Query 008165
Match_columns 575
No_of_seqs 213 out of 399
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 20:18:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008165hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10250 O-FucT: GDP-fucose pr 100.0 1.9E-56 4E-61 451.8 4.0 298 140-454 6-345 (351)
2 KOG3849 GDP-fucose protein O-f 97.7 2E-05 4.4E-10 81.4 3.2 281 130-452 26-368 (386)
3 PF05830 NodZ: Nodulation prot 95.5 0.12 2.7E-06 54.7 11.1 258 133-442 2-289 (321)
4 PLN02232 ubiquinone biosynthes 48.9 61 0.0013 30.4 6.8 111 257-380 37-153 (160)
5 PF14771 DUF4476: Domain of un 44.7 11 0.00023 32.8 1.0 36 352-402 39-74 (95)
6 PF00799 Gemini_AL1: Geminivir 38.2 35 0.00076 31.6 3.4 29 350-379 14-42 (114)
7 PF04561 RNA_pol_Rpb2_2: RNA p 30.0 19 0.00041 33.6 0.3 55 358-426 54-108 (190)
8 PF10892 DUF2688: Protein of u 27.9 42 0.00091 28.0 1.8 17 348-365 41-57 (60)
9 PRK10556 hypothetical protein; 25.9 46 0.001 30.6 1.9 26 353-382 3-28 (111)
10 PF09400 DUF2002: Protein of u 22.7 42 0.0009 31.1 1.0 26 353-382 3-28 (111)
11 smart00874 B5 tRNA synthetase 22.3 65 0.0014 26.1 2.0 23 346-369 13-35 (71)
No 1
>PF10250 O-FucT: GDP-fucose protein O-fucosyltransferase; InterPro: IPR019378 This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and Caenorhabditis elegans. Both features are characteristic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese []. ; PDB: 3ZY6_A 3ZY3_A 3ZY5_A 3ZY2_A 3ZY4_A.
Probab=100.00 E-value=1.9e-56 Score=451.81 Aligned_cols=298 Identities=40% Similarity=0.667 Sum_probs=207.9
Q ss_pred eCCCchhhHhhHhhHHHHHHHhcCcEEecccCCCCcccCCCC-----CcccccHHHHHHHhccccceeccCchhHHhhcC
Q 008165 140 ASGGLNQQRTGITDAVVVARILNATLVVPELDHHSYWKDDSD-----FANIFDVDHFISSLAKDVTIVKRVPDKVMRSME 214 (575)
Q Consensus 140 ~nGGLNQqR~~IcDaVaVARiLNATLViP~Ld~~s~WkD~S~-----F~DIFDvdhFI~sL~~dVrIVk~LP~~~~~~~~ 214 (575)
+.||+||||.++++||++|++||+|||||.+...+.|++.+. |+++||+++|+++++.+|.+.+.+|........
T Consensus 6 ~~GGfnNQr~~~~~a~~~A~~LnRTLVLPp~~~~~~~~~~~~~~~ipf~~~fD~~~l~~~~~~vi~~~ef~~~~~~~~~~ 85 (351)
T PF10250_consen 6 CMGGFNNQRMGFENAVVFAKALNRTLVLPPFIKHYHWKDQSKQRHIPFSDFFDVEHLRKFLRPVITMEEFLPKHWDEVFR 85 (351)
T ss_dssp -SSSHHHHHHHHHHHHHHHHHHT-EEE--EEEEESSSS----EEEEEHHHHB-HHHHTTTS--EE-HHHHHHHHS-GGG-
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCEEEcCCccccccccccccccccChhhhccHHHHHHHhhCceehheeccchhccccc
Confidence 889999999999999999999999999999999999999987 999999999999999999999999866543211
Q ss_pred ----------------------------CCCceecCCC-CCChhHHHhhhhhhhhhc------ceEEEeccccccccC-C
Q 008165 215 ----------------------------KPPYTMRVPR-KSTPEYYLDQVLPILLRR------RVVQLTKFDYRLAND-L 258 (575)
Q Consensus 215 ----------------------------~~~~~~~vp~-~s~~~yY~e~ilP~L~k~------~VI~l~~~d~RLa~~-l 258 (575)
+......... ++.+.+|.++++|.+.++ +|+.|.++..++.++ .
