Query 012011
Match_columns 473
No_of_seqs 179 out of 400
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 07:40:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012011.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012011hhsearch_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 1E-55 2.3E-60 445.1 2.7 306 63-412 5-343 (351)
2 KOG3849 GDP-fucose protein O-f 98.3 5.1E-06 1.1E-10 83.4 11.3 60 54-113 26-89 (386)
3 PF05830 NodZ: Nodulation prot 97.0 0.033 7.2E-07 57.4 16.6 255 57-402 2-289 (321)
4 PF14771 DUF4476: Domain of un 59.1 6.6 0.00014 33.2 2.0 56 311-383 39-94 (95)
5 KOG3705 Glycoprotein 6-alpha-L 50.6 82 0.0018 34.4 8.7 67 325-399 402-475 (580)
6 PLN02232 ubiquinone biosynthes 49.2 88 0.0019 28.7 7.9 29 311-339 125-153 (160)
7 PF00799 Gemini_AL1: Geminivir 42.6 28 0.00061 31.2 3.4 29 309-338 14-42 (114)
8 PF10892 DUF2688: Protein of u 33.2 31 0.00067 27.6 1.9 16 308-324 42-57 (60)
9 COG0763 LpxB Lipid A disacchar 31.9 72 0.0016 34.3 4.9 86 330-416 2-115 (381)
10 smart00874 B5 tRNA synthetase 29.1 48 0.001 26.1 2.4 25 303-328 11-35 (71)
11 PF04561 RNA_pol_Rpb2_2: RNA p 23.7 28 0.0006 31.9 0.2 17 317-333 54-70 (190)
12 PF03484 B5: tRNA synthetase B 21.8 53 0.0011 26.3 1.4 24 304-328 12-35 (70)
13 PF02845 CUE: CUE domain; Int 20.6 59 0.0013 23.5 1.3 35 345-386 4-40 (42)
14 COG0859 RfaF ADP-heptose:LPS h 20.3 1.7E+02 0.0036 30.1 5.0 76 315-410 198-273 (334)
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=1e-55 Score=445.11 Aligned_cols=306 Identities=35% Similarity=0.548 Sum_probs=207.5
Q ss_pred EecCChhhHHHHHHHHHHHHHHhcCeEeccccCCCCcccCCCC-----CCcccchHHHHHhccCCceEeccCChhhhhhh
Q 012011 63 FLDGGLNQQRMGICDAVAVTKILNATLVIPYLEVNPVWQDSSS-----FMDIYDVDHFINVLKDDISIVKELPNEFSWST 137 (473)
Q Consensus 63 ~~nGGLnqqR~~IcdaV~vAriLNATLViP~l~~~s~w~D~S~-----F~dIFD~dhFI~~L~~dV~Ivk~LP~~~~~~~ 137 (473)
.+.||+||||+++++||++|++||+|||||.+.....|++.++ |+++||+++|+++++++|.+.+.+|.......
T Consensus 5 p~~GGfnNQr~~~~~a~~~A~~LnRTLVLPp~~~~~~~~~~~~~~~ipf~~~fD~~~l~~~~~~vi~~~ef~~~~~~~~~ 84 (351)
T PF10250_consen 5 PCMGGFNNQRMGFENAVVFAKALNRTLVLPPFIKHYHWKDQSKQRHIPFSDFFDVEHLRKFLRPVITMEEFLPKHWDEVF 84 (351)
T ss_dssp --SSSHHHHHHHHHHHHHHHHHHT-EEE--EEEEESSSS----EEEEEHHHHB-HHHHTTTS--EE-HHHHHHHHS-GGG
T ss_pred CCCCCHHHHHHHHHHHHHHHHHhCCEEEcCCccccccccccccccccChhhhccHHHHHHHhhCceehheeccchhcccc
Confidence 3899999999999999999999999999999999999999987 99999999999999999999999987665432
Q ss_pred hhhh-----h---------------hcccccccccC-CC-cCChhHHHHhhhhhhhhc------ceEEEcCCCCcccCCC
Q 012011 138 REYY-----A---------------TAIRATRIKTA-PV-HASANWYLENVLPVLQSY------GVAAISPFSHRLTFDN 189 (473)
Q Consensus 138 ~~~~-----~---------------~~~~~~~i~~~-p~-~~~~~~Y~~~vlP~l~k~------~Vi~l~~~~~rL~~~~ 189 (473)
...+ . .......+... .. ++.+.+|+++++|.+.++ +|+.|.++..++..+.
