Query 012839
Match_columns 455
No_of_seqs 180 out of 417
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 06:50:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012839.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012839hhsearch_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 4E-47 8.7E-52 372.1 0.9 257 165-438 6-306 (351)
2 KOG3849 GDP-fucose protein O-f 96.2 0.054 1.2E-06 55.4 11.3 171 156-340 27-250 (386)
3 PF05830 NodZ: Nodulation prot 93.7 0.91 2E-05 47.1 11.9 208 158-426 2-242 (321)
4 PLN02232 ubiquinone biosynthes 49.1 33 0.00072 31.1 5.0 100 291-403 48-152 (160)
5 KOG3111 D-ribulose-5-phosphate 44.0 44 0.00095 33.3 5.2 108 298-422 42-171 (224)
6 PF00799 Gemini_AL1: Geminivir 38.3 30 0.00064 31.1 2.8 27 374-401 14-40 (114)
7 PF14771 DUF4476: Domain of un 36.2 18 0.00038 30.4 1.0 38 376-428 39-76 (95)
8 PF10892 DUF2688: Protein of u 33.8 30 0.00064 28.1 1.9 17 372-389 41-57 (60)
9 smart00874 B5 tRNA synthetase 29.7 44 0.00095 26.2 2.2 24 369-393 12-35 (71)
10 TIGR01354 cyt_deam_tetra cytid 27.5 79 0.0017 28.3 3.7 47 377-427 80-127 (127)
11 PF04561 RNA_pol_Rpb2_2: RNA p 25.0 23 0.00049 32.0 -0.2 17 382-398 54-70 (190)
12 PRK05578 cytidine deaminase; V 24.5 87 0.0019 28.5 3.5 41 384-428 91-131 (131)
13 COG4878 Uncharacterized protei 24.0 59 0.0013 33.8 2.5 58 382-440 93-151 (309)
14 PF13756 Stimulus_sens_1: Stim 21.0 1.1E+02 0.0023 27.0 3.3 28 377-404 1-30 (112)
15 PF03484 B5: tRNA synthetase B 20.3 56 0.0012 26.1 1.3 25 370-395 13-37 (70)
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=4e-47 Score=372.06 Aligned_cols=257 Identities=31% Similarity=0.485 Sum_probs=171.2
Q ss_pred EcCCchhhHHHHHHHHHHHHHhCCeEeecccccccccCCCCC-----CCCCCChHHHHHhccCCeEEeccCcccccccCC
Q 012839 165 VSGGMNQQRNQIVDAVVIARILGAALVVPILQVNVIWGDESE-----FSDIFDLEHFKSVLANDVRIVSSLPSTHIMTRP 239 (455)
Q Consensus 165 ~nGGLNQqR~~IcDAVaVARiLNATLViP~Ld~~s~W~D~S~-----F~DIFDvdhFI~sL~~DVrIVk~LP~~~~~~~~ 239 (455)
+.||+|+||.++++||++|++||+|||||.+.....|+|.++ |+|+||++||+++++++|.+.+.+|........
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 889999999999999999999999999999999999999998 999999999999999999999999865432111
Q ss_pred c------------------------------ccccCC-CCCChhhHHhHhhHhhhcc------ceEEEeccccccCCC-C
Q 012839 240 V------------------------------EEKRTP-LHVSPQWIRARYLRRLNRE------GVLLLRGLDSRLSKD-L 281 (455)
Q Consensus 240 ~------------------------------~~~~vp-~~~spswy~~~vlP~L~k~------~VI~l~~~d~RLa~~-l 281 (455)
. ...... .+..+.||.++++|.+.++ +|+.|.++..++.++ .
