Query 005403
Match_columns 698
No_of_seqs 206 out of 1185
Neff 4.1
Searched_HMMs 46136
Date Thu Mar 28 22:53:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005403.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005403hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03131 hypothetical protein; 100.0 1.1E-99 2E-104 830.9 39.2 603 1-678 1-680 (705)
2 PLN03119 putative ADP-ribosyla 100.0 2.7E-81 6E-86 682.1 36.7 564 1-679 1-628 (648)
3 KOG0702 Predicted GTPase-activ 100.0 2.3E-48 5E-53 419.2 31.0 504 1-631 1-523 (524)
4 KOG0703 Predicted GTPase-activ 100.0 1E-36 2.2E-41 314.7 10.3 118 6-126 7-127 (287)
5 PF01412 ArfGap: Putative GTPa 100.0 2.9E-35 6.4E-40 269.0 9.1 112 13-125 2-116 (116)
6 smart00105 ArfGap Putative GTP 100.0 1.3E-33 2.7E-38 257.1 10.5 107 22-128 1-110 (112)
7 COG5347 GTPase-activating prot 100.0 1.1E-30 2.3E-35 275.2 13.8 120 8-127 4-127 (319)
8 PLN03114 ADP-ribosylation fact 99.9 9.4E-25 2E-29 230.6 13.1 116 12-127 10-130 (395)
9 KOG0704 ADP-ribosylation facto 99.9 3E-24 6.5E-29 225.6 8.9 85 8-92 3-90 (386)
10 KOG0705 GTPase-activating prot 99.9 1.2E-23 2.7E-28 231.1 9.1 116 12-128 501-619 (749)
11 KOG0706 Predicted GTPase-activ 99.9 3.6E-23 7.8E-28 223.0 7.6 84 10-93 9-95 (454)
12 KOG0521 Putative GTPase activa 99.8 7.8E-21 1.7E-25 220.0 3.5 115 15-129 417-535 (785)
13 KOG0818 GTPase-activating prot 99.7 9.1E-18 2E-22 182.9 3.9 107 19-125 3-119 (669)
14 KOG1117 Rho- and Arf-GTPase ac 99.7 4.1E-17 8.8E-22 185.6 4.6 110 16-126 290-404 (1186)
15 KOG0702 Predicted GTPase-activ 97.0 0.16 3.4E-06 57.8 23.1 13 43-55 24-36 (524)
16 PLN03131 hypothetical protein; 95.7 0.21 4.6E-06 58.2 14.9 22 354-375 430-451 (705)
17 KOG0521 Putative GTPase activa 91.5 0.022 4.8E-07 68.1 -3.2 70 20-91 626-699 (785)
18 PF00643 zf-B_box: B-box zinc 84.2 0.89 1.9E-05 34.5 2.5 39 24-64 3-42 (42)
19 PRK12495 hypothetical protein; 73.8 2.8 6E-05 43.9 3.0 37 13-53 28-67 (226)
20 PRK00085 recO DNA repair prote 62.2 6.5 0.00014 40.1 2.9 37 16-52 137-178 (247)
21 TIGR00613 reco DNA repair prot 58.7 7.4 0.00016 39.6 2.6 38 16-53 135-177 (241)
22 COG1734 DksA DnaK suppressor p 52.2 5 0.00011 38.3 0.2 48 7-54 61-111 (120)
23 PF08271 TF_Zn_Ribbon: TFIIB z 50.9 8.4 0.00018 29.9 1.2 27 26-53 2-28 (43)
24 PLN03119 putative ADP-ribosyla 49.1 2.6E+02 0.0056 33.7 13.0 9 354-362 390-398 (648)
25 PF11781 RRN7: RNA polymerase 47.9 14 0.0003 28.3 1.9 27 22-51 6-32 (36)
26 COG1381 RecO Recombinational D 47.3 9.8 0.00021 39.9 1.4 27 25-51 155-182 (251)
27 PF14376 Haem_bd: Haem-binding 44.7 18 0.00038 34.9 2.6 24 11-38 32-55 (137)
28 KOG0119 Splicing factor 1/bran 43.3 6.4E+02 0.014 30.0 18.3 39 605-648 482-520 (554)
29 TIGR02419 C4_traR_proteo phage 43.3 13 0.00027 31.7 1.2 33 21-54 28-62 (63)
30 PF01286 XPA_N: XPA protein N- 42.8 7.8 0.00017 29.6 -0.1 27 25-51 4-31 (34)
31 PRK11019 hypothetical protein; 42.4 13 0.00028 33.9 1.2 32 24-56 36-69 (88)
32 smart00401 ZnF_GATA zinc finge 36.6 27 0.00059 28.5 2.1 36 23-58 2-39 (52)
33 KOG2236 Uncharacterized conser 35.5 74 0.0016 36.9 6.0 28 300-327 211-238 (483)
34 PHA00080 DksA-like zinc finger 33.3 23 0.0005 31.0 1.3 33 22-55 29-63 (72)
35 cd00194 UBA Ubiquitin Associat 32.8 4.8 0.0001 29.9 -2.6 27 178-205 5-31 (38)
36 PRK10778 dksA RNA polymerase-b 31.6 27 0.00058 34.5 1.6 36 21-56 108-144 (151)
37 TIGR02890 spore_yteA sporulati 31.3 28 0.00061 34.6 1.7 32 23-54 85-117 (159)
38 KOG2057 Predicted equilibrativ 30.7 5.8E+02 0.012 29.0 11.5 19 351-369 370-390 (499)
39 COG1997 RPL43A Ribosomal prote 30.1 56 0.0012 30.1 3.2 29 22-52 33-61 (89)
40 cd07171 NR_DBD_ER DNA-binding 29.9 37 0.0008 30.2 2.0 31 23-56 2-32 (82)
41 KOG3362 Predicted BBOX Zn-fing 29.8 21 0.00046 35.5 0.5 32 24-56 118-150 (156)
42 cd03031 GRX_GRX_like Glutaredo 28.6 31 0.00068 33.8 1.5 44 5-57 80-123 (147)
43 cd07173 NR_DBD_AR DNA-binding 28.5 36 0.00078 30.3 1.7 31 23-56 2-32 (82)
44 PRK13715 conjugal transfer pro 27.9 27 0.00059 30.6 0.9 30 25-54 35-65 (73)
45 cd06968 NR_DBD_ROR DNA-binding 27.9 40 0.00086 30.8 1.9 31 23-56 4-34 (95)
46 KOG4368 Predicted RNA binding 27.2 2.9E+02 0.0064 33.3 9.0 19 170-188 641-659 (757)
47 PF00320 GATA: GATA zinc finge 27.2 58 0.0013 24.7 2.4 30 27-56 1-32 (36)
48 TIGR00100 hypA hydrogenase nic 26.0 30 0.00064 32.5 0.8 43 21-67 67-113 (115)
49 cd07170 NR_DBD_ERR DNA-binding 25.8 42 0.00092 30.9 1.7 30 24-56 4-33 (97)
50 COG2158 Uncharacterized protei 25.7 38 0.00082 32.2 1.4 23 36-58 52-76 (112)
51 PRK00420 hypothetical protein; 25.3 1.1E+02 0.0024 29.2 4.4 45 6-53 3-49 (112)
52 PRK00423 tfb transcription ini 25.3 42 0.00092 36.3 1.9 34 22-56 9-42 (310)
53 KOG0457 Histone acetyltransfer 24.7 51 0.0011 37.8 2.4 92 21-125 10-126 (438)
54 cd07160 NR_DBD_LXR DNA-binding 24.4 47 0.001 30.8 1.8 31 23-56 17-47 (101)
55 PRK13844 recombination protein 24.4 53 0.0012 34.1 2.3 95 7-114 39-135 (200)
56 PTZ00255 60S ribosomal protein 23.8 74 0.0016 29.3 2.9 39 11-51 22-61 (90)
57 PF02318 FYVE_2: FYVE-type zin 23.1 1.2E+02 0.0027 28.3 4.3 51 5-55 23-90 (118)
58 PRK03681 hypA hydrogenase nick 22.2 27 0.00059 32.7 -0.2 43 21-66 67-113 (114)
59 PF01258 zf-dskA_traR: Prokary 22.1 16 0.00034 27.5 -1.5 30 25-54 4-34 (36)
60 PRK00564 hypA hydrogenase nick 21.1 31 0.00067 32.5 -0.1 43 22-67 69-115 (117)
61 PF12760 Zn_Tnp_IS1595: Transp 20.5 1.1E+02 0.0024 24.1 3.0 42 8-51 3-44 (46)
62 PF07282 OrfB_Zn_ribbon: Putat 20.4 56 0.0012 27.3 1.3 26 25-52 29-54 (69)
63 cd07169 NR_DBD_GCNF_like DNA-b 20.3 65 0.0014 29.2 1.8 32 22-56 4-35 (90)
No 1
>PLN03131 hypothetical protein; Provisional
Probab=100.00 E-value=1.1e-99 Score=830.92 Aligned_cols=603 Identities=34% Similarity=0.517 Sum_probs=487.3
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCCcceeecccCCCCHHHHHHHHhc
Q 005403 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (698)
Q Consensus 1 m~sr~kedernekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LGhrVKSLsLD~Wt~eEVe~m~~g 80 (698)
|++| |++|+++++|++|++.++|++|+||++++|+|||+|||||||++|+||||+|+||||||+||+|+++||++|+.+
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 ChHHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCcccccccc-cCCCCCCCCCCC
Q 005403 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPPY 159 (698)
Q Consensus 81 GN~~aN~iwEa~~~~~~~p~Pdssd~~~~reFIR~KYveKrF~~e~~~dkPpRl~~gd~eds~e~Rr-ss~q~~SRSppy 159 (698)
||+++|+|||++|+..+.+.|+..+.+++|+|||.|||+|||+.....++|++....-+.+..|+|| ++|++|+|||+|
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 9999999999999987777888888888999999999999999999999999887666777789999 999999999999
Q ss_pred cchhh-cccccCCCCCCCCccccccCCCCCCCCCchhhh--cccCCCccCCCCCcccccccccccccCCCC---CCCCcc
Q 005403 160 EDTYE-RRYNEQSSPGGRSDDKNSRYGYDERSPGNEQEN--RQFGDYRRTSPTRPEVINDWRRDDRFGNGR---KFEDRR 233 (698)
Q Consensus 160 ~d~~e-rrys~r~s~~~Rk~dkl~~mgy~d~~~~~d~l~--~~~Gd~~r~sP~r~e~~~d~~~~dr~~~~~---~~~~~r 233 (698)
+++|| ||||++..+++|+ +++|+.. +++|+|+| ||+|| +|||+||||+++. +.+|++
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 6899988877777 7777764 99999999 99995 9999999999995 677777
Q ss_pred cCCCCC--CcCCCCCCCCCCCCCCCCCccCchhhhccCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCChh
Q 005403 234 ISDGDS--KLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQA 311 (698)
Q Consensus 234 ~s~~~~--~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~~ 311 (698)
+|+++. +.+.+|||++||+.. || +|||+|+|||||||+|||++|+|++..++++|.++.|||+|+|+++|++|+++
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 776554 557899999999874 45 66999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCccccCCCCCCCChhhhhhhchhhcccccccCCCCCCCCCccccCCcCcccccCCCCCCchHHHhhccCCCCC
Q 005403 312 EVKLETTGSLIDFDADPKPSPAVAQAQQKTVAQSVVQPASSANDNNWASFDLAPQVKVSQTSSNLNTLETVFSQLSVPAS 391 (698)
Q Consensus 312 ~~k~~~s~sLiD~~~~~ep~~~~~~~~q~~~~~~~~~~~~s~~~~~wasfd~~~~~~~~~~~~~~n~le~~l~qls~~~s 391 (698)
++|+++++|||||++|+|+..+. .|.++.... + .......|+-|.+-..-++.+..+. .--.-|+||+..+.