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~ 164 (351)
T PF10250_consen 85 RLQYCWSPWESGSWDDNMKDGNPFGPFWDKFPIKFDPCEFWSSPSLYLEDVLPELREWNENSEHPVIAFTGFESRLPDNY 164 (351)
T ss_dssp -EEEESS-B--------TTSSTTHHHHHHHTT---SEEE-E-TTSTTTT-STTHHHHHHHHTT-SEEEESS-SS-SS--G
T ss_pred chhhcccccccccchhhccccccccccccccceeeccccccCCchhhHHHhhhHHhhhccccccccceeccccccchhcc
Confidence 2110 0 00001111111 11 567888889999999987 9999999999999887
Q ss_pred CCchhhhhcceecceeeeccHhHHHHHHHHHHHHcCCCCCCCCCcchhhhhhhhccccCCCCceEEEeeccchhhHhhhc
Q 012011 190 LPMDIQRLRCKANFQALIFVPHIRALGDALVSRLRYPSIKNRGLDDVHLEETAYTNKIQEPLKFVVLHLRFDKDMAAHSA 269 (473)
Q Consensus 190 lP~~iQrLRCrvnf~ALrF~~~I~~lg~~lv~Rmr~~~~~~~~~~~~~~~~~~~~~~~~~~g~yiAlHLR~E~Dmla~sg 269 (473)
++.++|| +|+|+++|+++|++++++|+.. .++|||+|||+|+|| +++
T Consensus 165 ~~~~~~r--------~l~~~~~i~~~a~~~i~~~~~~-----------------------~~~yiavHlR~~~D~--~~~ 211 (351)
T PF10250_consen 165 LDRDLQR--------YLRFSPEIRELADKFIKRLLAG-----------------------GGPYIAVHLRRGKDW--FSA 211 (351)
T ss_dssp GGGGGGG--------G--B-HHHHHHHHHHHHHH---------------------------SSEEEEEE--SHHH--HHH
T ss_pred cCccceE--------EEecCHHHHHHHHHHHHHhhcc-----------------------cCceEEEeecccCch--Hhh
Confidence 8888987 9999999999999999999931 389999999999999 888
Q ss_pred cCCCCChHHHHHHHHHHHhhhcccccCCCCChHHHhcCCCCCCCHHHHHHHHHHcCCCCCceEEEeeccccCCccchhHH
Q 012011 270 CDFGGGKAEKLALAKYRQMIWQGRVLNSQFTDEELRSQGRCPLTPEEIGLLLAALGFDKSTRLYLASHKVYGGEARISAL 349 (473)
Q Consensus 270 C~~~~~~~E~~eL~~~R~~~w~~~~~~~~~~~~~~R~~G~CPLtPeEvgl~L~alGf~~~T~IYlA~geiygg~~~l~~L 349 (473)
|.+++ ++..|..+|.. . ...+++...+..|.||++|++++.+++++|+.+.|.||||++++|||.+.|.+|
T Consensus 212 C~~~~---~~~~~~~~~~~--~----~~~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l 282 (351)
T PF10250_consen 212 CEFKG---ERHLLASPRCW--G----KKSINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPL 282 (351)
T ss_dssp HCT-T-------TTTHHHH-------GGGTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------
T ss_pred cccCC---chHHHHHhHhh--c----cccccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHH
Confidence 99955 77778888864 1 123456678899999999999999999999999999999999999999999999
Q ss_pred HHhCCCCcccccCCChHHHhccccchhhhhhhhheeecccceeeeCCCCchhhhhhhhhcccc
Q 012011 350 RRLFPLMEDKKSLASSEERAGVKGKASLLAALDYYVSMHSNIFISASPGNMHNALMGHRTYEN 412 (473)
Q Consensus 350 ~~~fPnl~tKe~L~s~eEL~~f~~~ss~lAAlDy~Vcl~SDvFv~t~~Gnfa~~v~GhR~y~g 412 (473)
++.||++++|+++.+.+|+++|.+ .++|+||++||++||+||+|..++|+.+|+++|+|.|
T Consensus 283 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~a~vD~~i~~~s~~Figt~~Stfs~~i~~~R~~~g 343 (351)