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 0 011122 2567778877788988886 999999999999965 8
Q ss_pred chhhhhhhhhhcccceeechhHHHHHHHHHHHHH-cCCCeeeeeccccchhhhhcccCCCchhhHHHHHHHhhhhhhhhc
Q 012839 282 PSDLQKLRCKVAFHALRFAPPILQLGNKLAERMR-SKGPYLSLHLRMEKDVWVRTGCLPGPEYDEMISNERKQRPELLTA 360 (455)
Q Consensus 282 P~eiQrLRCrvnf~ALrF~p~I~~Lg~~LV~Rmr-~~GpyIALHLRfEkDMlAfSgC~~g~e~~El~~~~R~~~~~~~~~ 360 (455)
+.++|| +|+|+++|+++|++++++++ ..++|||+|||+|+|| +++|.++. ..+.++..|.. +
T Consensus 166 ~~~~~r--------~l~~~~~i~~~a~~~i~~~~~~~~~yiavHlR~~~D~--~~~C~~~~-~~~~~~~~~~~------~ 228 (351)
T PF10250_consen 166 DRDLQR--------YLRFSPEIRELADKFIKRLLAGGGPYIAVHLRRGKDW--FSACEFKG-ERHLLASPRCW------G 228 (351)
T ss_dssp GGGGGG--------G--B-HHHHHHHHHHHHHH----SSEEEEEE--SHHH--HHHHCT-T-----TTTHHHH-------
T ss_pred CccceE--------EEecCHHHHHHHHHHHHHhhcccCceEEEeecccCch--HhhcccCC-chHHHHHhHhh------c
Confidence 888987 99999999999999999999 7899999999999999 99999965 55555666654 2
Q ss_pred ccCCChHhhhcCCCCCCCHHHHHHHHHHhCCCCCceEEEeeCCCCCCccccccHHhhCCCCcccccCCChhhhhhhhH
Q 012839 361 RSNMTYHERKLAGLCPLNAVEVTRLLKALGAPKIARIYWAGGEPLGGKEALLPLITEFPHLYNKEDLALPVTFSCLLM 438 (455)
Q Consensus 361 ~~~i~~~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAsGeiYGg~~~L~pL~~~FPnl~tKetLat~eEL~p~~~ 438 (455)
++.......+..|.||++|++++.+++++|+.+.|.||||++++|||.+.|++|+++||++++|+++.+.+|++++.-
T Consensus 229 ~~~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~ 306 (351)
T PF10250_consen 229 KKSINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLSHEELEPLND 306 (351)
T ss_dssp GGGTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--EE--S-----
T ss_pred cccccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCCHHHhhhccc
Confidence 334555567778999999999999999999999999999999999999999999999999999999999999976543
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=96.16 E-value=0.054 Score=55.42 Aligned_cols=171 Identities=23% Similarity=0.328 Sum_probs=97.4
Q ss_pred CCcceEEEE-EcCCchhhHHHHHHHHHHHHHhCCeEeeccc---ccccccCCCCCCCCCCChH------------HHHHh
Q 012839 156 DRRKYLLVV-VSGGMNQQRNQIVDAVVIARILGAALVVPIL---QVNVIWGDESEFSDIFDLE------------HFKSV 219 (455)
Q Consensus 156 ~snGYL~V~-~nGGLNQqR~~IcDAVaVARiLNATLViP~L---d~~s~W~D~S~F~DIFDvd------------hFI~s 219 (455)
..||||+.- |-|-.-+|-...--..|-|+.||.|||+|-. ++-.+-+---.|.-.|.++ .|++-
T Consensus 27 DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiEy~~pe~~n~~vpf~~yF~vepl~~YhRVitm~dFm~k 106 (386)
T KOG3849|consen 27 DPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIEYKHPETKNLMVPFEFYFQVEPLAKYHRVITMQDFMKK 106 (386)
