Query 008317
Match_columns 570
No_of_seqs 224 out of 408
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 22:17:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008317.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008317hhsearch_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 7.3E-56 1.6E-60 451.4 2.4 306 164-496 6-349 (351)
2 KOG3849 GDP-fucose protein O-f 97.3 0.00079 1.7E-08 69.8 8.4 274 155-489 27-367 (386)
3 PF05830 NodZ: Nodulation prot 95.2 0.5 1.1E-05 50.2 14.6 256 157-480 2-289 (321)
4 PLN02232 ubiquinone biosynthes 49.8 82 0.0018 29.6 7.9 101 294-417 47-153 (160)
5 PF14771 DUF4476: Domain of un 48.8 8.4 0.00018 33.4 1.0 56 389-461 39-94 (95)
6 PF00799 Gemini_AL1: Geminivir 36.4 35 0.00075 31.6 3.0 29 387-416 14-42 (114)
7 KOG3705 Glycoprotein 6-alpha-L 35.9 2E+02 0.0044 32.5 9.1 66 403-476 402-474 (580)
8 PF10892 DUF2688: Protein of u 29.7 34 0.00074 28.3 1.6 16 386-402 42-57 (60)
9 COG0859 RfaF ADP-heptose:LPS h 27.2 63 0.0014 34.0 3.6 69 393-481 198-266 (334)
10 PF04561 RNA_pol_Rpb2_2: RNA p 27.0 19 0.00042 33.7 -0.2 17 395-411 54-70 (190)
11 PF01531 Glyco_transf_11: Glyc 25.5 2.6E+02 0.0056 29.1 7.7 135 301-501 137-277 (298)
12 smart00874 B5 tRNA synthetase 24.9 45 0.00098 27.0 1.6 23 383-406 13-35 (71)
13 KOG3111 D-ribulose-5-phosphate 24.8 2.1E+02 0.0045 29.4 6.4 113 302-435 42-171 (224)
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=7.3e-56 Score=451.38 Aligned_cols=306 Identities=37% Similarity=0.634 Sum_probs=208.1
Q ss_pred ecCchhHHHHHHHHHHHHHHHhcCeEEeccccccccccCCCC-----CCCCCChHHHHHHhcccccccccCchHHHhhhc
Q 008317 164 ANGGLNQQRLSICDAVAVAGLLNATLVIPIFHLNSVWRDSSN-----FGDIFDEDFFMHALRSNVNVVKELPEDILQQFD 238 (570)
Q Consensus 164 ~nGGLNQqR~~IcDaVavAriLNATLVlP~l~~~s~W~D~S~-----F~dIFD~dhFI~sL~~dVrIVk~LP~~~~~~~~ 238 (570)
+.||+||||.++++||++|++||+|||||.+.....|+|.++ |+++||+++|++.++++|.+.+.+|..+.....
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 899999999999999999999999999999999999999988 999999999999999999999999876644221
Q ss_pred ccc-------------------------cceeeccccc-CCChhhHHhhhhhhhhhc------ceEEEccCCcccccC-C
Q 008317 239 HNI-------------------------SSIVNLRVKG-WSSPTHYLQKVLPKLQHL------GAVRIAPFSNRLAQG-V 285 (570)
Q Consensus 239 ~~~-------------------------~~~~~~~~~~-~s~~~yY~~~vlP~l~k~------~VI~l~~f~~rLa~~-l 285 (570)
... .....+.... |+.+.+|.++++|.+.++ +++.|.++..++..+ .
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 100 0112223333 788999999999999887 999999999999876 7
Q ss_pred CCccccccceecccccccchhHHHHHHHHHHHHhhcccCCCCceEEEeeccccchhhhccccCCCChhHHHHHHHHHHhh
Q 008317 286 PSNIQGLRCLANFEALRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLRFETDMVAFSCCEYDGGEEEKREMDIARERS 365 (570)
Q Consensus 286 p~diQrLRCrvnf~ALrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLRfE~DMlAfsgC~~~~~~~E~~eL~~~R~~~ 365 (570)
+.++|+ +|+|+++|+++|++++++|+. .+++|||+|||+|+|| +++|.+++ ++..|..+|..