T PF10250_consen 283 KNMFPNVVTKDDLLSHEELEPLND--DQLAMVDQEICSRSDVFIGTCGSTFSSNIARERHYRG 343 (351)
T ss_dssp HHHHHHHHGGGT--EE--S-------S--HHHHHHHHHHSSEEEE-TT-HHHHHHHHHHHHSS
T ss_pred HHHhhhhEeccccCCHHHhhhccc--cchhHHHHHHHhcCCEEEecCcchhHHHhhcccCcCC
Confidence 999999999999999999999988 6999999999999999999999999999999999999
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=98.30 E-value=5.1e-06 Score=83.45 Aligned_cols=60 Identities=23% Similarity=0.220 Sum_probs=46.3
Q ss_pred CCCCcEEEE-EecCChhhHHHHHHHHHHHHHHhcCeEeccccC---CCCcccCCCCCCcccchH
Q 012011 54 QKSQGYIQV-FLDGGLNQQRMGICDAVAVTKILNATLVIPYLE---VNPVWQDSSSFMDIYDVD 113 (473)
Q Consensus 54 ~~snGyl~V-~~nGGLnqqR~~IcdaV~vAriLNATLViP~l~---~~s~w~D~S~F~dIFD~d 113 (473)
...||||+. .|-|-+.||-....-..|.|+.||.|||+|-.- +-.+-.---.|...|.++
T Consensus 26 ~DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiEy~~pe~~n~~vpf~~yF~ve 89 (386)
T KOG3849|consen 26 WDPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIEYKHPETKNLMVPFEFYFQVE 89 (386)
T ss_pred CCCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchhccCCcccccccchhheeecc
Confidence 368999988 699999999999999999999999999998642 111101113788888765
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=97.02 E-value=0.033 Score=57.39 Aligned_cols=255 Identities=19% Similarity=0.228 Sum_probs=124.8
Q ss_pred CcEEEEEecCChhhHHHHHHHHHHHHHHhcCeEeccccCCCCcccCC----CCCCcccchHHHHHhcc--CCceEeccCC
Q 012011 57 QGYIQVFLDGGLNQQRMGICDAVAVTKILNATLVIPYLEVNPVWQDS----SSFMDIYDVDHFINVLK--DDISIVKELP 130 (473)
Q Consensus 57 nGyl~V~~nGGLnqqR~~IcdaV~vAriLNATLViP~l~~~s~w~D~----S~F~dIFD~dhFI~~L~--~dV~Ivk~LP 130 (473)
+.|++..--+|+|.-=-+++-|-.+|+-.|.||||= |+++ ..|...|++ |-+-.+ .-|+|+-.
T Consensus 2 ~r~~~~r~r~g~gd~l~~la~aw~~a~~~~r~l~id-------w~~s~~~~~~f~n~f~~--ffepv~~i~~~~~~~~-- 70 (321)
T PF05830_consen 2 QRFVVSRRRTGLGDCLWSLAAAWRYAKRTGRTLVID-------WRGSCYLDQPFTNAFPV--FFEPVEDIAGVRVICD-- 70 (321)
T ss_dssp --EEEEE--S-HHHHHHHHHHHHHHHHHHT-EEEEE--------BT-TT-SSTTSBSHHH--HB---SEETTEEEE-S--
T ss_pred CceEEEeccCCchhHHHHHHHHHHHHHHhCCeEEEE-------cCCceecCCcccccCCc--ccchhhhhcCceeEec--
Confidence 468888889999999999999999999999999983 7777 477777754 555554 34554421
Q ss_pred hhhhhhhhhhhhhcccccccccCCCcCC----------hhHH---HHhhhhhhh------hcceEEEcCCCCcccCCCCC
Q 012011 131 NEFSWSTREYYATAIRATRIKTAPVHAS----------ANWY---LENVLPVLQ------SYGVAAISPFSHRLTFDNLP 191 (473)
Q Consensus 131 ~~~~~~~~~~~~~~~~~~~i~~~p~~~~----------~~~Y---~~~vlP~l~------k~~Vi~l~~~~~rL~~~~lP 191 (473)
..+... . . .-+..|.+|. -.+. .+++--++. ...||+..-...+- .