T ss_pred CCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchhccCCcccccccchhheeecccHhhhhhheeHHHHHHH
Confidence 479998775 8899999989999999999999999999963 2222222224577777765 34554
Q ss_pred ccCCeE-------EeccCccccccc---CCcccccCCCCCChhh------------------------HHhHhhHhh--h
Q 012839 220 LANDVR-------IVSSLPSTHIMT---RPVEEKRTPLHVSPQW------------------------IRARYLRRL--N 263 (455)
Q Consensus 220 L~~DVr-------IVk~LP~~~~~~---~~~~~~~vp~~~spsw------------------------y~~~vlP~L--~ 263 (455)
|..+.= |--+- -..+ ++.+..+--+-..|-| ..++.+..+ +
T Consensus 107 lapthwp~~~Rva~c~k~---a~qr~pdkp~Ch~KeGNPFGPfWDqfhvsFv~sE~f~~i~Fd~~~~~~~~kW~~kfp~e 183 (386)
T KOG3849|consen 107 LAPTHWPGTPRVAICDKS---AAQRSPDKPGCHSKEGNPFGPFWDQFHVSFVGSEYFGDIGFDLNQMGSRKKWLEKFPSE 183 (386)
T ss_pred hCcccCCCCcceeeeehh---hhccCCCCCCCcccCCCCCCCchhheEeeeeccccccccccchhhcchHHHHHhhCCcc
Confidence 444321 10000 0000 1111011000001111 112222222 3
Q ss_pred ccceEEEeccccccC-CCCchhhhhhhhhhcccceeechhHHHHHHHHHHHHHcCCCeeeeeccccchhhhhcccCCC
Q 012839 264 REGVLLLRGLDSRLS-KDLPSDLQKLRCKVAFHALRFAPPILQLGNKLAERMRSKGPYLSLHLRMEKDVWVRTGCLPG 340 (455)
Q Consensus 264 k~~VI~l~~~d~RLa-~~lP~eiQrLRCrvnf~ALrF~p~I~~Lg~~LV~Rmr~~GpyIALHLRfEkDMlAfSgC~~g 340 (455)
+|-|+.|++.-.... ..---.+|| -||++.+|.+-|++.+..=-. .||+++|||---|++- .|.+-
T Consensus 184 eyPVLAf~gAPA~FPv~~e~~~lQk--------Yl~WS~r~~e~~k~fI~a~L~-rpfvgiHLRng~DWvr--aCehi 250 (386)
T KOG3849|consen 184 EYPVLAFSGAPAPFPVKGEVWSLQK--------YLRWSSRITEQAKKFISANLA-RPFVGIHLRNGADWVR--ACEHI 250 (386)
T ss_pred cCceeeecCCCCCCccccccccHHH--------HHHHHHHHHHHHHHHHHHhcC-cceeEEEeecCchHHH--HHHHh
Confidence 567777764322221 011124665 489999999999887654332 3999999999999986 37653
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=93.65 E-value=0.91 Score=47.07 Aligned_cols=208 Identities=19% Similarity=0.267 Sum_probs=103.8
Q ss_pred cceEEEEEcCCchhhHHHHHHHHHHHHHhCCeEeecccccccccCCC----CCCCCCCChHHHHHhcc--CCeEEeccCc
Q 012839 158 RKYLLVVVSGGMNQQRNQIVDAVVIARILGAALVVPILQVNVIWGDE----SEFSDIFDLEHFKSVLA--NDVRIVSSLP 231 (455)
Q Consensus 158 nGYL~V~~nGGLNQqR~~IcDAVaVARiLNATLViP~Ld~~s~W~D~----S~F~DIFDvdhFI~sL~--~DVrIVk~LP 231 (455)
+.|++.+--+|++.-=-+++-|-..|+-.|-||||= |+++ -.|...|++ |-+-.+ ..|+|+-+=+
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 578999999999999999999999999999999983 6665 345555543 444433 3445542211
Q ss_pred ccccccCCcccccCCCCCChhhHH-----------hHh------h-Hhhh------ccceEEEeccccccCCCCchhhhh
Q 012839 232 STHIMTRPVEEKRTPLHVSPQWIR-----------ARY------L-RRLN------REGVLLLRGLDSRLSKDLPSDLQK 287 (455)
Q Consensus 232 ~~~~~~~~~~~~~vp~~~spswy~-----------~~v------l-P~L~------k~~VI~l~~~d~RLa~~lP~eiQr 287 (455)
......|-...|.|.+ +.+ | -++. ..-||+.+.+.-|=. -+.