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---HQDKMPAFP---R-MAGSGSHASLDHFKAPVAPEAAAPM-APPIDLFQLPATSP 372 (705)
T ss_pred ceeecccccccccccCccccccc---cccccCCcc---c-ccccccccccccccccccccccccc-CCchhhhhccCCCC
Confidence 99999999999999999987663 333322221 1 1345556666655544444333221 22456899999999
Q ss_pred CCCCCCCCCCCCCCCcccCCCcccccCCCCCCCcccCCCccccccccCCCCCccccccccCCCCCCCCCCCCCCCCcccc
Q 005403 392 VPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLPVSV 471 (698)
Q Consensus 392 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~s~~s~~s~~~~~~~~~~~ 471 (698)
+|.++.+.++ ++.. ..++.++.+++.|++ ....++.-+
T Consensus 373 a~~vdlf~~s--------~l~~-------------------------------~p~~n~~q~~qts~p---~~~dlfag~ 410 (705)
T PLN03131 373 APPVDLFEIP--------PLDP-------------------------------APAINAYQPPQTSLP---SSIDLFGGI 410 (705)
T ss_pred CCcccccccC--------cccC-------------------------------CCccccCCCCcccCC---ccccccccc
Confidence 9998888773 1101 111234445555554 455667788
Q ss_pred CCCCCCcccCCC---CCcCCCCCCccccccCCCCcc--CCCC------------------------Ccc---ccccccCC
Q 005403 472 NAGNSFSMQHQP---PLFPTAGGQFTASQFTPPVAG--SSNN------------------------QQW---NTSLAQNA 519 (698)
Q Consensus 472 ~~~q~~~~q~qq---~~f~~~~~~~~~q~~t~~~~~--~~nn------------------------Q~w---~~~~~q~~ 519 (698)
++||..+..||. .-.|+++||.++...++++.. ..|= ..| +..+.|++
T Consensus 411 ~qqq~~~s~~~~~~~~s~pknegwa~fd~~~p~~s~~~~~n~t~~~v~~~~~~~~~~d~v~~~~~~~q~Pp~~~~~~~~s 490 (705)
T PLN03131 411 TQQQSINSLDEKSPELSIPKNEGWATFDGIQPIASTPGNENLTPFSIGPSMAGSANFDQVPSLDKGMQWPPFQNSSDEES 490 (705)
T ss_pred cccCccccccccCcccCCccccCcccccCCCcccccCCcccccccccccccccCcchhhccccccccccCCCcccccccc
Confidence 888877755555 778999999998644444422 2222 234 33333543
Q ss_pred --CCCCCCCCCCCCCCcccccCC--------------CCCCCCCCccccccCCccCcccccccccCCCCCCCCCCccCCC
Q 005403 520 --QGPPAAQPAQSVPKPALESAS--------------GGLSQPSPVEVKSTGRTALPEDLFTANYSSFPASVPGWQTVPP 583 (698)
Q Consensus 520 --~~~p~~~~~~~~~~~~~~~~~--------------~~~sq~~~~e~k~sgrkeLP~DlFt~~y~~~p~~vpGwq~~pp 583 (698)
+..||....+.|-++.+++.- .+.+....+|....--+.-.+|.|.....+......|.|+..|
T Consensus 491 ~s~~~pW~~~~~~V~~~~~~~~q~WnAF~~~ds~~~~~l~~~~~~s~~q~~~~~~~t~~q~~~~~~~~d~~~d~~~r~~p 570 (705)
T PLN03131 491 ASGPAPWLGDLHNVEAPDNTSAQNWNAFEFDDSVAGIPLEGIKQSSEPQTAANMPPTADQLIGCKALEDFNKDGIKRTAP 570 (705)
T ss_pred cccCCcccccchhcccCCccCccccccccccccccccccccccccccccccccCCCCcccccccccccccccccccccCC
Confidence 456777888889888775421 2345556677777777778888888888898899999999999
Q ss_pred CCc----eeceecCCCC-------------CCCCccccCCCCCCCCCCCCCCCccccCCCCcccccccCCCCCCCCCCCC
Q 005403 584 HGM----VYAMQYNTAA-------------PMPNFVHSKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLR 646 (698)
Q Consensus 584 ~gm----g~~mqy~~~~-------------p~~~~~~~~ks~NPFD~~~~~~~~Q~~~fPsm~~lqgalp~~~~~~~~~~ 646 (698)
+|| ||+.+-...+ .|++--+..||+|||||.+|....+.-||-.|.+||+|||+. .++
T Consensus 571 ~~~~~~~g~~~~~~~~~~ps~~~~~~~~~~~~~s~~~~~ks~npfdl~~dsd~~~~~mf~d~sslq~~lp~~-----~~~ 645 (705)
T PLN03131 571 HGQGELPGLDEPSDILAEPSYTPPAHPIMEHAQSHANDHKSINPFDLPYDSDLEPGNMFLDMSSLEAALPDA-----HLP 645 (705)
T ss_pred CCCcCCCCCCCCCccccCCCCCccccccccccccccCccCCCCCcCCccccccCcccceeehHHHHhhcCCC-----CCc
Confidence 999 5554422222 344445678999999999999999999999999999999954 445
Q ss_pred CC-CC-CCCCCCCCCCCC-CCCCCCCCCCcccccc
Q 005403 647 TS-SL-TPSPAWMPPQAS-PYPSAMPSQMPTYAAA 678 (698)
Q Consensus 647 ss-~~-~~s~~~~~~~~~-~y~~~~~~~~~~y~s~ 678 (698)
++ +| +.+..|++..+. +|+++.|++.++|.++
T Consensus 646 ~~f~g~~~tepw~~~~~~~~yip~~pqggl~y~ag 680 (705)
T PLN03131 646 SAFLGSGMTEPWFPQDLAMTYIPAAPQGGLAYMAG 680 (705)
T ss_pred hhhhcCCCCCccccCCCcccccCCCCCCCchhhcc
Confidence 55 66 899999999977 9999999999999776
No 2
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=100.00 E-value=2.7e-81 Score=682.13 Aligned_cols=564 Identities=31% Similarity=0.440 Sum_probs=422.5
Q ss_pred CcchhhhhHHHHHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCCcceeecccCCCCHHHHHHHHhc
Q 005403 1 MANRLKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEG 80 (698)
Q Consensus 1 m~sr~kedernekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LGhrVKSLsLD~Wt~eEVe~m~~g 80 (698)
|++| |++||++++|++|+++++|++|+||+..+|+|||+|||||||++|+||||+|+||||||+||+|+++||++|+.+
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 ChHHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCcccccccc-cCCCCCCCCCCC
Q 005403 81 GNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRR-DTYQGGSRSPPY 159 (698)
Q Consensus 81 GN~~aN~iwEa~~~~~~~p~Pdssd~~~~reFIR~KYveKrF~~e~~~dkPpRl~~gd~eds~e~Rr-ss~q~~SRSppy 159 (698)
||+++|+|||++|+..+.+.|...+.+++|+|||.|||+|+|+.....+++++.....+....+.|+ ++|+++++|++|
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 9999999999999887677788888888899999999999999999999888754344433446788 999999999999
Q ss_pred cchhh-cccccCCCCCCCCccccccCCCCCCCCCchhh-hcccCCCccCCCCCcccccccccccccCCCCCCCCcccCCC
Q 005403 160 EDTYE-RRYNEQSSPGGRSDDKNSRYGYDERSPGNEQE-NRQFGDYRRTSPTRPEVINDWRRDDRFGNGRKFEDRRISDG 237 (698)
Q Consensus 160 ~d~~e-rrys~r~s~~~Rk~dkl~~mgy~d~~~~~d~l-~~~~Gd~~r~sP~r~e~~~d~~~~dr~~~~~~~~~~r~s~~ 237 (698)
++.|| |||+++...+.|| ++.|+. .+++++|.+ ||+|+ +|||+||||+||... .|+||.
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 888876 599999999 99997 899999999998754 499873
Q ss_pred ------C-CCcCCCCCCCCCCCCCCCCCccCchhhhccCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCCh
Q 005403 238 ------D-SKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQ 310 (698)
Q Consensus 238 ------~-~~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~ 310 (698)
+ .+.+.+||+++ |.++++||+.+ .++++.. .. -.+ .++.|||+|+|+++|+|++.
T Consensus 221 s~ss~g~~~~~~~~sp~~~-~~~~~~~~~~~-~~~~~~~-------------~~--~~~-~~~sqRT~SsGs~gSfDs~s 282 (648)
T PLN03119 221 SVSSAGDPFRSDIQSPNFQ-QEAEFRSPQFQ-HSNAPPS-------------EN--LFP-GRQHQRTTSSGSVRSVDSNF 282 (648)
T ss_pred ccccCCcccccCcCCCCcc-cccccCCcccc-cccCcch-------------hh--ccc-cccccccccccccccccccc
Confidence 2 56678999999 55566665555 5654310 00 001 47789999999999999999
Q ss_pred hhhhhhccCccccCCCCCCCChhhhhhhchhhcccccccCCCCCCCCCccccCCcCcccccCCCCCCchHHHhhccCCCC
Q 005403 311 AEVKLETTGSLIDFDADPKPSPAVAQAQQKTVAQSVVQPASSANDNNWASFDLAPQVKVSQTSSNLNTLETVFSQLSVPA 390 (698)
Q Consensus 311 ~~~k~~~s~sLiD~~~~~ep~~~~~~~~q~~~~~~~~~~~~s~~~~~wasfd~~~~~~~~~~~~~~n~le~~l~qls~~~ 390 (698)
+++|++++++|.|+.+|.+..-+. .|.++... +..+.++ ..- -..|+||++.+
T Consensus 283 ~S~ks~~Sg~l~d~~~E~~~~~~~---~q~~~~~~---------------------~P~~~~~-~aa--pIDLFqlp~ts 335 (648)
T PLN03119 283 MSIKSYTSGGLGEAVSESRQNTGS---QQGKTSNH---------------------VPLVAES-TKA--PIDLFQLPGAP 335 (648)
T ss_pred ccccccccCCcccccccccccccc---cccccCCC---------------------Ccccccc-cCC--chhhhhccCCC
Confidence 999999999999999999876553 23222222 1111111 111 35689999999
Q ss_pred CCCCCCCCCCCCCCCCcccCCCcccccCCCCCCCcccCCCccccccccCCCCCccccccccCCCCCCCCCCCCCCCCccc
Q 005403 391 SVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLPVS 470 (698)
Q Consensus 391 s~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~s~~s~~s~~~~~~~~~~ 470 (698)
.+|+++.+.++ ++ |-+.++..+.+++.+++++- ..+.-
T Consensus 336 ~a~~vdlf~~~-------------------~~--------------------p~~p~~n~~q~~qts~p~~~---~~f~~ 373 (648)
T PLN03119 336 VAQSVDTFQPS-------------------IA--------------------PRSPPVNLQQAPQTYSFTPA---NSFAG 373 (648)
T ss_pred CCccccccccc-------------------cC--------------------CCCCccccCCCccccCCcch---hhhhc
Confidence 99999988873 00 11222334556666655422 12233
Q ss_pred cCCCCCCcccCCC-CCcCCCCCCccccccCCCCccCCCC---------------------Cccc---ccccc--CCCCCC
Q 005403 471 VNAGNSFSMQHQP-PLFPTAGGQFTASQFTPPVAGSSNN---------------------QQWN---TSLAQ--NAQGPP 523 (698)
Q Consensus 471 ~~~~q~~~~q~qq-~~f~~~~~~~~~q~~t~~~~~~~nn---------------------Q~w~---~~~~q--~~~~~p 523 (698)
+++||-. +-++ .-.|+++||.++.+.++++-+..|= ..|- ....| .++..|
T Consensus 374 ~~qqq~~--~~~~~~s~pkneGWA~fd~p~~s~~~~~ni~~~~~~~~~~~~d~v~~~~~~mq~Pp~~~~~~~~s~s~~~p 451 (648)
T PLN03119 374 NLGQQPT--SRPSELSAPKNEGWASFDNPMPAAKSTNVITSPGDFQLELKIEEILQPSTSMQLPPYPSTVDQHALSIPSP 451 (648)
T ss_pred ccccCcc--cCccccccccccCcccccccccccCCcccccCccccccCcchhhhcccccccccCCCcccccccccccCCc
Confidence 3333322 2333 6788999999987555555433221 2331 12222 234556
Q ss_pred CCCCCCCCCCcccccCC-----C-------CCCC--CCCccccccCCccCcccccccccCCCCCCCCCCccCC-CCCc-e
Q 005403 524 AAQPAQSVPKPALESAS-----G-------GLSQ--PSPVEVKSTGRTALPEDLFTANYSSFPASVPGWQTVP-PHGM-V 587 (698)
Q Consensus 524 ~~~~~~~~~~~~~~~~~-----~-------~~sq--~~~~e~k~sgrkeLP~DlFt~~y~~~p~~vpGwq~~p-p~gm-g 587 (698)
|....+.|.++.+++.- + +.+. +...+....--+--.+|.|.....+...+..|.|+.. |+|| |
T Consensus 452 W~~~~~~V~~~~~~~~q~WnAF~ds~~~~~l~~~~~~~~~~~~~~~~~~~t~~q~~~~r~~ed~~~dg~qr~~~p~g~~g 531 (648)
T PLN03119 452 WQEDLSNVLKDVVDNPQPWNAFPDSIEANPLDSSRNIHQQVDGASTSSYNTDHQHLESQVLEELSNDGTQTTRIPAGSSA 531 (648)
T ss_pred hhccchhcccCcccCccccccchhhhccCccccccccccccccccccCCCCcccccccccccccccccccccccCCCCCC
Confidence 77777788777655421 0 0000 0112222222344445666666777778899999999 8888 4
Q ss_pred eceecCCCCCCCCccc-------cCCCCCCCCCCCCCCCccccCCCCcccccccCCCCCCCCCCCCCC-CCCCCCCCCCC
Q 005403 588 YAMQYNTAAPMPNFVH-------SKSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS-SLTPSPAWMPP 659 (698)
Q Consensus 588 ~~mqy~~~~p~~~~~~-------~~ks~NPFD~~~~~~~~Q~~~fPsm~~lqgalp~~~~~~~~~~ss-~~~~s~~~~~~ 659 (698)
|+.+-...|+ |+|.- ..||+|||||.+|....+.-||-.|.+||++||+ ..++++ +|+.+..|++.
