Query 004602
Match_columns 743
No_of_seqs 201 out of 1175
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 02:02:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004602.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004602hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03131 hypothetical protein; 100.0 1E-102 3E-107 858.6 41.3 613 1-669 1-681 (705)
2 PLN03119 putative ADP-ribosyla 100.0 1.2E-84 2.5E-89 712.4 37.7 562 1-659 1-616 (648)
3 KOG0702 Predicted GTPase-activ 100.0 4.9E-46 1.1E-50 403.5 29.4 494 1-621 1-523 (524)
4 KOG0703 Predicted GTPase-activ 100.0 5E-37 1.1E-41 319.0 9.6 118 6-126 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 4.6E-35 9.9E-40 269.5 8.7 112 13-125 2-116 (116)
6 smart00105 ArfGap Putative GTP 100.0 1.6E-33 3.5E-38 258.0 10.5 107 22-128 1-110 (112)
7 COG5347 GTPase-activating prot 100.0 1.2E-30 2.7E-35 276.4 13.0 119 9-127 5-127 (319)
8 PLN03114 ADP-ribosylation fact 99.9 1.9E-25 4.1E-30 237.2 17.1 116 12-127 10-130 (395)
9 KOG0704 ADP-ribosylation facto 99.9 1.3E-24 2.9E-29 229.5 7.0 85 9-93 4-91 (386)
10 KOG0705 GTPase-activating prot 99.9 2.6E-24 5.7E-29 237.5 8.4 116 12-128 501-619 (749)
11 KOG0706 Predicted GTPase-activ 99.9 1.7E-23 3.7E-28 226.8 6.7 84 10-93 9-95 (454)
12 KOG0521 Putative GTPase activa 99.8 8.9E-21 1.9E-25 220.9 3.8 114 15-129 417-535 (785)
13 KOG0818 GTPase-activating prot 99.7 2.9E-18 6.3E-23 187.8 3.9 108 19-126 3-120 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 3.9E-17 8.5E-22 186.7 4.5 111 15-126 289-404 (1186)
15 KOG0702 Predicted GTPase-activ 97.6 0.011 2.5E-07 67.0 22.9 41 517-560 392-432 (524)
16 PLN03131 hypothetical protein; 95.3 1.9 4.1E-05 51.0 20.6 21 355-375 431-451 (705)
17 KOG0521 Putative GTPase activa 91.4 0.024 5.2E-07 68.3 -3.1 70 20-91 626-699 (785)
18 PF00643 zf-B_box: B-box zinc 81.2 1 2.2E-05 34.5 1.8 40 23-64 2-42 (42)
19 PRK12495 hypothetical protein; 74.3 2.2 4.8E-05 44.9 2.5 29 21-53 39-67 (226)
20 COG1734 DksA DnaK suppressor p 70.6 1.9 4E-05 41.5 0.9 49 6-54 60-111 (120)
21 PRK00085 recO DNA repair prote 62.1 6.5 0.00014 40.5 2.9 37 16-52 137-178 (247)
22 TIGR00613 reco DNA repair prot 57.2 6.9 0.00015 40.1 2.2 37 17-53 136-177 (241)
23 PLN03119 putative ADP-ribosyla 56.6 1.1E+02 0.0023 36.9 11.6 8 355-362 391-398 (648)
24 COG1381 RecO Recombinational D 50.1 8.1 0.00018 40.8 1.3 27 25-51 155-182 (251)
25 TIGR02419 C4_traR_proteo phage 49.0 9.7 0.00021 32.6 1.4 34 21-54 28-62 (63)
26 PF11781 RRN7: RNA polymerase 47.7 12 0.00025 29.0 1.5 28 22-52 6-33 (36)
27 PF01286 XPA_N: XPA protein N- 47.0 6.2 0.00014 30.4 -0.0 27 25-51 4-31 (34)
28 PRK10778 dksA RNA polymerase-b 46.9 12 0.00025 37.3 1.8 44 13-56 98-144 (151)
29 PF08271 TF_Zn_Ribbon: TFIIB z 45.4 7.9 0.00017 30.3 0.3 27 26-53 2-28 (43)
30 PRK11019 hypothetical protein; 44.0 16 0.00035 33.6 2.1 32 24-56 36-69 (88)
31 KOG4368 Predicted RNA binding 42.4 1.3E+02 0.0028 36.3 9.3 18 170-187 641-658 (757)
32 PHA00080 DksA-like zinc finger 40.5 15 0.00033 32.3 1.3 33 22-55 29-63 (72)
33 TIGR02890 spore_yteA sporulati 40.4 18 0.00039 36.3 2.0 30 25-54 87-117 (159)
34 PRK13715 conjugal transfer pro 37.2 16 0.00035 32.2 1.0 30 25-54 35-65 (73)
35 smart00401 ZnF_GATA zinc finge 35.2 25 0.00054 29.0 1.7 37 23-59 2-40 (52)
36 KOG2057 Predicted equilibrativ 34.7 7.5E+02 0.016 28.3 13.5 20 350-369 369-390 (499)
37 PF14376 Haem_bd: Haem-binding 34.3 49 0.0011 32.2 3.9 26 10-39 31-56 (137)
38 KOG3362 Predicted BBOX Zn-fing 33.6 15 0.00032 36.7 0.2 33 23-56 117-150 (156)
39 PRK00420 hypothetical protein; 32.4 63 0.0014 31.0 4.1 45 6-53 3-49 (112)
40 TIGR00100 hypA hydrogenase nic 31.0 22 0.00048 33.6 0.9 43 21-67 67-113 (115)
41 PF01258 zf-dskA_traR: Prokary 29.7 10 0.00022 28.7 -1.3 29 26-54 5-34 (36)
42 TIGR02420 dksA RNA polymerase- 29.1 29 0.00064 32.3 1.4 29 23-51 79-108 (110)
43 PRK03681 hypA hydrogenase nick 27.2 19 0.00042 34.0 -0.2 43 21-66 67-113 (114)
44 cd00194 UBA Ubiquitin Associat 26.9 7.1 0.00015 29.2 -2.6 26 179-205 6-31 (38)
45 KOG0119 Splicing factor 1/bran 26.9 1.2E+03 0.025 28.2 17.8 53 581-638 463-520 (554)
46 cd07171 NR_DBD_ER DNA-binding 25.3 40 0.00087 30.2 1.5 31 23-56 2-32 (82)
47 PRK00564 hypA hydrogenase nick 24.9 25 0.00054 33.4 0.1 43 22-67 69-115 (117)
48 PRK11295 hypothetical protein; 24.8 51 0.0011 31.8 2.1 33 1-33 1-33 (113)
49 PF00320 GATA: GATA zinc finge 24.0 54 0.0012 25.0 1.8 30 27-56 1-32 (36)
50 cd06968 NR_DBD_ROR DNA-binding 23.7 43 0.00093 30.9 1.4 31 23-56 4-34 (95)
51 cd07173 NR_DBD_AR DNA-binding 23.7 49 0.0011 29.7 1.7 31 23-56 2-32 (82)
52 cd03031 GRX_GRX_like Glutaredo 23.7 35 0.00076 33.8 0.8 43 6-57 81-123 (147)
53 COG1997 RPL43A Ribosomal prote 22.9 72 0.0016 29.6 2.6 30 22-53 33-62 (89)
54 COG2174 RPL34A Ribosomal prote 22.5 51 0.0011 30.7 1.6 33 20-52 30-79 (93)
55 PRK00423 tfb transcription ini 22.5 41 0.00088 36.7 1.1 34 22-56 9-42 (310)
56 COG2158 Uncharacterized protei 22.4 39 0.00084 32.3 0.8 30 27-58 45-76 (112)
57 cd07170 NR_DBD_ERR DNA-binding 21.3 48 0.001 30.7 1.2 30 24-56 4-33 (97)
58 PRK06266 transcription initiat 21.1 37 0.00081 34.5 0.5 30 26-56 119-148 (178)
59 PRK12380 hydrogenase nickel in 20.4 35 0.00076 32.2 0.1 42 21-66 67-112 (113)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.3e-102 Score=858.60 Aligned_cols=613 Identities=34% Similarity=0.502 Sum_probs=484.0
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCCCceeecccCCCCHHHHHHHHhc
Q 004602 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (743)
Q Consensus 1 M~sr~keder~ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LGhrVKSlsLD~Wt~eEV~~m~~g 80 (743)
|++| |++|+++++|++|+++++|++||||++++|+|||+|||||||++|+||||+|+||||||+||+|+++||++|+.+
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 004602 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPPY 159 (743)
Q Consensus 81 GN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIraKY~eKrF~~~~~~DkPpRl~~gdkeds~E~Rr-~s~~s~sRSppy 159 (743)
||+++|+|||++|+..+.+.|+..+.+++|+|||+|||+|||+.....+++++.....+.+..|+|| ++|++|+|||+|
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 9999999999999988778888888888999999999999999999999999887777777789999 999999999999
Q ss_pred chhhh-hccccCCCCCCCCccccccCCCCCCCCCchhhh--cccCCCccCCCCCcccccccccccccCCCC---CCCCcc
Q 004602 160 EDTYE-RRYNEQSSPGGRSDDKNSRYGYDERSPGNEQEN--RQFGDYRRTSPTRPEVINDWRRDDRFGNGR---KFEDRR 233 (743)
Q Consensus 160 dd~~e-rRy~~rss~~~R~~dkl~rmgydd~~~~~d~l~--~~~G~~~r~sP~~~e~v~d~~~~Dr~~~~~---~~~~~r 233 (743)
+++|| |||+++..+++|+ +++|+.. +|+|+|+| ||+|+ +|||+||||+++. +++|++
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 6899998888887 7777764 99999999 99996 9999999999996 667777
Q ss_pred cCCCC--CccCCCCCCCCCCCCCCCCCccCchhhhccCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCChh
Q 004602 234 ISDGD--SKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQA 311 (743)
Q Consensus 234 ~s~~~--~~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~~ 311 (743)
+|+++ .+.+.+|||++||+.. || +|||+|+||||||++|||++|+|++..++++|.+++|||+|+|+++|++|+++
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 004602 312 EVKLETTGSLIDFDADPKPSPAVAQAQQKTVAQSVVQPASSANDNNWASFDLAPQVKVSQTSSNLNTLETVFSQLSVPAS 391 (743)
Q Consensus 312 ~~k~~~s~sLiDf~~~~ep~~~~~~~~qt~~~~~~~~~~~s~~~~~wAsfd~~~~~~~~~~~s~~n~le~~l~qlsv~~s 391 (743)
++|+++++|||||++|+|+..+. .|.++..... .......|+-|.+-..-++.+..+. .--..|+||+..+.