T Consensus 166 ~~~~~r--------~l~~~~~i~~~a~~~i~~~~~----~~~~yiavHlR~~~D~--~~~C~~~~---~~~~~~~~~~~- 227 (351)
T PF10250_consen 166 DRDLQR--------YLRFSPEIRELADKFIKRLLA----GGGPYIAVHLRRGKDW--FSACEFKG---ERHLLASPRCW- 227 (351)
T ss_dssp GGGGGG--------G--B-HHHHHHHHHHHHHH--------SSEEEEEE--SHHH--HHHHCT-T-------TTTHHHH-
T ss_pred CccceE--------EEecCHHHHHHHHHHHHHhhc----ccCceEEEeecccCch--HhhcccCC---chHHHHHhHhh-
Confidence 788887 999999999999999999993 4689999999999999 89999955 66777777653
Q ss_pred hccccccCCcccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHH
Q 008317 366 WRGKFRKRGRVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEE 445 (570)
Q Consensus 366 wk~k~~k~~~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlA~GeiyGg~~~l~pL~~~FPnl~tKe~L~s~eE 445 (570)
.. +.+++.+.+..+.||++|++++.+++++|+.+.|.||||++++|||++.|.+|+++||++++|+++.+.+|
T Consensus 228 -~~------~~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~ 300 (351)
T PF10250_consen 228 -GK------KSINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLSHEE 300 (351)
T ss_dssp --G------GGTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--EE--
T ss_pred -cc------ccccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCCHHH
Confidence 11 25677888999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhcccchhhhhhhheeeeccceeeecCCCChhhhhhhccccccCCccce
Q 008317 446 LAAFKGHSSRLAALDYTVCLHSEVFVTTQGGNFPHFLMGHRRYLYGGHAKT 496 (570)
Q Consensus 446 L~pf~~~ss~~AALDYiVcl~SDVFv~t~~GNfa~~V~GhR~y~~~G~~kT 496 (570)
+++|.+ +++|+||++||++||+||+|..++|+.+|+++|+|.+..++||
T Consensus 301 ~~~~~~--~~~a~vD~~i~~~s~~Figt~~Stfs~~i~~~R~~~g~~~~~~ 349 (351)
T PF10250_consen 301 LEPLND--DQLAMVDQEICSRSDVFIGTCGSTFSSNIARERHYRGKPKRKS 349 (351)
T ss_dssp S-------S--HHHHHHHHHHSSEEEE-TT-HHHHHHHHHHHHSSSS---E
T ss_pred hhhccc--cchhHHHHHHHhcCCEEEecCcchhHHHhhcccCcCCCCCCCC
Confidence 999986 8999999999999999999998899999999999984444344
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.31 E-value=0.00079 Score=69.78 Aligned_cols=274 Identities=19% Similarity=0.263 Sum_probs=142.5
Q ss_pred CCCceEEEE-ecCchhHHHHHHHHHHHHHHHhcCeEEeccccccccccCC-----CCCCCCCChHHHHHHhccccccccc
Q 008317 155 KSNGFLIIE-ANGGLNQQRLSICDAVAVAGLLNATLVIPIFHLNSVWRDS-----SNFGDIFDEDFFMHALRSNVNVVKE 228 (570)
Q Consensus 155 ~snGYL~V~-~nGGLNQqR~~IcDaVavAriLNATLVlP~l~~~s~W~D~-----S~F~dIFD~dhFI~sL~~dVrIVk~ 228 (570)
..||||+.- |-|-..+|--...-..|.|+.||.|||+|..-. |-+-+ -.|...|.++- |+..-|||.-
T Consensus 27 DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiE--y~~pe~~n~~vpf~~yF~vep----l~~YhRVitm 100 (386)
T KOG3849|consen 27 DPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIE--YKHPETKNLMVPFEFYFQVEP----LAKYHRVITM 100 (386)
T ss_pred CCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchh--ccCCcccccccchhheeeccc----HhhhhhheeH
Confidence 589998765 999999999999999999999999999997642 21221 24777777653 3334444422
Q ss_pred CchHHHhhhcccc------------------cceeecc-------cccC-------CChhhHHh------h------hhh
Q 008317 229 LPEDILQQFDHNI------------------SSIVNLR-------VKGW-------SSPTHYLQ------K------VLP 264 (570)
Q Consensus 229 LP~~~~~~~~~~~------------------~~~~~~~-------~~~~-------s~~~yY~~------~------vlP 264 (570)
+++++...-.+ ..-++-+ -+-| ..-.||-. + -+.