T Consensus 532 ~~~~~~~~~~-Ps~~~~~~~~~~~~ks~npfdl~~~sd~~~~~mf~d~tslq~~lp~-----~~~~~~~~~~~t~~w~~~ 605 (648)
T PLN03119 532 FGFPGNIGMA-PSYSEEAWQHVNEQKSANPFDLPYDSEFDSNDMFLDMSSLQGALPD-----IQTPQAFLNGVSQPWLAA 605 (648)
T ss_pred CCCCCccccC-CCCCchhccccccccCCCCcCCccccccCcccceeehHHHHhhcCC-----CCCchhhhcCCCcccccC
Confidence 4555444332 56644 4599999999999999999999999999999996 344566 88999999999
Q ss_pred CCC-CCCCCCC--CCCccccccC
Q 005403 660 QAS-PYPSAMP--SQMPTYAAAI 679 (698)
Q Consensus 660 ~~~-~y~~~~~--~~~~~y~s~~ 679 (698)
.+. +|+++-| .+.++|.++-
T Consensus 606 ~~~~~yip~~~~~qggl~y~~~q 628 (648)
T PLN03119 606 DSVPSYLPAPAVAQGGLAYMAGQ 628 (648)
T ss_pred CCcccccCCCccccCCchhhhcc
Confidence 977 9999965 9999997763
No 3
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=2.3e-48 Score=419.19 Aligned_cols=504 Identities=29% Similarity=0.368 Sum_probs=363.3
Q ss_pred CcchhhhhHHH-HHHHHHHHcCCCCCCccCCCCCCC-CeeEccceeeeehhhhhhhhcCC--cceeecccCCCCHHHHHH
Q 005403 1 MANRLKEDEKN-ERIIRGLLKLQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGIHREFT--HRVKSVSMAKFTSQEVKA 76 (698)
Q Consensus 1 m~sr~kedern-ekiLr~Llk~PgNk~CADCGs~~P-qWaSvNfGVFVC~~CSGIHR~LG--hrVKSLsLD~Wt~eEVe~ 76 (698)
|++++||+|++ |++||+|+++|+|++|++|+...+ +|+++.-|-|||+.|+|+.|.|. ||||+|+|.+|++.||..
T Consensus 1 ~a~~~ke~E~~~ek~iR~l~kLP~NrrC~nCnsl~~~t~~~~~~g~fv~~~~sg~ls~l~~ahRvksiSmttft~qevs~ 80 (524)
T KOG0702|consen 1 YAGYKKEDEYDYEKEIRRLLKLPENRRCINCNSLVAATYVVYTVGSFVCTMCSGLLSGLNPAHRVKSISMTTFTDQEVSF 80 (524)
T ss_pred CCcccccchhHHHHHHHHHhcCCCCCceeeccccccceEEEeeccceeeeccchhhccCCCccccceeeeeeccccchHH
Confidence 78999999998 999999999999999999999987 99999999999999999999996 999999999999999999
Q ss_pred HHhcChHHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHhhccccccCCCCCCCCCCCCCCCcccccccccCCCCCCCC
Q 005403 77 LQEGGNQRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNYDKPPRVKMGDKEDSYDIRRDTYQGGSRS 156 (698)
Q Consensus 77 m~~gGN~~aN~iwEa~~~~~~~p~Pdssd~~~~reFIR~KYveKrF~~e~~~dkPpRl~~gd~eds~e~Rrss~q~~SRS 156 (698)
|+.+||+.+++||++-.+.++-..||..|.+++|+||+.||++|+|+.+....+-+... |- ..+.++
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 99999999999999999988888999999999999999999999999875543322211 11 112224
Q ss_pred CCCcchhhcccccCCCCCCCCccccccCCCCCCCCCchhhh--cccCCCccCCCCCcccccccccccccCCCCCCCCccc
Q 005403 157 PPYEDTYERRYNEQSSPGGRSDDKNSRYGYDERSPGNEQEN--RQFGDYRRTSPTRPEVINDWRRDDRFGNGRKFEDRRI 234 (698)
Q Consensus 157 ppy~d~~errys~r~s~~~Rk~dkl~~mgy~d~~~~~d~l~--~~~Gd~~r~sP~r~e~~~d~~~~dr~~~~~~~~~~r~ 234 (698)
+++.+.+.++ +-+|-.++|+.+.+.... -+...+-+ +|.|||+++||+ |+|+.-+.
T Consensus 148 ~~~~~s~~~~-------------~~lrs~~gd~~P~~~~~t~np~~~~~~~-~~~~~~~~~~rf--dlfg~~k~------ 205 (524)
T KOG0702|consen 148 RPVSESRPET-------------KSLRSLLGDHAPLLAESTKNPRSRGLPK-SPIRFEIVDDRF--DLFGLPKA------ 205 (524)
T ss_pred CcccccCCCc-------------cccccccCCCCcchhhcccCccccCCCC-CCchhhhhhhhh--hhhcCcCc------
Confidence 4444433333 344445666656554433 44567888 999999876554 66654332
Q ss_pred CCCCCCcCCCCCCCCCCCCCCCCCccCchhhhccCCCCCcccCCCCCCCCCccCCCCCcccccCCCCCCCCCCCChhhhh
Q 005403 235 SDGDSKLEGRSPEQPKDPESSSPPVVRPVREILGDNVLPLRISEPPKANGVRVADGSTNTQRTASSGNLGSANENQAEVK 314 (698)
Q Consensus 235 s~~~~~~~~~sp~~~Kd~~~sspp~~~~~~~ilg~~v~~lr~~~~~~~~~~~~~~g~~~~qrt~~~~~~~s~~~~~~~~k 314 (698)
+| -..++...-|+++.++|+..+++++|+++-+-.|+++|+.|....+...+++..---..+.+..+.+.++.+.+
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 23456778899999999999999999999999999999999999998888888776655557889999999999
Q ss_pred hhccCccccCCCCCCCC--hhhhhhhchhhcccccccCC-CCCCCCCccccCCcCcccccC---CCCCCchHHHhhccCC
Q 005403 315 LETTGSLIDFDADPKPS--PAVAQAQQKTVAQSVVQPAS-SANDNNWASFDLAPQVKVSQT---SSNLNTLETVFSQLSV 388 (698)
Q Consensus 315 ~~~s~sLiD~~~~~ep~--~~~~~~~q~~~~~~~~~~~~-s~~~~~wasfd~~~~~~~~~~---~~~~n~le~~l~qls~ 388 (698)
..+.++++||+...|-+ .++.+.+-.+..+.+.|+.+ +..+++|++|+.++....... ++..+.|.+.+.+|.|
T Consensus 282 i~s~~~~~~f~k~~e~paps~a~qlp~~ss~~~~~q~t~~~~~nd~~ssf~~~~~Ap~~~~~s~p~i~s~~~s~~~~l~~ 361 (524)
T KOG0702|consen 282 ITSPGSFADFLKFEEIPAPSVAMQLPPYSSTVDQHQPTIPSPWNDQGSSFGATPVAPPLWVASPPSIGSNLLSSSRALAV 361 (524)
T ss_pred ccCcccchhhcccccccCcchhhhcCCcCCCccccCCCCCCcccccCcccccccccCCccccCCCCcccccccccccccc
Confidence 99999999998877755 22222222222222223333 356899999999887755443 3566777888888888
Q ss_pred CCCCCCCCCCCCCCCCCCcccCCCcccccCCCCCCCcccCCCccccccccCCCCCccccccccCCCCCCCCCCCCCCCCc
Q 005403 389 PASVPGQVSGIPSGAGAPVIAPATNVNVLPGGGSPVASVGHTPFSVFSAAAPAAPAVSGFATFPSANAPAPAPGVTPLLP 468 (698)
Q Consensus 389 ~~s~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~s~~s~~s~~~~~~~~ 468 (698)
.++++|+ .+.+.+++++-.+++- -
T Consensus 362 ~~s~~gs-------------------------a~~~~~~~~~n~~~~e-------------------------------~ 385 (524)
T KOG0702|consen 362 QSSVFGS-------------------------AGYVPPHQPVNLGVLE-------------------------------E 385 (524)
T ss_pred ccccccc-------------------------cccCCCCccccccccc-------------------------------c
Confidence 8877652 1122233332211100 0
Q ss_pred cccCCCCCCcccCCC--CCcCCCCCCccccccCCCCccCCCCCccccccccCCCCCCCCCCCCCCCCcccccCCCCCCCC
Q 005403 469 VSVNAGNSFSMQHQP--PLFPTAGGQFTASQFTPPVAGSSNNQQWNTSLAQNAQGPPAAQPAQSVPKPALESASGGLSQP 546 (698)
Q Consensus 469 ~~~~~~q~~~~q~qq--~~f~~~~~~~~~q~~t~~~~~~~nnQ~w~~~~~q~~~~~p~~~~~~~~~~~~~~~~~~~~sq~ 546 (698)
..+...|..+-+.+. .+||++-|. +.+.| +|-.. -.+..+.+.-+ + .
T Consensus 386 ~~~s~~q~~s~ft~~~ts~~p~~~~~-----------~pssn-------~~~~~---~~Q~~~~~~~~--g--------~ 434 (524)
T KOG0702|consen 386 LSNSTTQTFSAFTNESTSGFPAPIGM-----------APSSN-------HHQDD---EFQPNHRNPQP--G--------A 434 (524)
T ss_pred cccccccccccccCcccccCcccccc-----------CCccc-------ccccc---cccccccCCCC--c--------c
Confidence 112223333333332 455554433 11111 11111 11222222111 1 1
Q ss_pred CCccccccCCccCc-ccccccccCCCCCCCCCCccCCCCCceecee-cCCCCCCCC--ccccCCCCCCCCCCCCCCCccc
Q 005403 547 SPVEVKSTGRTALP-EDLFTANYSSFPASVPGWQTVPPHGMVYAMQ-YNTAAPMPN--FVHSKSTTNPFDVNNDSHPVQA 622 (698)
Q Consensus 547 ~~~e~k~sgrkeLP-~DlFt~~y~~~p~~vpGwq~~pp~gmg~~mq-y~~~~p~~~--~~~~~ks~NPFD~~~~~~~~Q~ 622 (698)
...+.+..++.++| .++|++.|.-.-.|+++||...++||+|+|+ |.+....|+ .++.-+|+|||+.+-. .+.|.