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ 165 (351)
T PF10250_consen 86 LQYCWSPWESGSWDDNMKDGNPFGPFWDKFPIKFDPCEFWSSPSLYLEDVLPELREWNENSEHPVIAFTGFESRLPDNYL 165 (351)
T ss_dssp EEEESS-B--------TTSSTTHHHHHHHTT---SEEE-E-TTSTTTT-STTHHHHHHHHTT-SEEEESS-SS-SS--GG
T ss_pred hhhcccccccccchhhccccccccccccccceeeccccccCCchhhHHHhhhHHhhhccccccccceeccccccchhccc
Confidence 1112233333 788899999999999887 999999999999977 8
Q ss_pred chHhhhhheeeeccccccchhHHHHHHHHHHHHHhcCCCceEEeeccchhhhhhhcccCCCCchHhHHHHHHHhhhccCC
Q 008165 259 DEELQKMRCRVNYHALRFTKPIEELGQKLVMRMRSMAKRFIAVHLRFEPDMLAFSGCYYGGGDKERYELGEIRKRWATLP 338 (575)
Q Consensus 259 P~diQrLRCrvnF~ALrF~p~I~~Lg~~LV~RLR~~~~~fiALHLRfE~DMLAfsgC~~ggg~~E~~EL~~~R~~w~~~~ 338 (575)
+.++|| +|+|+++|+++|++++++|+..+++|||+|||+|+|| +++|.+++ ++..|..+|.. +.+
T Consensus 166 ~~~~~r--------~l~~~~~i~~~a~~~i~~~~~~~~~yiavHlR~~~D~--~~~C~~~~---~~~~~~~~~~~--~~~ 230 (351)
T PF10250_consen 166 DRDLQR--------YLRFSPEIRELADKFIKRLLAGGGPYIAVHLRRGKDW--FSACEFKG---ERHLLASPRCW--GKK 230 (351)
T ss_dssp GGGGGG--------G--B-HHHHHHHHHHHHHH----SSEEEEEE--SHHH--HHHHCT-T-------TTTHHHH---GG
T ss_pred CccceE--------EEecCHHHHHHHHHHHHHhhcccCceEEEeecccCch--HhhcccCC---chHHHHHhHhh--ccc
Confidence 899988 9999999999999999999955689999999999999 88999954 67777777765 234
Q ss_pred CCCchhhccCCCCCCCHHHHHHHHHHcCCCCCceEEEEeccccCccccccchHhhCCCccccccCCh-hhccCCcCcccc
Q 008165 339 DLSPEGERKRGKCPLTPHEVGLMLRALGFANDTHLYVASGEIYGGEETLRPLRELFPNFYTKEMLAD-EELKPFLQFSSR 417 (575)
Q Consensus 339 ~i~~~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYLAsgeiyGG~~~L~pL~~~FPnl~tKe~La~-eEL~pf~~~sS~ 417 (575)
.+++...+..+.||++|++++.+++++|+.+.|.||||++++|||.+.|.+|++.||++++|+.+.+ +|+++|.+ ++
T Consensus 231 ~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~--~~ 308 (351)
T PF10250_consen 231 SINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLSHEELEPLND--DQ 308 (351)
T ss_dssp GTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--EE--S-------S-
T ss_pred cccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCCHHHhhhccc--cc
Confidence 5677788889999999999999999999999999999999999999999999999999999999998 99999986 89
Q ss_pred hhhhhhhhhcCCceeeecCCCcHHHHHhhhhcccCCc
Q 008165 418 LAAIDYIVCDESDVFVTNNNGNMAKILAGRRRYMGHK 454 (575)
Q Consensus 418 lAALDYiVcl~SDVFV~t~~GNfa~~V~GhR~y~G~~ 454 (575)
+|+||++||++||+||+|..++|+.+|+++|.|.|+.
