Query 004446
Match_columns 753
No_of_seqs 199 out of 1187
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 23:35:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004446.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004446hhsearch_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-100 5E-105 842.3 41.5 622 1-679 1-681 (705)
2 PLN03119 putative ADP-ribosyla 100.0 7.8E-83 1.7E-87 699.1 38.2 571 1-669 1-616 (648)
3 KOG0702 Predicted GTPase-activ 100.0 3.2E-47 7E-52 413.3 30.5 504 1-631 1-523 (524)
4 KOG0703 Predicted GTPase-activ 100.0 1.6E-36 3.6E-41 315.7 11.2 118 6-126 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 5.3E-35 1.2E-39 269.7 6.7 112 13-125 2-116 (116)
6 smart00105 ArfGap Putative GTP 100.0 2E-33 4.2E-38 258.1 9.0 107 22-128 1-110 (112)
7 COG5347 GTPase-activating prot 100.0 2.5E-30 5.4E-35 274.7 13.9 119 9-127 5-127 (319)
8 PLN03114 ADP-ribosylation fact 99.9 3.3E-25 7.2E-30 235.7 12.7 116 12-127 10-130 (395)
9 KOG0705 GTPase-activating prot 99.9 1.7E-24 3.7E-29 239.4 8.9 116 12-128 501-619 (749)
10 KOG0704 ADP-ribosylation facto 99.9 1.9E-24 4.1E-29 228.7 8.9 86 8-93 3-91 (386)
11 KOG0706 Predicted GTPase-activ 99.9 1.6E-23 3.5E-28 227.3 7.8 84 10-93 9-95 (454)
12 KOG0521 Putative GTPase activa 99.8 6.3E-21 1.4E-25 222.6 3.5 115 14-129 416-535 (785)
13 KOG0818 GTPase-activating prot 99.7 1.5E-18 3.2E-23 190.3 3.1 108 19-126 3-120 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 4.9E-17 1.1E-21 186.2 5.8 110 16-126 290-404 (1186)
15 KOG0702 Predicted GTPase-activ 97.5 0.023 5E-07 64.7 23.3 41 517-560 392-432 (524)
16 PLN03131 hypothetical protein; 92.1 15 0.00033 44.0 20.1 21 355-375 431-451 (705)
17 KOG0521 Putative GTPase activa 91.2 0.023 5E-07 68.6 -3.5 70 20-91 626-699 (785)
18 PF00643 zf-B_box: B-box zinc 80.8 0.9 2E-05 34.8 1.4 40 23-64 2-42 (42)
19 PRK12495 hypothetical protein; 76.7 2.4 5.2E-05 44.7 3.5 30 21-54 39-68 (226)
20 PRK00085 recO DNA repair prote 73.5 4.5 9.7E-05 41.8 4.5 39 16-54 137-180 (247)
21 TIGR00613 reco DNA repair prot 60.9 6.8 0.00015 40.3 2.8 38 17-54 136-178 (241)
22 COG1734 DksA DnaK suppressor p 53.0 2.7 5.8E-05 40.5 -1.5 48 7-54 61-111 (120)
23 PF08271 TF_Zn_Ribbon: TFIIB z 51.6 8.8 0.00019 30.1 1.4 27 26-53 2-28 (43)
24 COG1381 RecO Recombinational D 50.2 8.2 0.00018 40.9 1.4 38 14-51 140-182 (251)
25 KOG4368 Predicted RNA binding 47.1 73 0.0016 38.3 8.3 15 251-265 711-725 (757)
26 PF01286 XPA_N: XPA protein N- 46.8 5.9 0.00013 30.6 -0.2 27 25-51 4-31 (34)
27 PF11781 RRN7: RNA polymerase 46.1 15 0.00032 28.5 1.8 29 22-53 6-34 (36)
28 PRK00420 hypothetical protein; 39.4 60 0.0013 31.2 5.2 46 6-54 3-50 (112)
29 TIGR02419 C4_traR_proteo phage 37.5 12 0.00025 32.2 0.1 33 21-54 28-62 (63)
30 PF14376 Haem_bd: Haem-binding 37.2 17 0.00037 35.4 1.2 25 10-38 31-55 (137)
31 TIGR00100 hypA hydrogenase nic 34.1 25 0.00053 33.4 1.7 43 21-67 67-113 (115)
32 PRK11019 hypothetical protein; 32.2 17 0.00037 33.5 0.3 31 24-55 36-68 (88)
33 COG1997 RPL43A Ribosomal prote 31.9 56 0.0012 30.3 3.5 31 22-54 33-63 (89)
34 KOG3362 Predicted BBOX Zn-fing 31.4 17 0.00037 36.4 0.2 34 22-56 116-150 (156)
35 TIGR02890 spore_yteA sporulati 30.8 18 0.00039 36.3 0.3 30 25-54 87-117 (159)
36 PRK10778 dksA RNA polymerase-b 30.6 17 0.00037 36.2 0.1 34 22-55 109-143 (151)
37 PRK03681 hypA hydrogenase nick 29.0 23 0.00051 33.5 0.7 43 21-66 67-113 (114)
38 PF02318 FYVE_2: FYVE-type zin 28.6 99 0.0021 29.2 4.8 51 5-55 23-90 (118)
39 cd03031 GRX_GRX_like Glutaredo 28.6 38 0.00083 33.5 2.1 43 6-57 81-123 (147)
40 PRK00564 hypA hydrogenase nick 28.2 26 0.00057 33.3 0.9 43 22-67 69-115 (117)
41 smart00401 ZnF_GATA zinc finge 28.2 42 0.00091 27.7 1.9 36 23-58 2-39 (52)
42 PRK00423 tfb transcription ini 28.1 43 0.00093 36.6 2.6 34 22-56 9-42 (310)
43 PF14803 Nudix_N_2: Nudix N-te 27.4 34 0.00073 26.4 1.2 30 25-55 1-33 (34)
44 KOG1985 Vesicle coat complex C 26.0 9.8E+02 0.021 30.5 13.3 12 690-701 84-95 (887)
45 PRK13844 recombination protein 25.9 67 0.0014 33.7 3.4 42 7-56 39-81 (200)
46 PHA00080 DksA-like zinc finger 25.9 19 0.0004 31.8 -0.5 32 22-54 29-62 (72)
47 COG2158 Uncharacterized protei 25.6 46 0.001 31.9 2.0 23 36-58 52-76 (112)
48 PTZ00255 60S ribosomal protein 24.9 81 0.0017 29.4 3.3 41 11-53 22-63 (90)
49 PRK00762 hypA hydrogenase nick 24.2 41 0.00088 32.4 1.4 46 21-67 67-119 (124)
50 KOG2236 Uncharacterized conser 24.2 1.9E+02 0.0041 34.0 6.8 20 586-611 410-429 (483)
51 PRK12380 hydrogenase nickel in 24.2 36 0.00078 32.2 1.0 42 21-66 67-112 (113)
52 PRK13715 conjugal transfer pro 23.8 19 0.00041 31.9 -0.8 30 25-54 35-65 (73)
53 PF12760 Zn_Tnp_IS1595: Transp 23.3 1E+02 0.0022 24.6 3.2 42 8-51 3-44 (46)
54 KOG2199 Signal transducing ada 23.1 2.1E+02 0.0046 33.3 6.7 27 179-205 215-241 (462)
55 PRK03824 hypA hydrogenase nick 22.4 58 0.0013 31.8 2.0 25 43-67 106-134 (135)
56 PRK06266 transcription initiat 22.2 43 0.00093 34.1 1.2 30 26-56 119-148 (178)
57 KOG2057 Predicted equilibrativ 22.2 1.2E+03 0.027 26.7 12.3 17 350-366 369-387 (499)
58 COG0675 Transposase and inacti 22.1 48 0.0011 34.6 1.6 25 25-56 310-335 (364)
59 KOG0119 Splicing factor 1/bran 21.1 82 0.0018 37.2 3.2 77 5-81 242-327 (554)
60 PF10058 DUF2296: Predicted in 21.0 94 0.002 26.1 2.7 41 12-52 3-52 (54)
61 PF07282 OrfB_Zn_ribbon: Putat 20.7 61 0.0013 27.3 1.6 26 25-52 29-54 (69)
62 TIGR02420 dksA RNA polymerase- 20.6 43 0.00093 31.3 0.7 29 23-51 79-108 (110)
63 TIGR00373 conserved hypothetic 20.5 52 0.0011 32.8 1.3 35 21-56 104-140 (158)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=2.3e-100 Score=842.26 Aligned_cols=622 Identities=34% Similarity=0.491 Sum_probs=483.8
Q ss_pred CcchhhhhHHHHHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCCcceeeeccCcCCHHHHHHHHhc
Q 004446 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (753)
Q Consensus 1 M~~r~kedernekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LGHRVKSlsLD~Wt~eEV~~m~~g 80 (753)
|++| |++|+++++|++|+++++|++|+||++++|+|||+|||||||++|+||||+|+||||||+||+|+++||++|+.+
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 004446 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPPY 159 (753)
Q Consensus 81 GN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIraKYveKrF~~~~~~dkPpRl~~gd~eds~e~Rr-~~~~s~srSpp~ 159 (753)
||+++|+|||++|+..+++.|+.++.+++|+|||.|||+|+|+.....++|++....-+.+..|+|| ++|++++|||+|
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 9999999999999987778888888888999999999999999999999999887666777779999 999999999999
Q ss_pred cchhh-hhccCCCCCCCCCCcccccCccCCCCCCchhhh--cccCCccccCCCCccccccccccccCCCCC---CCCCCc
Q 004446 160 EDTYE-RRYNEQSSPGGRSDDKNSRYGYDERSPGNEQEN--RQFGDYRRTSPTRPEVINDWRRDDRFGNGR---KFEDRR 233 (753)
Q Consensus 160 ~d~~e-rR~~~rss~~~Rs~dk~~r~gydd~~p~~d~~~--~~~G~~~r~SP~r~e~v~d~~rdDrf~~~~---~~~~~R 233 (753)
+++|| |||+++.++++|+ +++|+.. +|||+|+| ||+|| +||||||||+|+. +++|++
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 6899998888888 8888874 99999999 99997 9999999999996 666777
Q ss_pred cCCCC--CCCCCCCCCCCCCCCCCCCCcccchhhhccCCCCCCccCCCCCCCCCccCCCCcccccccCCCCCCCCCCchh
Q 004446 234 ISDGD--SKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQA 311 (753)
Q Consensus 234 ~S~~~--~~~~~~sp~~~Kd~~~sspp~vr~~~~iLg~~vp~lr~~~~pk~~~~~~s~g~~~~qrtass~s~~s~d~~~~ 311 (753)
.|+++ .+.+.+|||++||++. +| +|||+|+|||||||+|||.+++|++..++++|.++.|||+|+++++|+||+++
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 76554 4557799999999875 44 66999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCccccCCCCCCCChhhhhhhhhhhcccccccCCCCCCCCCccccCCcCcccccCC-CCcchhHHHhhccccCc
Q 004446 312 EVKLETTGSLIDFDADPKPSPAVAQAQQKTVAQSVVQPASSANDNNWASFDLAPQVKVSQTS-SNLNTLETVFSQLSVPA 390 (753)
Q Consensus 312 ~~k~~~s~sLiD~~s~~ep~~~~~~a~qt~~~~~~~q~~~s~~~~~wasFD~~~~~~~~q~~-~~~n~le~~l~qlsv~~ 390 (753)
++|+++++|||||++|+|+..+. .|.++.... -..+...+|+-|.+-..-++.+. +..-|+ -|+||...+
T Consensus 301 s~Ks~~s~sL~D~~~e~~~~~~~---~q~k~~~~~----~~~~~~~~~s~d~f~~~v~p~~~~~~a~pI--DLFqlp~ts 371 (705)
T PLN03131 301 SIKSFNSGSLADIVAEAEQAAGN---HQDKMPAFP----RMAGSGSHASLDHFKAPVAPEAAAPMAPPI--DLFQLPATS 371 (705)
T ss_pred ceeecccccccccccCccccccc---cccccCCcc----ccccccccccccccccccccccccccCCch--hhhhccCCC
Confidence 99999999999999999987663 332222221 12456667776665433333222 222334 477999999
Q ss_pred cCCCCCCCCCCCCCCCc-ccCCCccccCCCCCCCCcccCCCC-----cccc----cccCCCCCCcccccccCCCCCCCCC
Q 004446 391 SVPGQVSGIPSGAGAPV-IAPATNVNVLPGGGSPVASVGHTP-----FSVF----SAAAPAAPAVSGFATFPSANAPAPA 460 (753)
Q Consensus 391 s~p~~~~~~~~~~~~~~-~~~~~n~~~~~~~~s~~~~~~~~~-----~~~~----~~~~~~~~~~~~~~tf~~s~~s~~s 460 (753)
.+|.++.+.+ .|+ -+++.|.. ...-.|...+..... -+.+ ...+.-+|+.++|++|+......