T Consensus 73 --------i~~~~~~g~~fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~c~------~~a 138 (321)
T PF05830_consen 73 --------INQFSFPGPFFPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWRCD------EEA 138 (321)
T ss_dssp --------GGT----SSEESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTSS-------HHH
T ss_pred --------hhhhcCCCCcChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCcch------hHH
Confidence 1111122222233322 111 1 1222 345787777654432 223
Q ss_pred hhhhhcccceeechhHHHHHHHHHHHHHcCCCeeeeecccc--chhhhhcccCCCchhhHHHHHHHhhhhhhhhcccCCC
Q 012839 288 LRCKVAFHALRFAPPILQLGNKLAERMRSKGPYLSLHLRME--KDVWVRTGCLPGPEYDEMISNERKQRPELLTARSNMT 365 (455)
Q Consensus 288 LRCrvnf~ALrF~p~I~~Lg~~LV~Rmr~~GpyIALHLRfE--kDMlAfSgC~~g~e~~El~~~~R~~~~~~~~~~~~i~ 365 (455)
.| .-|..|+-+++|++..+.+-++-=.+..=|.+|.|.= +|...+ +|++-+++.-
T Consensus 139 eR--~if~slkpR~eIqarID~iy~ehf~g~~~IGVHVRhGngeD~~~h-~~~~~D~e~~-------------------- 195 (321)
T PF05830_consen 139 ER--EIFSSLKPRPEIQARIDAIYREHFAGYSVIGVHVRHGNGEDIMDH-APYWADEERA-------------------- 195 (321)
T ss_dssp HH--HHHHHS-B-HHHHHHHHHHHHHHTTTSEEEEEEE----------------HHHHHH--------------------
T ss_pred HH--HHHHhCCCCHHHHHHHHHHHHHHcCCCceEEEEEeccCCcchhcc-CccccCchHH--------------------
Confidence 33 3588999999999998888777655556899999932 122222 1221110000
Q ss_pred hHhhhcCCCCCCCH-HHHHHHHHHhCCCCCceEEEeeCCCCCCccccccHHhhCCCCccccc
Q 012839 366 YHERKLAGLCPLNA-VEVTRLLKALGAPKIARIYWAGGEPLGGKEALLPLITEFPHLYNKED 426 (455)
Q Consensus 366 ~~~~R~~G~CPLTP-eEVgl~LrALGf~~~T~IYlAsGeiYGg~~~L~pL~~~FPnl~tKet 426 (455)
|.. ......++++=.+.++.|+||+-. .+-++-+++.||.+++.+.
T Consensus 196 -----------L~~V~~ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k 242 (321)
T PF05830_consen 196 -----------LRQVCTAIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPK 242 (321)
T ss_dssp -----------HHHHHHHHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE----
T ss_pred -----------HHHHHHHHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEccc
Confidence 000 112233455666778999999995 5678999999999887643
No 4
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=49.15 E-value=33 Score=31.10 Aligned_cols=100 Identities=12% Similarity=-0.023 Sum_probs=57.8
Q ss_pred hhcccceeechhHHHHHHHHHHHHHcCCCeeeeeccccchhhhhc----ccC-CCchhhHHHHHHHhhhhhhhhcccCCC
Q 012839 291 KVAFHALRFAPPILQLGNKLAERMRSKGPYLSLHLRMEKDVWVRT----GCL-PGPEYDEMISNERKQRPELLTARSNMT 365 (455)
Q Consensus 291 rvnf~ALrF~p~I~~Lg~~LV~Rmr~~GpyIALHLRfEkDMlAfS----gC~-~g~e~~El~~~~R~~~~~~~~~~~~i~ 365 (455)
-++..+|++.++..+.-+.+.+.|+.+|.++-++..-+...+... -|. .+..-..+ ...+..+ .