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 1334555565555444343333221 12467999999999
Q ss_pred CCCCCCCCCCCCCCCc-ccCCCccccCCCCCCCCcccCCCc-----cccc----cccCCCCCCcccccccCCCCCCCCCC
Q 004602 392 VPGQVSGIPSGAGAPV-IAPATNVNVLPGGGSPVASVGHTP-----FSVF----SAAAPAAPAVSGFATFPSANAPAPAP 461 (743)
Q Consensus 392 ~P~~~~~~~~~~~~~~-~a~~~n~~~~~~~~s~~~~~g~~~-----~~~~----~~~~~~~~~~~~~~tf~~s~~s~~s~ 461 (743)
+|.++.+.+ .|+ -+++.|.. ...-.|...+..... -+.+ ...+.-+|+.++|++|+.....
T Consensus 373 a~~vdlf~~----s~l~~~p~~n~~-q~~qts~p~~~dlfag~~qqq~~~s~~~~~~~~s~pknegwa~fd~~~p~---- 443 (705)
T PLN03131 373 APPVDLFEI----PPLDPAPAINAY-QPPQTSLPSSIDLFGGITQQQSINSLDEKSPELSIPKNEGWATFDGIQPI---- 443 (705)
T ss_pred CCccccccc----CcccCCCccccC-CCCcccCCccccccccccccCccccccccCcccCCccccCcccccCCCcc----
Confidence 999998887 222 33444432 001111111111000 0000 1223337889999999855542
Q ss_pred CCCCCCccccCCCCCCccCCCCCCccCCCCCccccccCCCCcCCCCCCccccccc---c--CCCCCCCCCCCCCCCCCcc
Q 004602 462 GVTPLLPVSVNAGNSFSMQHQPPLFPTAGGQFTASQFTPPVAGSSNNQQWNTSLA---Q--NAQGPPAAQPAQSVPKPAL 536 (743)
Q Consensus 462 ~~~~~~~~~~~~~~~~~~q~~q~~fp~~~~~~~~q~~t~~~~~~~n~q~w~~~~~---q--~~~~~p~~~~~~~v~~~~~ 536 (743)
++.++ ++|++. ..+|.+...+. +.... ....+.++|.-+++ | .++..||....|+|.++.+
T Consensus 444 --~s~~~-~~n~t~--------~~v~~~~~~~~-~~d~v--~~~~~~~q~Pp~~~~~~~~s~s~~~pW~~~~~~V~~~~~ 509 (705)
T PLN03131 444 --ASTPG-NENLTP--------FSIGPSMAGSA-NFDQV--PSLDKGMQWPPFQNSSDEESASGPAPWLGDLHNVEAPDN 509 (705)
T ss_pred --cccCC-cccccc--------cccccccccCc-chhhc--cccccccccCCCcccccccccccCCcccccchhcccCCc
Confidence 22222 334432 23443333321 22222 33445589976654 4 4567889999999999988
Q ss_pred ccCC--------------CCCCCCCCccccccCCCCCcccccccccCCCCCCCCCCccCCCCCC-CC-------------
Q 004602 537 ESAS--------------GGLSQPSPVEVKSTGRTALPEDLFTANYSSFPASVPGWQTVPPHGM-PM------------- 588 (743)
Q Consensus 537 ~~~s--------------~~~s~~~~~e~k~sgrkeLP~DlFt~~y~~~p~~vpGwq~~pp~gm-p~------------- 588 (743)
++.- .+.+....+|.+++--+.-.+|.|.....+......|.|+..|+|| ++
T Consensus 510 ~~~q~WnAF~~~ds~~~~~l~~~~~~s~~q~~~~~~~t~~q~~~~~~~~d~~~d~~~r~~p~~~~~~~g~~~~~~~~~~p 589 (705)
T PLN03131 510 TSAQNWNAFEFDDSVAGIPLEGIKQSSEPQTAANMPPTADQLIGCKALEDFNKDGIKRTAPHGQGELPGLDEPSDILAEP 589 (705)
T ss_pred cCccccccccccccccccccccccccccccccccCCCCcccccccccccccccccccccCCCCCcCCCCCCCCCccccCC
Confidence 6522 3455667788888888888999999999999999999999999999 22
Q ss_pred -------------CCCCCCCCCCCCCCCCCCCCCcccccCCCcccccccCCCCCCCCCCCCCC-CC-CCCCCCCCCCCC-
Q 004602 589 -------------PNFVHSKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS-SL-TPSPAWMPPQAS- 652 (743)
Q Consensus 589 -------------~~~~~~~ks~NPFD~~~~~~~~Qa~~fpsm~~lqgalp~~~~~~~~~~ss-~~-~~s~~~~p~q~~- 652 (743)
++..++.||+|||||.+|....+.-||-.|.+||+|||+.- +++. +| +.+..|++.-+.
T Consensus 590 s~~~~~~~~~~~~~s~~~~~ks~npfdl~~dsd~~~~~mf~d~sslq~~lp~~~-----~~~~f~g~~~tepw~~~~~~~ 664 (705)
T PLN03131 590 SYTPPAHPIMEHAQSHANDHKSINPFDLPYDSDLEPGNMFLDMSSLEAALPDAH-----LPSAFLGSGMTEPWFPQDLAM 664 (705)
T ss_pred CCCccccccccccccccCccCCCCCcCCccccccCcccceeehHHHHhhcCCCC-----CchhhhcCCCCCccccCCCcc
Confidence 33447999999999999999999999999999999999643 4455 56 789999999877
Q ss_pred CCCCCCCCCCccccccC
Q 004602 653 PYPSAMPSQMPTYAAAI 669 (743)
Q Consensus 653 ~y~~~~~~~~~~~~~~~ 669 (743)
+|+++.|+++++|.|+.
T Consensus 665 ~yip~~pqggl~y~agq 681 (705)
T PLN03131 665 TYIPAAPQGGLAYMAGQ 681 (705)
T ss_pred cccCCCCCCCchhhccc
Confidence 99999998888777643
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=1.2e-84 Score=712.38 Aligned_cols=562 Identities=32% Similarity=0.440 Sum_probs=419.1
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCCCceeecccCCCCHHHHHHHHhc
Q 004602 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (743)
Q Consensus 1 M~sr~keder~ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LGhrVKSlsLD~Wt~eEV~~m~~g 80 (743)
|++| +++|+++++|++|+++++|++||||++.+|+|||+|||||||++|+||||+|+||||||+||+|+++||++|+.+
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 004602 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPPY 159 (743)
Q Consensus 81 GN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIraKY~eKrF~~~~~~DkPpRl~~gdkeds~E~Rr-~s~~s~sRSppy 159 (743)
||+++|+|||++|+..+.+.|...+.+++|+|||+|||+|+|+.....+++++.....+....++|| ++|+++++||+|
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 9999999999999987777788888888999999999999999999999988754344444446888 999999999999
Q ss_pred chhhh-hccccCCCCCCCCccccccCCCCCCCCCchhh-hcccCCCccCCCCCcccccccccccccCCCCCCCCcccCCC
Q 004602 160 EDTYE-RRYNEQSSPGGRSDDKNSRYGYDERSPGNEQE-NRQFGDYRRTSPTRPEVINDWRRDDRFGNGRKFEDRRISDG 237 (743)
Q Consensus 160 dd~~e-rRy~~rss~~~R~~dkl~rmgydd~~~~~d~l-~~~~G~~~r~sP~~~e~v~d~~~~Dr~~~~~~~~~~r~s~~ 237 (743)
++.|| |||+++...+.|| ++.|+. ++|+++|.+ ||+|+ +|||+||||+||... .|+||.
