Query 008243
Match_columns 573
No_of_seqs 190 out of 386
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 21:19:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008243.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008243hhsearch_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 4.8E-56 1E-60 448.3 2.2 296 120-432 6-345 (351)
2 KOG3849 GDP-fucose protein O-f 97.3 0.0056 1.2E-07 63.8 14.1 275 110-430 26-368 (386)
3 PF05830 NodZ: Nodulation prot 91.7 3.8 8.3E-05 43.8 13.7 249 113-419 2-288 (321)
4 PF14771 DUF4476: Domain of un 43.8 7.3 0.00016 33.7 -0.1 54 330-400 39-93 (95)
5 PF00799 Gemini_AL1: Geminivir 40.0 32 0.00069 31.8 3.4 28 328-356 14-41 (114)
6 PLN02232 ubiquinone biosynthes 38.4 33 0.00072 32.2 3.3 98 247-358 49-153 (160)
7 KOG1832 HIV-1 Vpr-binding prot 34.1 26 0.00056 42.7 2.2 13 461-473 1326-1338(1516)
8 PF10892 DUF2688: Protein of u 29.5 40 0.00086 28.2 2.0 16 327-343 42-57 (60)
9 COG1312 UxuA D-mannonate dehyd 27.3 77 0.0017 34.8 4.2 66 203-269 187-272 (362)
10 TIGR03006 pepcterm_polyde poly 25.6 3.3E+02 0.0072 28.3 8.3 118 208-361 28-149 (265)
11 TIGR01354 cyt_deam_tetra cytid 24.8 86 0.0019 28.9 3.6 47 331-381 80-127 (127)
12 smart00874 B5 tRNA synthetase 23.7 63 0.0014 26.2 2.2 24 323-347 12-35 (71)
13 PRK05578 cytidine deaminase; V 22.4 93 0.002 29.2 3.3 96 276-382 25-131 (131)
14 COG2241 CobL Precorrin-6B meth 21.5 3E+02 0.0066 28.1 6.9 116 210-359 59-178 (210)
15 cd02068 radical_SAM_B12_BD B12 20.0 75 0.0016 28.4 2.1 71 283-371 38-109 (127)
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=4.8e-56 Score=448.28 Aligned_cols=296 Identities=36% Similarity=0.639 Sum_probs=207.6
Q ss_pred ecCCchhhHHHHHHHHHHHHHhCCeEEeeccCCCcccCCCCC-----CCccccHHHHHHhccCceEEcccCCcccCCCC-
Q 008243 120 TSGGLNQQRTGIIDAVVAARILNATLVIPKLDQKSFWKDASD-----FSEIFDVDRFISVLSKDVKIIKQIPRKGGKSL- 193 (573)
Q Consensus 120 ~nGGLNQqR~~IcDaVaVARiLNATLViP~Ld~~s~W~D~S~-----F~DIFDvdhFI~sL~~dVrIVk~LP~~~~~~~- 193 (573)
|.||+||||.++++||++|++||+|||||.+.....|++.+. |+++||+++|+++++.+|.+.+.+|..+....
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 889999999999999999999999999999999999999988 99999999999999999999999986543210
Q ss_pred -----------------------------CCccccCCC-CCChHHHHHhhhHhHhhc------ceEEEecccccccCC-C
Q 008243 194 -----------------------------TPYHMRVPR-KCNEKCYQNRVLPVLLKR------HAVQLSKFDYRLANK-L 236 (573)
Q Consensus 194 -----------------------------~~~~~r~p~-~~s~~yY~~~vLP~l~k~------~VI~l~~fd~rLa~~-l 236 (573)
......... +..+.+|+++++|++.++ +|+.|..+..++.++ .