T Consensus 435 ~~~sl~~~~~~~~P~~~~fa~s~~qp~fP~qt~~~q~~~~~~~~~~~~~~p~~~P~~~v~~~G~S~nPF~as~~-S~aq~ 513 (524)
T KOG0702|consen 435 AMSSLPYGFEFASPFDMFFAMSFPQPAFPIQTPQVQQPGGSHFGLAGDSKPSYLPAPAVAQAGLSYNPFMASPN-SAAQF 513 (524)
T ss_pred ccccCCCCCCcCCCccccccccCcCcCCCCccccccCCCCCCccccccCCcccCccccccccccccCccccCCC-Ccccc
Confidence 34677889999999 9999999999888999999999999999999 888776666 9999999999999754 34455
Q ss_pred c-CCCCcccc
Q 005403 623 Q-TFPSMASL 631 (698)
Q Consensus 623 ~-~fPsm~~l 631 (698)
+ +||+|.++
T Consensus 514 ~~~~p~~nPF 523 (524)
T KOG0702|consen 514 PVAFPGTNPF 523 (524)
T ss_pred cccCCCCCCC
Confidence 4 47888765
No 4
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=100.00 E-value=1e-36 Score=314.73 Aligned_cols=118 Identities=28% Similarity=0.588 Sum_probs=107.8
Q ss_pred hhhHHHHHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC-c--ceeecccCCCCHHHHHHHHhcCh
Q 005403 6 KEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGN 82 (698)
Q Consensus 6 kedernekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG-h--rVKSLsLD~Wt~eEVe~m~~gGN 82 (698)
...++++++|++||+.++|+.|||||+++|+|||+|+|||||++|+||||.|| | |||||+||.|++|+|+.|+..||
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 HHHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHhhccccccCC
Q 005403 83 QRAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (698)
Q Consensus 83 ~~aN~iwEa~~~~~~~p~Pdssd~~~~reFIR~KYveKrF~~e~ 126 (698)
.+||++||++++.. ...|..+ +.+++|||+|||+|+|+.+.
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 99999999998754 4455433 36889999999999999865
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=2.9e-35 Score=269.00 Aligned_cols=112 Identities=33% Similarity=0.681 Sum_probs=92.5
Q ss_pred HHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC---cceeecccCCCCHHHHHHHHhcChHHHHHHH
Q 005403 13 RIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEVL 89 (698)
Q Consensus 13 kiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG---hrVKSLsLD~Wt~eEVe~m~~gGN~~aN~iw 89 (698)
++|++|++.++|++|||||+++|+|||++||||||+.|+|+||+|| |+||||+||+|+++||++|+.+||.++|++|
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 hhcCCCCCCCCCCCChHHHHHHHHHHHhhccccccC
Q 005403 90 LKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (698)
Q Consensus 90 Ea~~~~~~~p~Pdssd~~~~reFIR~KYveKrF~~e 125 (698)
|++.+ ...+.+..++.+.+++||++||++++|+.+
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 334445567888889999999999999863
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=1.3e-33 Score=257.05 Aligned_cols=107 Identities=28% Similarity=0.631 Sum_probs=97.9
Q ss_pred CCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC-c--ceeecccCCCCHHHHHHHHhcChHHHHHHHhhcCCCCCC
Q 005403 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEWDPQRQ 98 (698)
Q Consensus 22 PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG-h--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~iwEa~~~~~~~ 98 (698)
|+|++||||++++|+|||++||||||++|+|+||+|| | +||||+||+|++++|++|+.+||.++|++||++++....
T Consensus 1 ~~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~VkSl~md~w~~~~i~~~~~~GN~~~n~~~e~~~~~~~~ 80 (112)
T smart00105 1 PGNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKVRSLTLDTWTEEELRLLQKGGNENANSIWESNLDDFSL 80 (112)
T ss_pred CCCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCeeeecccCCCCHHHHHHHHHhhhHHHHHHHHhhCCcccc
Confidence 5899999999999999999999999999999999998 4 699999999999999999999999999999999987655
Q ss_pred CCCCCChHHHHHHHHHHHhhccccccCCCC
Q 005403 99 SFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (698)
Q Consensus 99 p~Pdssd~~~~reFIR~KYveKrF~~e~~~ 128 (698)
+.|..++.+.+++||+.||++|+|+.++..
T Consensus 81 ~~~~~~~~~~~~~fI~~KY~~k~f~~~~~~ 110 (112)
T smart00105 81 KPPDSDDQQKYESFIAAKYEEKLFVPPESA 110 (112)
T ss_pred CCCCCchHHHHHHHHHHHHHhhhccccccC
Confidence 556666677889999999999999987654
No 7
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=99.97 E-value=1.1e-30 Score=275.24 Aligned_cols=120 Identities=21% Similarity=0.528 Sum_probs=103.8
Q ss_pred hHHHHHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC-c--ceeecccCCCCHHHHHHHHhcChHH
Q 005403 8 DEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQR 84 (698)
Q Consensus 8 dernekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG-h--rVKSLsLD~Wt~eEVe~m~~gGN~~ 84 (698)
+...+++|..|.+.++|++|||||+++|+|||+|||||||++||||||+|| | +||||+||+|+++||++|+.+||.+
T Consensus 4 ~~~~~~~l~~l~~~~~Nk~CaDCga~~P~W~S~nlGvfiCi~CagvHRsLGvhiS~VKSitLD~wt~~~l~~m~~gGN~~ 83 (319)
T COG5347 4 KSEDRKLLKLLKSDSSNKKCADCGAPNPTWASVNLGVFLCIDCAGVHRSLGVHISKVKSLTLDNWTEEELRRMEVGGNSN 83 (319)
T ss_pred chHHHHHHHHHhhccccCccccCCCCCCceEecccCeEEEeecchhhhccccceeeeeeeecccCCHHHHHHHHHhcchh
Confidence 344577888888899999999999999999999999999999999999999 4 9999999999999999999999999
Q ss_pred HHHHHhhcCCCC-CCCCCCCChHHHHHHHHHHHhhccccccCCC
Q 005403 85 AKEVLLKEWDPQ-RQSFPDSSNVERLRNFIKHVYVDRRYTGERN 127 (698)
Q Consensus 85 aN~iwEa~~~~~-~~p~Pdssd~~~~reFIR~KYveKrF~~e~~ 127 (698)
||+||+++.-.. ..+.-...|...+++||++||++++|+....
T Consensus 84 a~~~~e~~~~~~~~~~~k~~yd~~v~~~y~~~ky~~~~~~~~~~ 127 (319)
T COG5347 84 ANRFYEKNLLDQLLLPIKAKYDSSVAKKYIRKKYELKKFIDDSS 127 (319)
T ss_pred hhhHhccCCCcccccccccccCHHHHHHHHHHHHHhhhcccccc
Confidence 999999977432 1222234566778999999999999998643
No 8
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=99.92 E-value=9.4e-25 Score=230.61 Aligned_cols=116 Identities=23% Similarity=0.405 Sum_probs=96.9
Q ss_pred HHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC-c--ceeecccCCCCHHHHHHHHhcChHHHHHH
Q 005403 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (698)
Q Consensus 12 ekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG-h--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~i 88 (698)
.++|++|++.++|++|+||++++|+||++|||||||++|+||||.|| | +||||+||.|++++|++|+.+||.++|++
T Consensus 10 ~~vfrkL~~kPgNk~CaDCga~nPtWASvn~GIFLCl~CSGVHRsLGvHISfVRSltLD~Ws~eqL~~Mk~GGN~rA~~f 89 (395)
T PLN03114 10 ISVFKKLKAKSDNKICFDCNAKNPTWASVTYGIFLCIDCSAVHRSLGVHISFVRSTNLDSWSSEQLKMMIYGGNNRAQVF 89 (395)
T ss_pred HHHHHHHHhCcCCCcCccCCCCCCCceeeccceeehhhhhHhhccCCCCCceeecccCCCCCHHHHHHHHHhcCHHHHHH
Confidence 45799999999999999999999999999999999999999999998 4 89999999999999999999999999999
Q ss_pred HhhcCCCCCCCCCC--CChHHHHHHHHHHHhhccccccCCC
Q 005403 89 LLKEWDPQRQSFPD--SSNVERLRNFIKHVYVDRRYTGERN 127 (698)
Q Consensus 89 wEa~~~~~~~p~Pd--ssd~~~~reFIR~KYveKrF~~e~~ 127 (698)
|+.+--........ .+....+.+-+.+|++++.+..+..
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 98743211111111 3445555567899999999986654
No 9
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=99.90 E-value=3e-24 Score=225.56 Aligned_cols=85 Identities=33% Similarity=0.703 Sum_probs=79.8
Q ss_pred hHHHHHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC-c--ceeecccCCCCHHHHHHHHhcChHH
Q 005403 8 DEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQR 84 (698)
Q Consensus 8 dernekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG-h--rVKSLsLD~Wt~eEVe~m~~gGN~~ 84 (698)
+.++++.|+.|....+|++|+||++.+|+|||++||||||++|+|+||.|| | .||||+||+|.+.||++|+.+||++
T Consensus 3 sprtrr~L~~lkp~deNk~CfeC~a~NPQWvSvsyGIfICLECSG~HRgLGVhiSFVRSVTMD~wkeiel~kMeaGGN~~ 82 (386)
T KOG0704|consen 3 SPRTRRVLLELKPQDENKKCFECGAPNPQWVSVSYGIFICLECSGKHRGLGVHISFVRSVTMDKWKEIELKKMEAGGNER 82 (386)
T ss_pred ChHHHHHHHhcCccccCCceeecCCCCCCeEeecccEEEEEecCCcccccceeeEEEEeeecccccHHHHHHHHhccchh
Confidence 457788888888888999999999999999999999999999999999999 5 9999999999999999999999999
Q ss_pred HHHHHhhc
Q 005403 85 AKEVLLKE 92 (698)
Q Consensus 85 aN~iwEa~ 92 (698)
+++|++..
T Consensus 83 ~~eFL~s~ 90 (386)
T KOG0704|consen 83 FREFLSSQ 90 (386)
T ss_pred HHHHHhhC
Confidence 99998764
No 10
>KOG0705 consensus GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms]
Probab=99.89 E-value=1.2e-23 Score=231.06 Aligned_cols=116 Identities=22% Similarity=0.463 Sum_probs=105.1
Q ss_pred HHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC---cceeecccCCCCHHHHHHHHhcChHHHHHH
Q 005403 12 ERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEV 88 (698)
Q Consensus 12 ekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG---hrVKSLsLD~Wt~eEVe~m~~gGN~~aN~i 88 (698)
.-.|+.|...+||..|+||+.++|.|+++|+|+++|++|+||||.|| +||++|.||.|..|.+..|..+||+.||++
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 34678888899999999999999999999999999999999999998 499999999999999999999999999999
Q ss_pred HhhcCCCCCCCCCCCChHHHHHHHHHHHhhccccccCCCC
Q 005403 89 LLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGERNY 128 (698)
Q Consensus 89 wEa~~~~~~~p~Pdssd~~~~reFIR~KYveKrF~~e~~~ 128 (698)
||.......+|.|+++.. ++|+||++||++|.|......