T Consensus 48 v~~~~~l~~~~d~~~~l~ei~rvLkpGG~l~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~y----------~ 116 (160)
T PLN02232 48 VTMGYGLRNVVDRLRAMKEMYRVLKPGSRVSILDFNKSNQSVTTFMQGWMIDNVVVPVATV-YDLAKEY----------E 116 (160)
T ss_pred EEecchhhcCCCHHHHHHHHHHHcCcCeEEEEEECCCCChHHHHHHHHHHccchHhhhhHH-hCChHHH----------H
Confidence 344557787788888888999999988998887765443211100 011 00000000 0000000 0
Q ss_pred hHhhhcCCCCCCCHHHHHHHHHHhCCCCCceEEEeeCC
Q 012839 366 YHERKLAGLCPLNAVEVTRLLKALGAPKIARIYWAGGE 403 (455)
Q Consensus 366 ~~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAsGe 403 (455)
+- ...... +++|+|..-+|+.-||.+-+.-+++.|-
T Consensus 117 yl-~~si~~-f~~~~el~~ll~~aGF~~~~~~~~~~g~ 152 (160)
T PLN02232 117 YL-KYSING-YLTGEELETLALEAGFSSACHYEISGGF 152 (160)
T ss_pred hH-HHHHHH-CcCHHHHHHHHHHcCCCcceEEECcchH
Confidence 00 001112 5899999999999999999888888774
No 5
>KOG3111 consensus D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=44.04 E-value=44 Score=33.29 Aligned_cols=108 Identities=21% Similarity=0.336 Sum_probs=65.9
Q ss_pred eechhHHHHHHHHHHHHHcC---CCeeeeeccccc-----hhhhhcccC----CC---chhhHHHHHHHhhhhhhhhccc
Q 012839 298 RFAPPILQLGNKLAERMRSK---GPYLSLHLRMEK-----DVWVRTGCL----PG---PEYDEMISNERKQRPELLTARS 362 (455)
Q Consensus 298 rF~p~I~~Lg~~LV~Rmr~~---GpyIALHLRfEk-----DMlAfSgC~----~g---~e~~El~~~~R~~~~~~~~~~~ 362 (455)
+|+|.| ..|.-+|++||.. -+|.-+||=.|. |=.|-.|-. |- +...|++++.|+.--+. ..
T Consensus 42 ~FVpNi-T~G~pvV~slR~~~~~~~ffD~HmMV~~Peq~V~~~a~agas~~tfH~E~~q~~~~lv~~ir~~Gmk~---G~ 117 (224)
T KOG3111|consen 42 HFVPNI-TFGPPVVESLRKHTGADPFFDVHMMVENPEQWVDQMAKAGASLFTFHYEATQKPAELVEKIREKGMKV---GL 117 (224)
T ss_pred cccCCc-ccchHHHHHHHhccCCCcceeEEEeecCHHHHHHHHHhcCcceEEEEEeeccCHHHHHHHHHHcCCee---eE
Confidence 466666 5788899999974 469999997774 222333322 11 22355555555431000 00
Q ss_pred CCChHhhhcCCCCCCCHHHHHHHHHHhCCCCCceEEEeeCCCCCCccccc-------cHHhhCCCCc
Q 012839 363 NMTYHERKLAGLCPLNAVEVTRLLKALGAPKIARIYWAGGEPLGGKEALL-------PLITEFPHLY 422 (455)
Q Consensus 363 ~i~~~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAsGeiYGg~~~L~-------pL~~~FPnl~ 422 (455)
-.=|=||-|....+.. .-|-.+-.+---.|||++.|. -||+-|||+.
T Consensus 118 ----------alkPgT~Ve~~~~~~~---~~D~vLvMtVePGFGGQkFme~mm~KV~~lR~kyp~l~ 171 (224)
T KOG3111|consen 118 ----------ALKPGTPVEDLEPLAE---HVDMVLVMTVEPGFGGQKFMEDMMPKVEWLREKYPNLD 171 (224)
T ss_pred ----------EeCCCCcHHHHHHhhc---cccEEEEEEecCCCchhhhHHHHHHHHHHHHHhCCCce
Confidence 1236788888777665 234445555555799999884 5899999984
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=38.30 E-value=30 Score=31.07 Aligned_cols=27 Identities=30% Similarity=0.383 Sum_probs=15.0
Q ss_pred CCCCCHHHHHHHHHHhCCCCCceEEEee
Q 012839 374 LCPLNAVEVTRLLKALGAPKIARIYWAG 401 (455)
Q Consensus 374 ~CPLTPeEVgl~LrALGf~~~T~IYlAs 401 (455)
+||||+||+...|++|--+. ...||..
