Query 009877
Match_columns 523
No_of_seqs 210 out of 387
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 18:24:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009877hhsearch_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 1.5E-56 3.3E-61 451.3 2.2 306 164-496 6-349 (351)
2 KOG3849 GDP-fucose protein O-f 97.5 0.00035 7.6E-09 71.7 9.1 57 155-213 27-89 (386)
3 PF05830 NodZ: Nodulation prot 95.1 0.48 1E-05 49.8 13.7 256 157-480 2-289 (321)
4 KOG3705 Glycoprotein 6-alpha-L 65.3 39 0.00084 37.4 9.4 66 403-476 402-474 (580)
5 PF14771 DUF4476: Domain of un 62.1 3.4 7.4E-05 35.4 0.8 36 389-439 39-74 (95)
6 PLN02232 ubiquinone biosynthes 56.0 61 0.0013 30.1 8.0 101 294-417 47-153 (160)
7 PF00799 Gemini_AL1: Geminivir 37.7 32 0.0007 31.4 3.0 29 387-416 14-42 (114)
8 PF01531 Glyco_transf_11: Glyc 31.0 1.4E+02 0.0031 30.6 6.9 135 301-501 137-277 (298)
9 PF10892 DUF2688: Protein of u 30.9 32 0.00069 28.2 1.6 16 386-402 42-57 (60)
10 COG0859 RfaF ADP-heptose:LPS h 28.5 58 0.0013 33.8 3.5 71 393-483 198-268 (334)
11 smart00874 B5 tRNA synthetase 28.3 37 0.00079 27.2 1.6 23 383-406 13-35 (71)
12 PF04561 RNA_pol_Rpb2_2: RNA p 24.1 22 0.00048 32.9 -0.4 17 395-411 54-70 (190)
13 PRK15451 tRNA cmo(5)U34 methyl 21.3 1.2E+02 0.0025 30.2 4.0 27 385-411 204-230 (247)
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=1.5e-56 Score=451.31 Aligned_cols=306 Identities=37% Similarity=0.635 Sum_probs=208.1
Q ss_pred ecCchhHHHHHHHHHHHHHHHhcCeEeccccccCccccCCCC-----CCCCCChHHHHHHhcccchhcccCchHHHhhhc
Q 009877 164 ANGGLNQQRLSICDAVAVAGLLNATLVIPIFHLNSVWRDSSN-----FGDIFDEDFFMHALRSNVNVVKELPEDILQQFD 238 (523)
Q Consensus 164 ~nGGLNQqR~~IcdaVavAriLNATLVlP~l~~~s~W~D~S~-----F~dIFD~dhFI~sL~~dVrIVk~LP~~~~~~~~ 238 (523)
|.||+||||.++++||++|++||+|||||.+.....|+|.++ |+++||+++|++.++++|.+.+.+|..+.....
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 999999999999999999999999876544221
Q ss_pred ccc-------------------------cceeeccccc-CCChhhHHhhhhhhhhhc------ceEEEcCCccccccC-C
Q 009877 239 HNI-------------------------SSIVNLRVKG-WSSPTHYLQKVLPKLQHL------GAVRIAPFSNRLAQG-V 285 (523)
Q Consensus 239 ~~~-------------------------~~~~~~~~~~-~s~~~yY~~~vlP~l~k~------~Vi~l~~f~~rLa~~-l 285 (523)
... .......... |+.+.+|.++++|.+.++ +++.|.++...+..+ .
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 0112222333 788999999999999887 999999999999876 7
Q ss_pred CCccccccceecccccccchhHHHHHHHHHHHHhhcccCCCCceEEEeecccchhhhhccccCCCChhHHHHHHHHHHhh
Q 009877 286 PSNIQGLRCLANFEALRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLRFETDMVAFSCCEYDGGEEEKREMDIARERS 365 (523)
Q Consensus 286 P~diQrLRCrvnf~ALrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLRfE~DMlAfsgC~~~~~~~E~~eL~~~R~~~ 365 (523)
+.++|+ +|+|+++|+++|++++++|+. .+++|||+|||+|+|| +++|.+++ ++..|..+|..