T Consensus 372 ~a~~vdlf~~----s~l~~~p~~n~~-q~~qts~p~~~dlfag~~qqq~~~s~~~~~~~~s~pknegwa~fd~~~p~~-- 444 (705)
T PLN03131 372 PAPPVDLFEI----PPLDPAPAINAY-QPPQTSLPSSIDLFGGITQQQSINSLDEKSPELSIPKNEGWATFDGIQPIA-- 444 (705)
T ss_pred CCCccccccc----CcccCCCccccC-CCCcccCCccccccccccccCccccccccCcccCCccccCcccccCCCccc--
Confidence 9999988876 222 33444432 001111111111000 0000 12233478899999998555421
Q ss_pred CCCCCCCccccCCCCCCccCCCCCCccCCCCCccccccCCCCcCCCCCcccccccc---cC--CCCCCCCCCCCCCCCcc
Q 004446 461 PGVTPLLPVSVNAGNSFSMQHQPPLFPTAGGQFTASQFTPPVAGSSNNQQWNTSLA---QN--AQGPPAAQPAQSVPKPA 535 (753)
Q Consensus 461 ~~~~~~~~~~~~~~~~~~~q~~~~~f~~~~~~~~~q~~t~~~~~~~n~q~w~~~~~---q~--~~~~p~~~~~~~~~~~~ 535 (753)
+.++ ++|++. ..++.+...+. +.... ....+.++|.-+++ |+ ++..||....+.|.++.
T Consensus 445 ----s~~~-~~n~t~--------~~v~~~~~~~~-~~d~v--~~~~~~~q~Pp~~~~~~~~s~s~~~pW~~~~~~V~~~~ 508 (705)
T PLN03131 445 ----STPG-NENLTP--------FSIGPSMAGSA-NFDQV--PSLDKGMQWPPFQNSSDEESASGPAPWLGDLHNVEAPD 508 (705)
T ss_pred ----ccCC-cccccc--------cccccccccCc-chhhc--cccccccccCCCcccccccccccCCcccccchhcccCC
Confidence 1222 233332 23333332211 22222 33445588875544 54 45567888888898887
Q ss_pred cccCC--------------CCCCCCCCccccccCCccCcccccccccCCCCCCCCCCccCCCCCc----eeceecCCCC-
Q 004446 536 LESAS--------------GGLSQPSPVEVKSTGRTALPEDLFTANYSSFPASVPGWQTVPPHGM----VYAMQYNTAA- 596 (753)
Q Consensus 536 ~~~~~--------------~~~s~~~~~e~k~sgrkeLP~DlFt~~y~~~p~~vpGwq~~p~~gm----g~~mqy~~~~- 596 (753)
+++.- .+.+....+|.+++--+.-.+|.|.....+......|.|+..|+|| ||+.+-...+
T Consensus 509 ~~~~q~WnAF~~~ds~~~~~l~~~~~~s~~q~~~~~~~t~~q~~~~~~~~d~~~d~~~r~~p~~~~~~~g~~~~~~~~~~ 588 (705)
T PLN03131 509 NTSAQNWNAFEFDDSVAGIPLEGIKQSSEPQTAANMPPTADQLIGCKALEDFNKDGIKRTAPHGQGELPGLDEPSDILAE 588 (705)
T ss_pred ccCccccccccccccccccccccccccccccccccCCCCcccccccccccccccccccccCCCCCcCCCCCCCCCccccC
Confidence 75421 2445667777888888888899999999999999999999999999 5555532222
Q ss_pred ------------CCCCcccccCCCCCCCCCCCCCCccccCCCCcccccccCCCCCCCCCCCCCC-CC-CCCCCCCCCCCC
Q 004446 597 ------------PMPNFVHSKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS-SL-TPSPAWMPPQAS 662 (753)
Q Consensus 597 ------------p~~~~~~~~ks~NPFD~~~~~~~~Q~~~fpsm~~lqgalp~~~~~~~~~~ss-~~-~~s~~~~p~q~~ 662 (753)
.|++--+..||+|||||.+|....+.-||-.|.+||+|||+. .+++. +| +.+..|++.-+.
T Consensus 589 ps~~~~~~~~~~~~~s~~~~~ks~npfdl~~dsd~~~~~mf~d~sslq~~lp~~-----~~~~~f~g~~~tepw~~~~~~ 663 (705)
T PLN03131 589 PSYTPPAHPIMEHAQSHANDHKSINPFDLPYDSDLEPGNMFLDMSSLEAALPDA-----HLPSAFLGSGMTEPWFPQDLA 663 (705)
T ss_pred CCCCccccccccccccccCccCCCCCcCCccccccCcccceeehHHHHhhcCCC-----CCchhhhcCCCCCccccCCCc
Confidence 344445678999999999999999999999999999999965 44555 66 789999999877
Q ss_pred -CCCCCCCCCCccccccC
Q 004446 663 -PYPSAMPSQMPTYAAAI 679 (753)
Q Consensus 663 -~y~~~~~~~~~~~~~~~ 679 (753)
+|+++.|+++++|.|+.
T Consensus 664 ~~yip~~pqggl~y~agq 681 (705)
T PLN03131 664 MTYIPAAPQGGLAYMAGQ 681 (705)
T ss_pred ccccCCCCCCCchhhccc
Confidence 99999998887766643
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=7.8e-83 Score=699.13 Aligned_cols=571 Identities=32% Similarity=0.449 Sum_probs=410.2
Q ss_pred CcchhhhhHHHHHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCCcceeeeccCcCCHHHHHHHHhc
Q 004446 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (753)
Q Consensus 1 M~~r~kedernekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LGHRVKSlsLD~Wt~eEV~~m~~g 80 (753)
|++| |++|+++++|++|+++++|++|+||+..+|+|||+|||||||++|+||||+|+||||||+||+|+++||++|+.+
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 004446 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPPY 159 (753)
Q Consensus 81 GN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIraKYveKrF~~~~~~dkPpRl~~gd~eds~e~Rr-~~~~s~srSpp~ 159 (753)
||+++|+|||++|+..+.+.|...+.+++|+|||.|||+|+|+.+...+++++.....+....+.|| ++|+++++||+|
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 9999999999999887777788788888999999999999999999999988754344444446788 999999999999
Q ss_pred cchhh-hhccCCCCCCCCCCcccccCccCCCCCCchhh-hcccCCccccCCCCccccccccccccCCCCCCCCCCccCCC
Q 004446 160 EDTYE-RRYNEQSSPGGRSDDKNSRYGYDERSPGNEQE-NRQFGDYRRTSPTRPEVINDWRRDDRFGNGRKFEDRRISDG 237 (753)
Q Consensus 160 ~d~~e-rR~~~rss~~~Rs~dk~~r~gydd~~p~~d~~-~~~~G~~~r~SP~r~e~v~d~~rdDrf~~~~~~~~~R~S~~ 237 (753)
++.|| |||+++.....|| ++.|+. ..|+++|.+ ||+|+ .|||.||||.||... .|+||.
T Consensus 160 ~~~ye~rr~~~~~~~~~~~-------------~~s~r~~~~k~~~~~~-s~~~~---~~~m~ed~f~~e~~~--~r~sd~ 220 (648)
T PLN03119 160 DYQYEERRYGKIPLGFTGK-------------SASVKGLHAKASSFVY-SPGRF---SDHMFEDQFSNEDSA--PRASDY 220 (648)
T ss_pred ccchhhhhccccccccccC-------------CCccccccccccceee-ccchH---HHHhhhhhcccCCCC--Cccccc
Confidence 99998 9999999999999 888877 599999999 99999 899999999999854 499873
Q ss_pred C-------CCCCCCCCCCCCCCCCCCCCcccchhhhccCCCCCCccCCCCCCCCCccCCCCcccccccCCCCCCCCCCch
Q 004446 238 D-------SKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQ 310 (753)
Q Consensus 238 ~-------~~~~~~sp~~~Kd~~~sspp~vr~~~~iLg~~vp~lr~~~~pk~~~~~~s~g~~~~qrtass~s~~s~d~~~ 310 (753)
. .+.+.+||+++ |.++++||+.+ .++++. . ..--..++.|||+|+|+++|+|++.