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 999777677777777554 568899999999999987654
No 11
>KOG0706 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=99.88 E-value=3.6e-23 Score=222.97 Aligned_cols=84 Identities=21% Similarity=0.561 Sum_probs=79.5
Q ss_pred HHHHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC-c--ceeecccCCCCHHHHHHHHhcChHHHH
Q 005403 10 KNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAK 86 (698)
Q Consensus 10 rnekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG-h--rVKSLsLD~Wt~eEVe~m~~gGN~~aN 86 (698)
...++++.|...++|++|+|||+++|+|++|+|||||||.|+++||.|| | +|||..||+|+.+||..|+.+||.+|+
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 005403 87 EVLLKEW 93 (698)
Q Consensus 87 ~iwEa~~ 93 (698)
.|+..+-
T Consensus 89 ~FFkqhg 95 (454)
T KOG0706|consen 89 VFFKQHG 95 (454)
T ss_pred HHHHHcC
Confidence 9998654
No 12
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=99.81 E-value=7.8e-21 Score=220.04 Aligned_cols=115 Identities=23% Similarity=0.445 Sum_probs=101.3
Q ss_pred HHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC---cceeecccCCCCHHHHHHHHhcChHHHHHHHhh
Q 005403 15 IRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMAKFTSQEVKALQEGGNQRAKEVLLK 91 (698)
Q Consensus 15 Lr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG---hrVKSLsLD~Wt~eEVe~m~~gGN~~aN~iwEa 91 (698)
+..+...++|..|||||++.|+|+++|+||.+||+|+||||+|| +||+||+||.|..+.+.+++++||..+|.|||+
T Consensus 417 ~~~vq~~pgN~~c~Dcg~p~ptw~S~NLgv~~CIecSGvhRslGvh~SkvrsLtLD~~~~~l~~l~~~lgn~~~N~i~e~ 496 (785)
T KOG0521|consen 417 IEEVQSVPGNAQCCDCGAPEPTWASINLGVLLCIECSGVHRSLGVHISKVRSLTLDVWEPELLLLFKNLGNKYVNEIYEA 496 (785)
T ss_pred hhhhhcCCchhhhhhcCCCCCchHhhhhchhhHhhccccccccCchhhhhhhhhhhccCcHHHHHHHHhCcchhhhhhhc
Confidence 67888899999999999999999999999999999999999999 499999999999999999999999999999999
Q ss_pred cCCCCCCCCCC-CChHHHHHHHHHHHhhccccccCCCCC
Q 005403 92 EWDPQRQSFPD-SSNVERLRNFIKHVYVDRRYTGERNYD 129 (698)
Q Consensus 92 ~~~~~~~p~Pd-ssd~~~~reFIR~KYveKrF~~e~~~d 129 (698)
.+.....+.|. .++...++.||++||++++|..+....
T Consensus 497 ~l~~~~~~~~~~~~~~~~r~~~i~~kyve~~F~~k~~~~ 535 (785)
T KOG0521|consen 497 LLPSYDSSKPTASSSRQAREAWIKAKYVERRFSVKEPQI 535 (785)
T ss_pred ccccccccCCCCccchhhhhHhhhcccceeeEeecccch
Confidence 98755333332 233666788999999999999775543
No 13
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=99.69 E-value=9.1e-18 Score=182.93 Aligned_cols=107 Identities=19% Similarity=0.405 Sum_probs=92.1
Q ss_pred HcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC-c--ceeecccCCCCHHHHHHHHhcChHHHHHHHhhcCC-
Q 005403 19 LKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLKEWD- 94 (698)
Q Consensus 19 lk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG-h--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~iwEa~~~- 94 (698)
++...-+.|+|||.++|.|+|||-|||||.+|..|||.|| | .||+|....|.++.|+++..+.|..+|.|||..+-
T Consensus 3 k~~l~~evC~DC~~~dp~WASvnrGt~lC~eCcsvHrsLGrhIS~vrhLR~s~W~pt~l~~V~tLn~~gaNsIWEh~Lld 82 (669)
T KOG0818|consen 3 KRLLSSEVCADCSGPDPSWASVNRGTFLCDECCSVHRSLGRHISQVRHLRHTPWPPTLLQMVETLNNNGANSIWEHSLLD 82 (669)
T ss_pred ccchhhhhhcccCCCCCcceeecCceEehHhhhHHHhhhcchHHHHHHhccCCCCHHHHHHHHHHHhcCcchhhhhhccC
Confidence 3455668999999999999999999999999999999999 4 89999999999999999999999999999998763
Q ss_pred C------CCCCCCCCChHHHHHHHHHHHhhccccccC
Q 005403 95 P------QRQSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (698)
Q Consensus 95 ~------~~~p~Pdssd~~~~reFIR~KYveKrF~~e 125 (698)
+ .+++.|...-...+.+|||+||+...|+.+
T Consensus 83 ~st~~sg~rk~~pqD~~Hp~K~eFIkaKy~~LtFv~~ 119 (669)
T KOG0818|consen 83 PATIMSGRRKANPQDKVHPNKAEFIRAKYQMLAFVHR 119 (669)
T ss_pred chhhhcccCCCCCcCCCCccHHHHHHHHHHheeeecc
Confidence 2 134555544444578899999999999984
No 14
>KOG1117 consensus Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms; Cytoskeleton]
Probab=99.66 E-value=4.1e-17 Score=185.61 Aligned_cols=110 Identities=26% Similarity=0.532 Sum_probs=99.3
Q ss_pred HHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcCC---cceeecccC--CCCHHHHHHHHhcChHHHHHHHh
Q 005403 16 RGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFT---HRVKSVSMA--KFTSQEVKALQEGGNQRAKEVLL 90 (698)
Q Consensus 16 r~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LG---hrVKSLsLD--~Wt~eEVe~m~~gGN~~aN~iwE 90 (698)
.++....+|+.|+||+++.|.||++|+++.||-.|+|-||.|| ++|+|++|| .|+.+.|+++..+||.++|.||-
T Consensus 290 eriW~ne~nr~cadC~ssrPdwasiNL~vvIck~caGqhrslgs~dSkvrslkmd~svwsneliElfivlgn~~an~Fwa 369 (1186)
T KOG1117|consen 290 ERIWLNEENRECADCGSSRPDWASINLCVVICKPCAGQHRSLGSGDSKVRSLKMDPSVWSNELIELFIVLGNPRANRFWA 369 (1186)
T ss_pred HHHHhccccccccccCCCCCcccccccceEEcccCCCccccCCCccccccccccCcccccchhhhhheeecCcccccccc
Confidence 4567788999999999999999999999999999999999998 699999999 79999999999999999999999
Q ss_pred hcCCCCCCCCCCCChHHHHHHHHHHHhhccccccCC
Q 005403 91 KEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGER 126 (698)
Q Consensus 91 a~~~~~~~p~Pdssd~~~~reFIR~KYveKrF~~e~ 126 (698)
.++++...-.|+++ ...+++||+.||.+.+|....
T Consensus 370 ~nl~~~e~lh~dss-p~~r~~fi~~Kykeg~fRk~~ 404 (1186)
T KOG1117|consen 370 GNLPPNEHLHPDSS-PSTRRQFIKEKYKEGKFRKEH 404 (1186)
T ss_pred cCCCCccccCCCCC-cchhhhHHHHHhhcccccccc
Confidence 99987766677764 345688999999999998653
No 15
>KOG0702 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=97.02 E-value=0.16 Score=57.82 Aligned_cols=13 Identities=23% Similarity=0.481 Sum_probs=9.9
Q ss_pred eeeeehhhhhhhh
Q 005403 43 WTFVCTNCSGIHR 55 (698)
Q Consensus 43 GVFVC~~CSGIHR 55 (698)
..--|++|.++|-
T Consensus 24 ~NrrC~nCnsl~~ 36 (524)
T KOG0702|consen 24 ENRRCINCNSLVA 36 (524)
T ss_pred CCCceeecccccc
Confidence 3447999999886
No 16
>PLN03131 hypothetical protein; Provisional
Probab=95.72 E-value=0.21 Score=58.21 Aligned_cols=22 Identities=23% Similarity=0.536 Sum_probs=15.0
Q ss_pred CCCCCccccCCcCcccccCCCC
Q 005403 354 NDNNWASFDLAPQVKVSQTSSN 375 (698)
Q Consensus 354 ~~~~wasfd~~~~~~~~~~~~~ 375 (698)
-+.+||+||...+-..++...|
T Consensus 430 knegwa~fd~~~p~~s~~~~~n 451 (705)
T PLN03131 430 KNEGWATFDGIQPIASTPGNEN 451 (705)
T ss_pred cccCcccccCCCcccccCCccc
Confidence 3889999997766555544444
No 17
>KOG0521 consensus Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms]
Probab=91.54 E-value=0.022 Score=68.13 Aligned_cols=70 Identities=17% Similarity=0.275 Sum_probs=56.2
Q ss_pred cCCCCCCccCCCC-CCCCeeEccceeeeehhhhhhhhcCC-c--ceeecccCCCCHHHHHHHHhcChHHHHHHHhh
Q 005403 20 KLQDNRRCINCNS-LGTQYVCTNFWTFVCTNCSGIHREFT-H--RVKSVSMAKFTSQEVKALQEGGNQRAKEVLLK 91 (698)
Q Consensus 20 k~PgNk~CADCGs-~~PqWaSvNfGVFVC~~CSGIHR~LG-h--rVKSLsLD~Wt~eEVe~m~~gGN~~aN~iwEa 91 (698)
+...+..|++|++ ....|+++|+.+-+|+.|+++|+.++ | .+.++.|++..+ |..+...|+...+..|..
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~s~lh~a~~~~~~~~~e~ll~~ga~--vn~~d~~g~~plh~~~~~ 699 (785)
T KOG0521|consen 626 KASSDGECLPRIATALAHGCCENWPVVLCIGCSLLHVAVGTGDSGAVELLLQNGAD--VNALDSKGRTPLHHATAS 699 (785)
T ss_pred HhccCccchhhhhhhhcchhhhccchhhhcccchhhhhhccchHHHHHHHHhcCCc--chhhhccCCCcchhhhhh
Confidence 3455789999998 57999999999999999999999996 4 667777777766 777777776666666543
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=84.22 E-value=0.89 Score=34.51 Aligned_cols=39 Identities=15% Similarity=0.475 Sum_probs=33.2
Q ss_pred CCCccCCCCCCCCeeEccceeeeehhhhhh-hhcCCcceeec
Q 005403 24 NRRCINCNSLGTQYVCTNFWTFVCTNCSGI-HREFTHRVKSV 64 (698)
Q Consensus 24 Nk~CADCGs~~PqWaSvNfGVFVC~~CSGI-HR~LGhrVKSL 64 (698)
+..|..|......|.+.+=.++||..|... |+. |+|..|
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~--H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG--HKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT--SEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCCC--CEEeEC
Confidence 578999999889999999999999999987 877 877664
No 19
>PRK12495 hypothetical protein; Provisional
Probab=73.84 E-value=2.8 Score=43.89 Aligned_cols=37 Identities=19% Similarity=0.237 Sum_probs=27.0
Q ss_pred HHHHHHHc---CCCCCCccCCCCCCCCeeEccceeeeehhhhhh
Q 005403 13 RIIRGLLK---LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (698)
Q Consensus 13 kiLr~Llk---~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGI 53 (698)
+++-.||. ...+..|-+||.+=|.+ -|+.+|..|..+
T Consensus 28 ~~ma~lL~~gatmsa~hC~~CG~PIpa~----pG~~~Cp~CQ~~ 67 (226)
T PRK12495 28 ERMSELLLQGATMTNAHCDECGDPIFRH----DGQEFCPTCQQP 67 (226)
T ss_pred HHHHHHHHhhcccchhhcccccCcccCC----CCeeECCCCCCc
Confidence 34444444 45678999999998832 599999999654
No 20
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=62.16 E-value=6.5 Score=40.13 Aligned_cols=37 Identities=27% Similarity=0.504 Sum_probs=28.8
Q ss_pred HHHHcC----CCCCCccCCCCCC-CCeeEccceeeeehhhhh
Q 005403 16 RGLLKL----QDNRRCINCNSLG-TQYVCTNFWTFVCTNCSG 52 (698)
Q Consensus 16 r~Llk~----PgNk~CADCGs~~-PqWaSvNfGVFVC~~CSG 52 (698)
.+|++. |.-..|+-||... ..|.+..-|.++|..|..
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 355553 4456999999875 478899999999999973
No 21
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=58.69 E-value=7.4 Score=39.60 Aligned_cols=38 Identities=24% Similarity=0.472 Sum_probs=29.0
Q ss_pred HHHHc----CCCCCCccCCCCCCC-CeeEccceeeeehhhhhh
Q 005403 16 RGLLK----LQDNRRCINCNSLGT-QYVCTNFWTFVCTNCSGI 53 (698)
Q Consensus 16 r~Llk----~PgNk~CADCGs~~P-qWaSvNfGVFVC~~CSGI 53 (698)
..|++ .|.-..|+.||..++ .|.+...|.|+|..|...