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 88999955 66777777754
Q ss_pred hccccccCCcccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHH
Q 009877 366 WRGKFRKRGRVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEE 445 (523)
Q Consensus 366 wk~k~~~~~~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlAsGeiyGg~~~m~pL~~~FPnl~tKe~L~s~eE 445 (523)
..+ .+++.+.+..+.||++|++++.+++++|+.+.|.||||++++|||++.|.+|+++||++++|+++.+.+|
T Consensus 228 -~~~------~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~ 300 (351)
T PF10250_consen 228 -GKK------SINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLSHEE 300 (351)
T ss_dssp --GG------GTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--EE--
T ss_pred -ccc------cccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCCHHH
Confidence 222 5678889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhhccccchhhhheeeeeccceeeecCCCChhhhhhhhhhcccCCcccc
Q 009877 446 LAAFKGHSSRLAALDYTVCLHSEVFVTTQGGNFPHFLMGHRRYLYGGHAKT 496 (523)
Q Consensus 446 L~pf~~~ss~lAALDYiVcl~SDVFv~t~~GNfa~~V~GhR~y~~~G~~kT 496 (523)
+++|.+ +++|+||++||++||+||+|..++|+.+|+++|+|.+..++||
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=97.54 E-value=0.00035 Score=71.69 Aligned_cols=57 Identities=25% Similarity=0.307 Sum_probs=45.4
Q ss_pred CCCcEEEEE-ecCchhHHHHHHHHHHHHHHHhcCeEeccccccCccccCC-----CCCCCCCChH
Q 009877 155 KSNGFLIIE-ANGGLNQQRLSICDAVAVAGLLNATLVIPIFHLNSVWRDS-----SNFGDIFDED 213 (523)
Q Consensus 155 ~snGYL~V~-~nGGLNQqR~~IcdaVavAriLNATLVlP~l~~~s~W~D~-----S~F~dIFD~d 213 (523)
..||||+.- |-|-..+|-....-..|.|+.||.|||+|..-. |-+-+ -.|...|.++
T Consensus 27 DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiE--y~~pe~~n~~vpf~~yF~ve 89 (386)
T KOG3849|consen 27 DPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIE--YKHPETKNLMVPFEFYFQVE 89 (386)
T ss_pred CCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchh--ccCCcccccccchhheeecc
Confidence 579998775 999999999999999999999999999997642 21221 2477777765
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=95.06 E-value=0.48 Score=49.84 Aligned_cols=256 Identities=18% Similarity=0.249 Sum_probs=119.3
Q ss_pred CcEEEEEecCchhHHHHHHHHHHHHHHHhcCeEeccccccCccccCC----CCCCCCCChHHHHHHhcc--cchhcccCc
Q 009877 157 NGFLIIEANGGLNQQRLSICDAVAVAGLLNATLVIPIFHLNSVWRDS----SNFGDIFDEDFFMHALRS--NVNVVKELP 230 (523)
Q Consensus 157 nGYL~V~~nGGLNQqR~~IcdaVavAriLNATLVlP~l~~~s~W~D~----S~F~dIFD~dhFI~sL~~--dVrIVk~LP 230 (523)
+.|++.+--+|+|.-=-+++-|-.+|+-.|.||||= |+++ -.|...|++ |-+-.++ .|+++-.-
T Consensus 2 ~r~~~~r~r~g~gd~l~~la~aw~~a~~~~r~l~id-------w~~s~~~~~~f~n~f~~--ffepv~~i~~~~~~~~d- 71 (321)
T PF05830_consen 2 QRFVVSRRRTGLGDCLWSLAAAWRYAKRTGRTLVID-------WRGSCYLDQPFTNAFPV--FFEPVEDIAGVRVICDD- 71 (321)
T ss_dssp --EEEEE--S-HHHHHHHHHHHHHHHHHHT-EEEEE--------BT-TT-SSTTSBSHHH--HB---SEETTEEEE-SG-
T ss_pred CceEEEeccCCchhHHHHHHHHHHHHHHhCCeEEEE-------cCCceecCCcccccCCc--ccchhhhhcCceeEecc-
Confidence 579999999999999999999999999999999983 7775 346666654 5444442 33332110
Q ss_pred hHHHhhhcccccceeecccccCCChhh---H-------H--hhhhhhhh------hcceEEEcCCccccccCCCCccccc
Q 009877 231 EDILQQFDHNISSIVNLRVKGWSSPTH---Y-------L--QKVLPKLQ------HLGAVRIAPFSNRLAQGVPSNIQGL 292 (523)
Q Consensus 231 ~~~~~~~~~~~~~~~~~~~~~~s~~~y---Y-------~--~~vlP~l~------k~~Vi~l~~f~~rLa~~lP~diQrL 292 (523)
.+. ..+.+.+.-+.-|-.|.- | . +++--+++ ...||+..=+.-+ -|-+..