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 877776 599999999 99999 899999999999854 499873
Q ss_pred ------C-CccCCCCCCCCCCCCCCCCCccCchhhhccCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCCh
Q 004602 238 ------D-SKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQ 310 (743)
Q Consensus 238 ------~-~~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~ 310 (743)
+ .+.+.+||+++ |.++++||+.+ .++++.. ..---.++.|||+|+|+++|+|+++
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 2 55677999999 55566676555 5554310 0000146789999999999999999
Q ss_pred hhhhhhccCccccCCCCCCCChhhhhhhhhhhcccccccCCCCCCCCCccccCCcCcccccCCCCCChhHHHhhccCCCC
Q 004602 311 AEVKLETTGSLIDFDADPKPSPAVAQAQQKTVAQSVVQPASSANDNNWASFDLAPQVKVSQTSSNLNTLETVFSQLSVPA 390 (743)
Q Consensus 311 ~~~k~~~s~sLiDf~~~~ep~~~~~~~~qt~~~~~~~~~~~s~~~~~wAsfd~~~~~~~~~~~s~~n~le~~l~qlsv~~ 390 (743)
+++|++++++|.|+..|.+..-+. .|.++.. | +..+.++ ..- -..|+||++.+
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 2322222 2 1111111 111 35689999999
Q ss_pred CCCCCCCCCCCCCCCCcccCCCccccCCCCCCCCcccCCC----c-cccccccCCCCCCcccccccCCCCCCCCCCCCCC
Q 004602 391 SVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHT----P-FSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTP 465 (743)
Q Consensus 391 s~P~~~~~~~~~~~~~~~a~~~n~~~~~~~~s~~~~~g~~----~-~~~~~~~~~~~~~~~~~~tf~~s~~s~~s~~~~~ 465 (743)
.+|.++.+.++-+ | -+++.|.. ...-.|...+.+.. . -..+...+.-+|+.++|++|+....++.++
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 9999999886211 1 33444442 11111111111111 0 111233344488899999999555544331
Q ss_pred CCccccCCCCCCccCCCCCCccCCCCCccccccCCCCcCCCCCCccccccc-----cCCCCCCCCCCCCCCCCCccccCC
Q 004602 466 LLPVSVNAGNSFSMQHQPPLFPTAGGQFTASQFTPPVAGSSNNQQWNTSLA-----QNAQGPPAAQPAQSVPKPALESAS 540 (743)
Q Consensus 466 ~~~~~~~~~~~~~~q~~q~~fp~~~~~~~~q~~t~~~~~~~n~q~w~~~~~-----q~~~~~p~~~~~~~v~~~~~~~~s 540 (743)
+|.+ + +++.....+..... ...+.++|.-+++ -.++..||....|+|.++.+++.-
T Consensus 408 -----~ni~---------~---~~~~~~~~~~d~v~--~~~~~mq~Pp~~~~~~~~s~s~~~pW~~~~~~V~~~~~~~~q 468 (648)
T PLN03119 408 -----NVIT---------S---PGDFQLELKIEEIL--QPSTSMQLPPYPSTVDQHALSIPSPWQEDLSNVLKDVVDNPQ 468 (648)
T ss_pred -----cccc---------C---ccccccCcchhhhc--ccccccccCCCcccccccccccCCchhccchhcccCcccCcc
Confidence 2111 0 12222222333333 3334488875544 456677888888898888765522
Q ss_pred -----CCCCCC---------CCccccccCCCCCcccccccccCCCCCCCCCCccCC-CCCCCCCCCC-------------
Q 004602 541 -----GGLSQP---------SPVEVKSTGRTALPEDLFTANYSSFPASVPGWQTVP-PHGMPMPNFV------------- 592 (743)
Q Consensus 541 -----~~~s~~---------~~~e~k~sgrkeLP~DlFt~~y~~~p~~vpGwq~~p-p~gmp~~~~~------------- 592 (743)
+-.-.+ ...+....--+.-.+|.|.....+...+..|.|+.. |.|||.++++
T Consensus 469 ~WnAF~ds~~~~~l~~~~~~~~~~~~~~~~~~~t~~q~~~~r~~ed~~~dg~qr~~~p~g~~g~~~~~~~~~~Ps~~~~~ 548 (648)
T PLN03119 469 PWNAFPDSIEANPLDSSRNIHQQVDGASTSSYNTDHQHLESQVLEELSNDGTQTTRIPAGSSAFGFPGNIGMAPSYSEEA 548 (648)
T ss_pred ccccchhhhccCccccccccccccccccccCCCCcccccccccccccccccccccccCCCCCCCCCCCccccCCCCCchh
Confidence 000011 122222233355566778888888888999999999 9999554443
Q ss_pred ----CCCCCCCCCCCCCCCCCcccccCCCcccccccCCCCCCCCCCCCCC-CCCCCCCCCCCCCC-CCCCCCC
Q 004602 593 ----HSKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS-SLTPSPAWMPPQAS-PYPSAMP 659 (743)
Q Consensus 593 ----~~~ks~NPFD~~~~~~~~Qa~~fpsm~~lqgalp~~~~~~~~~~ss-~~~~s~~~~p~q~~-~y~~~~~ 659 (743)
.+.||+|||||.+|....+.-||-.|.+||++||+ ..++++ +|+.+..|++.-+. +|+++.|
T Consensus 549 ~~~~~~~ks~npfdl~~~sd~~~~~mf~d~tslq~~lp~-----~~~~~~~~~~~t~~w~~~~~~~~yip~~~ 616 (648)
T PLN03119 549 WQHVNEQKSANPFDLPYDSEFDSNDMFLDMSSLQGALPD-----IQTPQAFLNGVSQPWLAADSVPSYLPAPA 616 (648)
T ss_pred ccccccccCCCCcCCccccccCcccceeehHHHHhhcCC-----CCCchhhhcCCCcccccCCCcccccCCCc
Confidence 38899999999999999999999999999999996 344556 88999999999876 8877755
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=4.9e-46 Score=403.52 Aligned_cols=494 Identities=30% Similarity=0.368 Sum_probs=354.3
Q ss_pred CcchhhhhHHH-HHHHHHHHcCCCCCCCcCCCCCCC-CeeEccceehhhhhhhhhhhcCC--CceeecccCCCCHHHHHH
Q 004602 1 MANRLKEDEKN-ERIIRGLLKLQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIHREFT--HRVKSVSMAKFTSQEVKA 76 (743)
Q Consensus 1 M~sr~keder~-ekiLr~Llk~pgNk~CADCGs~~P-~WaSiN~GVFVC~~CSGIHR~LG--hrVKSlsLD~Wt~eEV~~ 76 (743)
|++++||+|+. |++||+|+++|+|++|++|+...+ +|+++.-|-|||+.|+|+.|.|. ||||+|+|.+|+..||..
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 78899999997 999999999999999999999988 99999999999999999999996 999999999999999999
Q ss_pred HHhcChHHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccCCCCCCCCCCCCCCCCccccccccCCCCCCCC
Q 004602 77 LQEGGNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRRDTYQGGSRS 156 (743)
Q Consensus 77 m~~gGN~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIraKY~eKrF~~~~~~DkPpRl~~gdkeds~E~Rr~s~~s~sRS 156 (743)
|+.+||+.+++||++-.+.++--.||..+..++|+||++||++|||+.+....+-+... |- ..+.++
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 99999999999999999988888899999999999999999999999876544433221 10 112224
Q ss_pred CCCchhhhhccccCCCCCCCCccccccCCCCCCCCCchhhh--cccCCCccCCCCCcccccccccccccCCCCCCCCccc
Q 004602 157 PPYEDTYERRYNEQSSPGGRSDDKNSRYGYDERSPGNEQEN--RQFGDYRRTSPTRPEVINDWRRDDRFGNGRKFEDRRI 234 (743)
Q Consensus 157 ppydd~~erRy~~rss~~~R~~dkl~rmgydd~~~~~d~l~--~~~G~~~r~sP~~~e~v~d~~~~Dr~~~~~~~~~~r~ 234 (743)
+++.+.+.++| -+|..++|+.+...... -+...+-+ +|.|||+|+||+ |+|+.-+.