T Consensus 101 --~dFm~klapthwp~~~Rva~c~k~a~qr~pdkp~Ch~KeGNPFGPfWDqfhvsFv~sE~f~~i~Fd~~~~~~~~kW~~ 178 (386)
T KOG3849|consen 101 --QDFMKKLAPTHWPGTPRVAICDKSAAQRSPDKPGCHSKEGNPFGPFWDQFHVSFVGSEYFGDIGFDLNQMGSRKKWLE 178 (386)
T ss_pred --HHHHHHhCcccCCCCcceeeeehhhhccCCCCCCCcccCCCCCCCchhheEeeeeccccccccccchhhcchHHHHHh
Confidence 11111100000 0000000 0011 11111110 0 000
Q ss_pred h--hhhcceEEEccCCcccccCCCC-----ccccccceecccccccchhHHHHHHHHHHHHhhcccCCCCceEEEeeccc
Q 008317 265 K--LQHLGAVRIAPFSNRLAQGVPS-----NIQGLRCLANFEALRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLRFE 337 (570)
Q Consensus 265 ~--l~k~~VI~l~~f~~rLa~~lp~-----diQrLRCrvnf~ALrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLRfE 337 (570)
+ -+++-|+.|++.-. ..|. .||| -|+.+.+|.+.|++.+.-= -..|||++|||-.
T Consensus 179 kfp~eeyPVLAf~gAPA----~FPv~~e~~~lQk--------Yl~WS~r~~e~~k~fI~a~------L~rpfvgiHLRng 240 (386)
T KOG3849|consen 179 KFPSEEYPVLAFSGAPA----PFPVKGEVWSLQK--------YLRWSSRITEQAKKFISAN------LARPFVGIHLRNG 240 (386)
T ss_pred hCCcccCceeeecCCCC----CCccccccccHHH--------HHHHHHHHHHHHHHHHHHh------cCcceeEEEeecC
Confidence 0 02233444332100 0111 3444 3788899999888865432 3459999999999
Q ss_pred cchhhhccccCCCChhHHHHHHHHHHhhhccccccCCcccCCccccc-----CCCCCCCHHHH----HHHHhhcCCCCCc
Q 008317 338 TDMVAFSCCEYDGGEEEKREMDIARERSWRGKFRKRGRVIRPGANRV-----DGKCPLTPLEV----GMMLRGMGFDNTT 408 (570)
Q Consensus 338 ~DMlAfsgC~~~~~~~E~~eL~~~R~~~wk~k~~k~~~~i~~~~~R~-----~G~CPLTPeEv----gl~LralGf~~~T 408 (570)
.||+-- |.+.-...- +|. |+... -+ ...+. ...|-=+-+|+ .+-.+.+| .--
T Consensus 241 ~DWvra--Cehikd~~~---------~hl---fASpQ-Cl--Gy~~~~gaLt~e~C~Psk~~I~rqik~~v~si~--dak 301 (386)
T KOG3849|consen 241 ADWVRA--CEHIKDTTN---------RHL---FASPQ-CL--GYGHHLGALTKEICSPSKQQILRQIKEKVGSIG--DAK 301 (386)
T ss_pred chHHHH--HHHhcccCC---------Ccc---ccChh-hc--cccccccccchhhhCccHHHHHHHHHHHHhhhc--ccc
Confidence 999875 754222110 000 00000 00 00111 13453333443 22223344 223
Q ss_pred EEEEeeccccCccccchhHH-hhCCCccccccCCCHHHHhhhcccchhhhhhhheeeeccceeeecCCCChhhhhhhccc
Q 008317 409 SVYVAAGKIYKAEKYVAPLR-QMFPRLETKDTLATPEELAAFKGHSSRLAALDYTVCLHSEVFVTTQGGNFPHFLMGHRR 487 (570)
Q Consensus 409 ~IYlA~GeiyGg~~~l~pL~-~~FPnl~tKe~L~s~eEL~pf~~~ss~~AALDYiVcl~SDVFv~t~~GNfa~~V~GhR~ 487 (570)
.+|||+-. +..+..|. +++|-=+.-..|-. --+-+|..|.-+||.||++--++|+.+|--.|-
T Consensus 302 SVfVAsDs----~hmi~Eln~aL~~~~i~vh~l~p------------dd~y~dLaIlGqadhFiGNCvSsfsafvKRERD 365 (386)
T KOG3849|consen 302 SVFVASDS----DHMIDELNEALKPYEIEVHRLEP------------DDMYTDLAILGQADHFIGNCVSSFSAFVKRERD 365 (386)
T ss_pred eEEEeccc----hhhhHHHHHhhcccceeEEecCc------------ccchhhhhhhcccchhhhhhHHHHHHHHhhhhc
Confidence 59999876 44333443 33332221111111 125578999999999999999999999987775
Q ss_pred cc
Q 008317 488 YL 489 (570)
Q Consensus 488 y~ 489 (570)
..