T Consensus 135 l~lL~~~G~~p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 135 LKLLQILGYALDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred HHHHHHcCCCcccCccCCCCCcCCCceEchhcCeEEChhhCcc
Confidence 35555 345579999998543 688999999999999764
No 22
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=52.17 E-value=5 Score=38.32 Aligned_cols=48 Identities=15% Similarity=0.246 Sum_probs=27.9
Q ss_pred hhHHHHHHHHHHHcCCCC--CCccCCCCCCC-CeeEccceeeeehhhhhhh
Q 005403 7 EDEKNERIIRGLLKLQDN--RRCINCNSLGT-QYVCTNFWTFVCTNCSGIH 54 (698)
Q Consensus 7 edernekiLr~Llk~PgN--k~CADCGs~~P-qWaSvNfGVFVC~~CSGIH 54 (698)
+.....++-..|.+.... .+|.+||.+=| .=.-..-+..+|+.|.-.|
T Consensus 61 ~r~~l~~i~~al~rIe~gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~ 111 (120)
T COG1734 61 ERKLLRKIESALDRIEEGTYGICEECGEPIPEARLEARPTARLCIECQERA 111 (120)
T ss_pred HHHHHHHHHHHHHHHHcCCccchhccCCcCCHHHHhhCcchHHHHHHHHHH
Confidence 333344444445444434 38999999622 2222233667999998776
No 23
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=50.90 E-value=8.4 Score=29.92 Aligned_cols=27 Identities=30% Similarity=0.563 Sum_probs=21.1
Q ss_pred CccCCCCCCCCeeEccceeeeehhhhhh
Q 005403 26 RCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (698)
Q Consensus 26 ~CADCGs~~PqWaSvNfGVFVC~~CSGI 53 (698)
+|-.||+.. ......-|-+||..|.-|
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 555677899999999544
No 24
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=49.14 E-value=2.6e+02 Score=33.66 Aligned_cols=9 Identities=56% Similarity=1.287 Sum_probs=8.0
Q ss_pred CCCCCcccc
Q 005403 354 NDNNWASFD 362 (698)
Q Consensus 354 ~~~~wasfd 362 (698)
-+.+||+||
T Consensus 390 kneGWA~fd 398 (648)
T PLN03119 390 KNEGWASFD 398 (648)
T ss_pred cccCccccc
Confidence 388999999
No 25
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=47.85 E-value=14 Score=28.34 Aligned_cols=27 Identities=22% Similarity=0.551 Sum_probs=22.8
Q ss_pred CCCCCccCCCCCCCCeeEccceeeeehhhh
Q 005403 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCS 51 (698)
Q Consensus 22 PgNk~CADCGs~~PqWaSvNfGVFVC~~CS 51 (698)
..|..|..|++. |...+=|-++|.+|-
T Consensus 6 ~~~~~C~~C~~~---~~~~~dG~~yC~~cG 32 (36)
T PF11781_consen 6 GPNEPCPVCGSR---WFYSDDGFYYCDRCG 32 (36)
T ss_pred cCCCcCCCCCCe---EeEccCCEEEhhhCc
Confidence 345679999998 888899999999994
No 26
>COG1381 RecO Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=47.27 E-value=9.8 Score=39.94 Aligned_cols=27 Identities=22% Similarity=0.657 Sum_probs=24.8
Q ss_pred CCccCCCCCC-CCeeEccceeeeehhhh
Q 005403 25 RRCINCNSLG-TQYVCTNFWTFVCTNCS 51 (698)
Q Consensus 25 k~CADCGs~~-PqWaSvNfGVFVC~~CS 51 (698)
..|+.||.+. +..+++-.|-+||.+|.
T Consensus 155 ~~Ca~cg~~~~~~~~s~~~~~~~C~~~~ 182 (251)
T COG1381 155 TSCARCGTPVDPVYFSPKSGGFLCSKCA 182 (251)
T ss_pred HHHhCcCCcCCCcceeeccCcccchhcc
Confidence 6999999975 57999999999999998
No 27
>PF14376 Haem_bd: Haem-binding domain
Probab=44.70 E-value=18 Score=34.91 Aligned_cols=24 Identities=29% Similarity=0.606 Sum_probs=16.3
Q ss_pred HHHHHHHHHcCCCCCCccCCCCCCCCee
Q 005403 11 NERIIRGLLKLQDNRRCINCNSLGTQYV 38 (698)
Q Consensus 11 nekiLr~Llk~PgNk~CADCGs~~PqWa 38 (698)
..+.++.|++ +-|.||++.+..|-
T Consensus 32 ~p~~v~~il~----~~CydCHSn~T~~P 55 (137)
T PF14376_consen 32 APEEVKIILK----NSCYDCHSNNTRYP 55 (137)
T ss_pred chHHHHHHHH----ccccccCCCCCCCc
Confidence 3344555554 57999999887764
No 28
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=43.32 E-value=6.4e+02 Score=30.01 Aligned_cols=39 Identities=28% Similarity=0.375 Sum_probs=25.5
Q ss_pred CCCCCCCCCCCCCCCccccCCCCcccccccCCCCCCCCCCCCCC
Q 005403 605 KSTTNPFDVNNDSHPVQAQTFPSMASLQGALPNVSHPPGLLRTS 648 (698)
Q Consensus 605 ~ks~NPFD~~~~~~~~Q~~~fPsm~~lqgalp~~~~~~~~~~ss 648 (698)
-.++-|||-. .|+.--|.+-.-.|+-..|+++.+|.+.+
T Consensus 482 ~~~~pp~~r~-----a~~~a~Pg~p~~~~~~~~vPpp~g~~p~~ 520 (554)
T KOG0119|consen 482 TTSIPPGDRQ-----AQAAAPPGAPFHGGNYNAVPPPPGLQPAN 520 (554)
T ss_pred cccCCccccc-----ccccCCCCCCCCCCCCCCCCCCCCCCCCC
Confidence 4667777774 24444466666667767777788877766
No 29
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=43.30 E-value=13 Score=31.70 Aligned_cols=33 Identities=18% Similarity=0.236 Sum_probs=22.7
Q ss_pred CCCCCCccCCCCCCC--CeeEccceeeeehhhhhhh
Q 005403 21 LQDNRRCINCNSLGT--QYVCTNFWTFVCTNCSGIH 54 (698)
Q Consensus 21 ~PgNk~CADCGs~~P--qWaSvNfGVFVC~~CSGIH 54 (698)
..+...|.|||..=| .+. ..-|+..|+.|...+
T Consensus 28 ~~s~g~C~~Cg~~Ip~~Rl~-a~p~~~~Cv~Cq~~~ 62 (63)
T TIGR02419 28 GPSLRECEDCGEPIPEARRE-ALPGVTRCVSCQEIL 62 (63)
T ss_pred CCCCCeeccCCCcChHHHHh-hcCCcCCcHHHHhhc
Confidence 455679999999632 232 234788999998754
No 30
>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=42.76 E-value=7.8 Score=29.65 Aligned_cols=27 Identities=30% Similarity=0.653 Sum_probs=16.8
Q ss_pred CCccCCCCC-CCCeeEccceeeeehhhh
Q 005403 25 RRCINCNSL-GTQYVCTNFWTFVCTNCS 51 (698)
Q Consensus 25 k~CADCGs~-~PqWaSvNfGVFVC~~CS 51 (698)
.+|.+|+.. .-+|..-+|+.-||.+|.
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~VCD~CR 31 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPVCDKCR 31 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S--TTT-
T ss_pred chHhHhCCHHHHHHHHHhCCcccccccc
Confidence 479999995 578999999999999994
No 31
>PRK11019 hypothetical protein; Provisional
Probab=42.36 E-value=13 Score=33.88 Aligned_cols=32 Identities=13% Similarity=0.186 Sum_probs=22.8
Q ss_pred CCCccCCCCCCC--CeeEccceeeeehhhhhhhhc
Q 005403 24 NRRCINCNSLGT--QYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 24 Nk~CADCGs~~P--qWaSvNfGVFVC~~CSGIHR~ 56 (698)
-..|.|||.+=| .|.-+ -++-.|+.|...+-.
T Consensus 36 yg~C~~CG~~Ip~~Rl~A~-P~a~~Cv~Cq~~~E~ 69 (88)
T PRK11019 36 LTECEECGEPIPEARRKAI-PGVRLCVACQQEKDL 69 (88)
T ss_pred CCeeCcCCCcCcHHHHhhc-CCccccHHHHHHHHH
Confidence 469999999633 34322 377899999987644
No 32
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=36.60 E-value=27 Score=28.51 Aligned_cols=36 Identities=17% Similarity=0.359 Sum_probs=29.2
Q ss_pred CCCCccCCCCC-CCCeeEcccee-eeehhhhhhhhcCC
Q 005403 23 DNRRCINCNSL-GTQYVCTNFWT-FVCTNCSGIHREFT 58 (698)
Q Consensus 23 gNk~CADCGs~-~PqWaSvNfGV-FVC~~CSGIHR~LG 58 (698)
....|.+|+.. -|.|=.-..|. +||-.|.-..+..+
T Consensus 2 ~~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k~~ 39 (52)
T smart00401 2 SGRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKKHG 39 (52)
T ss_pred CCCCcCCCCCCCCCccccCCCCCCcEeecccHHHHHcC
Confidence 35799999985 58898888886 99999987777655
No 33
>KOG2236 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.55 E-value=74 Score=36.87 Aligned_cols=28 Identities=18% Similarity=0.247 Sum_probs=15.0
Q ss_pred CCCCCCCCCChhhhhhhccCccccCCCC
Q 005403 300 SGNLGSANENQAEVKLETTGSLIDFDAD 327 (698)
Q Consensus 300 ~~~~~s~~~~~~~~k~~~s~sLiD~~~~ 327 (698)
.|-+-++...-+-++.-....++|+++-
T Consensus 211 lG~V~svv~~~VII~s~~~~~vlde~Sv 238 (483)
T KOG2236|consen 211 LGKVSSVVDQQVIIESTCNKEVLDEDSV 238 (483)
T ss_pred hhHHHHHhhhceEEEeccCcccccccce
Confidence 3334444455555555555667776543
No 34
>PHA00080 DksA-like zinc finger domain containing protein
Probab=33.32 E-value=23 Score=30.96 Aligned_cols=33 Identities=15% Similarity=0.271 Sum_probs=22.0
Q ss_pred CCCCCccCCCCCC--CCeeEccceeeeehhhhhhhh
Q 005403 22 QDNRRCINCNSLG--TQYVCTNFWTFVCTNCSGIHR 55 (698)
Q Consensus 22 PgNk~CADCGs~~--PqWaSvNfGVFVC~~CSGIHR 55 (698)
.+...|.|||..= ..|.- .-++..|+.|...+-
T Consensus 29 ~~~~~C~~Cg~~Ip~~Rl~a-~P~~~~Cv~Cq~~~E 63 (72)
T PHA00080 29 PSATHCEECGDPIPEARREA-VPGCRTCVSCQEILE 63 (72)
T ss_pred CCCCEecCCCCcCcHHHHHh-CCCccCcHHHHHHHH
Confidence 3445899999953 33332 236678999988653
No 35
>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=32.83 E-value=4.8 Score=29.86 Aligned_cols=27 Identities=11% Similarity=0.176 Sum_probs=22.9
Q ss_pred ccccccCCCCCCCCCchhhhcccCCCcc
Q 005403 178 DDKNSRYGYDERSPGNEQENRQFGDYRR 205 (698)
Q Consensus 178 ~dkl~~mgy~d~~~~~d~l~~~~Gd~~r 205 (698)
.+++.+|||+ ++....+|+..+||+++
T Consensus 5 v~~L~~mGf~-~~~~~~AL~~~~~d~~~ 31 (38)
T cd00194 5 LEQLLEMGFS-REEARKALRATNNNVER 31 (38)
T ss_pred HHHHHHcCCC-HHHHHHHHHHhCCCHHH
Confidence 3578899999 66888999999999877
No 36
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=31.59 E-value=27 Score=34.53 Aligned_cols=36 Identities=14% Similarity=0.210 Sum_probs=22.0
Q ss_pred CCCCCCccCCCCCC-CCeeEccceeeeehhhhhhhhc
Q 005403 21 LQDNRRCINCNSLG-TQYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 21 ~PgNk~CADCGs~~-PqWaSvNfGVFVC~~CSGIHR~ 56 (698)
...-..|-+||.+= ..=.-+-=++..|+.|...|-.