T Consensus 71 d~i~~~---~----~---~g~~fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~c-----~ 135 (321)
T PF05830_consen 71 DRINQF---S----F---PGPFFPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWRC-----D 135 (321)
T ss_dssp GGGGT--------------SSEESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTSS------
T ss_pred chhhhh---c----C---CCCcChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCcc-----h
Confidence 111100 0 0 0001122211 1111 122223332 24577765444332 2
Q ss_pred chhhhhcceecceeeeccHhHHHHHHHHHHHHcCCCCCCCCCcchhhhhhhhccccCCCCceEEEeeccc--hhhHhhhc
Q 012011 192 MDIQRLRCKANFQALIFVPHIRALGDALVSRLRYPSIKNRGLDDVHLEETAYTNKIQEPLKFVVLHLRFD--KDMAAHSA 269 (473)
Q Consensus 192 ~~iQrLRCrvnf~ALrF~~~I~~lg~~lv~Rmr~~~~~~~~~~~~~~~~~~~~~~~~~~g~yiAlHLR~E--~Dmla~sg 269 (473)
.++.| .-|..|+-+++|++..+.+.+.-=. +..=|++|.|.- +|.+.+ +
T Consensus 136 ~~aeR----~if~slkpR~eIqarID~iy~ehf~------------------------g~~~IGVHVRhGngeD~~~h-~ 186 (321)
T PF05830_consen 136 EEAER----EIFSSLKPRPEIQARIDAIYREHFA------------------------GYSVIGVHVRHGNGEDIMDH-A 186 (321)
T ss_dssp HHHHH----HHHHHS-B-HHHHHHHHHHHHHHTT------------------------TSEEEEEEE-------------
T ss_pred hHHHH----HHHHhCCCCHHHHHHHHHHHHHHcC------------------------CCceEEEEEeccCCcchhcc-C
Confidence 33443 2588999999999999998776433 245799999932 233333 2
Q ss_pred cCCCCChHHHHHHHHHHHhhhcccccCCCCChHHHhcCCCCCCCHHHHHHHHHHcCCCCCceEEEeeccccCCccchhHH
Q 012011 270 CDFGGGKAEKLALAKYRQMIWQGRVLNSQFTDEELRSQGRCPLTPEEIGLLLAALGFDKSTRLYLASHKVYGGEARISAL 349 (473)
Q Consensus 270 C~~~~~~~E~~eL~~~R~~~w~~~~~~~~~~~~~~R~~G~CPLtPeEvgl~L~alGf~~~T~IYlA~geiygg~~~l~~L 349 (473)
|++ ..++..|.+.. .....++++-...++.|+||+=. ...++-+
T Consensus 187 ~~~---~D~e~~L~~V~-----------------------------~ai~~ak~~~~~k~~~IFLATDS----aeVid~f 230 (321)
T PF05830_consen 187 PYW---ADEERALRQVC-----------------------------TAIDKAKALAPPKPVRIFLATDS----AEVIDQF 230 (321)
T ss_dssp ------HHHHHHHHHHH-----------------------------HHHHHHHTS--SS-EEEEEEES-----HHHHHHH
T ss_pred ccc---cCchHHHHHHH-----------------------------HHHHHHHhccCCCCeeEEEecCc----HHHHHHH
Confidence 321 11111111111 11122344555678899999988 6779999
Q ss_pred HHhCCCCcccccCCChHHHhccccch-----hhhhhhhheeecccceee-eCCCCchhh
Q 012011 350 RRLFPLMEDKKSLASSEERAGVKGKA-----SLLAALDYYVSMHSNIFI-SASPGNMHN 402 (473)
Q Consensus 350 ~~~fPnl~tKe~L~s~eEL~~f~~~s-----s~lAAlDy~Vcl~SDvFv-~t~~Gnfa~ 402 (473)
++.||.+++-++=..+..-.++.+.. -..|-+|.+...++|+-| .+-.+.|.+
T Consensus 231 r~~FPdiiti~k~F~~~~~g~Lhs~~~g~~gg~~ALIDM~LLSrCD~LIr~~ptS~Fsr 289 (321)
T PF05830_consen 231 RKKFPDIITIPKQFPASQAGPLHSAAVGIEGGESALIDMYLLSRCDYLIRFPPTSAFSR 289 (321)
T ss_dssp HHHSTTEE----------------HHHHHHHHHHHHHHHHHHTTSSEEEEESTT-GGGH