T Consensus 309 ~a~vD~~i~~~s~~Figt~~Stfs~~i~~~R~~~g~~ 345 (351)
T PF10250_consen 309 LAMVDQEICSRSDVFIGTCGSTFSSNIARERHYRGKP 345 (351)
T ss_dssp -HHHHHHHHHHSSEEEE-TT-HHHHHHHHHHHHSSSS
T ss_pred hhHHHHHHHhcCCEEEecCcchhHHHhhcccCcCCCC
Confidence 9999999999999999999999999999999999954
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.72 E-value=2e-05 Score=81.36 Aligned_cols=281 Identities=23% Similarity=0.313 Sum_probs=153.4
Q ss_pred CCCCcEEEEE-eCCCchhhHhhHhhHHHHHHHhcCcEEecccC---CCCcccCCCCCcccccHH------------HHHH
Q 008165 130 RSSNGYLLIA-ASGGLNQQRTGITDAVVVARILNATLVVPELD---HHSYWKDDSDFANIFDVD------------HFIS 193 (575)
Q Consensus 130 ~~snGYL~V~-~nGGLNQqR~~IcDaVaVARiLNATLViP~Ld---~~s~WkD~S~F~DIFDvd------------hFI~ 193 (575)
...||||+.- |-|-+.+|-....-..|.|+.||.|||+|..- +-.+-+---.|...|.++ .|+.
T Consensus 26 ~DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiEy~~pe~~n~~vpf~~yF~vepl~~YhRVitm~dFm~ 105 (386)
T KOG3849|consen 26 WDPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIEYKHPETKNLMVPFEFYFQVEPLAKYHRVITMQDFMK 105 (386)
T ss_pred CCCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchhccCCcccccccchhheeecccHhhhhhheeHHHHHH
Confidence 3578998876 99999999999999999999999999998542 222222225788888775 3444
Q ss_pred Hhccccceecc----CchhHH-hhcCC--------CCc-----eecCCCCCChhHH------Hhhh---hhhh-----hh
Q 008165 194 SLAKDVTIVKR----VPDKVM-RSMEK--------PPY-----TMRVPRKSTPEYY------LDQV---LPIL-----LR 241 (575)
Q Consensus 194 sL~~dVrIVk~----LP~~~~-~~~~~--------~~~-----~~~vp~~s~~~yY------~e~i---lP~L-----~k 241 (575)
-|..+.=.-.. +=+.-. ++-++ +|+ .+.|- -..-.|| +++. -..+ ++
T Consensus 106 klapthwp~~~Rva~c~k~a~qr~pdkp~Ch~KeGNPFGPfWDqfhvs-Fv~sE~f~~i~Fd~~~~~~~~kW~~kfp~ee 184 (386)
T KOG3849|consen 106 KLAPTHWPGTPRVAICDKSAAQRSPDKPGCHSKEGNPFGPFWDQFHVS-FVGSEYFGDIGFDLNQMGSRKKWLEKFPSEE 184 (386)
T ss_pred HhCcccCCCCcceeeeehhhhccCCCCCCCcccCCCCCCCchhheEee-eeccccccccccchhhcchHHHHHhhCCccc
Confidence 44333110000 000000 00000 110 00000 0111111 1111 1122 45
Q ss_pred cceEEEeccccc---cccCCchHhhhhheeeeccccccchhHHHHHHHHHHHHHhcCCCceEEeeccchhhhhhhcccCC
Q 008165 242 RRVVQLTKFDYR---LANDLDEELQKMRCRVNYHALRFTKPIEELGQKLVMRMRSMAKRFIAVHLRFEPDMLAFSGCYYG 318 (575)
Q Consensus 242 ~~VI~l~~~d~R---La~~lP~diQrLRCrvnF~ALrF~p~I~~Lg~~LV~RLR~~~~~fiALHLRfE~DMLAfsgC~~g 318 (575)