T Consensus 72 -~i~-----~~~~~g~~fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~------c~~~ae 139 (321)
T PF05830_consen 72 -RIN-----QFSFPGPFFPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWR------CDEEAE 139 (321)
T ss_dssp -GGG-----T----SSEESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTS------S-HHHH
T ss_pred -hhh-----hhcCCCCcChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCc------chhHHH
Confidence 000 001111111222222211 1 1 11111111 2345544422222 122222
Q ss_pred cceecccccccchhHHHHHHHHHHHHhhcccCCCCceEEEeeccc--chhhhhccccCCCChhHHHHHHHHHHhhhcccc
Q 009877 293 RCLANFEALRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLRFE--TDMVAFSCCEYDGGEEEKREMDIARERSWRGKF 370 (523)
Q Consensus 293 RCrvnf~ALrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLRfE--~DMlAfsgC~~~~~~~E~~eL~~~R~~~wk~k~ 370 (523)
|| -|..|+-+++|++..+.+.+.-= .+..=|++|-|.- +|.+.+ +|++ ..++..|.+..
T Consensus 140 R~--if~slkpR~eIqarID~iy~ehf-----~g~~~IGVHVRhGngeD~~~h-~~~~---~D~e~~L~~V~-------- 200 (321)
T PF05830_consen 140 RE--IFSSLKPRPEIQARIDAIYREHF-----AGYSVIGVHVRHGNGEDIMDH-APYW---ADEERALRQVC-------- 200 (321)
T ss_dssp HH--HHHHS-B-HHHHHHHHHHHHHHT-----TTSEEEEEEE-------------------HHHHHHHHHHH--------
T ss_pred HH--HHHhCCCCHHHHHHHHHHHHHHc-----CCCceEEEEEeccCCcchhcc-Cccc---cCchHHHHHHH--------
Confidence 22 48899999999999998876643 2445899999932 222222 1221 01111111100
Q ss_pred ccCCcccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhh
Q 009877 371 RKRGRVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFK 450 (523)
Q Consensus 371 ~~~~~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlAsGeiyGg~~~m~pL~~~FPnl~tKe~L~s~eEL~pf~ 450 (523)
.....++++=...++.|+||+-. .+-++-+++.||.+++-++=..+..-.+..
T Consensus 201 -----------------------~ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k~F~~~~~g~Lh 253 (321)
T PF05830_consen 201 -----------------------TAIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPKQFPASQAGPLH 253 (321)
T ss_dssp -----------------------HHHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE---------------
T ss_pred -----------------------HHHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEcccccCCCCCCcCc
Confidence 11123355556678999999988 677999999999998876544322211221
Q ss_pred cc-----ccchhhhheeeeeccceee-ecCCCChhh
Q 009877 451 GH-----SSRLAALDYTVCLHSEVFV-TTQGGNFPH 480 (523)
Q Consensus 451 ~~-----ss~lAALDYiVcl~SDVFv-~t~~GNfa~ 480 (523)
+. .-..|-+|-+....+|+-| .+-.+.|.+
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 11 1134889999999999999 565555554
No 4
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=65.30 E-value=39 Score=37.44 Aligned_cols=66 Identities=17% Similarity=0.270 Sum_probs=37.1
Q ss_pred CCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhhccccc------h-hhhheeeeeccceeeecCC
Q 009877 403 GFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFKGHSSR------L-AALDYTVCLHSEVFVTTQG 475 (523)
Q Consensus 403 Gf~~~T~IYlAsGeiyGg~~~m~pL~~~FPnl~tKe~L~s~eEL~pf~~~ss~------l-AALDYiVcl~SDVFv~t~~ 475 (523)
|=+-.-+||||+-+ ..-+..-+..|||. .+.+..|.+.-....++ + --+|..+...+|..|.|.+
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 33444589999998 45566778889986 34444555544332221 1 2345555555555555544
Q ss_pred C
Q 009877 476 G 476 (523)
Q Consensus 476 G 476 (523)
+
T Consensus 474 S 474 (580)
T KOG3705|consen 474 S 474 (580)
T ss_pred H
Confidence 3
No 5
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=62.13 E-value=3.4 Score=35.44 Aligned_cols=36 Identities=19% Similarity=0.346 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCcccccc
Q 009877 389 PLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDT 439 (523)
Q Consensus 389 PLTPeEvgl~LralGf~~~T~IYlAsGeiyGg~~~m~pL~~~FPnl~tKe~ 439 (523)
++|-.|++-+|+-..|+ +.+|+.++-++|++++++.