T Consensus 221 s~ss~g~~~~~~~~sp~~~-~~~~~~~~~~~-~~~~~~-----~-----------~~~~~~~~sqRT~SsGs~gSfDs~s 282 (648)
T PLN03119 221 SVSSAGDPFRSDIQSPNFQ-QEAEFRSPQFQ-HSNAPP-----S-----------ENLFPGRQHQRTTSSGSVRSVDSNF 282 (648)
T ss_pred ccccCCcccccCcCCCCcc-cccccCCcccc-cccCcc-----h-----------hhccccccccccccccccccccccc
Confidence 2 55677999999 55666676665 454421 0 0000147789999999999999999
Q ss_pred hhhhhhccCccccCCCCCCCChhhhhhhhhhhcccccccCCCCCCCCCccccCCcCcccccCCCCcchhHHHhhccccCc
Q 004446 311 AEVKLETTGSLIDFDADPKPSPAVAQAQQKTVAQSVVQPASSANDNNWASFDLAPQVKVSQTSSNLNTLETVFSQLSVPA 390 (753)
Q Consensus 311 ~~~k~~~s~sLiD~~s~~ep~~~~~~a~qt~~~~~~~q~~~s~~~~~wasFD~~~~~~~~q~~~~~n~le~~l~qlsv~~ 390 (753)
+++|++++++|.|+.+|.+..-+. .|.++...+ +. +.+ +..-|+ -|+||.+.+
T Consensus 283 ~S~ks~~Sg~l~d~~~E~~~~~~~---~q~~~~~~~------------------P~---~~~-~~aapI--DLFqlp~ts 335 (648)
T PLN03119 283 MSIKSYTSGGLGEAVSESRQNTGS---QQGKTSNHV------------------PL---VAE-STKAPI--DLFQLPGAP 335 (648)
T ss_pred ccccccccCCcccccccccccccc---cccccCCCC------------------cc---ccc-ccCCch--hhhhccCCC
Confidence 999999999999999998876653 222121111 11 111 112223 366888888
Q ss_pred cCCCCCCCCCCCCCCCcccCCCccccCCCCCCCCcccCCC----C-cccccccCCCCCCcccccccCCCCCCCCCCCCCC
Q 004446 391 SVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHT----P-FSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTP 465 (753)
Q Consensus 391 s~p~~~~~~~~~~~~~~~~~~~n~~~~~~~~s~~~~~~~~----~-~~~~~~~~~~~~~~~~~~tf~~s~~s~~s~~~~~ 465 (753)
.+|.++.+.++-+ | -+++.|.. ...-.|+..+.+.. . -..+...+.-+|+.++|++|+....++.++
T Consensus 336 ~a~~vdlf~~~~~--p-~~p~~n~~-q~~qts~p~~~~~f~~~~qqq~~~~~~~~s~pkneGWA~fd~p~~s~~~~---- 407 (648)
T PLN03119 336 VAQSVDTFQPSIA--P-RSPPVNLQ-QAPQTYSFTPANSFAGNLGQQPTSRPSELSAPKNEGWASFDNPMPAAKST---- 407 (648)
T ss_pred CCccccccccccC--C-CCCccccC-CCccccCCcchhhhhcccccCcccCccccccccccCcccccccccccCCc----
Confidence 8888888776211 1 23333332 11111111111111 0 111233344488899999999555544331
Q ss_pred CCccccCCCCCCccCCCCCCccCCCCCccccccCCCCcCCCCCcccccccc-----cCCCCCCCCCCCCCCCCcccccCC
Q 004446 466 LLPVSVNAGNSFSMQHQPPLFPTAGGQFTASQFTPPVAGSSNNQQWNTSLA-----QNAQGPPAAQPAQSVPKPALESAS 540 (753)
Q Consensus 466 ~~~~~~~~~~~~~~q~~~~~f~~~~~~~~~q~~t~~~~~~~n~q~w~~~~~-----q~~~~~p~~~~~~~~~~~~~~~~~ 540 (753)
+|.+- +++.....+..... ...+.++|.-+.+ -.++..||....+.|.++.+++.-
T Consensus 408 -----~ni~~------------~~~~~~~~~~d~v~--~~~~~mq~Pp~~~~~~~~s~s~~~pW~~~~~~V~~~~~~~~q 468 (648)
T PLN03119 408 -----NVITS------------PGDFQLELKIEEIL--QPSTSMQLPPYPSTVDQHALSIPSPWQEDLSNVLKDVVDNPQ 468 (648)
T ss_pred -----ccccC------------ccccccCcchhhhc--ccccccccCCCcccccccccccCCchhccchhcccCcccCcc
Confidence 11110 11222112222222 2233366654433 233445566666666666544311
Q ss_pred -----CCCCCC---------CCccccccCCccCcccccccccCCCCCCCCCCccCC-CCCc-eeceecCCCCCCCCccc-
Q 004446 541 -----GGLSQP---------SPVEVKSTGRTALPEDLFTANYSSFPASVPGWQTVP-PHGM-VYAMQYNTAAPMPNFVH- 603 (753)
Q Consensus 541 -----~~~s~~---------~~~e~k~sgrkeLP~DlFt~~y~~~p~~vpGwq~~p-~~gm-g~~mqy~~~~p~~~~~~- 603 (753)
+-.-.+ ...+....--+.-.+|.|.....+...+..|.|+.. |+|| ||+.+-...++ |+|.-
T Consensus 469 ~WnAF~ds~~~~~l~~~~~~~~~~~~~~~~~~~t~~q~~~~r~~ed~~~dg~qr~~~p~g~~g~~~~~~~~~~-Ps~~~~ 547 (648)
T PLN03119 469 PWNAFPDSIEANPLDSSRNIHQQVDGASTSSYNTDHQHLESQVLEELSNDGTQTTRIPAGSSAFGFPGNIGMA-PSYSEE 547 (648)
T ss_pred ccccchhhhccCccccccccccccccccccCCCCcccccccccccccccccccccccCCCCCCCCCCCccccC-CCCCch
Confidence 000000 111222223344556777777788888999999999 8887 44555443332 56643
Q ss_pred ------ccCCCCCCCCCCCCCCccccCCCCcccccccCCCCCCCCCCCCCC-CCCCCCCCCCCCCC-CCCCCCC
Q 004446 604 ------SKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS-SLTPSPAWMPPQAS-PYPSAMP 669 (753)
Q Consensus 604 ------~~ks~NPFD~~~~~~~~Q~~~fpsm~~lqgalp~~~~~~~~~~ss-~~~~s~~~~p~q~~-~y~~~~~ 669 (753)
..||+|||||.+|....+.-||-.|.+||++||+. .++++ +|+.+..|++.-+. +|+++.|
T Consensus 548 ~~~~~~~~ks~npfdl~~~sd~~~~~mf~d~tslq~~lp~~-----~~~~~~~~~~t~~w~~~~~~~~yip~~~ 616 (648)
T PLN03119 548 AWQHVNEQKSANPFDLPYDSEFDSNDMFLDMSSLQGALPDI-----QTPQAFLNGVSQPWLAADSVPSYLPAPA 616 (648)
T ss_pred hccccccccCCCCcCCccccccCcccceeehHHHHhhcCCC-----CCchhhhcCCCcccccCCCcccccCCCc
Confidence 44999999999999999999999999999999963 45566 88999999999876 8877755
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=3.2e-47 Score=413.34 Aligned_cols=504 Identities=29% Similarity=0.370 Sum_probs=361.1
Q ss_pred CcchhhhhHHH-HHHHHHHHccCCCCCCcCCCCCCC-CeeEeceeeeeecccccccccCC--cceeeeccCcCCHHHHHH
Q 004446 1 MANRLKEDEKN-ERIIRGLLKLQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIHREFT--HRVKSVSMAKFTSQEVKA 76 (753)
Q Consensus 1 M~~r~kedern-ekiLr~Llk~pgNk~CADCGs~~P-~WaSvN~GVFVC~~CSGIHR~LG--HRVKSlsLD~Wt~eEV~~ 76 (753)
|++++||+|+. |++||+|+|+|+|++|++|+...+ +|+++.-|-|||+.|+|+-|.|. ||||+|+|.+|+..||..
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 004446 77 LQEGGNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRRDTYQGGSRS 156 (753)
Q Consensus 77 m~~gGN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIraKYveKrF~~~~~~dkPpRl~~gd~eds~e~Rr~~~~s~srS 156 (753)
|+.+||+.+++||++-.+.++-..||..+..++|+||+.||+.|+|+.+....+-+... |- ..+.++
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----------RG---SLSEDS 147 (524)
T ss_pred HhhcchhhhhhhhhcchhhhhccCCCcccchhhHHHHhhhhccceeecCcccccccccc----------cc---cccccC
Confidence 99999999999999999988888999999999999999999999999776544422211 10 111223
Q ss_pred CCCcchhhhhccCCCCCCCCCCcccccCccCCCCCCchhh--hcccCCccccCCCCccccccccccccCCCCCCCCCCcc
Q 004446 157 PPYEDTYERRYNEQSSPGGRSDDKNSRYGYDERSPGNEQE--NRQFGDYRRTSPTRPEVINDWRRDDRFGNGRKFEDRRI 234 (753)
Q Consensus 157 pp~~d~~erR~~~rss~~~Rs~dk~~r~gydd~~p~~d~~--~~~~G~~~r~SP~r~e~v~d~~rdDrf~~~~~~~~~R~ 234 (753)
+++. .+|...+.+|..++|+.|..... +-+...+.+ +|.|||+++||+ |+|+.-+.