|-|+.|++.-.. +..+++ |||- |+.+.+|.+.|++.+.-- ..+||+++|||...||+-- |.+-
T Consensus 185 yPVLAf~gAPA~FPv~~e~~~--lQkY--------l~WS~r~~e~~k~fI~a~--L~rpfvgiHLRng~DWvra--Cehi 250 (386)
T KOG3849|consen 185 YPVLAFSGAPAPFPVKGEVWS--LQKY--------LRWSSRITEQAKKFISAN--LARPFVGIHLRNGADWVRA--CEHI 250 (386)
T ss_pred CceeeecCCCCCCcccccccc--HHHH--------HHHHHHHHHHHHHHHHHh--cCcceeEEEeecCchHHHH--HHHh
Confidence 677777655322 112333 5664 889999999999877652 3469999999999999865 7643
Q ss_pred CCchHhHHHHHHHhhhccCCCCCchhhcc-----CCCCCCCHHHHHHH----HHHcCCCCCceEEEEeccccCcccccc-
Q 008165 319 GGDKERYELGEIRKRWATLPDLSPEGERK-----RGKCPLTPHEVGLM----LRALGFANDTHLYVASGEIYGGEETLR- 388 (575)
Q Consensus 319 gg~~E~~EL~~~R~~w~~~~~i~~~~~R~-----~G~CPLTPeEVgl~----LrALGf~~~T~IYLAsgeiyGG~~~L~- 388 (575)
.... -|. .....+- -...+. ...|-=+.+||-.- .+.+| .-..+|+|+.. ..|.
T Consensus 251 kd~~-------~~h-lfASpQC-lGy~~~~gaLt~e~C~Psk~~I~rqik~~v~si~--dakSVfVAsDs-----~hmi~ 314 (386)
T KOG3849|consen 251 KDTT-------NRH-LFASPQC-LGYGHHLGALTKEICSPSKQQILRQIKEKVGSIG--DAKSVFVASDS-----DHMID 314 (386)
T ss_pred cccC-------CCc-cccChhh-ccccccccccchhhhCccHHHHHHHHHHHHhhhc--ccceEEEeccc-----hhhhH
Confidence 2110 000 0000000 000111 23454444554322 22333 34479999876 2232
Q ss_pred chH-hhCCCccccccCChhhccCCcCcccchhhhhhhhhcCCceeeecCCCcHHHHHhhhhcccC
Q 008165 389 PLR-ELFPNFYTKEMLADEELKPFLQFSSRLAAIDYIVCDESDVFVTNNNGNMAKILAGRRRYMG 452 (575)
Q Consensus 389 pL~-~~FPnl~tKe~La~eEL~pf~~~sS~lAALDYiVcl~SDVFV~t~~GNfa~~V~GhR~y~G 452 (575)
.|. +++|-=+.-.. |+| .-+-+|..|.-+||-||+|--+.|+..|--.|-..|
T Consensus 315 Eln~aL~~~~i~vh~-----l~p------dd~y~dLaIlGqadhFiGNCvSsfsafvKRERD~~G 368 (386)
T KOG3849|consen 315 ELNEALKPYEIEVHR-----LEP------DDMYTDLAILGQADHFIGNCVSSFSAFVKRERDHAG 368 (386)
T ss_pred HHHHhhcccceeEEe-----cCc------ccchhhhhhhcccchhhhhhHHHHHHHHhhhhcccC
Confidence 221 23331111111 111 125689999999999999999999999999998888
No 3
>PF05830 NodZ: Nodulation protein Z (NodZ); InterPro: IPR008716 The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal [].; GO: 0016758 transferase activity, transferring hexosyl groups, 0009312 oligosaccharide biosynthetic process, 0009877 nodulation; PDB: 3SIX_A 2HLH_A 2HHC_A 3SIW_A 2OCX_A.
