confidence 4667799 999652 2222221 11 36799999877665 32 89998876
No 52
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=22.11 E-value=1.2e+03 Score=26.62 Aligned_cols=19 Identities=26% Similarity=0.333 Sum_probs=11.5
Q ss_pred CCCCCC--CCCccccCCcCcc
Q 005151 350 ASSAND--NNWASFDLAPQVK 368 (711)
Q Consensus 350 ~~s~~~--~~wAsfd~~~~~~ 368 (711)
+.|.++ ++|--|..++.-+
T Consensus 369 A~Sg~GdfgD~~AF~aAPsgp 389 (499)
T KOG2057|consen 369 APSGGGDFGDLFAFGAAPSGP 389 (499)
T ss_pred ccCCCCcchhhhhhcCCCCcc
Confidence 343444 5788888776543
No 53
>PRK11295 hypothetical protein; Provisional
Probab=21.56 E-value=85 Score=30.13 Aligned_cols=32 Identities=19% Similarity=-0.015 Sum_probs=20.8
Q ss_pred cchhhhhHHHHHHHHHHHcCCCCCCCcCCCCC
Q 005151 2 ANRLKEDEKNERIIRGLLKLQDNRRCINCNSL 33 (711)
Q Consensus 2 ~sr~keder~ekiLr~Llk~PgNk~CADCGs~ 33 (711)
+...++..+.++-+|.......+-.|..|+..
T Consensus 2 ~~~~~~~~~~~~~~R~~~L~r~p~lC~~Cgr~ 33 (113)
T PRK11295 2 AIIPKNYARLESGYREKALKLYPWVCGRCSRE 33 (113)
T ss_pred ccchHHHHHHHHHHHHHHHHHCcchhhhhcCh
Confidence 33345555666666666544556689999997
No 54
>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=46 Score=30.48 Aligned_cols=31 Identities=19% Similarity=0.578 Sum_probs=25.8
Q ss_pred CCCCCcCCCCCCCCeeEccchhhhhhhhhhhhcc
Q 005151 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (711)
Q Consensus 23 gNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~ 56 (711)
++..|.=||...-. ..||++.|..|.+..|.
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 46789999986643 58999999999998876
No 55
>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=21.32 E-value=48 Score=30.77 Aligned_cols=31 Identities=13% Similarity=0.290 Sum_probs=17.9
Q ss_pred CCCCCCcCCCCCCC-CeeEccchhhhhhhhhh
Q 005151 22 QDNRRCINCNSLGT-QYVCTNFWTFVCTNCSG 52 (711)
Q Consensus 22 PgNk~CADCGs~~P-~WaSiNfGVFVCi~CSG 52 (711)
..-.+|.|||.+=| .=.-.--++..|+.|..
T Consensus 78 g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq~ 109 (110)
T TIGR02420 78 GEYGYCEECGEEIGLRRLEARPTATLCIDCKT 109 (110)
T ss_pred CCCCchhccCCcccHHHHhhCCCccccHHhHc
Confidence 34479999998621 11111224468999963
No 56
>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=21.16 E-value=49 Score=29.52 Aligned_cols=31 Identities=16% Similarity=0.591 Sum_probs=25.6
Q ss_pred CCCCCcCCCCCCCCeeEccchhhhhhhhhhhhcc
Q 005151 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (711)
Q Consensus 23 gNk~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~ 56 (711)
.|..|.=||...- ...||++.|..|.+..|.
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 4678999997654 469999999999998866
No 57
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=20.81 E-value=50 Score=31.94 Aligned_cols=25 Identities=12% Similarity=0.355 Sum_probs=17.9
Q ss_pred hhhhhhhhhhhhccC--Cc--ceeecccc
Q 005151 43 WTFVCTNCSGIHREF--TH--RVKSVSMA 67 (711)
Q Consensus 43 GVFVCi~CSGIHR~L--GH--rVKSLsLD 67 (711)
..+.|-.|-+.+-.+ |. +|++|.++
T Consensus 106 ~~~~CP~Cgs~~~~i~~G~el~i~~ie~e 134 (135)
T PRK03824 106 AFLKCPKCGSRDFEIVKGRGVYIEEIKIE 134 (135)
T ss_pred cCcCCcCCCCCCcEEecCceEEEEEEEEe
Confidence 446799999876454 43 88888765
No 58
>PRK13844 recombination protein RecR; Provisional
Probab=20.78 E-value=68 Score=33.44 Aligned_cols=42 Identities=31% Similarity=0.629 Sum_probs=29.7
Q ss_pred hhHHHHHHHHHHHcCCCC-CCCcCCCCCCCCeeEccchhhhhhhhhhhhcc
Q 005151 7 EDEKNERIIRGLLKLQDN-RRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (711)
Q Consensus 7 eder~ekiLr~Llk~PgN-k~CADCGs~~P~WaSiNfGVFVCi~CSGIHR~ 56 (711)
.++..+++.+.|.....| +.|--|+...= .-+|.-|+.-.|.
T Consensus 39 ~~~~~~~la~~i~~~~~~i~~C~~C~~lte--------~~~C~IC~d~~Rd 81 (200)
T PRK13844 39 SPETAIAIANSLLDATANIKKCVYCQALTE--------DDVCNICSNTNRD 81 (200)
T ss_pred CHHHHHHHHHHHHHHHHhCCcCCCCCCCCC--------CCCCCCCCCCCCC
Confidence 445567777777776666 79999987542 1268888888876
No 59
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=20.77 E-value=1.5e+02 Score=26.80 Aligned_cols=31 Identities=16% Similarity=0.423 Sum_probs=22.6
Q ss_pred CCcCCCCCCC---CeeEccch---hhhhhhhhhhhcc
Q 005151 26 RCINCNSLGT---QYVCTNFW---TFVCTNCSGIHRE 56 (711)
Q Consensus 26 ~CADCGs~~P---~WaSiNfG---VFVCi~CSGIHR~ 56 (711)
.|..||..-| .|...--| .|-|..|.+|+.-
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~ 38 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQL 38 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHH
Confidence 6999999865 34333234 8999999999843
Done!