T Consensus 148 ~~~~-------------~s~~~~~~lrs~~gd~~P~~~~~t~np~~~~~~~-~~~~~~~~~~rf--dlfg~~k~------ 205 (524)
T KOG0702|consen 148 RPVS-------------ESRPETKSLRSLLGDHAPLLAESTKNPRSRGLPK-SPIRFEIVDDRF--DLFGLPKA------ 205 (524)
T ss_pred Cccc-------------ccCCCccccccccCCCCcchhhcccCccccCCCC-CCchhhhhhhhh--hhhcCcCc------
Confidence 3444 34444455555666665655433 244456778 899999876655 55544332
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCcccchhhhccCCCCCCccCCCCCCCCCccCCCCcccccccCCCCCCCCCCchhhhh
Q 004446 235 SDGDSKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQAEVK 314 (753)
Q Consensus 235 S~~~~~~~~~sp~~~Kd~~~sspp~vr~~~~iLg~~vp~lr~~~~pk~~~~~~s~g~~~~qrtass~s~~s~d~~~~~~k 314 (753)
++. ..++...-|+++.++|+..+++++|+++-+-.+++.|+.|....+...+++....-..+.+..+.+.++.+.+
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 SDA----QSQSTFQSSIAPSSSPPNHQSVPQAYSDSPANIFAGEPFKQPVSRPSFASAPKNEGWASLSDNPVNEAKSENV 281 (524)
T ss_pred ccc----cccCcccccccccCCCCccccchhhcccccccccccCCCCCCccCccccccccccCCcccccCcccccccccc
Confidence 222 3356778889999999999999999999999999999999888888888887765555557788899999999
Q ss_pred hhccCccccCCCCCCCC--hhhhhhhhhhhcccccccCC-CCCCCCCccccCCcCcccc---cCCCCcchhHHHhhcccc
Q 004446 315 LETTGSLIDFDADPKPS--PAVAQAQQKTVAQSVVQPAS-SANDNNWASFDLAPQVKVS---QTSSNLNTLETVFSQLSV 388 (753)
Q Consensus 315 ~~~s~sLiD~~s~~ep~--~~~~~a~qt~~~~~~~q~~~-s~~~~~wasFD~~~~~~~~---q~~~~~n~le~~l~qlsv 388 (753)
..+..+++||+...|-+ ..+.+.+.-+..+.+.|+.+ +..+++|++|+........ +.+...+.|...+.+|.|
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 99999999998877755 22323333222222234433 3568999999988665433 333555777778888888
Q ss_pred CccCCCCCCCCCCCCCCCcccCCCccccCCCCCCCCcccCCCCcccccccCCCCCCcccccccCCCCCCCCCCCCCCCCc
Q 004446 389 PASVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLP 468 (753)
Q Consensus 389 ~~s~p~~~~~~~~~~~~~~~~~~~n~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~tf~~s~~s~~s~~~~~~~~ 468 (753)
.++++|+... +++++++-.+++ .-
T Consensus 362 ~~s~~gsa~~-------------------------~~~~~~~n~~~~-------------------------------e~ 385 (524)
T KOG0702|consen 362 QSSVFGSAGY-------------------------VPPHQPVNLGVL-------------------------------EE 385 (524)
T ss_pred cccccccccc-------------------------CCCCcccccccc-------------------------------cc
Confidence 7777644321 222222211100 00
Q ss_pred cccCCCCCCccCCCC--CCccCCCCCccccccCCCCcCCCCCcccccccccCCCCCCCCCCCCCCCCcccccCCCCCCCC
Q 004446 469 VSVNAGNSFSMQHQP--PLFPTAGGQFTASQFTPPVAGSSNNQQWNTSLAQNAQGPPAAQPAQSVPKPALESASGGLSQP 546 (753)
Q Consensus 469 ~~~~~~~~~~~q~~~--~~f~~~~~~~~~q~~t~~~~~~~n~q~w~~~~~q~~~~~p~~~~~~~~~~~~~~~~~~~~s~~ 546 (753)
..+...|..+-+.+. ++||.+-|. +.+ .++|-.+ -.+..+.+..+ + .
T Consensus 386 ~~~s~~q~~s~ft~~~ts~~p~~~~~-----------~ps-------sn~~~~~---~~Q~~~~~~~~--g--------~ 434 (524)
T KOG0702|consen 386 LSNSTTQTFSAFTNESTSGFPAPIGM-----------APS-------SNHHQDD---EFQPNHRNPQP--G--------A 434 (524)
T ss_pred cccccccccccccCcccccCcccccc-----------CCc-------ccccccc---cccccccCCCC--c--------c
Confidence 112233333333322 455544433 111 1112222 12222222211 1 2
Q ss_pred CCccccccCCccCc-ccccccccCCCCCCCCCCccCCCCCceecee-cCCCCCCCC--cccccCCCCCCCCCCCCCCccc
Q 004446 547 SPVEVKSTGRTALP-EDLFTANYSSFPASVPGWQTVPPHGMVYAMQ-YNTAAPMPN--FVHSKSTTNPFDVNNDSHPVQA 622 (753)
Q Consensus 547 ~~~e~k~sgrkeLP-~DlFt~~y~~~p~~vpGwq~~p~~gmg~~mq-y~~~~p~~~--~~~~~ks~NPFD~~~~~~~~Q~ 622 (753)
...+.+..++.++| .++|++.|.-...|+++||...++||+|+|+ |.+....|+ .++.-+|+|||+.+-. .+.|.
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 888886666 9999999999999754 34455
Q ss_pred c-CCCCcccc
Q 004446 623 Q-TFPSMASL 631 (753)
Q Consensus 623 ~-~fpsm~~l 631 (753)
+ +||+|.++
T Consensus 514 ~~~~p~~nPF 523 (524)
T KOG0702|consen 514 PVAFPGTNPF 523 (524)
T ss_pred cccCCCCCCC
Confidence 4 47887765
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1.6e-36 Score=315.68 Aligned_cols=118 Identities=28% Similarity=0.588 Sum_probs=107.3
Q ss_pred hhhHHHHHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcCh
Q 004446 6 KEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGN 82 (753)
Q Consensus 6 kedernekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN 82 (753)
...++++++|++||+.++|++||||++++|.|||+|+|||||++|+||||+|| | |||||+||.|++|+|+.|+..||
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 45688999999999999999999999999999999999999999999999998 5 99999999999999999999999
Q ss_pred HHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHhhhcccccCC
Q 004446 83 QRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (753)
Q Consensus 83 ~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIraKYveKrF~~~~ 126 (753)
.+||++||++++.. ..+|..+ +.+++|||+|||.|+|+.+.
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 99999999997654 4455432 26789999999999999865
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=5.3e-35 Score=269.69 Aligned_cols=112 Identities=33% Similarity=0.681 Sum_probs=92.5
Q ss_pred HHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC---cceeeeccCcCCHHHHHHHHhcChHHHHHHH
Q 004446 13 RIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEVL 89 (753)
Q Consensus 13 kiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG---HRVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~ 89 (753)
++|++|++.++|++|||||+++|+|||++||||||+.|+||||+|| |+||||+||+|+++||++|+.+||.++|++|
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 004446 90 LKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (753)
Q Consensus 90 Ea~~~~~~~p~Pdssd~~~lreFIraKYveKrF~~~ 125 (753)
|++.. ...+.+..++.+.+++||++||++|+|+.+
T Consensus 82 e~~~~-~~~~~~~~~~~~~~~~fI~~KY~~k~f~~~ 116 (116)
T PF01412_consen 82 EANSP-PPKKPPPSSDQEKREQFIRAKYVEKAFISK 116 (116)
T ss_dssp TTTST-TTTTHCTTSHHHHHHHHHHHHHTTHTTS-C
T ss_pred HcCCC-CCCCCCCCCcHHHHHHHHHHHHHhhhhccC
Confidence 99933 334445567788889999999999999853
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=2e-33 Score=258.06 Aligned_cols=107 Identities=28% Similarity=0.631 Sum_probs=98.0
Q ss_pred CCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcChHHHHHHHhhcCCCCCC
Q 004446 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEWDPQRQ 98 (753)
Q Consensus 22 pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~Ea~~~~~~~ 98 (753)
++|++||||++++|+|||++||||||++|+||||+|| | +||||+||+|++++|++|+.+||+++|++||++++....
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 004446 99 SFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (753)
Q Consensus 99 p~Pdssd~~~lreFIraKYveKrF~~~~~~ 128 (753)
+.+..++.+.+++||+.||++|+|+.++..
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 556666677889999999999999987654
No 7
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.97 E-value=2.5e-30 Score=274.72 Aligned_cols=119 Identities=21% Similarity=0.531 Sum_probs=103.3
Q ss_pred HHHHHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcChHHH
Q 004446 9 EKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRA 85 (753)
Q Consensus 9 ernekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN~~a 85 (753)
...++++..|.+.++|++|||||+++|+|||+|||||||++||||||+|| | +||||+||+|+++||++|+.+||.+|
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 34567888888899999999999999999999999999999999999999 4 99999999999999999999999999
Q ss_pred HHHHhhcCCCC-CCCCCCCChHHHHHHHHHHHhhhcccccCCC
Q 004446 86 KEVLLKEWDPQ-RQSFPDSSNVERLRNFIKHVYVDRRYTGERN 127 (753)
Q Consensus 86 N~i~Ea~~~~~-~~p~Pdssd~~~lreFIraKYveKrF~~~~~ 127 (753)
|+|||++.-.. ..+.-...|...+++||++||++++|+....
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~ 127 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSS 127 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccccc
Confidence 99999987542 1222234556678899999999999998643
No 8
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.92 E-value=3.3e-25 Score=235.70 Aligned_cols=116 Identities=23% Similarity=0.397 Sum_probs=97.4
Q ss_pred HHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcChHHHHHH
Q 004446 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (753)
Q Consensus 12 ekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN~~aN~i 88 (753)
.++|++|+++++|++|+||++++|+||++|||||||++|+||||.|| | +||||+||+|++++|++|+.+||.++|+|
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 45799999999999999999999999999999999999999999998 4 89999999999999999999999999999
Q ss_pred HhhcCCCCCCCCC--CCChHHHHHHHHHHHhhhcccccCCC
Q 004446 89 LLKEWDPQRQSFP--DSSNVERLRNFIKHVYVDRRYTGERN 127 (753)
Q Consensus 89 ~Ea~~~~~~~p~P--dssd~~~lreFIraKYveKrF~~~~~ 127 (753)
|+.+.-....... ..+....+.+-+.+|++++.+..+..