Probab=95.49 E-value=0.12 Score=54.68 Aligned_cols=258 Identities=17% Similarity=0.278 Sum_probs=120.3
Q ss_pred CcEEEEEeCCCchhhHhhHhhHHHHHHHhcCcEEecccCCCCcccCC----CCCcccccHHHHHHHhcc--ccceecc--
Q 008165 133 NGYLLIAASGGLNQQRTGITDAVVVARILNATLVVPELDHHSYWKDD----SDFANIFDVDHFISSLAK--DVTIVKR-- 204 (575)
Q Consensus 133 nGYL~V~~nGGLNQqR~~IcDaVaVARiLNATLViP~Ld~~s~WkD~----S~F~DIFDvdhFI~sL~~--dVrIVk~-- 204 (575)
+.|++..--+|+|.-=-+++-|-.+|+-.|.||||- |+++ ..|...|++ |-+-.++ .|+|+-.
T Consensus 2 ~r~~~~r~r~g~gd~l~~la~aw~~a~~~~r~l~id-------w~~s~~~~~~f~n~f~~--ffepv~~i~~~~~~~~d~ 72 (321)
T PF05830_consen 2 QRFVVSRRRTGLGDCLWSLAAAWRYAKRTGRTLVID-------WRGSCYLDQPFTNAFPV--FFEPVEDIAGVRVICDDR 72 (321)
T ss_dssp --EEEEE--S-HHHHHHHHHHHHHHHHHHT-EEEEE--------BT-TT-SSTTSBSHHH--HB---SEETTEEEE-SGG
T ss_pred CceEEEeccCCchhHHHHHHHHHHHHHHhCCeEEEE-------cCCceecCCcccccCCc--ccchhhhhcCceeEecch
Confidence 578999999999999999999999999999999995 7766 677777765 5555542 3444411
Q ss_pred -----CchhHHhhcCCCCceecCCCCCChhHHHh--hhhhhhh------hcceEEEeccccccccCCchHhhhhheeeec
Q 008165 205 -----VPDKVMRSMEKPPYTMRVPRKSTPEYYLD--QVLPILL------RRRVVQLTKFDYRLANDLDEELQKMRCRVNY 271 (575)
Q Consensus 205 -----LP~~~~~~~~~~~~~~~vp~~s~~~yY~e--~ilP~L~------k~~VI~l~~~d~RLa~~lP~diQrLRCrvnF 271 (575)
+|-.+....=+.| +++.-....+.-+.| ++--+++ ...||+.. .|...=..++.| | -|
T Consensus 73 i~~~~~~g~~fp~~w~~p-~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~----c~~~~c~~~aeR--~--if 143 (321)
T PF05830_consen 73 INQFSFPGPFFPAWWNKP-SIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDA----CLMWRCDEEAER--E--IF 143 (321)
T ss_dssp GGT----SSEESGGGGS--GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S------TTSS-HHHHH--H--HH
T ss_pred hhhhcCCCCcChhHHhCC-CcceecCChHHHhhhhHHHHHHhhcccccccchhhhHh----hcCCcchhHHHH--H--HH
Confidence 1111100000000 111000111111111 1222232 22355443 332222233333 2 28
Q ss_pred cccccchhHHHHHHHHHHHHHhcCCCceEEeeccc--hhhhhhhcccCCCCchHhHHHHHHHhhhccCCCCCchhhccCC
Q 008165 272 HALRFTKPIEELGQKLVMRMRSMAKRFIAVHLRFE--PDMLAFSGCYYGGGDKERYELGEIRKRWATLPDLSPEGERKRG 349 (575)
Q Consensus 272 ~ALrF~p~I~~Lg~~LV~RLR~~~~~fiALHLRfE--~DMLAfsgC~~ggg~~E~~EL~~~R~~w~~~~~i~~~~~R~~G 349 (575)
..|+-+++|++..+.+.+.-=. +..=|++|-|.= +|.+.+ +|++ .++...|.+...