T Consensus 108 ~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~ 144 (151)
T PRK10778 108 DEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEI 144 (151)
T ss_pred CCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHH
Confidence 34446999999851 1111122245689999987643
No 37
>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=31.29 E-value=28 Score=34.65 Aligned_cols=32 Identities=13% Similarity=0.192 Sum_probs=20.0
Q ss_pred CCCCccCCCCC-CCCeeEccceeeeehhhhhhh
Q 005403 23 DNRRCINCNSL-GTQYVCTNFWTFVCTNCSGIH 54 (698)
Q Consensus 23 gNk~CADCGs~-~PqWaSvNfGVFVC~~CSGIH 54 (698)
.=..|.+||.. ...=.-+.-++-.|+.|...+
T Consensus 85 ~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~ 117 (159)
T TIGR02890 85 TYGICEVCGKPIPYERLEAIPTATTCVECQNRK 117 (159)
T ss_pred CCCeecccCCcccHHHHhhCCCcchhHHHHHHh
Confidence 33589999985 111111222556999998865
No 38
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=30.69 E-value=5.8e+02 Score=28.99 Aligned_cols=19 Identities=21% Similarity=0.319 Sum_probs=11.6
Q ss_pred CCCCC--CCCccccCCcCccc
Q 005403 351 SSAND--NNWASFDLAPQVKV 369 (698)
Q Consensus 351 ~s~~~--~~wasfd~~~~~~~ 369 (698)
.|.++ ++|--|..++.-+.
T Consensus 370 ~Sg~GdfgD~~AF~aAPsgpm 390 (499)
T KOG2057|consen 370 PSGGGDFGDLFAFGAAPSGPM 390 (499)
T ss_pred cCCCCcchhhhhhcCCCCccc
Confidence 33444 57888887765433
No 39
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=30.08 E-value=56 Score=30.07 Aligned_cols=29 Identities=14% Similarity=0.352 Sum_probs=22.9
Q ss_pred CCCCCccCCCCCCCCeeEccceeeeehhhhh
Q 005403 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSG 52 (698)
Q Consensus 22 PgNk~CADCGs~~PqWaSvNfGVFVC~~CSG 52 (698)
..--.|-.|+.. .---+..||+.|..|-.
T Consensus 33 ~~~~~Cp~C~~~--~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 33 RAKHVCPFCGRT--TVKRIATGIWKCRKCGA 61 (89)
T ss_pred hcCCcCCCCCCc--ceeeeccCeEEcCCCCC
Confidence 345689999998 55567899999999944
No 40
>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=29.90 E-value=37 Score=30.21 Aligned_cols=31 Identities=16% Similarity=0.591 Sum_probs=25.7
Q ss_pred CCCCccCCCCCCCCeeEccceeeeehhhhhhhhc
Q 005403 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 23 gNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~ 56 (698)
.|..|.=||...- ...||++.|..|.++.|.
T Consensus 2 ~~~~C~VCg~~~~---g~hyGv~sC~aC~~FFRR 32 (82)
T cd07171 2 DTHFCAVCSDYAS---GYHYGVWSCEGCKAFFKR 32 (82)
T ss_pred CCCCCeecCCcCc---ceEECceeehhhHHhHHH
Confidence 4678999997654 358999999999999876
No 41
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=29.80 E-value=21 Score=35.48 Aligned_cols=32 Identities=31% Similarity=0.709 Sum_probs=26.9
Q ss_pred CCCccCCCCCCCCeeEccceeeee-hhhhhhhhc
Q 005403 24 NRRCINCNSLGTQYVCTNFWTFVC-TNCSGIHRE 56 (698)
Q Consensus 24 Nk~CADCGs~~PqWaSvNfGVFVC-~~CSGIHR~ 56 (698)
-+.|+-|| -..-|.|++-|.-.| ..|-.+|.+
T Consensus 118 r~fCaVCG-~~S~ysC~~CG~kyCsv~C~~~Hne 150 (156)
T KOG3362|consen 118 RKFCAVCG-YDSKYSCVNCGTKYCSVRCLKTHNE 150 (156)
T ss_pred chhhhhcC-CCchhHHHhcCCceeechhhhhccc
Confidence 35899999 677899999999887 479999965
No 42
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=28.63 E-value=31 Score=33.84 Aligned_cols=44 Identities=20% Similarity=0.546 Sum_probs=31.1
Q ss_pred hhhhHHHHHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcC
Q 005403 5 LKEDEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF 57 (698)
Q Consensus 5 ~kedernekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~L 57 (698)
+.|+.+.+++|+.+....+...|.-||.. +-.+|..|.|-|+.+
T Consensus 80 L~e~G~L~~lL~~~~~~~~~~~C~~Cgg~---------rfv~C~~C~Gs~k~~ 123 (147)
T cd03031 80 LNESGELRKLLKGIRARAGGGVCEGCGGA---------RFVPCSECNGSCKVF 123 (147)
T ss_pred HHHcCCHHHHHhhcccccCCCCCCCCCCc---------CeEECCCCCCcceEE
Confidence 34555666777776555566679999853 345899999988764
No 43
>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=28.45 E-value=36 Score=30.33 Aligned_cols=31 Identities=13% Similarity=0.566 Sum_probs=25.6
Q ss_pred CCCCccCCCCCCCCeeEccceeeeehhhhhhhhc
Q 005403 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 23 gNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~ 56 (698)
..+.|.=||...-. ..||++.|..|.++.|.
T Consensus 2 ~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 32 (82)
T cd07173 2 PQKTCLICGDEASG---CHYGALTCGSCKVFFKR 32 (82)
T ss_pred CCCCCeecCCcCcc---eEECcchhhhHHHHHHH
Confidence 46679999986543 58999999999999876
No 44
>PRK13715 conjugal transfer protein TraR; Provisional
Probab=27.93 E-value=27 Score=30.62 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=20.3
Q ss_pred CCccCCCCCCCC-eeEccceeeeehhhhhhh
Q 005403 25 RRCINCNSLGTQ-YVCTNFWTFVCTNCSGIH 54 (698)
Q Consensus 25 k~CADCGs~~Pq-WaSvNfGVFVC~~CSGIH 54 (698)
..|.|||..=|. =.-.--|+..|+.|...+
T Consensus 35 ~~C~~Cg~~Ip~~Rl~a~p~~~~Cv~Cq~~~ 65 (73)
T PRK13715 35 YLCEACGNPIPEARRKIFPGVTLCVECQAYQ 65 (73)
T ss_pred ccHhhcCCcCCHHHHhcCCCcCCCHHHHHHH
Confidence 589999996332 112233778999998765
No 45
>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=27.87 E-value=40 Score=30.83 Aligned_cols=31 Identities=19% Similarity=0.578 Sum_probs=26.0
Q ss_pred CCCCccCCCCCCCCeeEccceeeeehhhhhhhhc
Q 005403 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 23 gNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~ 56 (698)
++..|.=||...-. ..||++.|..|.++.|.
T Consensus 4 ~~~~C~VCg~~~~g---~hyGv~sC~aC~~FFRR 34 (95)
T cd06968 4 EVIPCKICGDKSSG---IHYGVITCEGCKGFFRR 34 (95)
T ss_pred cccCCcccCCcCcc---eEECceeehhhHHhhHH
Confidence 56789999986644 48999999999999876
No 46
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=27.24 E-value=2.9e+02 Score=33.28 Aligned_cols=19 Identities=26% Similarity=0.410 Sum_probs=9.7
Q ss_pred CCCCCCCCccccccCCCCC
Q 005403 170 QSSPGGRSDDKNSRYGYDE 188 (698)
Q Consensus 170 r~s~~~Rk~dkl~~mgy~d 188 (698)
++++.+|+.++-+.|.|+.
T Consensus 641 ~SsSrSrs~SRsrS~srs~ 659 (757)
T KOG4368|consen 641 RSSSRSRSQSRSRSKSYSP 659 (757)
T ss_pred CCccccccCCcccccccCC
Confidence 3344455555555555553
No 47
>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=27.19 E-value=58 Score=24.67 Aligned_cols=30 Identities=20% Similarity=0.417 Sum_probs=21.8
Q ss_pred ccCCCCC-CCCeeEccceee-eehhhhhhhhc
Q 005403 27 CINCNSL-GTQYVCTNFWTF-VCTNCSGIHRE 56 (698)
Q Consensus 27 CADCGs~-~PqWaSvNfGVF-VC~~CSGIHR~ 56 (698)
|.+|+.. .|.|=....|-. ||-.|.-.+|.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~kk 32 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYKK 32 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHHH
Confidence 8999985 699998888887 99999776665
No 48
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=25.99 E-value=30 Score=32.50 Aligned_cols=43 Identities=21% Similarity=0.452 Sum_probs=29.2
Q ss_pred CCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcC--C--cceeecccC
Q 005403 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--T--HRVKSVSMA 67 (698)
Q Consensus 21 ~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~L--G--hrVKSLsLD 67 (698)
.|.--+|.+||. +..+..-.|.|-.|.+..-.+ | -+|++|.++
T Consensus 67 ~p~~~~C~~Cg~----~~~~~~~~~~CP~Cgs~~~~i~~G~El~I~~ie~~ 113 (115)
T TIGR00100 67 EPVECECEDCSE----EVSPEIDLYRCPKCHGIMLQVRAGKELNLKSIEVE 113 (115)
T ss_pred eCcEEEcccCCC----EEecCCcCccCcCCcCCCcEEecCCeEEEEEEEEE
Confidence 466779999994 223332358899999876555 3 288888764
No 49
>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=25.84 E-value=42 Score=30.86 Aligned_cols=30 Identities=17% Similarity=0.621 Sum_probs=24.7
Q ss_pred CCCccCCCCCCCCeeEccceeeeehhhhhhhhc
Q 005403 24 NRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 24 Nk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~ 56 (698)
+..|.=||...-. ..||++.|..|.++.|.
T Consensus 4 ~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 33 (97)
T cd07170 4 KRLCLVCGDIASG---YHYGVASCEACKAFFKR 33 (97)
T ss_pred CCCCeecCCcCcc---eEECceeehhhhHHHHH
Confidence 3579999986644 48999999999999876
No 50
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=25.66 E-value=38 Score=32.19 Aligned_cols=23 Identities=22% Similarity=0.563 Sum_probs=20.8
Q ss_pred CeeEccce--eeeehhhhhhhhcCC
Q 005403 36 QYVCTNFW--TFVCTNCSGIHREFT 58 (698)
Q Consensus 36 qWaSvNfG--VFVC~~CSGIHR~LG 58 (698)
.|++-.-| |.-|.+|--|||.=+
T Consensus 52 ewi~~~~G~~VwSC~dC~~iH~ke~ 76 (112)
T COG2158 52 EWISDSNGRKVWSCSDCHWIHRKEG 76 (112)
T ss_pred ceeEcCCCCEEeeccccceecccch
Confidence 99998889 999999999999854
No 51
>PRK00420 hypothetical protein; Validated
Probab=25.31 E-value=1.1e+02 Score=29.22 Aligned_cols=45 Identities=16% Similarity=0.174 Sum_probs=30.5
Q ss_pred hhhHHHHHHHHHHHc--CCCCCCccCCCCCCCCeeEccceeeeehhhhhh
Q 005403 6 KEDEKNERIIRGLLK--LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGI 53 (698)
Q Consensus 6 kedernekiLr~Llk--~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGI 53 (698)
++++..+++-+.|++ .--+..|-.||.+-.. ++-|-.+|-.|..+
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 345556666566666 3346899999976433 36788999999654
No 52
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=25.30 E-value=42 Score=36.31 Aligned_cols=34 Identities=21% Similarity=0.354 Sum_probs=23.7
Q ss_pred CCCCCccCCCCCCCCeeEccceeeeehhhhhhhhc
Q 005403 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 22 PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~ 56 (698)
....+|-+||... -=....-|-.||.+|--|..+
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 222456799999999876543
No 53
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=24.67 E-value=51 Score=37.80 Aligned_cols=92 Identities=18% Similarity=0.248 Sum_probs=46.9
Q ss_pred CCCCC-CccCCCC--CCCCeeEccce--eeeehhhhhhhhcCC-----c--ce-eecc----cCCCCH-HHHHHHHh---
Q 005403 21 LQDNR-RCINCNS--LGTQYVCTNFW--TFVCTNCSGIHREFT-----H--RV-KSVS----MAKFTS-QEVKALQE--- 79 (698)
Q Consensus 21 ~PgNk-~CADCGs--~~PqWaSvNfG--VFVC~~CSGIHR~LG-----h--rV-KSLs----LD~Wt~-eEVe~m~~--- 79 (698)
.++++ .|..|-. .+...+.+.-+ ..||+.|-.+=-+++ | +| ...+ --.|+. |||.+|..