T Consensus 39 ~~T~~Qv~~il~~f~fd---------------~~kl~~lk~l~p~i~D~~n 74 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFD---------------NDKLKALKLLYPYIVDPQN 74 (95)
T ss_pred ceeHHHHHHHHHHcCCC---------------HHHHHHHHHHhhhccCHHH
Confidence 39999999999999998 4579999999999999963
No 6
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=56.00 E-value=61 Score=30.08 Aligned_cols=101 Identities=11% Similarity=-0.055 Sum_probs=57.1
Q ss_pred ceecccccccchhHHHHHHHHHHHHhhcccCCCCceEEEeecccchhhhh----ccccCCCChhHHH--HHHHHHHhhhc
Q 009877 294 CLANFEALRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLRFETDMVAF----SCCEYDGGEEEKR--EMDIARERSWR 367 (523)
Q Consensus 294 Crvnf~ALrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLRfE~DMlAf----sgC~~~~~~~E~~--eL~~~R~~~wk 367 (523)
+.++..+|++.++..+.-+.+.+.|+ .+|.++-++.-.+...+.. .-|...+..-+.- ...+|++- |
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 34445677877888887788888887 5788887766544322110 0011000000000 00011110 0
Q ss_pred cccccCCcccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccc
Q 009877 368 GKFRKRGRVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKI 417 (523)
Q Consensus 368 ~k~~~~~~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlAsGei 417 (523)
..... +++|+|+..+|+..||.+-+.-+++.|-+
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 7
>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=37.73 E-value=32 Score=31.39 Aligned_cols=29 Identities=21% Similarity=0.311 Sum_probs=16.7
Q ss_pred CCCCCHHHHHHHHhhcCCCCCcEEEEeecc
Q 009877 387 KCPLTPLEVGMMLRGMGFDNTTSVYVAAGK 416 (523)
Q Consensus 387 ~CPLTPeEvgl~LralGf~~~T~IYlAsGe 416 (523)
+|||||||+...|+++--+ ....||..++
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 4677876664
No 8
>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=30.98 E-value=1.4e+02 Score=30.63 Aligned_cols=135 Identities=13% Similarity=0.218 Sum_probs=0.0
Q ss_pred cccchhHHHHHHHHHHHHhhcccCCCCceEEEeec---ccchhhh---hccccCCCChhHHHHHHHHHHhhhccccccCC
Q 009877 301 LRFSEPIRMLAEKMVDRMVKNSSQSGGKYVSVHLR---FETDMVA---FSCCEYDGGEEEKREMDIARERSWRGKFRKRG 374 (523)
Q Consensus 301 LrF~~~I~~lg~~lV~Rmr~~s~~~~g~yiAlHLR---fE~DMlA---fsgC~~~~~~~E~~eL~~~R~~~wk~k~~~~~ 374 (523)
..+.++|++..+.....+...-.......|+||.| |-..+-. +..|. .+=-+++++.++++
T Consensus 137 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~V~VHIRRGDy~~~~~~~~~~~~~~---~~Yy~~Ai~~i~~~---------- 203 (298)
T PF01531_consen 137 FDIKDELREEFKEFLRELNLEIIIKNSNSVCVHIRRGDYVSNGNHNWKHGICD---KDYYKKAIEYIREK---------- 203 (298)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEEEEEchhccccccccccCCCCC---HHHHHHHHHHHHHh----------
Q ss_pred cccCCcccccCCCCCCCHHHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhhcccc
Q 009877 375 RVIRPGANRVDGKCPLTPLEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFKGHSS 454 (523)
Q Consensus 375 ~~i~~~~~R~~G~CPLTPeEvgl~LralGf~~~T~IYlAsGeiyGg~~~m~pL~~~FPnl~tKe~L~s~eEL~pf~~~ss 454 (523)
..+..+||.|-+ ++-.++.++...........