T Consensus 144 ~slkpR~eIqarID~iy~ehf~-g~~~IGVHVRhGngeD~~~h-~~~~---~D~e~~L~~V~~----------------- 201 (321)
T PF05830_consen 144 SSLKPRPEIQARIDAIYREHFA-GYSVIGVHVRHGNGEDIMDH-APYW---ADEERALRQVCT----------------- 201 (321)
T ss_dssp HHS-B-HHHHHHHHHHHHHHTT-TSEEEEEEE-------------------HHHHHHHHHHHH-----------------
T ss_pred HhCCCCHHHHHHHHHHHHHHcC-CCceEEEEEeccCCcchhcc-Cccc---cCchHHHHHHHH-----------------
Confidence 8999999999999998776422 345799999931 233332 2322 111111111000
Q ss_pred CCCCCHHHHHHHHHHcCCCCCceEEEEeccccCccccccchHhhCCCccccccCC-hhhccCCcCcc-----cchhhhhh
Q 008165 350 KCPLTPHEVGLMLRALGFANDTHLYVASGEIYGGEETLRPLRELFPNFYTKEMLA-DEELKPFLQFS-----SRLAAIDY 423 (575)
Q Consensus 350 ~CPLTPeEVgl~LrALGf~~~T~IYLAsgeiyGG~~~L~pL~~~FPnl~tKe~La-~eEL~pf~~~s-----S~lAALDY 423 (575)
....++++-...++.|+||+-. .+.++-+++.||.+++-+.=. ...-.++.+.. -..|-+|-
T Consensus 202 --------ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k~F~~~~~g~Lhs~~~g~~gg~~ALIDM 269 (321)
T PF05830_consen 202 --------AIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPKQFPASQAGPLHSAAVGIEGGESALIDM 269 (321)
T ss_dssp --------HHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE----------------HHHHHHHHHHHHHHH
T ss_pred --------HHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEcccccCCCCCCcCcccccccchHHHHHHHH
Confidence 0112345556678999999987 466889999999988775321 11111232211 12488999
Q ss_pred hhhcCCceee-ecCCCcHHH
Q 008165 424 IVCDESDVFV-TNNNGNMAK 442 (575)
Q Consensus 424 iVcl~SDVFV-~t~~GNfa~ 442 (575)
+....+|+-| .+..+.|.+
T Consensus 270 ~LLSrCD~LIr~~ptS~Fsr 289 (321)
T PF05830_consen 270 YLLSRCDYLIRFPPTSAFSR 289 (321)
T ss_dssp HHHTTSSEEEEESTT-GGGH
T ss_pred HHHHhCCeEEEcCCCchhhh
Confidence 9999999999 555555544
No 4
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=48.85 E-value=61 Score=30.41 Aligned_cols=111 Identities=12% Similarity=-0.034 Sum_probs=62.5
Q ss_pred CCchHhhhhheeeeccccccchhHHHHHHHHHHHHHhcCCCceEEeeccchhhhhh----hcccCCCCchHhH--HHHHH
Q 008165 257 DLDEELQKMRCRVNYHALRFTKPIEELGQKLVMRMRSMAKRFIAVHLRFEPDMLAF----SGCYYGGGDKERY--ELGEI 330 (575)
Q Consensus 257 ~lP~diQrLRCrvnF~ALrF~p~I~~Lg~~LV~RLR~~~~~fiALHLRfE~DMLAf----sgC~~ggg~~E~~--EL~~~ 330 (575)
++|..-...-+-++..+|++.++..+.-+.+.+.|+. +|.++.++...+...+.. .-|...+..-+.. ...++
T Consensus 37 ~lp~~~~~fD~v~~~~~l~~~~d~~~~l~ei~rvLkp-GG~l~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y 115 (160)
T PLN02232 37 DLPFDDCEFDAVTMGYGLRNVVDRLRAMKEMYRVLKP-GSRVSILDFNKSNQSVTTFMQGWMIDNVVVPVATVYDLAKEY 115 (160)
T ss_pred hCCCCCCCeeEEEecchhhcCCCHHHHHHHHHHHcCc-CeEEEEEECCCCChHHHHHHHHHHccchHhhhhHHhCChHHH
Confidence 3553333344455566788888888888888888875 678877766543321110 0011000000000 00111
Q ss_pred HhhhccCCCCCchhhccCCCCCCCHHHHHHHHHHcCCCCCceEEEEeccc
Q 008165 331 RKRWATLPDLSPEGERKRGKCPLTPHEVGLMLRALGFANDTHLYVASGEI 380 (575)