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 9875421111111 13445555556899999999987654
No 9
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.90 E-value=1.7e-24 Score=239.40 Aligned_cols=116 Identities=22% Similarity=0.463 Sum_probs=106.5
Q ss_pred HHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC---cceeeeccCcCCHHHHHHHHhcChHHHHHH
Q 004446 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (753)
Q Consensus 12 ekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG---HRVKSlsLD~Wt~eEV~~m~~gGN~~aN~i 88 (753)
...|+.|...+||.+|+||+.++|.||++|+|+++|++|+||||.|| +||++|.||.|..|.+.+|..+||+.||++
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 45678888999999999999999999999999999999999999998 499999999999999999999999999999
Q ss_pred HhhcCCCCCCCCCCCChHHHHHHHHHHHhhhcccccCCCC
Q 004446 89 LLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (753)
Q Consensus 89 ~Ea~~~~~~~p~Pdssd~~~lreFIraKYveKrF~~~~~~ 128 (753)
||.......+|.|+++.+ ++|+||++||++|.|......
T Consensus 581 WE~~~~G~~KPs~~s~RE-EkErwIr~KYeqklFLaPl~~ 619 (749)
T KOG0705|consen 581 WEGSSQGQTKPSPDSSRE-EKERWIRAKYEQKLFLAPLPC 619 (749)
T ss_pred hhhhccCCcCCCccccHH-HHHHHHHHHHHHHhhcCCCCC
Confidence 999877777888877655 468899999999999987665
No 10
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.90 E-value=1.9e-24 Score=228.66 Aligned_cols=86 Identities=33% Similarity=0.680 Sum_probs=80.1
Q ss_pred hHHHHHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcChHH
Q 004446 8 DEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQR 84 (753)
Q Consensus 8 dernekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN~~ 84 (753)
+.++++.|+.|....+|++|+||++.+|+|||++||||||++|+|+||.|| | +||||+||+|.+.||++|+++||++
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 356788888888888999999999999999999999999999999999999 5 9999999999999999999999999
Q ss_pred HHHHHhhcC
Q 004446 85 AKEVLLKEW 93 (753)
Q Consensus 85 aN~i~Ea~~ 93 (753)
+++|++..-
T Consensus 83 ~~eFL~s~~ 91 (386)
T KOG0704|consen 83 FREFLSSQG 91 (386)
T ss_pred HHHHHhhCc
Confidence 999998753
No 11
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.88 E-value=1.6e-23 Score=227.30 Aligned_cols=84 Identities=21% Similarity=0.561 Sum_probs=79.8
Q ss_pred HHHHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcChHHHH
Q 004446 10 KNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAK 86 (753)
Q Consensus 10 rnekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN~~aN 86 (753)
...++++.|...++||+|+||++++|+|++|+|||||||+|+++||+|| | +|||..||+|+.++|.+|+.+||.+|+
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 HHHhhcC
Q 004446 87 EVLLKEW 93 (753)
Q Consensus 87 ~i~Ea~~ 93 (753)
.|+..+-
T Consensus 89 ~FFkqhg 95 (454)
T KOG0706|consen 89 VFFKQHG 95 (454)
T ss_pred HHHHHcC
Confidence 9998754
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.81 E-value=6.3e-21 Score=222.63 Aligned_cols=115 Identities=22% Similarity=0.451 Sum_probs=101.6
Q ss_pred HHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcChHHHHHHHh
Q 004446 14 IIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLL 90 (753)
Q Consensus 14 iLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~E 90 (753)
.+..+.+.++|..|+|||++.|+|+++|+||.+||+|+||||+|| | ||+||+||.|..+.+.+++.+||..+|.|||
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 004446 91 KEWDPQR--QSFPDSSNVERLRNFIKHVYVDRRYTGERNYD 129 (753)
Q Consensus 91 a~~~~~~--~p~Pdssd~~~lreFIraKYveKrF~~~~~~d 129 (753)
+.+.... ++.+..+ ...++.||++||++++|.-+....
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 9987543 3334333 666788999999999999776543
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.72 E-value=1.5e-18 Score=190.28 Aligned_cols=108 Identities=19% Similarity=0.395 Sum_probs=93.8
Q ss_pred HccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcChHHHHHHHhhcCC-
Q 004446 19 LKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEWD- 94 (753)
Q Consensus 19 lk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~Ea~~~- 94 (753)
++...-+.|+||+.++|.|||||-|+|||.+|+.|||.|| | .||+|....|.++.|+++..+.|..+|.|||..+-
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 3455668999999999999999999999999999999999 4 89999999999999999999999999999998763
Q ss_pred C------CCCCCCCCChHHHHHHHHHHHhhhcccccCC
Q 004446 95 P------QRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (753)
Q Consensus 95 ~------~~~p~Pdssd~~~lreFIraKYveKrF~~~~ 126 (753)
+ .+++.|.+.....+.+|||+||+...|+.+.
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~~ 120 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHRL 120 (669)
T ss_pred chhhhcccCCCCCcCCCCccHHHHHHHHHHheeeeccC
Confidence 2 2456666555556788999999999999843
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.66 E-value=4.9e-17 Score=186.24 Aligned_cols=110 Identities=26% Similarity=0.534 Sum_probs=99.5
Q ss_pred HHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccCC---cceeeeccC--cCCHHHHHHHHhcChHHHHHHHh
Q 004446 16 RGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMA--KFTSQEVKALQEGGNQRAKEVLL 90 (753)
Q Consensus 16 r~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~LG---HRVKSlsLD--~Wt~eEV~~m~~gGN~~aN~i~E 90 (753)
.++....+|+.|+||++..|.||++|++|.||..|+|-||.|| ++|+|++|| .|+.+.|+++..+||.++|.||-
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 4567788999999999999999999999999999999999998 699999999 69999999999999999999999
Q ss_pred hcCCCCCCCCCCCChHHHHHHHHHHHhhhcccccCC
Q 004446 91 KEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (753)
Q Consensus 91 a~~~~~~~p~Pdssd~~~lreFIraKYveKrF~~~~ 126 (753)
.++.+...-.|+++- ..+++||+.||.+.+|....
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 999887777777644 45688999999999998653
No 15
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=97.50 E-value=0.023 Score=64.74 Aligned_cols=41 Identities=10% Similarity=0.054 Sum_probs=24.8
Q ss_pred cCCCCCCCCCCCCCCCCcccccCCCCCCCCCCccccccCCccCc
Q 004446 517 QNAQGPPAAQPAQSVPKPALESASGGLSQPSPVEVKSTGRTALP 560 (753)
Q Consensus 517 q~~~~~p~~~~~~~~~~~~~~~~~~~~s~~~~~e~k~sgrkeLP 560 (753)
|+...+-+++++.....-+... ..+.+..+|....+|+++|
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 6666666666553333222222 2456677788888888887
No 16
>PLN03131 hypothetical protein; Provisional
Probab=92.10 E-value=15 Score=44.02 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=13.4
Q ss_pred CCCCccccCCcCcccccCCCC
Q 004446 355 DNNWASFDLAPQVKVSQTSSN 375 (753)
Q Consensus 355 ~~~wasFD~~~~~~~~q~~~~ 375 (753)
+.+||+||...+-..++...+
T Consensus 431 negwa~fd~~~p~~s~~~~~n 451 (705)
T PLN03131 431 NEGWATFDGIQPIASTPGNEN 451 (705)
T ss_pred ccCcccccCCCcccccCCccc
Confidence 789999997655444443333
No 17
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=91.21 E-value=0.023 Score=68.58 Aligned_cols=70 Identities=17% Similarity=0.275 Sum_probs=56.1
Q ss_pred ccCCCCCCcCCCC-CCCCeeEeceeeeeecccccccccCC-c--ceeeeccCcCCHHHHHHHHhcChHHHHHHHhh
Q 004446 20 KLQDNRRCINCNS-LGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLK 91 (753)
Q Consensus 20 k~pgNk~CADCGs-~~P~WaSvN~GVFVC~~CSGIHR~LG-H--RVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~Ea 91 (753)
+...+..|++|.+ ..-.|+|+|+.+-+|+.|+++|+.++ | .+.++.|++..+ |..+...|+..++..|..