T Consensus 366 ~~ 367 (386)
T KOG3849|consen 366 HA 367 (386)
T ss_pred cc
Confidence 43
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=95.24 E-value=0.5 Score=50.20 Aligned_cols=256 Identities=19% Similarity=0.264 Sum_probs=120.3
Q ss_pred CceEEEEecCchhHHHHHHHHHHHHHHHhcCeEEeccccccccccCC----CCCCCCCChHHHHHHhc--ccccccccCc
Q 008317 157 NGFLIIEANGGLNQQRLSICDAVAVAGLLNATLVIPIFHLNSVWRDS----SNFGDIFDEDFFMHALR--SNVNVVKELP 230 (570)
Q Consensus 157 nGYL~V~~nGGLNQqR~~IcDaVavAriLNATLVlP~l~~~s~W~D~----S~F~dIFD~dhFI~sL~--~dVrIVk~LP 230 (570)
+.|++.+--+|+|.-=-+++-|-.+|+-.|.||||= |+++ -.|...|++ |-+-.+ ..|+|+-.-+
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 579999999999999999999999999999999984 7775 346665544 444444 2333331100
Q ss_pred hHHHhhhcccccceeecccccCCChhh---HH--hhh------hh-hhh------hcceEEEccCCcccccCCCCccccc
Q 008317 231 EDILQQFDHNISSIVNLRVKGWSSPTH---YL--QKV------LP-KLQ------HLGAVRIAPFSNRLAQGVPSNIQGL 292 (570)
Q Consensus 231 ~~~~~~~~~~~~~~~~~~~~~~s~~~y---Y~--~~v------lP-~l~------k~~VI~l~~f~~rLa~~lp~diQrL 292 (570)
+.+ .+.+.++-+.-|-.|.- |. ++| |- ++. ...||+..-+..+ -|-+..
T Consensus 73 --i~~-----~~~~g~~fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~------c~~~ae 139 (321)
T PF05830_consen 73 --INQ-----FSFPGPFFPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWR------CDEEAE 139 (321)
T ss_dssp --GGT---------SSEESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTS------S-HHHH
T ss_pred --hhh-----hcCCCCcChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCc------chhHHH
Confidence 100 00111111222322221 11 111 11 111 2346664322211 122222
Q ss_pred cceecccccccchhHHHHHHHHHHHHhhcccCCCCceEEEeeccc--cchhhhccccCCCChhHHHHHHHHHHhhhcccc
Q 008317 293 RCLANFEALRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLRFE--TDMVAFSCCEYDGGEEEKREMDIARERSWRGKF 370 (570)
Q Consensus 293 RCrvnf~ALrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLRfE--~DMlAfsgC~~~~~~~E~~eL~~~R~~~wk~k~ 370 (570)
|| -|..|+-+++|++..+.+.+.-= .+..=|++|-|.- +|.+.+ +|++ .+. +..|.+.