Q Consensus 331 R~~w~~~~~i~~~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYLAsgei 380 (575)
++-|. .... +++|+|+..+|+..||.+-+.-+++.|-+
T Consensus 116 ~yl~~-----------si~~-f~~~~el~~ll~~aGF~~~~~~~~~~g~~ 153 (160)
T PLN02232 116 EYLKY-----------SING-YLTGEELETLALEAGFSSACHYEISGGFM 153 (160)
T ss_pred HhHHH-----------HHHH-CcCHHHHHHHHHHcCCCcceEEECcchHh
Confidence 21110 0112 48999999999999999998888887753
No 5
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=44.65 E-value=11 Score=32.75 Aligned_cols=36 Identities=25% Similarity=0.424 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHcCCCCCceEEEEeccccCccccccchHhhCCCcccccc
Q 008165 352 PLTPHEVGLMLRALGFANDTHLYVASGEIYGGEETLRPLRELFPNFYTKEM 402 (575)
Q Consensus 352 PLTPeEVgl~LrALGf~~~T~IYLAsgeiyGG~~~L~pL~~~FPnl~tKe~ 402 (575)
++|-.+++-+|+-..|++ .+|..|+-++|++++++.
T Consensus 39 ~~T~~Qv~~il~~f~fd~---------------~kl~~lk~l~p~i~D~~n 74 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDN---------------DKLKALKLLYPYIVDPQN 74 (95)
T ss_pred ceeHHHHHHHHHHcCCCH---------------HHHHHHHHHhhhccCHHH
Confidence 499999999999999983 369999999999999973
No 6
>PF00799 Gemini_AL1: Geminivirus Rep catalytic domain; InterPro: IPR022690 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome []. For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer []. It is found in association with PF08283 from PFAM. ; GO: 0006260 DNA replication; PDB: 1L5I_A 1L2M_A.
Probab=38.22 E-value=35 Score=31.58 Aligned_cols=29 Identities=24% Similarity=0.306 Sum_probs=16.4
Q ss_pred CCCCCHHHHHHHHHHcCCCCCceEEEEecc
Q 008165 350 KCPLTPHEVGLMLRALGFANDTHLYVASGE 379 (575)
Q Consensus 350 ~CPLTPeEVgl~LrALGf~~~T~IYLAsge 379 (575)
+|||||||+...|++|--+ ....||..++
T Consensus 14 qC~l~ke~~l~~L~~l~~~-~~~~yI~v~r 42 (114)
T PF00799_consen 14 QCSLTKEEALEQLKNLLTP-SNKKYIRVCR 42 (114)
T ss_dssp T----HHHHHHHHHH---S-S-EEEEEEEE
T ss_pred CCCCCHHHHHHHHHHhCCc-cCceEEEeec
Confidence 6999999999999999765 4677876543
No 7
>PF04561 RNA_pol_Rpb2_2: RNA polymerase Rpb2, domain 2; InterPro: IPR007642 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain []. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, a region known as dispensable region 1 (DRI).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_B 3LTI_A 3IYD_C 3LU0_C 2Y0S_R 1SMY_M 3DXJ_M 3AOI_C 2A68_M 1ZYR_C ....
Probab=30.04 E-value=19 Score=33.60 Aligned_cols=55 Identities=29% Similarity=0.343 Sum_probs=27.7
Q ss_pred HHHHHHHcCCCCCceEEEEeccccCccccccchHhhCCCccccccCChhhccCCcCcccchhhhhhhhh
Q 008165 358 VGLMLRALGFANDTHLYVASGEIYGGEETLRPLRELFPNFYTKEMLADEELKPFLQFSSRLAAIDYIVC 426 (575)
Q Consensus 358 Vgl~LrALGf~~~T~IYLAsgeiyGG~~~L~pL~~~FPnl~tKe~La~eEL~pf~~~sS~lAALDYiVc 426 (575)
+.++|+|||+.++.-||=.-+. .+. .......+..+++. .....++..|++|+-.