T ss_pred HHHCCCeEEcccccCCCCCCcCcccccccchHHHHHHHHHHHHhCCeEEEcCCCchhhh
Confidence 99999988775544322222333211 134889999999999999 566666654
No 4
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=59.11 E-value=6.6 Score=33.19 Aligned_cols=56 Identities=18% Similarity=0.303 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHcCCCCCceEEEeeccccCCccchhHHHHhCCCCcccccCCChHHHhccccchhhhhhhhh
Q 012011 311 PLTPEEIGLLLAALGFDKSTRLYLASHKVYGGEARISALRRLFPLMEDKKSLASSEERAGVKGKASLLAALDY 383 (473)
Q Consensus 311 PLtPeEvgl~L~alGf~~~T~IYlA~geiygg~~~l~~L~~~fPnl~tKe~L~s~eEL~~f~~~ss~lAAlDy 383 (473)
++|-.+++-+|+...|+ +.+|..|+-++|++++++.--+-.+.-.|. +++..|-+|
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 CFTCAQVKQILSLFSFD---------------NDKLKALKLLYPYIVDPQNYYTIIDAFSFS--SDKDKAREI 94 (95)
T ss_pred ceeHHHHHHHHHHcCCC---------------HHHHHHHHHHhhhccCHHHHHHHHHHhcCc--ccHHHHHHh
Confidence 49999999999999998 457999999999999997443333332232 344444443
No 5
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=50.59 E-value=82 Score=34.41 Aligned_cols=67 Identities=19% Similarity=0.281 Sum_probs=44.8
Q ss_pred CCCCCceEEEeeccccCCccchhHHHHhCCCCcccccCCChHHHhccccc------hhhh-hhhhheeecccceeeeCCC
Q 012011 325 GFDKSTRLYLASHKVYGGEARISALRRLFPLMEDKKSLASSEERAGVKGK------ASLL-AALDYYVSMHSNIFISASP 397 (473)
Q Consensus 325 Gf~~~T~IYlA~geiygg~~~l~~L~~~fPnl~tKe~L~s~eEL~~f~~~------ss~l-AAlDy~Vcl~SDvFv~t~~ 397 (473)
|=+-.-+||||+-+ ...+..-|..|||. .+.+..|.+.-.+- ++.+ --+|..+...+|..|.|++
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 33334589999998 35567778999996 45566666654432 2222 4568888888888888866
Q ss_pred Cc
Q 012011 398 GN 399 (473)
Q Consensus 398 Gn 399 (473)
+-
T Consensus 474 SQ 475 (580)
T KOG3705|consen 474 SQ 475 (580)
T ss_pred HH
Confidence 53
No 6
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=49.19 E-value=88 Score=28.67 Aligned_cols=29 Identities=24% Similarity=0.277 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHHcCCCCCceEEEeeccc
Q 012011 311 PLTPEEIGLLLAALGFDKSTRLYLASHKV 339 (473)
Q Consensus 311 PLtPeEvgl~L~alGf~~~T~IYlA~gei 339 (473)
+++|+|...+|+..||.+-+.-+++.|-+
T Consensus 125 f~~~~el~~ll~~aGF~~~~~~~~~~g~~ 153 (160)
T PLN02232 125 YLTGEELETLALEAGFSSACHYEISGGFM 153 (160)
T ss_pred CcCHHHHHHHHHHcCCCcceEEECcchHh
Confidence 48999999999999999998888887753
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=42.65 E-value=28 Score=31.22 Aligned_cols=29 Identities=31% Similarity=0.353 Sum_probs=16.8
Q ss_pred CCCCCHHHHHHHHHHcCCCCCceEEEeecc
Q 012011 309 RCPLTPEEIGLLLAALGFDKSTRLYLASHK 338 (473)
Q Consensus 309 ~CPLtPeEvgl~L~alGf~~~T~IYlA~ge 338 (473)
.|||+|||+...|+++--+ ....||..+.