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 chhhhheeeeeccceeeecCCCChhhhhhhhhhcccCCcccccccCh
Q 009877 455 RLAALDYTVCLHSEVFVTTQGGNFPHFLMGHRRYLYGGHAKTIKPDK 501 (523)
Q Consensus 455 ~lAALDYiVcl~SDVFv~t~~GNfa~~V~GhR~y~~~G~~kTi~Pdr 501 (523)
.-+..|+....++|.+|.+ .|+|++-.+ |+..|..++|.|.+
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 9
>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=30.90 E-value=32 Score=28.22 Aligned_cols=16 Identities=38% Similarity=0.692 Sum_probs=13.8
Q ss_pred CCCCCCHHHHHHHHhhc
Q 009877 386 GKCPLTPLEVGMMLRGM 402 (523)
Q Consensus 386 G~CPLTPeEvgl~Lral 402 (523)
|-| +||||-+.+++++
T Consensus 42 ~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDC-ITPEEDREILEAT 57 (60)
T ss_pred hcc-CCHHHHHHHHHHH
Confidence 568 9999999999875
No 10
>COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=28.51 E-value=58 Score=33.85 Aligned_cols=71 Identities=20% Similarity=0.244 Sum_probs=47.2
Q ss_pred HHHHHHHhhcCCCCCcEEEEeeccccCccccchhHHhhCCCccccccCCCHHHHhhhhccccchhhhheeeeeccceeee
Q 009877 393 LEVGMMLRGMGFDNTTSVYVAAGKIYKAEKYVAPLRQMFPRLETKDTLATPEELAAFKGHSSRLAALDYTVCLHSEVFVT 472 (523)
Q Consensus 393 eEvgl~LralGf~~~T~IYlAsGeiyGg~~~m~pL~~~FPnl~tKe~L~s~eEL~pf~~~ss~lAALDYiVcl~SDVFv~ 472 (523)
.|+...|.+-| ..|.+.+|. .-++..+-+.+..++.+. |+.+..|..+ +||- ..||.||+
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 36777888888 689999888 445556677778887655 5554444333 2222 67899999
Q ss_pred cCCCChhhhhh
Q 009877 473 TQGGNFPHFLM 483 (523)
Q Consensus 473 t~~GNfa~~V~ 483 (523)
+++|-|.=+-+
T Consensus 258 ~DSg~~HlAaA 268 (334)
T COG0859 258 NDSGPMHLAAA 268 (334)
T ss_pred cCChHHHHHHH
Confidence 99995544433
No 11
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=28.26 E-value=37 Score=27.22 Aligned_cols=23 Identities=30% Similarity=0.520 Sum_probs=19.4
Q ss_pred ccCCCCCCCHHHHHHHHhhcCCCC
Q 009877 383 RVDGKCPLTPLEVGMMLRGMGFDN 406 (523)
Q Consensus 383 R~~G~CPLTPeEvgl~LralGf~~ 406 (523)
+..|.. ++++|+..+|+.|||+-
T Consensus 13 ~llG~~-i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 13 RLLGLD-LSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHCCC-CCHHHHHHHHHHCCCeE
Confidence 455654 99999999999999974
No 12
>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=24.09 E-value=22 Score=32.89 Aligned_cols=17 Identities=18% Similarity=0.608 Sum_probs=11.9
Q ss_pred HHHHHhhcCCCCCcEEE
Q 009877 395 VGMMLRGMGFDNTTSVY 411 (523)
Q Consensus 395 vgl~LralGf~~~T~IY 411 (523)
+.++|+|||+.++.-||
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 57999999998776554
No 13
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=21.33 E-value=1.2e+02 Score=30.21 Aligned_cols=27 Identities=11% Similarity=0.070 Sum_probs=21.8
Q ss_pred CCCCCCCHHHHHHHHhhcCCCCCcEEE
Q 009877 385 DGKCPLTPLEVGMMLRGMGFDNTTSVY 411 (523)
Q Consensus 385 ~G~CPLTPeEvgl~LralGf~~~T~IY 411 (523)
+-..|+|++|...+|+.-||..-..+|
T Consensus 204 ~~~~~~~~~~~~~~L~~aGF~~v~~~~ 230 (247)
T PRK15451 204 NVMLTDSVETHKARLHKAGFEHSELWF 230 (247)
T ss_pred hhcccCCHHHHHHHHHHcCchhHHHHH
Confidence 346789999999999999998655443
Done!