T Consensus 140 R~--if~slkpR~eIqarID~iy~ehf-----~g~~~IGVHVRhGngeD~~~h-~~~~--~D~-e~~L~~V--------- 199 (321)
T PF05830_consen 140 RE--IFSSLKPRPEIQARIDAIYREHF-----AGYSVIGVHVRHGNGEDIMDH-APYW--ADE-ERALRQV--------- 199 (321)
T ss_dssp HH--HHHHS-B-HHHHHHHHHHHHHHT-----TTSEEEEEEE------------------HHH-HHHHHHH---------
T ss_pred HH--HHHhCCCCHHHHHHHHHHHHHHc-----CCCceEEEEEeccCCcchhcc-Cccc--cCc-hHHHHHH---------
Confidence 22 48899999999999998876643 2445899999932 222222 1211 111 0111100
Q ss_pred ccCCcccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhc
Q 008317 371 RKRGRVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFK 450 (570)
Q Consensus 371 ~k~~~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlA~GeiyGg~~~l~pL~~~FPnl~tKe~L~s~eEL~pf~ 450 (570)
......++++=...++.|+||+-. .+.++-|++.||.+++-++=..+..-.+..
T Consensus 200 ----------------------~~ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k~F~~~~~g~Lh 253 (321)
T PF05830_consen 200 ----------------------CTAIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPKQFPASQAGPLH 253 (321)
T ss_dssp ----------------------HHHHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE---------------
T ss_pred ----------------------HHHHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEcccccCCCCCCcCc
Confidence 011223455666778999999988 678999999999998875544322111221
Q ss_pred cc-----chhhhhhhheeeeccceee-ecCCCChhh
Q 008317 451 GH-----SSRLAALDYTVCLHSEVFV-TTQGGNFPH 480 (570)
Q Consensus 451 ~~-----ss~~AALDYiVcl~SDVFv-~t~~GNfa~ 480 (570)
+. .-..|-+|-+....+|+-| .+-.+.|.+
T Consensus 254 s~~~g~~gg~~ALIDM~LLSrCD~LIr~~ptS~Fsr 289 (321)
T PF05830_consen 254 SAAVGIEGGESALIDMYLLSRCDYLIRFPPTSAFSR 289 (321)
T ss_dssp -HHHHHHHHHHHHHHHHHHTTSSEEEEESTT-GGGH
T ss_pred ccccccchHHHHHHHHHHHHhCCeEEEcCCCchhhh
Confidence 10 1134889999999999999 565555554
No 4
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=49.80 E-value=82 Score=29.61 Aligned_cols=101 Identities=11% Similarity=-0.055 Sum_probs=56.6
Q ss_pred ceecccccccchhHHHHHHHHHHHHhhcccCCCCceEEEeeccccchhhh----ccccCCCChhHHH--HHHHHHHhhhc
Q 008317 294 CLANFEALRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLRFETDMVAF----SCCEYDGGEEEKR--EMDIARERSWR 367 (570)
Q Consensus 294 Crvnf~ALrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLRfE~DMlAf----sgC~~~~~~~E~~--eL~~~R~~~wk 367 (570)
+.++..+|++.++..+.-+.+.+.|+ .+|.++-++.-.+...+.. .-|.....+.+.- ...++++- |
T Consensus 47 ~v~~~~~l~~~~d~~~~l~ei~rvLk-----pGG~l~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~yl-~- 119 (160)
T PLN02232 47 AVTMGYGLRNVVDRLRAMKEMYRVLK-----PGSRVSILDFNKSNQSVTTFMQGWMIDNVVVPVATVYDLAKEYEYL-K- 119 (160)
T ss_pred EEEecchhhcCCCHHHHHHHHHHHcC-----cCeEEEEEECCCCChHHHHHHHHHHccchHhhhhHHhCChHHHHhH-H-
Confidence 34445577777788887788888887 5788887766544321110 0011000000000 00001100 0
Q ss_pred cccccCCcccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccc
Q 008317 368 GKFRKRGRVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKI 417 (570)
Q Consensus 368 ~k~~k~~~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlA~Gei 417 (570)
..... +++|+|+..+|+..||.+-+.-+++.|-+
T Consensus 120 ---------------~si~~-f~~~~el~~ll~~aGF~~~~~~~~~~g~~ 153 (160)