T Consensus 10 ~~g~ky~C~~C~~dit~~i~ikCaeCp~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t 89 (438)
T KOG0457|consen 10 DPGGKYNCDYCSLDITGLIRIKCAECPDFDLCLQCFSVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAET 89 (438)
T ss_pred cCCCCCCCccHhHHhccceEEEeecCCCcchhHHHHhcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHH
Confidence 45555 4444665 23333322222 468999987654554 3 43 3322 227994 67777764
Q ss_pred --cChH--HHHHHHhhcCCCCCCCCCCCChHHHHHHHHHHHhhccccccC
Q 005403 80 --GGNQ--RAKEVLLKEWDPQRQSFPDSSNVERLRNFIKHVYVDRRYTGE 125 (698)
Q Consensus 80 --gGN~--~aN~iwEa~~~~~~~p~Pdssd~~~~reFIR~KYveKrF~~e 125 (698)
.||= .|+.| = ..+.+..++.-...|++..+...
T Consensus 90 ~G~GNW~dIA~hI------------G-tKtkeeck~hy~k~fv~s~~~~~ 126 (438)
T KOG0457|consen 90 YGFGNWQDIADHI------------G-TKTKEECKEHYLKHFVNSPIFPL 126 (438)
T ss_pred hCCCcHHHHHHHH------------c-ccchHHHHHHHHHHHhcCccccc
Confidence 3551 22211 0 12334455555667777766543
No 54
>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family 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. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq
Probab=24.42 E-value=47 Score=30.81 Aligned_cols=31 Identities=23% Similarity=0.631 Sum_probs=25.9
Q ss_pred CCCCccCCCCCCCCeeEccceeeeehhhhhhhhc
Q 005403 23 DNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 23 gNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~ 56 (698)
.+..|.=|+...-. ..||+..|..|.++.|.
T Consensus 17 ~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 47 (101)
T cd07160 17 GNEVCSVCGDKASG---FHYNVLSCEGCKGFFRR 47 (101)
T ss_pred CCCCCeecCCcCcc---eEECcceehhhhhhhhh
Confidence 46789999986544 58999999999999876
No 55
>PRK13844 recombination protein RecR; Provisional
Probab=24.40 E-value=53 Score=34.12 Aligned_cols=95 Identities=25% Similarity=0.370 Sum_probs=51.1
Q ss_pred hhHHHHHHHHHHHcCCCC-CCccCCCCCCCCeeEccceeeeehhhhhhhhcCCcceeecccCCCCHHHHHHHHhcChHHH
Q 005403 7 EDEKNERIIRGLLKLQDN-RRCINCNSLGTQYVCTNFWTFVCTNCSGIHREFTHRVKSVSMAKFTSQEVKALQEGGNQRA 85 (698)
Q Consensus 7 edernekiLr~Llk~PgN-k~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~LGhrVKSLsLD~Wt~eEVe~m~~gGN~~a 85 (698)
.++..+++.+.|.....| +.|--||...- .-+|.-|+.-.|.-. .|. =.=+..+|..|...|.-+.
T Consensus 39 ~~~~~~~la~~i~~~~~~i~~C~~C~~lte--------~~~C~IC~d~~Rd~~-~iC----VVE~~~Dv~aiE~t~~y~G 105 (200)
T PRK13844 39 SPETAIAIANSLLDATANIKKCVYCQALTE--------DDVCNICSNTNRDDT-KLC----IIESMLDMIAIEEAGIYRG 105 (200)
T ss_pred CHHHHHHHHHHHHHHHHhCCcCCCCCCCCC--------CCCCCCCCCCCCCCC-EEE----EECCHHHHHHHHhhCccce
Confidence 445567777777777777 79999998542 126888988888622 111 1124555666655443221
Q ss_pred -HHHHhhcCCCCCCCCCCCChHHHHHHHHH
Q 005403 86 -KEVLLKEWDPQRQSFPDSSNVERLRNFIK 114 (698)
Q Consensus 86 -N~iwEa~~~~~~~p~Pdssd~~~~reFIR 114 (698)
-.++...+.+.....|+.-+.+.+.+.|+
T Consensus 106 ~YhVL~G~ispl~gi~p~~l~i~~L~~Ri~ 135 (200)
T PRK13844 106 KYFVLNGRISPLDGIGPSELKLDILQQIIA 135 (200)
T ss_pred EEEEccCccCccCCCChhhcCHHHHHHHHh
Confidence 11222333333333444444455555554
No 56
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=23.82 E-value=74 Score=29.35 Aligned_cols=39 Identities=13% Similarity=0.279 Sum_probs=27.7
Q ss_pred HHHHHHHHHc-CCCCCCccCCCCCCCCeeEccceeeeehhhh
Q 005403 11 NERIIRGLLK-LQDNRRCINCNSLGTQYVCTNFWTFVCTNCS 51 (698)
Q Consensus 11 nekiLr~Llk-~PgNk~CADCGs~~PqWaSvNfGVFVC~~CS 51 (698)
.++.+++|-. ...--.|--||........+ ||+.|..|.
T Consensus 22 lRK~v~kie~~q~a~y~CpfCgk~~vkR~a~--GIW~C~~C~ 61 (90)
T PTZ00255 22 LRKQIKKIEISQHAKYFCPFCGKHAVKRQAV--GIWRCKGCK 61 (90)
T ss_pred HHHHHHHHHHHHhCCccCCCCCCCceeeeee--EEEEcCCCC
Confidence 3455555544 44456999999877776654 999999994
No 57
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=23.13 E-value=1.2e+02 Score=28.31 Aligned_cols=51 Identities=24% Similarity=0.531 Sum_probs=31.3
Q ss_pred hhhhHHHHHHHHHH----Hc----CC----CCCCccCCCCC-----CCCeeEccceeeeehhhhhhhh
Q 005403 5 LKEDEKNERIIRGL----LK----LQ----DNRRCINCNSL-----GTQYVCTNFWTFVCTNCSGIHR 55 (698)
Q Consensus 5 ~kedernekiLr~L----lk----~P----gNk~CADCGs~-----~PqWaSvNfGVFVC~~CSGIHR 55 (698)
.+|+++..+....| .+ .. +.+.|+-|+.+ +..=.+.+-.--||..|...++
T Consensus 23 ~~E~~Ri~kLk~~L~~e~~r~~~~~~~~~~~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~ 90 (118)
T PF02318_consen 23 KKEEERIRKLKQELQKEKMRREALGNSQKYGERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSK 90 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCSCSTTHCCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETS
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccccccccCCcchhhhCCcccccCCCCCcCCcCCccccCccCCcCC
Confidence 45556655555555 11 12 55799999874 4555677778888888877643
No 58
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=22.19 E-value=27 Score=32.73 Aligned_cols=43 Identities=12% Similarity=0.307 Sum_probs=29.7
Q ss_pred CCCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcC--C--cceeeccc
Q 005403 21 LQDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--T--HRVKSVSM 66 (698)
Q Consensus 21 ~PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~L--G--hrVKSLsL 66 (698)
.|..-+|-+||. .|....+..|.|-.|.+..-.+ | -+|++|.+
T Consensus 67 ~p~~~~C~~Cg~---~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~iEv 113 (114)
T PRK03681 67 QEAECWCETCQQ---YVTLLTQRVRRCPQCHGDMLRIVADDGLQIRRIEI 113 (114)
T ss_pred eCcEEEcccCCC---eeecCCccCCcCcCcCCCCcEEccCCeEEEEEEEE
Confidence 466779999995 2333344557899999877666 3 27888754
No 59
>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=22.13 E-value=16 Score=27.49 Aligned_cols=30 Identities=13% Similarity=0.299 Sum_probs=17.0
Q ss_pred CCccCCCCCC-CCeeEccceeeeehhhhhhh
Q 005403 25 RRCINCNSLG-TQYVCTNFWTFVCTNCSGIH 54 (698)
Q Consensus 25 k~CADCGs~~-PqWaSvNfGVFVC~~CSGIH 54 (698)
.+|.+||..= ..=.-+.-+..+|+.|+..|
T Consensus 4 g~C~~CGe~I~~~Rl~~~p~~~~C~~C~~~~ 34 (36)
T PF01258_consen 4 GICEDCGEPIPEERLVAVPGATLCVECQERR 34 (36)
T ss_dssp SB-TTTSSBEEHHHHHHCTTECS-HHHHHHH
T ss_pred CCccccCChHHHHHHHhCCCcEECHHHhCcc
Confidence 3599999752 11122223778999998765
No 60
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=21.09 E-value=31 Score=32.51 Aligned_cols=43 Identities=19% Similarity=0.354 Sum_probs=27.4
Q ss_pred CCCCCccCCCCCCCCeeEccceeeeehhhhhhhhcC--C--cceeecccC
Q 005403 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHREF--T--HRVKSVSMA 67 (698)
Q Consensus 22 PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~L--G--hrVKSLsLD 67 (698)
|.--+|-+||.. |-...+..+.|-.|.+..-.+ | -+|++|.++
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 445589999943 222234445699999876555 3 278887653
No 61
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=20.52 E-value=1.1e+02 Score=24.08 Aligned_cols=42 Identities=17% Similarity=0.335 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHHcCCCCCCccCCCCCCCCeeEccceeeeehhhh
Q 005403 8 DEKNERIIRGLLKLQDNRRCINCNSLGTQYVCTNFWTFVCTNCS 51 (698)
Q Consensus 8 dernekiLr~Llk~PgNk~CADCGs~~PqWaSvNfGVFVC~~CS 51 (698)
|+.-.+.|..+. =++.-.|--||.....++. +.+.|-|-.|.
T Consensus 3 e~~c~~~l~~~R-W~~g~~CP~Cg~~~~~~~~-~~~~~~C~~C~ 44 (46)
T PF12760_consen 3 EEACREYLEEIR-WPDGFVCPHCGSTKHYRLK-TRGRYRCKACR 44 (46)
T ss_pred HHHHHHHHHHhc-CCCCCCCCCCCCeeeEEeC-CCCeEECCCCC
Confidence 344444544443 3444789999998555544 37999999884
No 62
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.41 E-value=56 Score=27.26 Aligned_cols=26 Identities=23% Similarity=0.549 Sum_probs=22.0
Q ss_pred CCccCCCCCCCCeeEccceeeeehhhhh
Q 005403 25 RRCINCNSLGTQYVCTNFWTFVCTNCSG 52 (698)
Q Consensus 25 k~CADCGs~~PqWaSvNfGVFVC~~CSG 52 (698)
+.|..||..... ..+-.+|+|..|--
T Consensus 29 q~C~~CG~~~~~--~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 29 QTCPRCGHRNKK--RRSGRVFTCPNCGF 54 (69)
T ss_pred cCccCccccccc--ccccceEEcCCCCC
Confidence 689999998777 67888999999954
No 63
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=20.27 E-value=65 Score=29.17 Aligned_cols=32 Identities=22% Similarity=0.686 Sum_probs=26.0
Q ss_pred CCCCCccCCCCCCCCeeEccceeeeehhhhhhhhc
Q 005403 22 QDNRRCINCNSLGTQYVCTNFWTFVCTNCSGIHRE 56 (698)
Q Consensus 22 PgNk~CADCGs~~PqWaSvNfGVFVC~~CSGIHR~ 56 (698)
.++..|.=|+..... ..||+..|..|.++.|.
T Consensus 4 ~~~~~C~VCg~~a~g---~hyGv~sC~aCk~FFRR 35 (90)
T cd07169 4 AEQRTCLICGDRATG---LHYGIISCEGCKGFFKR 35 (90)
T ss_pred ccCCCCeecCCcCcc---eEECcceehhhHHHHHH
Confidence 356789999986543 58999999999999876
Done!