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~ 699 (785)
T KOG0521|consen 626 KASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATAS 699 (785)
T ss_pred HhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhh
Confidence 3455789999998 57999999999999999999999996 4 667777777766 777777776666666544
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=80.75 E-value=0.9 Score=34.82 Aligned_cols=40 Identities=15% Similarity=0.471 Sum_probs=33.7
Q ss_pred CCCCCcCCCCCCCCeeEeceeeeeecccccc-cccCCcceeee
Q 004446 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGI-HREFTHRVKSV 64 (753)
Q Consensus 23 gNk~CADCGs~~P~WaSvN~GVFVC~~CSGI-HR~LGHRVKSl 64 (753)
.+..|..|......|.+.+=.++||..|... |+. |+|..|
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 3578999999889999999999999999998 877 877664
No 19
>PRK12495 hypothetical protein; Provisional
Probab=76.74 E-value=2.4 Score=44.66 Aligned_cols=30 Identities=17% Similarity=0.209 Sum_probs=24.3
Q ss_pred cCCCCCCcCCCCCCCCeeEeceeeeeeccccccc
Q 004446 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 21 ~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIH 54 (753)
...++.|-+||.+-|.+ -|+.+|..|..+-
T Consensus 39 tmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH----DGQEFCPTCQQPV 68 (226)
T ss_pred ccchhhcccccCcccCC----CCeeECCCCCCcc
Confidence 35678999999998832 6999999999653
No 20
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=73.47 E-value=4.5 Score=41.75 Aligned_cols=39 Identities=26% Similarity=0.440 Sum_probs=29.8
Q ss_pred HHHHcc----CCCCCCcCCCCCCC-CeeEeceeeeeeccccccc
Q 004446 16 RGLLKL----QDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 16 r~Llk~----pgNk~CADCGs~~P-~WaSvN~GVFVC~~CSGIH 54 (753)
.+|++. +.-..|+.||.... .|.+..-|.|+|..|...|
T Consensus 137 ~~lL~~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~~~ 180 (247)
T PRK00085 137 LRLLAELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGDPY 180 (247)
T ss_pred HHHHHHcCCccchhhHhcCCCCCCceEEecccCCcccccccCcc
Confidence 355553 44469999998744 7889999999999998433
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=60.87 E-value=6.8 Score=40.30 Aligned_cols=38 Identities=24% Similarity=0.530 Sum_probs=29.3
Q ss_pred HHHcc----CCCCCCcCCCCCCC-CeeEeceeeeeeccccccc
Q 004446 17 GLLKL----QDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 17 ~Llk~----pgNk~CADCGs~~P-~WaSvN~GVFVC~~CSGIH 54 (753)
+|++. |.-..|+.||..++ .|.+...|.|+|.+|...+
T Consensus 136 ~lL~~~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~~ 178 (241)
T TIGR00613 136 KLLQILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEKD 178 (241)
T ss_pred HHHHHcCCCcccCccCCCCCcCCCceEchhcCeEEChhhCccC
Confidence 55553 45579999998544 6889999999999998753
No 22
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=53.00 E-value=2.7 Score=40.48 Aligned_cols=48 Identities=15% Similarity=0.252 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHHHccCCCC--CCcCCCCCCC-CeeEeceeeeeeccccccc
Q 004446 7 EDEKNERIIRGLLKLQDNR--RCINCNSLGT-QYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 7 edernekiLr~Llk~pgNk--~CADCGs~~P-~WaSvN~GVFVC~~CSGIH 54 (753)
+.....++-..|.++.... +|.+||.+=| .=.-..-++.+|+.|.-.|
T Consensus 61 ~r~~l~~i~~al~rIe~gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~ 111 (120)
T COG1734 61 ERKLLRKIESALDRIEEGTYGICEECGEPIPEARLEARPTARLCIECQERA 111 (120)
T ss_pred HHHHHHHHHHHHHHHHcCCccchhccCCcCCHHHHhhCcchHHHHHHHHHH
Confidence 3334444444555544443 8999999722 1122233567999998765
No 23
>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=51.64 E-value=8.8 Score=30.12 Aligned_cols=27 Identities=30% Similarity=0.563 Sum_probs=21.1
Q ss_pred CCcCCCCCCCCeeEeceeeeeecccccc
Q 004446 26 RCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (753)
Q Consensus 26 ~CADCGs~~P~WaSvN~GVFVC~~CSGI 53 (753)
+|-.||+.. ......-|.+||..|--|
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 455667899999999654
No 24
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=50.22 E-value=8.2 Score=40.93 Aligned_cols=38 Identities=21% Similarity=0.451 Sum_probs=29.5
Q ss_pred HHHHHHcc----CCCCCCcCCCCCC-CCeeEeceeeeeecccc
Q 004446 14 IIRGLLKL----QDNRRCINCNSLG-TQYVCTNFWTFVCTNCS 51 (753)
Q Consensus 14 iLr~Llk~----pgNk~CADCGs~~-P~WaSvN~GVFVC~~CS 51 (753)
...+||.. +.=..|+.||.+. +..+++-.|-+||.+|.
T Consensus 140 fel~lL~~~G~~~~l~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 140 FELKLLGELGIGPNLTSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHHHHHHcCCccchHHHhCcCCcCCCcceeeccCcccchhcc
Confidence 33455553 3336999999975 57999999999999999
No 25
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=47.06 E-value=73 Score=38.29 Aligned_cols=15 Identities=27% Similarity=0.043 Sum_probs=7.2
Q ss_pred CCCCCCCCcccchhh
Q 004446 251 DPESSSPPVVRPVRE 265 (753)
Q Consensus 251 d~~~sspp~vr~~~~ 265 (753)
+.|..+-+.||--+|
T Consensus 711 I~DPiSGGEVRdR~E 725 (757)
T KOG4368|consen 711 IQDPISGGEVRDRWE 725 (757)
T ss_pred ccCcccCccccchhh
Confidence 444444455554444
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=46.83 E-value=5.9 Score=30.56 Aligned_cols=27 Identities=30% Similarity=0.653 Sum_probs=16.9
Q ss_pred CCCcCCCCC-CCCeeEeceeeeeecccc
Q 004446 25 RRCINCNSL-GTQYVCTNFWTFVCTNCS 51 (753)
Q Consensus 25 k~CADCGs~-~P~WaSvN~GVFVC~~CS 51 (753)
.+|.+|+.. .-.|..-+|+.-||.+|.
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 479999995 678999999999999995
No 27
>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=46.09 E-value=15 Score=28.48 Aligned_cols=29 Identities=21% Similarity=0.475 Sum_probs=24.0
Q ss_pred CCCCCCcCCCCCCCCeeEeceeeeeecccccc
Q 004446 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (753)
Q Consensus 22 pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGI 53 (753)
..|..|..|++. |...+=|-++|.+|-.+
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCceE
Confidence 345679999998 88889999999999643
No 28
>PRK00420 hypothetical protein; Validated
Probab=39.35 E-value=60 Score=31.19 Aligned_cols=46 Identities=15% Similarity=0.155 Sum_probs=31.4
Q ss_pred hhhHHHHHHHHHHHc--cCCCCCCcCCCCCCCCeeEeceeeeeeccccccc
Q 004446 6 KEDEKNERIIRGLLK--LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 6 kedernekiLr~Llk--~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIH 54 (753)
++++..+++-+.|++ .--+..|-.||.+-.. ++-|-.+|..|..+.
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 345555666566666 3346899999976433 267899999998754
No 29
>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=37.52 E-value=12 Score=32.21 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=22.1
Q ss_pred cCCCCCCcCCCCCCC--CeeEeceeeeeeccccccc
Q 004446 21 LQDNRRCINCNSLGT--QYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 21 ~pgNk~CADCGs~~P--~WaSvN~GVFVC~~CSGIH 54 (753)
..+...|.|||..=| .+. ..-|+..|+.|...+
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 355679999999633 222 234778899997654
No 30
>PF14376 Haem_bd: Haem-binding domain
Probab=37.23 E-value=17 Score=35.41 Aligned_cols=25 Identities=32% Similarity=0.624 Sum_probs=17.5
Q ss_pred HHHHHHHHHHccCCCCCCcCCCCCCCCee
Q 004446 10 KNERIIRGLLKLQDNRRCINCNSLGTQYV 38 (753)
Q Consensus 10 rnekiLr~Llk~pgNk~CADCGs~~P~Wa 38 (753)
...+.++.|++ +-|.||++.+..|-
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 34455566664 57999999877765
No 31
>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=34.12 E-value=25 Score=33.36 Aligned_cols=43 Identities=21% Similarity=0.471 Sum_probs=29.6
Q ss_pred cCCCCCCcCCCCCCCCeeEeceeeeeecccccccccC--Cc--ceeeeccC
Q 004446 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSMA 67 (753)
Q Consensus 21 ~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~L--GH--RVKSlsLD 67 (753)
.|.--+|.+|+.. ..+..-.|.|-.|.+..-.+ |. +|++|.++
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 4666799999942 23322358899999876555 32 88888765
No 32
>PRK11019 hypothetical protein; Provisional
Probab=32.23 E-value=17 Score=33.49 Aligned_cols=31 Identities=13% Similarity=0.199 Sum_probs=21.7
Q ss_pred CCCCcCCCCCCC--CeeEeceeeeeecccccccc
Q 004446 24 NRRCINCNSLGT--QYVCTNFWTFVCTNCSGIHR 55 (753)
Q Consensus 24 Nk~CADCGs~~P--~WaSvN~GVFVC~~CSGIHR 55 (753)
-.+|.|||.+=| .|.- --++-.|+.|...+-
T Consensus 36 yg~C~~CG~~Ip~~Rl~A-~P~a~~Cv~Cq~~~E 68 (88)
T PRK11019 36 LTECEECGEPIPEARRKA-IPGVRLCVACQQEKD 68 (88)
T ss_pred CCeeCcCCCcCcHHHHhh-cCCccccHHHHHHHH
Confidence 469999999733 3322 236779999998753
No 33
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=31.86 E-value=56 Score=30.34 Aligned_cols=31 Identities=13% Similarity=0.306 Sum_probs=24.1
Q ss_pred CCCCCCcCCCCCCCCeeEeceeeeeeccccccc
Q 004446 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 22 pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIH 54 (753)
..-..|-.|+.+ .---+..||+.|..|-..-
T Consensus 33 ~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~~f 63 (89)
T COG1997 33 RAKHVCPFCGRT--TVKRIATGIWKCRKCGAKF 63 (89)
T ss_pred hcCCcCCCCCCc--ceeeeccCeEEcCCCCCee
Confidence 445699999998 4446789999999997543
No 34
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=31.39 E-value=17 Score=36.37 Aligned_cols=34 Identities=29% Similarity=0.641 Sum_probs=27.9
Q ss_pred CCCCCCcCCCCCCCCeeEeceeeeeec-cccccccc
Q 004446 22 QDNRRCINCNSLGTQYVCTNFWTFVCT-NCSGIHRE 56 (753)
Q Consensus 22 pgNk~CADCGs~~P~WaSvN~GVFVC~-~CSGIHR~ 56 (753)
|--+.|+-|| -.--|.|++-|.-.|. .|-.+|.+
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 3346899999 6778999999998874 79999965
No 35
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=30.83 E-value=18 Score=36.33 Aligned_cols=30 Identities=13% Similarity=0.189 Sum_probs=18.7
Q ss_pred CCCcCCCCCC-CCeeEeceeeeeeccccccc
Q 004446 25 RRCINCNSLG-TQYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 25 k~CADCGs~~-P~WaSvN~GVFVC~~CSGIH 54 (753)
-+|.+||..= ..=.-+--++-.|+.|...+
T Consensus 87 G~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 87 GICEVCGKPIPYERLEAIPTATTCVECQNRK 117 (159)
T ss_pred CeecccCCcccHHHHhhCCCcchhHHHHHHh
Confidence 5899999861 11111222456899998765
No 36
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=30.58 E-value=17 Score=36.23 Aligned_cols=34 Identities=15% Similarity=0.283 Sum_probs=20.4
Q ss_pred CCCCCCcCCCCCCC-CeeEeceeeeeecccccccc
Q 004446 22 QDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIHR 55 (753)