T PLN02232 120 ---------------YSING-YLTGEELETLALEAGFSSACHYEISGGFM 153 (160)
T ss_pred ---------------HHHHH-CcCHHHHHHHHHHcCCCcceEEECcchHh
Confidence 00012 48999999999999999998888887754
No 5
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=48.81 E-value=8.4 Score=33.43 Aligned_cols=56 Identities=21% Similarity=0.274 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhcccchhhhhhhh
Q 008317 389 PLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFKGHSSRLAALDY 461 (570)
Q Consensus 389 PLTPeEvgl~LralGf~~~T~IYlA~GeiyGg~~~l~pL~~~FPnl~tKe~L~s~eEL~pf~~~ss~~AALDY 461 (570)
++|-.|++-+|+-..|++ .+|+.++.++|++++++.--+-.+.-.|. +++..|-+|
T Consensus 39 ~~T~~Qv~~il~~f~fd~---------------~kl~~lk~l~p~i~D~~n~~~i~~~f~f~--s~k~~~~~~ 94 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDN---------------DKLKALKLLYPYIVDPQNYYTIIDAFSFS--SDKDKAREI 94 (95)
T ss_pred ceeHHHHHHHHHHcCCCH---------------HHHHHHHHHhhhccCHHHHHHHHHHhcCc--ccHHHHHHh
Confidence 499999999999999987 25999999999999996332222222222 445555444
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=36.36 E-value=35 Score=31.55 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=16.7
Q ss_pred CCCCCHHHHHHHHhhcCCCCCcEEEEeecc
Q 008317 387 KCPLTPLEVGMMLRGMGFDNTTSVYVAAGK 416 (570)
Q Consensus 387 ~CPLTPeEvgl~LralGf~~~T~IYlA~Ge 416 (570)
+|||||||+...|+++--+ ....||..++
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 6999999999999999754 4677876654
No 7
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=35.94 E-value=2e+02 Score=32.48 Aligned_cols=66 Identities=15% Similarity=0.202 Sum_probs=39.5
Q ss_pred CCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhcccch-------hhhhhhheeeeccceeeecCC
Q 008317 403 GFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFKGHSS-------RLAALDYTVCLHSEVFVTTQG 475 (570)
Q Consensus 403 Gf~~~T~IYlA~GeiyGg~~~l~pL~~~FPnl~tKe~L~s~eEL~pf~~~ss-------~~AALDYiVcl~SDVFv~t~~ 475 (570)
|=+-.-+||||+-+ ..-+..-+.-|||. .+.+..|.+.-...++ .---+|..+...+|..|.|.+
T Consensus 402 g~~~~rRiflAsDD----p~vv~EAk~kYPnY----e~igd~eia~~A~l~nRYTd~sL~GvIlDIh~LS~~d~LVCTFS 473 (580)
T KOG3705|consen 402 GKPLERRIFLASDD----PTVVPEAKNKYPNY----EVIGDTEIAKTAQLNNRYTDASLMGVILDIHILSKVDYLVCTFS 473 (580)
T ss_pred CCchhheEEEecCC----chhchHhhccCCCc----EEeccHHHHHHhhccccchhhhhhheeeeeeeecccceEEEech
Confidence 44555689999998 45567778889986 3445555555443322 123345555555665555544
Q ss_pred C
Q 008317 476 G 476 (570)
Q Consensus 476 G 476 (570)
+
T Consensus 474 S 474 (580)
T KOG3705|consen 474 S 474 (580)
T ss_pred H
Confidence 4
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=29.66 E-value=34 Score=28.34 Aligned_cols=16 Identities=38% Similarity=0.692 Sum_probs=13.9
Q ss_pred CCCCCCHHHHHHHHhhc
Q 008317 386 GKCPLTPLEVGMMLRGM 402 (570)
Q Consensus 386 G~CPLTPeEvgl~Lral 402 (570)
|-| +||||-+.+++++
T Consensus 42 ~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDC-ITPEEDREILEAT 57 (60)
T ss_pred hcc-CCHHHHHHHHHHH
Confidence 668 9999999999875
No 9
>COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=27.16 E-value=63 Score=34.00 Aligned_cols=69 Identities=20% Similarity=0.261 Sum_probs=46.4
Q ss_pred HHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhcccchhhhhhhheeeeccceeee
Q 008317 393 LEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFKGHSSRLAALDYTVCLHSEVFVT 472 (570)
Q Consensus 393 eEvgl~LralGf~~~T~IYlA~GeiyGg~~~l~pL~~~FPnl~tKe~L~s~eEL~pf~~~ss~~AALDYiVcl~SDVFv~ 472 (570)
.|+...|.+-| ..|.|.+|. .-++..+-+.+..++.+. |+.+..|..+ +||- ..||.||+
T Consensus 198 ~~l~~~l~~~~----~~Vvl~g~~--~e~e~~~~i~~~~~~~~~---l~~k~sL~e~-------~~li----~~a~l~I~ 257 (334)
T COG0859 198 AELAELLIAKG----YQVVLFGGP--DEEERAEEIAKGLPNAVI---LAGKTSLEEL-------AALI----AGADLVIG 257 (334)
T ss_pred HHHHHHHHHCC----CEEEEecCh--HHHHHHHHHHHhcCCccc---cCCCCCHHHH-------HHHH----hcCCEEEc
Confidence 46788888888 779999888 445556677777777655 5554433333 2222 67899999
Q ss_pred cCCCChhhh
Q 008317 473 TQGGNFPHF 481 (570)
Q Consensus 473 t~~GNfa~~ 481 (570)
+++|-|.=+
T Consensus 258 ~DSg~~HlA 266 (334)
T COG0859 258 NDSGPMHLA 266 (334)
T ss_pred cCChHHHHH
Confidence 999954433
No 10
>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=26.96 E-value=19 Score=33.68 Aligned_cols=17 Identities=18% Similarity=0.608 Sum_probs=11.8
Q ss_pred HHHHHhhcCCCCCcEEE
Q 008317 395 VGMMLRGMGFDNTTSVY 411 (570)
Q Consensus 395 vgl~LralGf~~~T~IY 411 (570)
+.++|+|||+.++.-||
T Consensus 54 i~ilLrALG~~sd~eI~ 70 (190)
T PF04561_consen 54 IVILLRALGIESDKEII 70 (190)
T ss_dssp HHHHHHHTT--STCHHH
T ss_pred eEEeehhhcCcCccccc
Confidence 68999999997766554
No 11
>PF01531 Glyco_transf_11: Glycosyl transferase family 11; InterPro: IPR002516 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Glycosyltransferase family 11 GT11 from CAZY comprises enzymes with only one known activity; galactoside 2-L-fucosyltransferase (2.4.1.69 from EC). Some of the proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Galactoside 2-L-fucosyltransferase 1 (2.4.1.69 from EC) and Galactoside 2-L-fucosyltransferase 2 (2.4.1.69 from EC) belong to the Hh blood group system and are associated with H/h and Se/se antigens.; GO: 0008107 galactoside 2-alpha-L-fucosyltransferase activity, 0005975 carbohydrate metabolic process, 0016020 membrane
Probab=25.55 E-value=2.6e+02 Score=29.14 Aligned_cols=135 Identities=13% Similarity=0.216 Sum_probs=0.0
Q ss_pred cccchhHHHHHHHHHHHHhhcccCCCCceEEEeec---cccchhh---hccccCCCChhHHHHHHHHHHhhhccccccCC
Q 008317 301 LRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLR---FETDMVA---FSCCEYDGGEEEKREMDIARERSWRGKFRKRG 374 (570)
Q Consensus 301 LrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLR---fE~DMlA---fsgC~~~~~~~E~~eL~~~R~~~wk~k~~k~~ 374 (570)
..+.++|++..+.....+...-.......|+||.| |-..+-. +..|.. +--++.+..++++
T Consensus 137 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~V~VHIRRGDy~~~~~~~~~~~~~~~---~Yy~~Ai~~i~~~---------- 203 (298)
T PF01531_consen 137 FDIKDELREEFKEFLRELNLEIIIKNSNSVCVHIRRGDYVSNGNHNWKHGICDK---DYYKKAIEYIREK---------- 203 (298)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEEEEEchhccccccccccCCCCCH---HHHHHHHHHHHHh----------
Q ss_pred cccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhcccch
Q 008317 375 RVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFKGHSS 454 (570)
Q Consensus 375 ~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlA~GeiyGg~~~l~pL~~~FPnl~tKe~L~s~eEL~pf~~~ss 454 (570)
..+..+||.|=+ ++-.++.++...........