T Consensus 14 qC~l~ke~~l~~L~~l~~~~-~~~yI~v 40 (114)
T PF00799_consen 14 QCSLTKEEALEQLKNLLTPS-NKKYIRV 40 (114)
T ss_dssp T----HHHHHHHHHH---SS--EEEEEE
T ss_pred CCCCCHHHHHHHHHHhCCcc-CceEEEe
Confidence 79999999999999998654 5667644
No 7
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=36.23 E-value=18 Score=30.40 Aligned_cols=38 Identities=13% Similarity=0.268 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHhCCCCCceEEEeeCCCCCCccccccHHhhCCCCcccccCC
Q 012839 376 PLNAVEVTRLLKALGAPKIARIYWAGGEPLGGKEALLPLITEFPHLYNKEDLA 428 (455)
Q Consensus 376 PLTPeEVgl~LrALGf~~~T~IYlAsGeiYGg~~~L~pL~~~FPnl~tKetLa 428 (455)
++|-.+++-+|+-..|++ .+|..|+-++|++++++.--
T Consensus 39 ~~T~~Qv~~il~~f~fd~---------------~kl~~lk~l~p~i~D~~n~~ 76 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDN---------------DKLKALKLLYPYIVDPQNYY 76 (95)
T ss_pred ceeHHHHHHHHHHcCCCH---------------HHHHHHHHHhhhccCHHHHH
Confidence 499999999999999975 36999999999999997543
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=33.82 E-value=30 Score=28.10 Aligned_cols=17 Identities=29% Similarity=0.516 Sum_probs=14.4
Q ss_pred CCCCCCCHHHHHHHHHHh
Q 012839 372 AGLCPLNAVEVTRLLKAL 389 (455)
Q Consensus 372 ~G~CPLTPeEVgl~LrAL 389 (455)
-|-| +||||-+-+++++
T Consensus 41 C~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 41 CGDC-ITPEEDREILEAT 57 (60)
T ss_pred hhcc-CCHHHHHHHHHHH
Confidence 3578 9999999999875
No 9
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=29.71 E-value=44 Score=26.20 Aligned_cols=24 Identities=42% Similarity=0.571 Sum_probs=20.1
Q ss_pred hhcCCCCCCCHHHHHHHHHHhCCCC
Q 012839 369 RKLAGLCPLNAVEVTRLLKALGAPK 393 (455)
Q Consensus 369 ~R~~G~CPLTPeEVgl~LrALGf~~ 393 (455)
++.-|.. ++++|+.-+|+.|||.-
T Consensus 12 ~~llG~~-i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 12 NRLLGLD-LSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHHCCC-CCHHHHHHHHHHCCCeE
Confidence 3556664 99999999999999975
No 10
>TIGR01354 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine.
Probab=27.45 E-value=79 Score=28.26 Aligned_cols=47 Identities=15% Similarity=0.277 Sum_probs=35.1
Q ss_pred CCHHHH-HHHHHHhCCCCCceEEEeeCCCCCCccccccHHhhCCCCcccccC
Q 012839 377 LNAVEV-TRLLKALGAPKIARIYWAGGEPLGGKEALLPLITEFPHLYNKEDL 427 (455)
Q Consensus 377 LTPeEV-gl~LrALGf~~~T~IYlAsGeiYGg~~~L~pL~~~FPnl~tKetL 427 (455)
++|--+ --+|..++ +.++.|++...+ |+....+|+++.|.-+.+++|
T Consensus 80 ~sPCG~Crq~l~e~~-~~~~~v~~~~~~---~~~~~~~l~eLLP~~f~~~~l 127 (127)
T TIGR01354 80 VSPCGACRQVLAEFA-GPDTPIYMTNND---GTYKVYTVGELLPFGFGPSDL 127 (127)
T ss_pred cCccHHHHHHHHHhC-CCCcEEEEECCC---CCEEEEEHHHhCcCcCCcCcC
Confidence 455443 35788887 679999999886 555568999999998887764
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=25.04 E-value=23 Score=31.97 Aligned_cols=17 Identities=35% Similarity=0.446 Sum_probs=13.4