T Consensus 54 i~ilLrALG~~sd~eI~~~i~~---~~~----------~~~~~~~~~~~~~~-~~~~~t~~~al~~i~~ 108 (190)
T PF04561_consen 54 IVILLRALGIESDKEIIELICY---SEE----------DFEDIEELMLSELE-EEEIYTQEQALEYIGK 108 (190)
T ss_dssp HHHHHHHTT--STCHHHHHHCC---CST----------CHSCSTTTHHHHCC-CTSSCSCHHHHHHHHH
T ss_pred eEEeehhhcCcCcccccceeec---ccc----------cccccccccccccc-cccccccccceeEecc
Confidence 5799999999877655421110 000 01111222222222 2334678999999987
No 8
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=27.86 E-value=42 Score=28.03 Aligned_cols=17 Identities=41% Similarity=0.679 Sum_probs=14.0
Q ss_pred CCCCCCCHHHHHHHHHHc
Q 008165 348 RGKCPLTPHEVGLMLRAL 365 (575)
Q Consensus 348 ~G~CPLTPeEVgl~LrAL 365 (575)
-|-| +||||-+.+++++
T Consensus 41 C~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 41 CGDC-ITPEEDREILEAT 57 (60)
T ss_pred hhcc-CCHHHHHHHHHHH
Confidence 3567 9999999999874
No 9
>PRK10556 hypothetical protein; Provisional
Probab=25.87 E-value=46 Score=30.65 Aligned_cols=26 Identities=38% Similarity=0.687 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHcCCCCCceEEEEeccccC
Q 008165 353 LTPHEVGLMLRALGFANDTHLYVASGEIYG 382 (575)
Q Consensus 353 LTPeEVgl~LrALGf~~~T~IYLAsgeiyG 382 (575)
|-|.||+.+|...||..+. .+.+.||
T Consensus 3 LRPDEVArVLe~aGF~~D~----vt~~aYG 28 (111)
T PRK10556 3 LRPDEVARVLEKAGFTVDV----VTQKAYG 28 (111)
T ss_pred cChHHHHHHHHhcCceEEE----eechhcc
Confidence 6799999999999998665 2345555
No 10
>PF09400 DUF2002: Protein of unknown function (DUF2002); InterPro: IPR018994 This entry represents a group of putative cytoplasmic proteins. The structure of these proteins form an antiparallel beta sheet and contain some alpha helical regions. ; PDB: 2G7J_A.
Probab=22.65 E-value=42 Score=31.14 Aligned_cols=26 Identities=38% Similarity=0.701 Sum_probs=17.6
Q ss_pred CCHHHHHHHHHHcCCCCCceEEEEeccccC
Q 008165 353 LTPHEVGLMLRALGFANDTHLYVASGEIYG 382 (575)
Q Consensus 353 LTPeEVgl~LrALGf~~~T~IYLAsgeiyG 382 (575)
|-|.||+.+|...||..+. .+.+.||
T Consensus 3 lrpdeva~vle~~gf~~d~----v~~~ayg 28 (111)
T PF09400_consen 3 LRPDEVARVLEKAGFERDY----VTDKAYG 28 (111)
T ss_dssp --HHHHHHHHHHTT-EEEE----EETTEEE
T ss_pred cChHHHHHHHHhcCceEEE----eeccccc
Confidence 6799999999999998654 2345555
No 11
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=22.34 E-value=65 Score=26.09 Aligned_cols=23 Identities=35% Similarity=0.508 Sum_probs=19.3
Q ss_pred ccCCCCCCCHHHHHHHHHHcCCCC
Q 008165 346 RKRGKCPLTPHEVGLMLRALGFAN 369 (575)
Q Consensus 346 R~~G~CPLTPeEVgl~LrALGf~~ 369 (575)
+..|.. ++++|+.-+|+.|||+-
T Consensus 13 ~llG~~-i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 13 RLLGLD-LSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHCCC-CCHHHHHHHHHHCCCeE
Confidence 446654 99999999999999984
Done!