T Consensus 148 ~~~~~s~~~~~-------------~lrs~~gd~~P~~~~~t~np~~~~~~~-~~~~~~~~~~rf--dlfg~~k~------ 205 (524)
T KOG0702|consen 148 RPVSESRPETK-------------SLRSLLGDHAPLLAESTKNPRSRGLPK-SPIRFEIVDDRF--DLFGLPKA------ 205 (524)
T ss_pred CcccccCCCcc-------------ccccccCCCCcchhhcccCccccCCCC-CCchhhhhhhhh--hhhcCcCc------
Confidence 44444443443 44455555545544332 44567888 999999876655 55544332
Q ss_pred CCCCCccCCCCCCCCCCCCCCCCCccCchhhhccCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCChhhhh
Q 004602 235 SDGDSKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQAEVK 314 (743)
Q Consensus 235 s~~~~~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~~~~k 314 (743)
+| -..++...-|+++.++|+..+++++|+++-+-.|+++|+.|....+...+++..---..+.+..+.+.+..+.+
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 23457778899999999999999999999999999999999999998888888765555557889999999999
Q ss_pred hhccCccccCCCCCCCCh--hhhhhhhhhhcccccccCC-CCCCCCCccccCCcCcccccC---CCCCChhHHHhhccCC
Q 004602 315 LETTGSLIDFDADPKPSP--AVAQAQQKTVAQSVVQPAS-SANDNNWASFDLAPQVKVSQT---SSNLNTLETVFSQLSV 388 (743)
Q Consensus 315 ~~~s~sLiDf~~~~ep~~--~~~~~~qt~~~~~~~~~~~-s~~~~~wAsfd~~~~~~~~~~---~s~~n~le~~l~qlsv 388 (743)
..+.++++||+...|-++ ++.+.+--+..+.+.|+.+ +..+++|++|+.++....... ++..+.|.+.+.+|.|
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 2222221111122223333 456899999999887755443 3666788888888888
Q ss_pred CCCCCCCCCCCCCCCCCCcccCCCccccCCCCCCCCcccCCCccccccccCCCCCCcccccccCCCCCCCCCCCCCCCCc
Q 004602 389 PASVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLP 468 (743)
Q Consensus 389 ~~s~P~~~~~~~~~~~~~~~a~~~n~~~~~~~~s~~~~~g~~~~~~~~~~~~~~~~~~~~~tf~~s~~s~~s~~~~~~~~ 468 (743)
.++++|+... +++++++-.+++ .-
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 8888654322 222222211100 00
Q ss_pred cccCCCCCCccCCCC--CCccCCCCCccccccCCCCcCCCCCCccccccccCCCCCCCCCCCCCCCCCccccCCCCCCCC
Q 004602 469 VSVNAGNSFSMQHQP--PLFPTAGGQFTASQFTPPVAGSSNNQQWNTSLAQNAQGPPAAQPAQSVPKPALESASGGLSQP 546 (743)
Q Consensus 469 ~~~~~~~~~~~q~~q--~~fp~~~~~~~~q~~t~~~~~~~n~q~w~~~~~q~~~~~p~~~~~~~v~~~~~~~~s~~~s~~ 546 (743)
..+...|..+-+.+. ++||.+-|. +.+ .++|-.+ -.|..+.+..+ + .
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 22222332221 1 2
Q ss_pred CCccccccCCCCCc-ccccccccCCCCCCCCCCccCCCCCC-------------CCCCCCCCCCCCCCCCCCCCCCCccc
Q 004602 547 SPVEVKSTGRTALP-EDLFTANYSSFPASVPGWQTVPPHGM-------------PMPNFVHSKSTTNPFDVNNDSHPVQA 612 (743)
Q Consensus 547 ~~~e~k~sgrkeLP-~DlFt~~y~~~p~~vpGwq~~pp~gm-------------p~~~~~~~~ks~NPFD~~~~~~~~Qa 612 (743)
...+.+..++.++| .++|++.|.-...|+++||...++|| |.+.+++.-+|+|||+.+-.+ +.|.
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 AMSSLPYGFEFASPFDMFFAMSFPQPAFPIQTPQVQQPGGSHFGLAGDSKPSYLPAPAVAQAGLSYNPFMASPNS-AAQF 513 (524)
T ss_pred ccccCCCCCCcCCCccccccccCcCcCCCCccccccCCCCCCccccccCCcccCccccccccccccCccccCCCC-cccc
Confidence 34678889999999 99999999998899999999999888 445599999999999998643 4455
Q ss_pred c-cCCCcccc
Q 004602 613 Q-TFPSMASL 621 (743)
Q Consensus 613 ~-~fpsm~~l 621 (743)
+ +||+|.++
T Consensus 514 ~~~~p~~nPF 523 (524)
T KOG0702|consen 514 PVAFPGTNPF 523 (524)
T ss_pred cccCCCCCCC
Confidence 4 47888776
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=5e-37 Score=318.97 Aligned_cols=118 Identities=28% Similarity=0.588 Sum_probs=107.7
Q ss_pred hhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcCh
Q 004602 6 KEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGN 82 (743)
Q Consensus 6 keder~ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN 82 (743)
...++++++|++||+.++|++|||||+++|+|||+|+|||||++|+||||.|| | |||||+||.|++|+|+.|+..||
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 004602 83 QRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (743)
Q Consensus 83 ~~aN~i~Ea~~~~~~~p~Pdssd~~~lreFIraKY~eKrF~~~~ 126 (743)
.+||++||++++.. ...|..+ +.++.|||+|||.|+|+.+.
T Consensus 87 ~~an~~~ea~~p~~-~~~p~~d--~~~e~FIR~KYE~kkf~~~~ 127 (287)
T KOG0703|consen 87 AKANSYYEAKLPDP-FRRPGPD--DLVEQFIRDKYERKKFLDPE 127 (287)
T ss_pred hhhhhhccccCCcc-ccCCChH--HHHHHHHHHHHhhhhhccch
Confidence 99999999998765 4455443 36788999999999999865
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=4.6e-35 Score=269.47 Aligned_cols=112 Identities=33% Similarity=0.681 Sum_probs=92.7
Q ss_pred HHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC---CceeecccCCCCHHHHHHHHhcChHHHHHHH
Q 004602 13 RIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEVL 89 (743)
Q Consensus 13 kiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG---hrVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~ 89 (743)
++|++|++.++|++|||||+++|+|||++||||||++|+|+||+|| |+||||+||+|+++||++|+.+||.++|++|
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 004602 90 LKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (743)
Q Consensus 90 Ea~~~~~~~p~Pdssd~~~lreFIraKY~eKrF~~~ 125 (743)
|++.. ...+.+..++.+.+++||++||++|+|+.+
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 334455567888889999999999999853
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=1.6e-33 Score=258.01 Aligned_cols=107 Identities=28% Similarity=0.631 Sum_probs=98.1
Q ss_pred CCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcChHHHHHHHhhcCCCCCC
Q 004602 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEWDPQRQ 98 (743)
Q Consensus 22 pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~Ea~~~~~~~ 98 (743)
++|++||||++++|+|||++||||||++|+||||+|| | +||||+||+|++++|++|+.+||.++|++||++++....
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 004602 99 SFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (743)
Q Consensus 99 p~Pdssd~~~lreFIraKY~eKrF~~~~~~ 128 (743)
+.+..++.+.+++||+.||++|+|+.++..
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=1.2e-30 Score=276.42 Aligned_cols=119 Identities=21% Similarity=0.531 Sum_probs=103.7
Q ss_pred HHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcChHHH
Q 004602 9 EKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRA 85 (743)
Q Consensus 9 er~ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN~~a 85 (743)
...++++..|.+.++|++|||||+++|+|||+|||||||++||||||+|| | +||||+||+|+++||++|+.+||.+|
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 HHHHhhcCCCCC-CCCCCCChHHHHHHHHHHHHhhcccccCCC
Q 004602 86 KEVLLKEWDPQR-QSFPDSSNVERLRNFIKHVYVDRRYTGERN 127 (743)
Q Consensus 86 N~i~Ea~~~~~~-~p~Pdssd~~~lreFIraKY~eKrF~~~~~ 127 (743)
|+|||++.-... .+.-...|...+++||++||++++|.....
T Consensus 85 ~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~ 127 (319)
T COG5347 85 NRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSS 127 (319)
T ss_pred hhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccccc
Confidence 999999875421 222234566778899999999999998743
No 8
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.93 E-value=1.9e-25 Score=237.24 Aligned_cols=116 Identities=23% Similarity=0.397 Sum_probs=97.9
Q ss_pred HHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcChHHHHHH
Q 004602 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (743)
Q Consensus 12 ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN~~aN~i 88 (743)
.++|++|++.++|++|+||++++|+||++|||||||++|+||||.|| | +||||+||+|++++|++|+.+||.++|+|
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 56799999999999999999999999999999999999999999998 4 89999999999999999999999999999
Q ss_pred HhhcCCCCCCCCC--CCChHHHHHHHHHHHHhhcccccCCC
Q 004602 89 LLKEWDPQRQSFP--DSSNVERLRNFIKHVYVDRRYTGERN 127 (743)
Q Consensus 89 ~Ea~~~~~~~p~P--dssd~~~lreFIraKY~eKrF~~~~~ 127 (743)
|+.+.-....... ..+....+.+-+.+|++++.+..+..