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 6999999999999999654 4677886654
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=33.17 E-value=31 Score=27.56 Aligned_cols=16 Identities=50% Similarity=0.796 Sum_probs=13.6
Q ss_pred CCCCCCHHHHHHHHHHc
Q 012011 308 GRCPLTPEEIGLLLAAL 324 (473)
Q Consensus 308 G~CPLtPeEvgl~L~al 324 (473)
|-| +||||-+.+++++
T Consensus 42 ~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDC-ITPEEDREILEAT 57 (60)
T ss_pred hcc-CCHHHHHHHHHHH
Confidence 567 9999999999875
No 9
>COG0763 LpxB Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]
Probab=31.88 E-value=72 Score=34.33 Aligned_cols=86 Identities=20% Similarity=0.261 Sum_probs=60.6
Q ss_pred ceEEEeeccccC---CccchhHHHHhCCCC------------cccccCCChHHHhccccch-----------hhhhhhhh
Q 012011 330 TRLYLASHKVYG---GEARISALRRLFPLM------------EDKKSLASSEERAGVKGKA-----------SLLAALDY 383 (473)
Q Consensus 330 T~IYlA~geiyg---g~~~l~~L~~~fPnl------------~tKe~L~s~eEL~~f~~~s-----------s~lAAlDy 383 (473)
.+|+|.+||.-| |..-+..||+.||++ .--++|...+||+- .|+. -+...+-+
T Consensus 2 ~ki~i~AGE~SGDllGa~LikaLk~~~~~~efvGvgG~~m~aeG~~sl~~~~elsv-mGf~EVL~~lp~llk~~~~~~~~ 80 (381)
T COG0763 2 LKIALSAGEASGDLLGAGLIKALKARYPDVEFVGVGGEKMEAEGLESLFDMEELSV-MGFVEVLGRLPRLLKIRRELVRY 80 (381)
T ss_pred ceEEEEecccchhhHHHHHHHHHHhhCCCeEEEEeccHHHHhccCccccCHHHHHH-hhHHHHHHHHHHHHHHHHHHHHH
Confidence 368888777655 445689999999866 23456666677652 2222 12356678
Q ss_pred eeecccceeeeCCCCchhhhhhhhhcccc--cccc
Q 012011 384 YVSMHSNIFISASPGNMHNALMGHRTYEN--LKTI 416 (473)
Q Consensus 384 ~Vcl~SDvFv~t~~Gnfa~~v~GhR~y~g--~kTI 416 (473)
++...-|+||.-.++.|---|+..=+-.| .|+|
T Consensus 81 i~~~kpD~~i~IDsPdFnl~vak~lrk~~p~i~ii 115 (381)
T COG0763 81 ILANKPDVLILIDSPDFNLRVAKKLRKAGPKIKII 115 (381)
T ss_pred HHhcCCCEEEEeCCCCCchHHHHHHHHhCCCCCeE
Confidence 89999999999999999988886655566 6665
No 10
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=29.13 E-value=48 Score=26.10 Aligned_cols=25 Identities=40% Similarity=0.458 Sum_probs=20.7
Q ss_pred HHhcCCCCCCCHHHHHHHHHHcCCCC
Q 012011 303 ELRSQGRCPLTPEEIGLLLAALGFDK 328 (473)
Q Consensus 303 ~~R~~G~CPLtPeEvgl~L~alGf~~ 328 (473)
-.+..|.. ++++|+.-+|+.|||+-
T Consensus 11 i~~llG~~-i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 11 INRLLGLD-LSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHHHCCC-CCHHHHHHHHHHCCCeE
Confidence 34666764 99999999999999974
No 11
>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=23.69 E-value=28 Score=31.92 Aligned_cols=17 Identities=35% Similarity=0.604 Sum_probs=11.6