Q Consensus 22 pgNk~CADCGs~~P-~WaSvN~GVFVC~~CSGIHR 55 (753)
..-.+|.+||.+=| .=.-+-=++..|+.|...|-
T Consensus 109 gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E 143 (151)
T PRK10778 109 EDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAE 143 (151)
T ss_pred CCCceeccCCCcccHHHHhcCCCccccHHHHHHHH
Confidence 44469999998611 11111223468999987653
No 37
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=28.98 E-value=23 Score=33.49 Aligned_cols=43 Identities=12% Similarity=0.338 Sum_probs=30.1
Q ss_pred cCCCCCCcCCCCCCCCeeEeceeeeeecccccccccC--Cc--ceeeecc
Q 004446 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSM 66 (753)
Q Consensus 21 ~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~L--GH--RVKSlsL 66 (753)
.|..-+|-+||.. |....+..+.|-.|-+..-.+ |. +|++|.+
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 4667799999953 222344557899999987666 32 8888765
No 38
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=28.61 E-value=99 Score=29.22 Aligned_cols=51 Identities=24% Similarity=0.531 Sum_probs=32.3
Q ss_pred hhhhHHHHHHHHHH----Hc----cC----CCCCCcCCCCC-----CCCeeEeceeeeeecccccccc
Q 004446 5 LKEDEKNERIIRGL----LK----LQ----DNRRCINCNSL-----GTQYVCTNFWTFVCTNCSGIHR 55 (753)
Q Consensus 5 ~kedernekiLr~L----lk----~p----gNk~CADCGs~-----~P~WaSvN~GVFVC~~CSGIHR 55 (753)
.+|+++..++..+| .+ .. +.+.|+-|+.+ +..-.|.+-.--||..|...++
T Consensus 23 ~~E~~Ri~kLk~~L~~e~~r~~~~~~~~~~~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~ 90 (118)
T PF02318_consen 23 KKEEERIRKLKQELQKEKMRREALGNSQKYGERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSK 90 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCSCSTTHCCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETS
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccccccccCCcchhhhCCcccccCCCCCcCCcCCccccCccCCcCC
Confidence 44555555555555 11 12 55799999874 4556677888889999988754
No 39
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=28.59 E-value=38 Score=33.54 Aligned_cols=43 Identities=19% Similarity=0.528 Sum_probs=30.2
Q ss_pred hhhHHHHHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccccccccC
Q 004446 6 KEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF 57 (753)
Q Consensus 6 kedernekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~L 57 (753)
.++.+.+++|+.+........|.-||.. +-.+|..|.|-|+.+
T Consensus 81 ~e~G~L~~lL~~~~~~~~~~~C~~Cgg~---------rfv~C~~C~Gs~k~~ 123 (147)
T cd03031 81 NESGELRKLLKGIRARAGGGVCEGCGGA---------RFVPCSECNGSCKVF 123 (147)
T ss_pred HHcCCHHHHHhhcccccCCCCCCCCCCc---------CeEECCCCCCcceEE
Confidence 3455566666666555566679999853 345899999988764
No 40
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.20 E-value=26 Score=33.31 Aligned_cols=43 Identities=19% Similarity=0.373 Sum_probs=27.9
Q ss_pred CCCCCCcCCCCCCCCeeEeceeeeeecccccccccC--Cc--ceeeeccC
Q 004446 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSMA 67 (753)
Q Consensus 22 pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~L--GH--RVKSlsLD 67 (753)
+.--+|.+||.. |-...+..+.|-.|.+..-.+ |. +|++|.++
T Consensus 69 p~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~~~i~~G~El~I~~iE~~ 115 (117)
T PRK00564 69 KVELECKDCSHV---FKPNALDYGVCEKCHSKNVIITQGNEMRLLSLEML 115 (117)
T ss_pred CCEEEhhhCCCc---cccCCccCCcCcCCCCCceEEecCCEEEEEEEEEE
Confidence 444589999943 222234455699999876565 32 88888764
No 41
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=28.17 E-value=42 Score=27.71 Aligned_cols=36 Identities=17% Similarity=0.359 Sum_probs=28.9
Q ss_pred CCCCCcCCCCC-CCCeeEeceee-eeecccccccccCC
Q 004446 23 DNRRCINCNSL-GTQYVCTNFWT-FVCTNCSGIHREFT 58 (753)
Q Consensus 23 gNk~CADCGs~-~P~WaSvN~GV-FVC~~CSGIHR~LG 58 (753)
..+.|.+|+.. -|.|=.-..|. +||-.|.--.+..+
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 99999987666654
No 42
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=28.11 E-value=43 Score=36.64 Aligned_cols=34 Identities=21% Similarity=0.354 Sum_probs=24.2
Q ss_pred CCCCCCcCCCCCCCCeeEeceeeeeeccccccccc
Q 004446 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (753)
Q Consensus 22 pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~ 56 (753)
....+|-+||... -=....-|..||.+|--|..+
T Consensus 9 ~~~~~Cp~Cg~~~-iv~d~~~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 9 EEKLVCPECGSDK-LIYDYERGEIVCADCGLVIEE 42 (310)
T ss_pred ccCCcCcCCCCCC-eeEECCCCeEeecccCCcccc
Confidence 3446899999742 222456799999999987644
No 43
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=27.39 E-value=34 Score=26.35 Aligned_cols=30 Identities=23% Similarity=0.419 Sum_probs=16.0
Q ss_pred CCCcCCCCCCCCeeE---eceeeeeecccccccc
Q 004446 25 RRCINCNSLGTQYVC---TNFWTFVCTNCSGIHR 55 (753)
Q Consensus 25 k~CADCGs~~P~WaS---vN~GVFVC~~CSGIHR 55 (753)
|.|-.||.+- ++.. -+.-=+||..|..||-
T Consensus 1 kfC~~CG~~l-~~~ip~gd~r~R~vC~~Cg~IhY 33 (34)
T PF14803_consen 1 KFCPQCGGPL-ERRIPEGDDRERLVCPACGFIHY 33 (34)
T ss_dssp -B-TTT--B--EEE--TT-SS-EEEETTTTEEE-
T ss_pred CccccccChh-hhhcCCCCCccceECCCCCCEEe
Confidence 5788999872 3322 2455679999999984
No 44
>KOG1985 consensus Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.00 E-value=9.8e+02 Score=30.47 Aligned_cols=12 Identities=33% Similarity=0.567 Sum_probs=8.9
Q ss_pred CCCCCCcCCCCC
Q 004446 690 MPPRPYLGPQVP 701 (753)
Q Consensus 690 ~~~~~ym~qQ~~ 701 (753)
.++..|+.+|.|
T Consensus 84 ~~~~Sy~~~~~p 95 (887)
T KOG1985|consen 84 VGPPSYQQLQAP 95 (887)
T ss_pred CCCcchhhccCC
Confidence 566778887777
No 45
>PRK13844 recombination protein RecR; Provisional
Probab=25.91 E-value=67 Score=33.73 Aligned_cols=42 Identities=31% Similarity=0.629 Sum_probs=31.4
Q ss_pred hhHHHHHHHHHHHccCCC-CCCcCCCCCCCCeeEeceeeeeeccccccccc
Q 004446 7 EDEKNERIIRGLLKLQDN-RRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (753)
Q Consensus 7 edernekiLr~Llk~pgN-k~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~ 56 (753)
.++..+++.+.|.....| +.|--|+...- .-+|.-|+.-.|.
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 445567777888887777 79999997542 1379999998886
No 46
>PHA00080 DksA-like zinc finger domain containing protein
Probab=25.91 E-value=19 Score=31.83 Aligned_cols=32 Identities=16% Similarity=0.275 Sum_probs=20.9
Q ss_pred CCCCCCcCCCCCC--CCeeEeceeeeeeccccccc
Q 004446 22 QDNRRCINCNSLG--TQYVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 22 pgNk~CADCGs~~--P~WaSvN~GVFVC~~CSGIH 54 (753)
....+|.|||..= ..|.- .-++..|+.|...+
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 3345899999963 23322 23566799998764
No 47
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=25.65 E-value=46 Score=31.89 Aligned_cols=23 Identities=22% Similarity=0.563 Sum_probs=20.9
Q ss_pred CeeEecee--eeeecccccccccCC
Q 004446 36 QYVCTNFW--TFVCTNCSGIHREFT 58 (753)
Q Consensus 36 ~WaSvN~G--VFVC~~CSGIHR~LG 58 (753)
.|++-.-| |.-|.+|--|||.-+
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~ 76 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEG 76 (112)
T ss_pred ceeEcCCCCEEeeccccceecccch
Confidence 99998889 999999999999844
No 48
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=24.94 E-value=81 Score=29.38 Aligned_cols=41 Identities=12% Similarity=0.252 Sum_probs=28.7
Q ss_pred HHHHHHHHHc-cCCCCCCcCCCCCCCCeeEeceeeeeecccccc
Q 004446 11 NERIIRGLLK-LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (753)
Q Consensus 11 nekiLr~Llk-~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGI 53 (753)
.++.+++|.. ...--.|--|+........+ ||..|..|.-.
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vkR~a~--GIW~C~~C~~~ 63 (90)
T PTZ00255 22 LRKQIKKIEISQHAKYFCPFCGKHAVKRQAV--GIWRCKGCKKT 63 (90)
T ss_pred HHHHHHHHHHHHhCCccCCCCCCCceeeeee--EEEEcCCCCCE
Confidence 3445555544 44556999999887776654 99999999743
No 49
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.23 E-value=41 Score=32.36 Aligned_cols=46 Identities=15% Similarity=0.405 Sum_probs=29.5
Q ss_pred cCCCCCCcCCCCCC-CCeeEecee--eeeecccccccccC--Cc--ceeeeccC
Q 004446 21 LQDNRRCINCNSLG-TQYVCTNFW--TFVCTNCSGIHREF--TH--RVKSVSMA 67 (753)
Q Consensus 21 ~pgNk~CADCGs~~-P~WaSvN~G--VFVC~~CSGIHR~L--GH--RVKSlsLD 67 (753)
.+.--+| +||... ..+..+..- .+.|-.|-+.+-.+ |. +|++|.++
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 4666799 999652 222222111 36799999877665 33 89999876
No 50
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.22 E-value=1.9e+02 Score=34.03 Aligned_cols=20 Identities=10% Similarity=-0.011 Sum_probs=12.5
Q ss_pred ceeceecCCCCCCCCcccccCCCCCC
Q 004446 586 MVYAMQYNTAAPMPNFVHSKSTTNPF 611 (753)
Q Consensus 586 mg~~mqy~~~~p~~~~~~~~ks~NPF 611 (753)
-|..+||+| |+.++-+-|+|
T Consensus 410 s~p~pq~qN------yppp~p~f~m~ 429 (483)
T KOG2236|consen 410 SGPSPQQQN------YPPPSPSFPMF 429 (483)
T ss_pred CCCCcccCC------CCCCCCCCCcc
Confidence 355677666 56666666666
No 51
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=24.16 E-value=36 Score=32.22 Aligned_cols=42 Identities=21% Similarity=0.426 Sum_probs=28.3
Q ss_pred cCCCCCCcCCCCCCCCeeEeceeeeeecccccccccC--Cc--ceeeecc
Q 004446 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSM 66 (753)
Q Consensus 21 ~pgNk~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~L--GH--RVKSlsL 66 (753)
.|..-+|-+||.. ..+....|.|-.|-+....+ |. +|++|.+
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 22333456699999876555 43 8888765
No 52
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=23.77 E-value=19 Score=31.87 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=19.8
Q ss_pred CCCcCCCCCCCC-eeEeceeeeeeccccccc
Q 004446 25 RRCINCNSLGTQ-YVCTNFWTFVCTNCSGIH 54 (753)
Q Consensus 25 k~CADCGs~~P~-WaSvN~GVFVC~~CSGIH 54 (753)
..|.|||.+=|. =.-.--|+..|+.|...+
T Consensus 35 ~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 35 YLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred ccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 589999997332 111223778999998653
No 53
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=23.31 E-value=1e+02 Score=24.59 Aligned_cols=42 Identities=17% Similarity=0.335 Sum_probs=27.4
Q ss_pred hHHHHHHHHHHHccCCCCCCcCCCCCCCCeeEeceeeeeecccc
Q 004446 8 DEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCS 51 (753)
Q Consensus 8 dernekiLr~Llk~pgNk~CADCGs~~P~WaSvN~GVFVC~~CS 51 (753)
|+.-.+.|+.+. =++.-+|-.||.....++. +.+.|-|..|.