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 9875322111111 13455555667999999999986654
No 9
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.90 E-value=1.3e-24 Score=229.53 Aligned_cols=85 Identities=33% Similarity=0.686 Sum_probs=79.1
Q ss_pred HHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcChHHH
Q 004602 9 EKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRA 85 (743)
Q Consensus 9 er~ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN~~a 85 (743)
.++++.|+.|....+|++|+||++.+|+|||++||||||++|+|+||.|| | +|||||||+|.+.||++|+.+||+++
T Consensus 4 prtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~~ 83 (386)
T KOG0704|consen 4 PRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNERF 83 (386)
T ss_pred hHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchhH
Confidence 46677888887888999999999999999999999999999999999999 5 99999999999999999999999999
Q ss_pred HHHHhhcC
Q 004602 86 KEVLLKEW 93 (743)
Q Consensus 86 N~i~Ea~~ 93 (743)
++|++..-
T Consensus 84 ~eFL~s~~ 91 (386)
T KOG0704|consen 84 REFLSSQG 91 (386)
T ss_pred HHHHhhCc
Confidence 99988653
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=2.6e-24 Score=237.54 Aligned_cols=116 Identities=22% Similarity=0.463 Sum_probs=106.3
Q ss_pred HHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC---CceeecccCCCCHHHHHHHHhcChHHHHHH
Q 004602 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (743)
Q Consensus 12 ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG---hrVKSlsLD~Wt~eEV~~m~~gGN~~aN~i 88 (743)
...|+.|...+||.+|+||+.++|.||++|+|+++|++|+||||.|| +||++|.||.|..|.+..|..+||+.||.+
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 44677888899999999999999999999999999999999999998 499999999999999999999999999999
Q ss_pred HhhcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccCCCC
Q 004602 89 LLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (743)
Q Consensus 89 ~Ea~~~~~~~p~Pdssd~~~lreFIraKY~eKrF~~~~~~ 128 (743)
||.......+|.|+++.+ ++|+|||+||++|.|......
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 999887788888887665 458899999999999987655
No 11
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.88 E-value=1.7e-23 Score=226.80 Aligned_cols=84 Identities=21% Similarity=0.561 Sum_probs=79.8
Q ss_pred HHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcChHHHH
Q 004602 10 KNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAK 86 (743)
Q Consensus 10 r~ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN~~aN 86 (743)
...++++.|...++|++|+|||+++|+|++|+|||||||+|+++||+|| | +|||..||+|+.++|++|+.+||.+|+
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 004602 87 EVLLKEW 93 (743)
Q Consensus 87 ~i~Ea~~ 93 (743)
.|+..+-
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=8.9e-21 Score=220.89 Aligned_cols=114 Identities=22% Similarity=0.446 Sum_probs=101.3
Q ss_pred HHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcChHHHHHHHhh
Q 004602 15 IRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLK 91 (743)
Q Consensus 15 Lr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~Ea 91 (743)
+..+.+.++|..|+|||++.|+|+++|+||.+||+|+||||+|| | ||+|++||.|..+.+.+++++||..+|.|||+
T Consensus 417 ~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~ 496 (785)
T KOG0521|consen 417 IEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEA 496 (785)
T ss_pred hhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhc
Confidence 67888899999999999999999999999999999999999999 4 99999999999999999999999999999999
Q ss_pred cCCCCC--CCCCCCChHHHHHHHHHHHHhhcccccCCCCC
Q 004602 92 EWDPQR--QSFPDSSNVERLRNFIKHVYVDRRYTGERNYD 129 (743)
Q Consensus 92 ~~~~~~--~p~Pdssd~~~lreFIraKY~eKrF~~~~~~D 129 (743)
.+.... ++.+... ...++.||++||++++|.-+....
T Consensus 497 ~l~~~~~~~~~~~~~-~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 497 LLPSYDSSKPTASSS-RQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred ccccccccCCCCccc-hhhhhHhhhcccceeeEeecccch
Confidence 987553 3334333 566788999999999999876543
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.71 E-value=2.9e-18 Score=187.75 Aligned_cols=108 Identities=18% Similarity=0.369 Sum_probs=93.7
Q ss_pred HcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcChHHHHHHHhhcCCC
Q 004602 19 LKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEWDP 95 (743)
Q Consensus 19 lk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~Ea~~~~ 95 (743)
.+...-+.|+||++++|.|||||-|+|||.+|+.|||.|| | .||+|....|.++.|+++..+.|..+|.|||..+-.
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 899999999999999999999999999999987642
Q ss_pred -------CCCCCCCCChHHHHHHHHHHHHhhcccccCC
Q 004602 96 -------QRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (743)
Q Consensus 96 -------~~~p~Pdssd~~~lreFIraKY~eKrF~~~~ 126 (743)
.+++.|.+.-...+.+|||+||+...|+.+.
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 2456666544555688999999999999853
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.66 E-value=3.9e-17 Score=186.75 Aligned_cols=111 Identities=26% Similarity=0.527 Sum_probs=100.5
Q ss_pred HHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcCC---CceeecccC--CCCHHHHHHHHhcChHHHHHHH
Q 004602 15 IRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMA--KFTSQEVKALQEGGNQRAKEVL 89 (743)
Q Consensus 15 Lr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~LG---hrVKSlsLD--~Wt~eEV~~m~~gGN~~aN~i~ 89 (743)
-.+++...+|+.||||++..|.||++|++|.||-.|+|-||.|| ++|+|++|| .|+.+.|+++..+||.++|.||
T Consensus 289 aeriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fw 368 (1186)
T KOG1117|consen 289 AERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFW 368 (1186)
T ss_pred HHHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCccccccc
Confidence 35678889999999999999999999999999999999999998 699999999 5999999999999999999999
Q ss_pred hhcCCCCCCCCCCCChHHHHHHHHHHHHhhcccccCC
Q 004602 90 LKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (743)
Q Consensus 90 Ea~~~~~~~p~Pdssd~~~lreFIraKY~eKrF~~~~ 126 (743)
-.++++...-.|+++- ..+++||+.||.+.+|....
T Consensus 369 a~nl~~~e~lh~dssp-~~r~~fi~~Kykeg~fRk~~ 404 (1186)
T KOG1117|consen 369 AGNLPPNEHLHPDSSP-STRRQFIKEKYKEGKFRKEH 404 (1186)
T ss_pred ccCCCCccccCCCCCc-chhhhHHHHHhhcccccccc
Confidence 9999888777777644 45688999999999998654
No 15
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=97.61 E-value=0.011 Score=66.99 Aligned_cols=41 Identities=10% Similarity=0.054 Sum_probs=24.8
Q ss_pred cCCCCCCCCCCCCCCCCCccccCCCCCCCCCCccccccCCCCCc
Q 004602 517 QNAQGPPAAQPAQSVPKPALESASGGLSQPSPVEVKSTGRTALP 560 (743)
Q Consensus 517 q~~~~~p~~~~~~~v~~~~~~~~s~~~s~~~~~e~k~sgrkeLP 560 (743)
|+...+-+++++.....-+... ..+.+..+|....+|+++|
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 5555555555553332222222 3456777889999999988
No 16
>PLN03131 hypothetical protein; Provisional
Probab=95.29 E-value=1.9 Score=51.05 Aligned_cols=21 Identities=24% Similarity=0.548 Sum_probs=14.4
Q ss_pred CCCCccccCCcCcccccCCCC
Q 004602 355 DNNWASFDLAPQVKVSQTSSN 375 (743)
Q Consensus 355 ~~~wAsfd~~~~~~~~~~~s~ 375 (743)
+.+||+||...+-..++...|
T Consensus 431 negwa~fd~~~p~~s~~~~~n 451 (705)
T PLN03131 431 NEGWATFDGIQPIASTPGNEN 451 (705)
T ss_pred ccCcccccCCCcccccCCccc
Confidence 889999997665554444444
No 17
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=91.41 E-value=0.024 Score=68.30 Aligned_cols=70 Identities=17% Similarity=0.275 Sum_probs=56.5
Q ss_pred cCCCCCCCcCCCC-CCCCeeEccceehhhhhhhhhhhcCC-C--ceeecccCCCCHHHHHHHHhcChHHHHHHHhh
Q 004602 20 KLQDNRRCINCNS-LGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLK 91 (743)
Q Consensus 20 k~pgNk~CADCGs-~~P~WaSiN~GVFVC~~CSGIHR~LG-h--rVKSlsLD~Wt~eEV~~m~~gGN~~aN~i~Ea 91 (743)
+...+-.|++|++ ..-.|+++|+.+-+|+.|+++|+.++ | .+.++.|++..+ |..+...|+...+..|..