Q ss_pred HHHHHHHcCCCCCceEE
Q 012011 317 IGLLLAALGFDKSTRLY 333 (473)
Q Consensus 317 vgl~L~alGf~~~T~IY 333 (473)
+.++|+|||+.++.-||
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 67899999997765544
No 12
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=21.84 E-value=53 Score=26.32 Aligned_cols=24 Identities=38% Similarity=0.497 Sum_probs=17.0
Q ss_pred HhcCCCCCCCHHHHHHHHHHcCCCC
Q 012011 304 LRSQGRCPLTPEEIGLLLAALGFDK 328 (473)
Q Consensus 304 ~R~~G~CPLtPeEvgl~L~alGf~~ 328 (473)
.+..|.. ++++|+.-+|+.|||.-
T Consensus 12 ~~~lG~~-i~~~~i~~~L~~lg~~~ 35 (70)
T PF03484_consen 12 NKLLGID-ISPEEIIKILKRLGFKV 35 (70)
T ss_dssp HHHHTS----HHHHHHHHHHTT-EE
T ss_pred HHHhCCC-CCHHHHHHHHHHCCCEE
Confidence 4666765 99999999999999983
No 13
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=20.62 E-value=59 Score=23.48 Aligned_cols=35 Identities=23% Similarity=0.365 Sum_probs=21.8
Q ss_pred chhHHHHhCCCCcccccCCChHHHhccc--cchhhhhhhhheee
Q 012011 345 RISALRRLFPLMEDKKSLASSEERAGVK--GKASLLAALDYYVS 386 (473)
Q Consensus 345 ~l~~L~~~fPnl~tKe~L~s~eEL~~f~--~~ss~lAAlDy~Vc 386 (473)
.+.-|+++||++ +.+.+..-. +..+..+|+|.+.+
T Consensus 4 ~v~~L~~mFP~~-------~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 4 MVQQLQEMFPDL-------DREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHSSSS--------HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHCCCC-------CHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 467899999997 334433322 23346788887654
No 14
>COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=20.29 E-value=1.7e+02 Score=30.13 Aligned_cols=76 Identities=26% Similarity=0.230 Sum_probs=51.6
Q ss_pred HHHHHHHHHcCCCCCceEEEeeccccCCccchhHHHHhCCCCcccccCCChHHHhccccchhhhhhhhheeecccceeee
Q 012011 315 EEIGLLLAALGFDKSTRLYLASHKVYGGEARISALRRLFPLMEDKKSLASSEERAGVKGKASLLAALDYYVSMHSNIFIS 394 (473)
Q Consensus 315 eEvgl~L~alGf~~~T~IYlA~geiygg~~~l~~L~~~fPnl~tKe~L~s~eEL~~f~~~ss~lAAlDy~Vcl~SDvFv~ 394 (473)
.|+...|.+-| ..|.|.+|. .-....+.+.+..++.+. |+.+..|. +++||- ..||.||+
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---LAGKTSLE-------ELAALI----AGADLVIG 257 (334)
T ss_pred HHHHHHHHHCC----CEEEEecCh--HHHHHHHHHHHhcCCccc---cCCCCCHH-------HHHHHH----hcCCEEEc
Confidence 46778888888 679999888 445556677778877554 33322221 123322 68999999
Q ss_pred CCCCchhhhhhhhhcc
Q 012011 395 ASPGNMHNALMGHRTY 410 (473)
Q Consensus 395 t~~Gnfa~~v~GhR~y 410 (473)
+.+|-|+-+-+.++-.
T Consensus 258 ~DSg~~HlAaA~~~P~ 273 (334)
T COG0859 258 NDSGPMHLAAALGTPT 273 (334)
T ss_pred cCChHHHHHHHcCCCE
Confidence 9999988887766633
Done!