Q ss_pred HHHHHHHhCCCCCceEE
Q 012839 382 VTRLLKALGAPKIARIY 398 (455)
Q Consensus 382 Vgl~LrALGf~~~T~IY 398 (455)
+.++|||||+.++.-||
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 78999999999888777
No 12
>PRK05578 cytidine deaminase; Validated
Probab=24.50 E-value=87 Score=28.49 Aligned_cols=41 Identities=17% Similarity=0.286 Sum_probs=32.0
Q ss_pred HHHHHhCCCCCceEEEeeCCCCCCccccccHHhhCCCCcccccCC
Q 012839 384 RLLKALGAPKIARIYWAGGEPLGGKEALLPLITEFPHLYNKEDLA 428 (455)
Q Consensus 384 l~LrALGf~~~T~IYlAsGeiYGg~~~L~pL~~~FPnl~tKetLa 428 (455)
-+|.-++ +.+|.||+...+ |+..-..|+++.|.-+++++|+
T Consensus 91 Q~l~e~~-~~~~~v~l~~~~---~~~~~~~l~eLLP~~f~~~~l~ 131 (131)
T PRK05578 91 QVLAEFG-GPDLLVTLVAKD---GPTGEMTLGELLPYAFTPDDLG 131 (131)
T ss_pred HHHHHhC-CCCcEEEEEcCC---CCEEEEEHHHhCcCcCChhhcC
Confidence 4566664 679999999876 4555689999999999988874
No 13
>COG4878 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.97 E-value=59 Score=33.82 Aligned_cols=58 Identities=10% Similarity=0.070 Sum_probs=47.4
Q ss_pred HHHHHHHhCCC-CCceEEEeeCCCCCCccccccHHhhCCCCcccccCCChhhhhhhhHHh
Q 012839 382 VTRLLKALGAP-KIARIYWAGGEPLGGKEALLPLITEFPHLYNKEDLALPVTFSCLLMEE 440 (455)
Q Consensus 382 Vgl~LrALGf~-~~T~IYlAsGeiYGg~~~L~pL~~~FPnl~tKetLat~eEL~p~~~e~ 440 (455)
++.++..|--. -+|.||++.+.|- -++.-..|.+-||++-|-.++.+.+|+.++..|.
T Consensus 93 L~~y~~~ls~~~y~~~vfVppSnil-~q~gk~alvk~~p~lktissiy~~deykd~~se~ 151 (309)
T COG4878 93 LADYGDILSITGYDTFVFVPPSNIL-LQKGKFALVKQAPSLKTISSIYNTDEYKDFNSES 151 (309)
T ss_pred HHHHHHHHhccccceEEEeCccccc-chhHHHHHHHhCCCcceeeeEecccccCcccchh
Confidence 44555555433 5799999999987 4556789999999999999999999999999985
No 14
>PF13756 Stimulus_sens_1: Stimulus-sensing domain
Probab=21.00 E-value=1.1e+02 Score=26.96 Aligned_cols=28 Identities=32% Similarity=0.452 Sum_probs=22.6
Q ss_pred CCHHHHHHHHHHhCCCCCce--EEEeeCCC
Q 012839 377 LNAVEVTRLLKALGAPKIAR--IYWAGGEP 404 (455)
Q Consensus 377 LTPeEVgl~LrALGf~~~T~--IYlAsGei 404 (455)
|+||.|+-||+-|.-+.+|+ ||=+.|..
T Consensus 1 l~pe~a~plLrrL~~Pt~~RARlyd~dG~L 30 (112)
T PF13756_consen 1 LNPERARPLLRRLISPTRTRARLYDPDGNL 30 (112)
T ss_pred CCHHHHHHHHHHhCCCCCceEEEECCCCCE
Confidence 68999999999999999996 66444443
No 15
>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=20.31 E-value=56 Score=26.12 Aligned_cols=25 Identities=32% Similarity=0.473 Sum_probs=17.2
Q ss_pred hcCCCCCCCHHHHHHHHHHhCCCCCc
Q 012839 370 KLAGLCPLNAVEVTRLLKALGAPKIA 395 (455)
Q Consensus 370 R~~G~CPLTPeEVgl~LrALGf~~~T 395 (455)
|.-|.. ++++|+.-+|+.|||.-+-
T Consensus 13 ~~lG~~-i~~~~i~~~L~~lg~~~~~ 37 (70)
T PF03484_consen 13 KLLGID-ISPEEIIKILKRLGFKVEK 37 (70)
T ss_dssp HHHTS----HHHHHHHHHHTT-EEEE
T ss_pred HHhCCC-CCHHHHHHHHHHCCCEEEE
Confidence 445665 9999999999999997554
Done!