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 47999999999999999999999996 4 677777877766 777777777766666654
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=81.25 E-value=1 Score=34.51 Aligned_cols=40 Identities=15% Similarity=0.471 Sum_probs=33.6
Q ss_pred CCCCCcCCCCCCCCeeEccceehhhhhhhhh-hhcCCCceeec
Q 004602 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGI-HREFTHRVKSV 64 (743)
Q Consensus 23 gNk~CADCGs~~P~WaSiN~GVFVC~~CSGI-HR~LGhrVKSl 64 (743)
.+..|..|......|.+.+=.++||..|... |+. |+|..|
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 3568999999889999999999999999998 877 877654
No 19
>PRK12495 hypothetical protein; Provisional
Probab=74.35 E-value=2.2 Score=44.89 Aligned_cols=29 Identities=17% Similarity=0.239 Sum_probs=23.8
Q ss_pred CCCCCCCcCCCCCCCCeeEccceehhhhhhhhh
Q 004602 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (743)
Q Consensus 21 ~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGI 53 (743)
...+..|-+||.+-|.+ -|+.+|..|..+
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 35678999999998832 699999999865
No 20
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=70.63 E-value=1.9 Score=41.47 Aligned_cols=49 Identities=14% Similarity=0.283 Sum_probs=30.7
Q ss_pred hhhHHHHHHHHHHHcCCCCC--CCcCCCCC-CCCeeEccceehhhhhhhhhh
Q 004602 6 KEDEKNERIIRGLLKLQDNR--RCINCNSL-GTQYVCTNFWTFVCTNCSGIH 54 (743)
Q Consensus 6 keder~ekiLr~Llk~pgNk--~CADCGs~-~P~WaSiN~GVFVC~~CSGIH 54 (743)
++.....++-..|.++.... +|.+||.+ ...-.-..-++.+|+.|.-.|
T Consensus 60 r~r~~l~~i~~al~rIe~gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~ 111 (120)
T COG1734 60 RERKLLRKIESALDRIEEGTYGICEECGEPIPEARLEARPTARLCIECQERA 111 (120)
T ss_pred HHHHHHHHHHHHHHHHHcCCccchhccCCcCCHHHHhhCcchHHHHHHHHHH
Confidence 33344444445555555554 89999997 222333444778999999876
No 21
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=62.14 E-value=6.5 Score=40.48 Aligned_cols=37 Identities=27% Similarity=0.507 Sum_probs=28.9
Q ss_pred HHHHcC----CCCCCCcCCCCCCC-CeeEccceehhhhhhhh
Q 004602 16 RGLLKL----QDNRRCINCNSLGT-QYVCTNFWTFVCTNCSG 52 (743)
Q Consensus 16 r~Llk~----pgNk~CADCGs~~P-~WaSiN~GVFVC~~CSG 52 (743)
.+|++. +.-..|+.||.... .|.+..-|.|+|..|..
T Consensus 137 ~~lL~~~G~~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~ 178 (247)
T PRK00085 137 LRLLAELGYGLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGD 178 (247)
T ss_pred HHHHHHcCCccchhhHhcCCCCCCceEEecccCCcccccccC
Confidence 355554 44469999998744 78999999999999973
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=57.22 E-value=6.9 Score=40.10 Aligned_cols=37 Identities=24% Similarity=0.540 Sum_probs=28.8
Q ss_pred HHHcC----CCCCCCcCCCCCCC-CeeEccceehhhhhhhhh
Q 004602 17 GLLKL----QDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGI 53 (743)
Q Consensus 17 ~Llk~----pgNk~CADCGs~~P-~WaSiN~GVFVC~~CSGI 53 (743)
+|++. |.-..|+.||..++ .|.+...|.|+|.+|...
T Consensus 136 ~lL~~~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 136 KLLQILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred HHHHHcCCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 45553 44569999998544 688999999999999864
No 23
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=56.65 E-value=1.1e+02 Score=36.91 Aligned_cols=8 Identities=63% Similarity=1.415 Sum_probs=7.6
Q ss_pred CCCCcccc
Q 004602 355 DNNWASFD 362 (743)
Q Consensus 355 ~~~wAsfd 362 (743)
+.+||+||
T Consensus 391 neGWA~fd 398 (648)
T PLN03119 391 NEGWASFD 398 (648)
T ss_pred ccCccccc
Confidence 78999999
No 24
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=50.11 E-value=8.1 Score=40.85 Aligned_cols=27 Identities=22% Similarity=0.657 Sum_probs=24.8
Q ss_pred CCCcCCCCCC-CCeeEccceehhhhhhh
Q 004602 25 RRCINCNSLG-TQYVCTNFWTFVCTNCS 51 (743)
Q Consensus 25 k~CADCGs~~-P~WaSiN~GVFVC~~CS 51 (743)
..|+.||.+. +..+++-.|-+||.+|.
T Consensus 155 ~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 155 TSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHhCcCCcCCCcceeeccCcccchhcc
Confidence 5999999975 57999999999999999
No 25
>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=48.99 E-value=9.7 Score=32.63 Aligned_cols=34 Identities=18% Similarity=0.182 Sum_probs=23.0
Q ss_pred CCCCCCCcCCCCCCC-CeeEccceehhhhhhhhhh
Q 004602 21 LQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIH 54 (743)
Q Consensus 21 ~pgNk~CADCGs~~P-~WaSiN~GVFVC~~CSGIH 54 (743)
..+...|.|||..=| .=.-..-|+..|+.|...+
T Consensus 28 ~~s~g~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 28 GPSLRECEDCGEPIPEARREALPGVTRCVSCQEIL 62 (63)
T ss_pred CCCCCeeccCCCcChHHHHhhcCCcCCcHHHHhhc
Confidence 355679999999633 2222344788999998764
No 26
>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=47.68 E-value=12 Score=28.98 Aligned_cols=28 Identities=21% Similarity=0.515 Sum_probs=23.7
Q ss_pred CCCCCCcCCCCCCCCeeEccceehhhhhhhh
Q 004602 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSG 52 (743)
Q Consensus 22 pgNk~CADCGs~~P~WaSiN~GVFVC~~CSG 52 (743)
..|..|..|++. |...+=|.++|.+|-.
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 8888999999999964
No 27
>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=47.02 E-value=6.2 Score=30.42 Aligned_cols=27 Identities=30% Similarity=0.653 Sum_probs=16.8
Q ss_pred CCCcCCCCC-CCCeeEccceehhhhhhh
Q 004602 25 RRCINCNSL-GTQYVCTNFWTFVCTNCS 51 (743)
Q Consensus 25 k~CADCGs~-~P~WaSiN~GVFVC~~CS 51 (743)
.+|.+|+.. .=.|..-+|+.-||.+|.
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 28
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=46.93 E-value=12 Score=37.34 Aligned_cols=44 Identities=20% Similarity=0.381 Sum_probs=25.9
Q ss_pred HHHHHHHcC--CCCCCCcCCCCC-CCCeeEccceehhhhhhhhhhhc
Q 004602 13 RIIRGLLKL--QDNRRCINCNSL-GTQYVCTNFWTFVCTNCSGIHRE 56 (743)
Q Consensus 13 kiLr~Llk~--pgNk~CADCGs~-~P~WaSiN~GVFVC~~CSGIHR~ 56 (743)
+|-+.|.++ ..--+|-+||.+ ...=.-.--++..|+.|...|-.
T Consensus 98 ~I~~AL~Ri~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~ 144 (151)
T PRK10778 98 KIEKTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEI 144 (151)
T ss_pred HHHHHHHHHhCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHH
Confidence 333344333 334599999986 22222223355799999987643
No 29
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=45.38 E-value=7.9 Score=30.32 Aligned_cols=27 Identities=30% Similarity=0.563 Sum_probs=21.3
Q ss_pred CCcCCCCCCCCeeEccceehhhhhhhhh
Q 004602 26 RCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (743)
Q Consensus 26 ~CADCGs~~P~WaSiN~GVFVC~~CSGI 53 (743)
+|-.||+.. ......-|-+||.+|.-|
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 555677899999999644
No 30
>PRK11019 hypothetical protein; Provisional
Probab=44.00 E-value=16 Score=33.58 Aligned_cols=32 Identities=13% Similarity=0.164 Sum_probs=22.8
Q ss_pred CCCCcCCCCCCC--CeeEccceehhhhhhhhhhhc
Q 004602 24 NRRCINCNSLGT--QYVCTNFWTFVCTNCSGIHRE 56 (743)
Q Consensus 24 Nk~CADCGs~~P--~WaSiN~GVFVC~~CSGIHR~ 56 (743)
-.+|.|||..=| .|. .--++-.|+.|...+-.