T Consensus 3 e~~c~~~l~~~R-W~~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 3 EEACREYLEEIR-WPDGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred HHHHHHHHHHhc-CCCCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 344444554443 3444789999998554443 36999999985
No 54
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=23.14 E-value=2.1e+02 Score=33.25 Aligned_cols=27 Identities=19% Similarity=0.177 Sum_probs=12.6
Q ss_pred cccccCccCCCCCCchhhhcccCCccc
Q 004446 179 DKNSRYGYDERSPGNEQENRQFGDYRR 205 (753)
Q Consensus 179 dk~~r~gydd~~p~~d~~~~~~G~~~r 205 (753)
.|..|..||=.----+-|.=+.|+|.-
T Consensus 215 ~rkVRALYDFeAaE~nELsFkaGdIIt 241 (462)
T KOG2199|consen 215 VRKVRALYDFEAAEDNELSFKAGDIIT 241 (462)
T ss_pred chhhhhhhcccccCCCccceecCcEEE
Confidence 334566666221111234456667665
No 55
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.38 E-value=58 Score=31.77 Aligned_cols=25 Identities=12% Similarity=0.355 Sum_probs=17.8
Q ss_pred eeeeecccccccccC--Cc--ceeeeccC
Q 004446 43 WTFVCTNCSGIHREF--TH--RVKSVSMA 67 (753)
Q Consensus 43 GVFVC~~CSGIHR~L--GH--RVKSlsLD 67 (753)
..+.|-.|-+.+-.+ |. +|++|.++
T Consensus 106 ~~~~CP~Cgs~~~~i~~G~el~i~~ie~e 134 (135)
T PRK03824 106 AFLKCPKCGSRDFEIVKGRGVYIEEIKIE 134 (135)
T ss_pred cCcCCcCCCCCCcEEecCceEEEEEEEEe
Confidence 446799999875444 43 88888765
No 56
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.24 E-value=43 Score=34.14 Aligned_cols=30 Identities=27% Similarity=0.512 Sum_probs=20.4
Q ss_pred CCcCCCCCCCCeeEeceeeeeeccccccccc
Q 004446 26 RCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (753)
Q Consensus 26 ~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~ 56 (753)
.|-+|+.....-=-+++ -|.|..|-+.-..
T Consensus 119 ~Cp~C~~rytf~eA~~~-~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEY-GFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhhc-CCcCCCCCCCCee
Confidence 79999975322222344 5999999987544
No 57
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=22.21 E-value=1.2e+03 Score=26.74 Aligned_cols=17 Identities=29% Similarity=0.448 Sum_probs=10.8
Q ss_pred CCCCCC--CCCccccCCcC
Q 004446 350 ASSAND--NNWASFDLAPQ 366 (753)
Q Consensus 350 ~~s~~~--~~wasFD~~~~ 366 (753)
+.|.++ ..|--|..++.
T Consensus 369 A~Sg~GdfgD~~AF~aAPs 387 (499)
T KOG2057|consen 369 APSGGGDFGDLFAFGAAPS 387 (499)
T ss_pred ccCCCCcchhhhhhcCCCC
Confidence 344555 67888877654
No 58
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.10 E-value=48 Score=34.56 Aligned_cols=25 Identities=24% Similarity=0.635 Sum_probs=20.8
Q ss_pred CCCcCCCCCCCCeeEeceeeeeecccccc-ccc
Q 004446 25 RRCINCNSLGTQYVCTNFWTFVCTNCSGI-HRE 56 (753)
Q Consensus 25 k~CADCGs~~P~WaSvN~GVFVC~~CSGI-HR~ 56 (753)
+.|.-||. +.-+.|.|..|... ||.
T Consensus 310 ~~C~~cg~-------~~~r~~~C~~cg~~~~rD 335 (364)
T COG0675 310 KTCPCCGH-------LSGRLFKCPRCGFVHDRD 335 (364)
T ss_pred ccccccCC-------ccceeEECCCCCCeehhh
Confidence 79999999 56789999999985 444
No 59
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=21.12 E-value=82 Score=37.20 Aligned_cols=77 Identities=30% Similarity=0.499 Sum_probs=0.0
Q ss_pred hhhhHHHHHHHHHHHccCCCCCCcCCCCCC-CCeeEece---eeeeecccccc-cccCCcceeeeccC----cCCHHHHH
Q 004446 5 LKEDEKNERIIRGLLKLQDNRRCINCNSLG-TQYVCTNF---WTFVCTNCSGI-HREFTHRVKSVSMA----KFTSQEVK 75 (753)
Q Consensus 5 ~kedernekiLr~Llk~pgNk~CADCGs~~-P~WaSvN~---GVFVC~~CSGI-HR~LGHRVKSlsLD----~Wt~eEV~ 75 (753)
.+..-+-...|..-++..+|+.|-.||..+ -+|.|-+- ..-||..|-.+ |-...-+++.-.|+ +|..|-..
T Consensus 242 ~~~Qlrela~lNgt~r~~d~~~c~~cg~~~H~q~~cp~r~~~~~n~c~~cg~~gH~~~dc~~~~q~~~~~~~~~d~ey~~ 321 (554)
T KOG0119|consen 242 KRLQLRELARLNGTLRDDDNRACRNCGSTGHKQYDCPGRIPNTTNVCKICGPLGHISIDCKVNDQQMPMSSANFDREYAS 321 (554)
T ss_pred cHHHHHHHHHhCCCCCccccccccccCCCccccccCCcccccccccccccCCcccccccCCCcccccchhhhccCHHHHh
Q ss_pred HHHhcC
Q 004446 76 ALQEGG 81 (753)
Q Consensus 76 ~m~~gG 81 (753)
+|.++|
T Consensus 322 lm~e~~ 327 (554)
T KOG0119|consen 322 LMLELG 327 (554)
T ss_pred hhcccc
No 60
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=21.00 E-value=94 Score=26.14 Aligned_cols=41 Identities=24% Similarity=0.378 Sum_probs=27.7
Q ss_pred HHHHHHHHccCC----CC---CCcCCCCCCCCe--eEeceeeeeeccccc
Q 004446 12 ERIIRGLLKLQD----NR---RCINCNSLGTQY--VCTNFWTFVCTNCSG 52 (753)
Q Consensus 12 ekiLr~Llk~pg----Nk---~CADCGs~~P~W--aSvN~GVFVC~~CSG 52 (753)
+|+|.-|+-..+ |+ +|..|...+=.. .....-.|+|..|-.
T Consensus 3 Dki~d~L~G~d~~~~~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 3 DKILDVLLGDDPTSPSNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred HHHHHHHhCCCCccccCceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 567777776444 54 899998864333 344555899999964
No 61
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.69 E-value=61 Score=27.33 Aligned_cols=26 Identities=23% Similarity=0.549 Sum_probs=22.4
Q ss_pred CCCcCCCCCCCCeeEeceeeeeeccccc
Q 004446 25 RRCINCNSLGTQYVCTNFWTFVCTNCSG 52 (753)
Q Consensus 25 k~CADCGs~~P~WaSvN~GVFVC~~CSG 52 (753)
+.|..||..... ..+-.+|+|..|--
T Consensus 29 q~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 29 QTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred cCccCccccccc--ccccceEEcCCCCC
Confidence 689999998777 67888999999975
No 62
>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=20.55 E-value=43 Score=31.31 Aligned_cols=29 Identities=14% Similarity=0.298 Sum_probs=16.6
Q ss_pred CCCCCcCCCCCCCC-eeEeceeeeeecccc
Q 004446 23 DNRRCINCNSLGTQ-YVCTNFWTFVCTNCS 51 (753)
Q Consensus 23 gNk~CADCGs~~P~-WaSvN~GVFVC~~CS 51 (753)
.-.+|.|||.+=|. =.-.-=++..|+.|.
T Consensus 79 ~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq 108 (110)
T TIGR02420 79 EYGYCEECGEEIGLRRLEARPTATLCIDCK 108 (110)
T ss_pred CCCchhccCCcccHHHHhhCCCccccHHhH
Confidence 44699999986211 111111345788885
No 63
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=20.47 E-value=52 Score=32.80 Aligned_cols=35 Identities=20% Similarity=0.282 Sum_probs=22.0
Q ss_pred cCCCC--CCcCCCCCCCCeeEeceeeeeeccccccccc
Q 004446 21 LQDNR--RCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (753)
Q Consensus 21 ~pgNk--~CADCGs~~P~WaSvN~GVFVC~~CSGIHR~ 56 (753)
..+|. .|-.|+.....==-+++ -|.|..|.+.-..
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~~-~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAMEL-NFTCPRCGAMLDY 140 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHHc-CCcCCCCCCEeee
Confidence 33444 79999965322222344 5999999987433
Done!