T Consensus 204 ------------------------------~~~~~f~ifSDD-------~~w~k~~l~~~~~~~~~~~~----------- 235 (298)
T PF01531_consen 204 ------------------------------VKNPKFFIFSDD-------IEWCKENLKFSNGDVYFSGN----------- 235 (298)
T ss_pred ------------------------------CCCCEEEEEcCC-------HHHHHHHHhhcCCcEEEECC-----------
Q ss_pred hhhhhhheeeeccceeeecCCCChhhhhhhccccccCCccceeccCh
Q 008317 455 RLAALDYTVCLHSEVFVTTQGGNFPHFLMGHRRYLYGGHAKTIKPDK 501 (570)
Q Consensus 455 ~~AALDYiVcl~SDVFv~t~~GNfa~~V~GhR~y~~~G~~kTI~Pdr 501 (570)
.-+..|+....++|.+|.+ .|+|++-.+ |+..|...+|.|.+
T Consensus 236 ~~~~~Dl~lms~C~~~Iis-nSTFswW~a----~L~~~~~i~i~p~~ 277 (298)
T PF01531_consen 236 NSPYEDLYLMSQCKHFIIS-NSTFSWWAA----YLSKNDKIVIAPIK 277 (298)
T ss_pred CCHHHHHHHHHhCCcEEEC-CChHHHHHH----HHCCCCCEEEECCc
No 12
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=24.89 E-value=45 Score=27.02 Aligned_cols=23 Identities=30% Similarity=0.520 Sum_probs=19.5
Q ss_pred ccCCCCCCCHHHHHHHHhhcCCCC
Q 008317 383 RVDGKCPLTPLEVGMMLRGMGFDN 406 (570)
Q Consensus 383 R~~G~CPLTPeEvgl~LralGf~~ 406 (570)
+..|.. ++++|+..+|+.|||+-
T Consensus 13 ~llG~~-i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 13 RLLGLD-LSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHCCC-CCHHHHHHHHHHCCCeE
Confidence 445654 99999999999999976
No 13
>KOG3111 consensus D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=24.76 E-value=2.1e+02 Score=29.45 Aligned_cols=113 Identities=20% Similarity=0.331 Sum_probs=63.0
Q ss_pred ccchhHHHHHHHHHHHHhhcccCCCCceEEEeecccc-----chhhhccc----cCCCChhHHHHH-HHHHHhhhccccc
Q 008317 302 RFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLRFET-----DMVAFSCC----EYDGGEEEKREM-DIARERSWRGKFR 371 (570)
Q Consensus 302 rF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLRfE~-----DMlAfsgC----~~~~~~~E~~eL-~~~R~~~wk~k~~ 371 (570)
+|+|.| .+|--+|++||++- ...+|+-+||=.|. |=+|-.|- -|-...++-.++ +++|++.-|
T Consensus 42 ~FVpNi-T~G~pvV~slR~~~--~~~~ffD~HmMV~~Peq~V~~~a~agas~~tfH~E~~q~~~~lv~~ir~~Gmk---- 114 (224)
T KOG3111|consen 42 HFVPNI-TFGPPVVESLRKHT--GADPFFDVHMMVENPEQWVDQMAKAGASLFTFHYEATQKPAELVEKIREKGMK---- 114 (224)
T ss_pred cccCCc-ccchHHHHHHHhcc--CCCcceeEEEeecCHHHHHHHHHhcCcceEEEEEeeccCHHHHHHHHHHcCCe----
Confidence 566766 47888999999843 22369999997764 11222111 111111111222 334544322
Q ss_pred cCCcccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccch-------hHHhhCCCcc
Q 008317 372 KRGRVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVA-------PLRQMFPRLE 435 (570)
Q Consensus 372 k~~~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlA~GeiyGg~~~l~-------pL~~~FPnl~ 435 (570)
-|-.++ |=||-|.-..+-. .-+-.+-.+.---|||++.|. -||+-|||+.
T Consensus 115 -~G~alk----------PgT~Ve~~~~~~~---~~D~vLvMtVePGFGGQkFme~mm~KV~~lR~kyp~l~ 171 (224)
T KOG3111|consen 115 -VGLALK----------PGTPVEDLEPLAE---HVDMVLVMTVEPGFGGQKFMEDMMPKVEWLREKYPNLD 171 (224)
T ss_pred -eeEEeC----------CCCcHHHHHHhhc---cccEEEEEEecCCCchhhhHHHHHHHHHHHHHhCCCce
Confidence 122223 5577776655544 234455555566699999984 5778888874
Done!