T Consensus 36 yg~C~~CG~~Ip~~Rl~-A~P~a~~Cv~Cq~~~E~ 69 (88)
T PRK11019 36 LTECEECGEPIPEARRK-AIPGVRLCVACQQEKDL 69 (88)
T ss_pred CCeeCcCCCcCcHHHHh-hcCCccccHHHHHHHHH
Confidence 469999999743 333 23377899999987644
No 31
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=42.41 E-value=1.3e+02 Score=36.34 Aligned_cols=18 Identities=28% Similarity=0.442 Sum_probs=9.1
Q ss_pred CCCCCCCCccccccCCCC
Q 004602 170 QSSPGGRSDDKNSRYGYD 187 (743)
Q Consensus 170 rss~~~R~~dkl~rmgyd 187 (743)
+++..+|+.++-+.|.|+
T Consensus 641 ~SsSrSrs~SRsrS~srs 658 (757)
T KOG4368|consen 641 RSSSRSRSQSRSRSKSYS 658 (757)
T ss_pred CCccccccCCcccccccC
Confidence 344444555555555555
No 32
>PHA00080 DksA-like zinc finger domain containing protein
Probab=40.48 E-value=15 Score=32.30 Aligned_cols=33 Identities=15% Similarity=0.272 Sum_probs=22.0
Q ss_pred CCCCCCcCCCCCC--CCeeEccceehhhhhhhhhhh
Q 004602 22 QDNRRCINCNSLG--TQYVCTNFWTFVCTNCSGIHR 55 (743)
Q Consensus 22 pgNk~CADCGs~~--P~WaSiN~GVFVC~~CSGIHR 55 (743)
....+|.|||..= ..|. ..-++..|+.|...+-
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~-a~P~~~~Cv~Cq~~~E 63 (72)
T PHA00080 29 PSATHCEECGDPIPEARRE-AVPGCRTCVSCQEILE 63 (72)
T ss_pred CCCCEecCCCCcCcHHHHH-hCCCccCcHHHHHHHH
Confidence 3345899999963 2332 2336778999998753
No 33
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=40.37 E-value=18 Score=36.26 Aligned_cols=30 Identities=13% Similarity=0.221 Sum_probs=20.2
Q ss_pred CCCcCCCCC-CCCeeEccceehhhhhhhhhh
Q 004602 25 RRCINCNSL-GTQYVCTNFWTFVCTNCSGIH 54 (743)
Q Consensus 25 k~CADCGs~-~P~WaSiN~GVFVC~~CSGIH 54 (743)
-+|.+||.. ...=.-+.-++-.|+.|...+
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 489999986 222222333567999999875
No 34
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=37.25 E-value=16 Score=32.25 Aligned_cols=30 Identities=13% Similarity=0.191 Sum_probs=21.0
Q ss_pred CCCcCCCCCCC-CeeEccceehhhhhhhhhh
Q 004602 25 RRCINCNSLGT-QYVCTNFWTFVCTNCSGIH 54 (743)
Q Consensus 25 k~CADCGs~~P-~WaSiN~GVFVC~~CSGIH 54 (743)
..|.|||..=| .-.-.--|+..|+.|...+
T Consensus 35 ~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 35 YLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred ccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 58999999733 2222334788999998764
No 35
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=35.20 E-value=25 Score=28.98 Aligned_cols=37 Identities=16% Similarity=0.336 Sum_probs=30.3
Q ss_pred CCCCCcCCCCC-CCCeeEcccee-hhhhhhhhhhhcCCC
Q 004602 23 DNRRCINCNSL-GTQYVCTNFWT-FVCTNCSGIHREFTH 59 (743)
Q Consensus 23 gNk~CADCGs~-~P~WaSiN~GV-FVC~~CSGIHR~LGh 59 (743)
....|.+|+.. -|.|=....|. +||-.|.-..+..+.
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~~ 40 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHGG 40 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcCC
Confidence 35799999985 58898888886 999999988777653
No 36
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=34.66 E-value=7.5e+02 Score=28.32 Aligned_cols=20 Identities=25% Similarity=0.343 Sum_probs=12.6
Q ss_pred CCCCCC--CCCccccCCcCccc
Q 004602 350 ASSAND--NNWASFDLAPQVKV 369 (743)
Q Consensus 350 ~~s~~~--~~wAsfd~~~~~~~ 369 (743)
+.|.++ ++|--|..++.-..
T Consensus 369 A~Sg~GdfgD~~AF~aAPsgpm 390 (499)
T KOG2057|consen 369 APSGGGDFGDLFAFGAAPSGPM 390 (499)
T ss_pred ccCCCCcchhhhhhcCCCCccc
Confidence 344445 67888887775443
No 37
>PF14376 Haem_bd: Haem-binding domain
Probab=34.26 E-value=49 Score=32.16 Aligned_cols=26 Identities=31% Similarity=0.588 Sum_probs=17.3
Q ss_pred HHHHHHHHHHcCCCCCCCcCCCCCCCCeeE
Q 004602 10 KNERIIRGLLKLQDNRRCINCNSLGTQYVC 39 (743)
Q Consensus 10 r~ekiLr~Llk~pgNk~CADCGs~~P~WaS 39 (743)
...+.++.|++ +-|.||++.+..|--
T Consensus 31 ~~p~~v~~il~----~~CydCHSn~T~~Pw 56 (137)
T PF14376_consen 31 KAPEEVKIILK----NSCYDCHSNNTRYPW 56 (137)
T ss_pred cchHHHHHHHH----ccccccCCCCCCCcc
Confidence 34445556664 479999998766653
No 38
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=33.56 E-value=15 Score=36.75 Aligned_cols=33 Identities=30% Similarity=0.648 Sum_probs=27.0
Q ss_pred CCCCCcCCCCCCCCeeEccceehhh-hhhhhhhhc
Q 004602 23 DNRRCINCNSLGTQYVCTNFWTFVC-TNCSGIHRE 56 (743)
Q Consensus 23 gNk~CADCGs~~P~WaSiN~GVFVC-~~CSGIHR~ 56 (743)
--+.|+-|| -.--|.|++-|.-.| ..|-.+|.+
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 667799999999887 579999965
No 39
>PRK00420 hypothetical protein; Validated
Probab=32.38 E-value=63 Score=31.00 Aligned_cols=45 Identities=16% Similarity=0.174 Sum_probs=30.2
Q ss_pred hhhHHHHHHHHHHHc--CCCCCCCcCCCCCCCCeeEccceehhhhhhhhh
Q 004602 6 KEDEKNERIIRGLLK--LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (743)
Q Consensus 6 keder~ekiLr~Llk--~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGI 53 (743)
++++..+++-+.|++ .--+..|-.||.+-.. ++-|-.+|..|..+
T Consensus 3 ~~~~~~k~~a~~Ll~Ga~ml~~~CP~Cg~pLf~---lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 3 ESEDIVKKAAELLLKGAKMLSKHCPVCGLPLFE---LKDGEVVCPVHGKV 49 (112)
T ss_pred ccHHHHHHHHHHHHhHHHHccCCCCCCCCccee---cCCCceECCCCCCe
Confidence 345555555555665 3346899999976432 36788899999864
No 40
>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=30.99 E-value=22 Score=33.59 Aligned_cols=43 Identities=21% Similarity=0.471 Sum_probs=29.5
Q ss_pred CCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcC--CC--ceeecccC
Q 004602 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSMA 67 (743)
Q Consensus 21 ~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~L--Gh--rVKSlsLD 67 (743)
.|.--+|.+||.. ..+..-.|.|-.|.+..-.+ |. +|++|.++
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 33332358899999876555 33 88888765
No 41
>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=29.72 E-value=10 Score=28.73 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=17.4
Q ss_pred CCcCCCCCC-CCeeEccceehhhhhhhhhh
Q 004602 26 RCINCNSLG-TQYVCTNFWTFVCTNCSGIH 54 (743)
Q Consensus 26 ~CADCGs~~-P~WaSiN~GVFVC~~CSGIH 54 (743)
+|.+||..= ..-.-+.-+..+|+.|+..|
T Consensus 5 ~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 5 ICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp B-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 599999852 22222334778999998765
No 42
>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=29.13 E-value=29 Score=32.34 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=17.8
Q ss_pred CCCCCcCCCCCC-CCeeEccceehhhhhhh
Q 004602 23 DNRRCINCNSLG-TQYVCTNFWTFVCTNCS 51 (743)
Q Consensus 23 gNk~CADCGs~~-P~WaSiN~GVFVC~~CS 51 (743)
.-.+|.|||.+= ..=.-.--++..|+.|.
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 446999999862 12222223456899996
No 43
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=27.18 E-value=19 Score=33.99 Aligned_cols=43 Identities=12% Similarity=0.338 Sum_probs=30.0
Q ss_pred CCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcC--CC--ceeeccc
Q 004602 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSM 66 (743)
Q Consensus 21 ~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~L--Gh--rVKSlsL 66 (743)
.|..-+|-+||.. |....+..|.|-.|.+..-.+ |. +|++|.+
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 333345557899999887666 32 7888764
No 44
>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=26.95 E-value=7.1 Score=29.18 Aligned_cols=26 Identities=12% Similarity=0.234 Sum_probs=22.2
Q ss_pred cccccCCCCCCCCCchhhhcccCCCcc
Q 004602 179 DKNSRYGYDERSPGNEQENRQFGDYRR 205 (743)
Q Consensus 179 dkl~rmgydd~~~~~d~l~~~~G~~~r 205 (743)
++|.+|||+ ++....+|...+||+++
T Consensus 6 ~~L~~mGf~-~~~~~~AL~~~~~d~~~ 31 (38)
T cd00194 6 EQLLEMGFS-REEARKALRATNNNVER 31 (38)
T ss_pred HHHHHcCCC-HHHHHHHHHHhCCCHHH
Confidence 568899999 66788899999999877
No 45
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=26.93 E-value=1.2e+03 Score=28.16 Aligned_cols=53 Identities=28% Similarity=0.428 Sum_probs=32.0
Q ss_pred CCCCCC---CCCCCCCC--CCCCCCCCCCCCCCCcccccCCCcccccccCCCCCCCCCCCCCC
Q 004602 581 VPPHGM---PMPNFVHS--KSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS 638 (743)
Q Consensus 581 ~pp~gm---p~~~~~~~--~ks~NPFD~~~~~~~~Qa~~fpsm~~lqgalp~~~~~~~~~~ss 638 (743)
.|++|| .++..|++ -.++-|||-. + |+.--|.+-.-.|+-..|+++.+|.+.+
T Consensus 463 ~p~Pg~~s~~~s~~P~q~s~~~~pp~~r~-a----~~~a~Pg~p~~~~~~~~vPpp~g~~p~~ 520 (554)
T KOG0119|consen 463 PPPPGMQSAQSSSLPQQASTTSIPPGDRQ-A----QAAAPPGAPFHGGNYNAVPPPPGLQPAN 520 (554)
T ss_pred CCCCCccccccccCCcccccccCCccccc-c----cccCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence 777888 44444433 4566777765 1 3333366655666766677777777665
No 46
>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=25.35 E-value=40 Score=30.23 Aligned_cols=31 Identities=16% Similarity=0.564 Sum_probs=25.7
Q ss_pred CCCCCcCCCCCCCCeeEccceehhhhhhhhhhhc
Q 004602 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (743)
Q Consensus 23 gNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~ 56 (743)
.|..|.-|+... ....||++.|..|.++.|.
T Consensus 2 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYA---SGYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcC---cceEECceeehhhHHhHHH
Confidence 467899999754 3579999999999998876
No 47
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.95 E-value=25 Score=33.39 Aligned_cols=43 Identities=19% Similarity=0.373 Sum_probs=27.9
Q ss_pred CCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcC--CC--ceeecccC
Q 004602 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSMA 67 (743)
Q Consensus 22 pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~L--Gh--rVKSlsLD 67 (743)
+.--+|-+||.. |-...+..+.|-.|.+..-.+ |. +|++|.++
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 222234455699999876555 33 88887664
No 48
>PRK11295 hypothetical protein; Provisional
Probab=24.81 E-value=51 Score=31.77 Aligned_cols=33 Identities=21% Similarity=0.029 Sum_probs=22.5
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCCcCCCCC
Q 004602 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSL 33 (743)
Q Consensus 1 M~sr~keder~ekiLr~Llk~pgNk~CADCGs~ 33 (743)
|+...++..+.++.+|.......+-.|..|+..
T Consensus 1 ~~~~~~~~~~~~~~~R~~~L~r~p~lC~~Cgr~ 33 (113)
T PRK11295 1 MAIIPKNYARLESGYREKALKLYPWVCGRCSRE 33 (113)
T ss_pred CccchHHHHHHHHHHHHHHHHHCcchhhhhcCh
Confidence 344445666666777766655666689999997
No 49
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=24.04 E-value=54 Score=25.04 Aligned_cols=30 Identities=20% Similarity=0.417 Sum_probs=22.1
Q ss_pred CcCCCCC-CCCeeEccceeh-hhhhhhhhhhc
Q 004602 27 CINCNSL-GTQYVCTNFWTF-VCTNCSGIHRE 56 (743)
Q Consensus 27 CADCGs~-~P~WaSiN~GVF-VC~~CSGIHR~ 56 (743)
|.+|+.. -|.|=....|-. ||-.|.-.+|.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk 32 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKK 32 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHH
Confidence 8999986 699998888877 99999877765
No 50
>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=23.74 E-value=43 Score=30.88 Aligned_cols=31 Identities=19% Similarity=0.540 Sum_probs=25.8
Q ss_pred CCCCCcCCCCCCCCeeEccceehhhhhhhhhhhc
Q 004602 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (743)
Q Consensus 23 gNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~ 56 (743)
++..|.-||... ....||++.|..|.++.|.
T Consensus 4 ~~~~C~VCg~~~---~g~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKS---SGIHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcC---cceEECceeehhhHHhhHH
Confidence 567899999865 3468999999999999876
No 51
>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=23.73 E-value=49 Score=29.72 Aligned_cols=31 Identities=13% Similarity=0.555 Sum_probs=25.5
Q ss_pred CCCCCcCCCCCCCCeeEccceehhhhhhhhhhhc
Q 004602 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (743)
Q Consensus 23 gNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~ 56 (743)
..+.|.-|+...- ...||++.|..|.++.|.
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 4567999997653 568999999999998876
No 52
>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=23.69 E-value=35 Score=33.76 Aligned_cols=43 Identities=19% Similarity=0.528 Sum_probs=29.5
Q ss_pred hhhHHHHHHHHHHHcCCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcC
Q 004602 6 KEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF 57 (743)
Q Consensus 6 keder~ekiLr~Llk~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~L 57 (743)
.++.+.+++|+.+........|.-||.. +-.+|..|.|-|+.+
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 3445556666666455566679999854 345899999988764
No 53
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=22.92 E-value=72 Score=29.64 Aligned_cols=30 Identities=13% Similarity=0.317 Sum_probs=23.3
Q ss_pred CCCCCCcCCCCCCCCeeEccceehhhhhhhhh
Q 004602 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (743)
Q Consensus 22 pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGI 53 (743)
..-..|-.|+.+ .---+..||+.|..|-..
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 345699999998 444568899999999754
No 54
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=22.54 E-value=51 Score=30.74 Aligned_cols=33 Identities=18% Similarity=0.429 Sum_probs=22.5
Q ss_pred cCCCCCCCcCCCCC-------CC----------CeeEccceehhhhhhhh
Q 004602 20 KLQDNRRCINCNSL-------GT----------QYVCTNFWTFVCTNCSG 52 (743)
Q Consensus 20 k~pgNk~CADCGs~-------~P----------~WaSiN~GVFVC~~CSG 52 (743)
+.+.--+|++||.+ -| .-+.=.||-.+|.+|.-
T Consensus 30 K~~~~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c~~ 79 (93)
T COG2174 30 KKPTIPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANCVR 79 (93)
T ss_pred ccCCCCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHHHH
Confidence 45556699999986 11 11244689999999974
No 55
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=22.54 E-value=41 Score=36.72 Aligned_cols=34 Identities=21% Similarity=0.354 Sum_probs=24.2
Q ss_pred CCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhc
Q 004602 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (743)
Q Consensus 22 pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~ 56 (743)
....+|-+||... -=....-|-.||.+|.-|..+
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 222456799999999987543
No 56
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=22.36 E-value=39 Score=32.34 Aligned_cols=30 Identities=27% Similarity=0.598 Sum_probs=23.7
Q ss_pred CcCCCCCCCCeeEccce--ehhhhhhhhhhhcCC
Q 004602 27 CINCNSLGTQYVCTNFW--TFVCTNCSGIHREFT 58 (743)
Q Consensus 27 CADCGs~~P~WaSiN~G--VFVC~~CSGIHR~LG 58 (743)
|.||+. + .|++-.-| |.-|.+|--|||.=+
T Consensus 45 c~~~~~-g-ewi~~~~G~~VwSC~dC~~iH~ke~ 76 (112)
T COG2158 45 CENEEL-G-EWISDSNGRKVWSCSDCHWIHRKEG 76 (112)
T ss_pred cccccc-C-ceeEcCCCCEEeeccccceecccch
Confidence 344443 4 89998889 999999999999844
No 57
>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription
Probab=21.28 E-value=48 Score=30.74 Aligned_cols=30 Identities=17% Similarity=0.610 Sum_probs=24.5
Q ss_pred CCCCcCCCCCCCCeeEccceehhhhhhhhhhhc
Q 004602 24 NRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (743)
Q Consensus 24 Nk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~ 56 (743)
+..|.-|+...- ...||++.|..|.++.|.
T Consensus 4 ~~~C~VCg~~a~---g~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIAS---GYHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCc---ceEECceeehhhhHHHHH
Confidence 457999997653 468999999999999876
No 58
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.05 E-value=37 Score=34.51 Aligned_cols=30 Identities=27% Similarity=0.512 Sum_probs=20.3
Q ss_pred CCcCCCCCCCCeeEccceehhhhhhhhhhhc
Q 004602 26 RCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (743)
Q Consensus 26 ~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~ 56 (743)
+|-+|+.....-=-+++ -|.|..|.+.-..
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 79999975322223444 5999999987543
No 59
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=20.39 E-value=35 Score=32.22 Aligned_cols=42 Identities=21% Similarity=0.426 Sum_probs=28.1
Q ss_pred CCCCCCCcCCCCCCCCeeEccceehhhhhhhhhhhcC--CC--ceeeccc
Q 004602 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--TH--RVKSVSM 66 (743)
Q Consensus 21 ~pgNk~CADCGs~~P~WaSiN~GVFVC~~CSGIHR~L--Gh--rVKSlsL 66 (743)
.|..-+|-+||.. ..+....|.|-.|.+....+ |. +|++|.+
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 22333456699999875555 33 7888765
Done!