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 011122222 667889899999999987 999999999999874 7
Q ss_pred chHHHhhhhhccccccccchHHHHHHHHHHHHHHhcCCceEEEEeecccchhhhccCCCCCChHHHHHHHHHHHHhhhhc
Q 008243 237 DTDLQKLRCRVNYHALSFTDSIQKMGEKLVHQMRMKGKHYIALHLRFEPDMLAFSGCYYGGGDKERKELGAIRKRWKTLH 316 (573)
Q Consensus 237 p~eiQrLRCrvnf~ALrF~p~I~~lg~~LV~RLR~~~gpfIALHLRfE~DMLAfsgC~~gg~~~E~~EL~~~R~~wk~~~ 316 (573)
+.++|| +|+|+++|+++|++++++|+..+++|||+|||+|+|| +++|.+++ ++..|..+|.. .++
T Consensus 166 ~~~~~r--------~l~~~~~i~~~a~~~i~~~~~~~~~yiavHlR~~~D~--~~~C~~~~---~~~~~~~~~~~--~~~ 230 (351)
T PF10250_consen 166 DRDLQR--------YLRFSPEIRELADKFIKRLLAGGGPYIAVHLRRGKDW--FSACEFKG---ERHLLASPRCW--GKK 230 (351)
T ss_dssp GGGGGG--------G--B-HHHHHHHHHHHHHH----SSEEEEEE--SHHH--HHHHCT-T-------TTTHHHH---GG
T ss_pred CccceE--------EEecCHHHHHHHHHHHHHhhcccCceEEEeecccCch--HhhcccCC---chHHHHHhHhh--ccc
Confidence 888987 9999999999999999999955689999999999999 99999954 77778888865 223
Q ss_pred CCCchhhhcCCCCCCCHHHHHHHHHHhCCCCcceEEEEeccccCCcccccchHhhcCCcccccccccc-ccCCCCCcccc
Q 008243 317 ISNPDKERRHGKCPLTPLEVGLMLRALGYGSDVHIYVASGEVYGGEETLAPLKALFPNFYSKETIASK-ELEPFSSFSSR 395 (573)
Q Consensus 317 ~~~~~~~R~~G~CPLTPeEvgl~LrALGf~~~T~IYlAaGeiyGG~~~l~pL~~~FPnl~tKetLas~-EL~pF~~~ss~ 395 (573)
.+++...|..|.||++|++++.+++++|+.+.|.||||++++|||.+.|.+|++.||++++|+++.+. |+++|.. .+
T Consensus 231 ~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~--~~ 308 (351)
T PF10250_consen 231 SINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLSHEELEPLND--DQ 308 (351)
T ss_dssp GTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--EE--S-------S-
T ss_pred cccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCCHHHhhhccc--cc
Confidence 35777889999999999999999999999999999999999999999999999999999999999999 9999976 89
Q ss_pred cchhheeeecCCceeeeCCCCchhhhhhhhccccCCC
Q 008243 396 MAALDFIVCDESDIFVTNNNGNMAKILAGRRKYFGHK 432 (573)
Q Consensus 396 ~AALDY~Vc~~SDVFVpt~~GNma~~V~GhR~y~G~~ 432 (573)
+|+||++||++||+||+|..++|+.+|+++|.|.|+.
T Consensus 309 ~a~vD~~i~~~s~~Figt~~Stfs~~i~~~R~~~g~~ 345 (351)
T PF10250_consen 309 LAMVDQEICSRSDVFIGTCGSTFSSNIARERHYRGKP 345 (351)
T ss_dssp -HHHHHHHHHHSSEEEE-TT-HHHHHHHHHHHHSSSS
T ss_pred hhHHHHHHHhcCCEEEecCcchhHHHhhcccCcCCCC
Confidence 9999999999999999999889999999999999954
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.27 E-value=0.0056 Score=63.83 Aligned_cols=275 Identities=21% Similarity=0.288 Sum_probs=151.5
Q ss_pred CCCCcEEEEE-ecCCchhhHHHHHHHHHHHHHhCCeEEeeccC---CCcccCCCCCCCccccHHH------------HHH
Q 008243 110 THSNRYLAIV-TSGGLNQQRTGIIDAVVAARILNATLVIPKLD---QKSFWKDASDFSEIFDVDR------------FIS 173 (573)
Q Consensus 110 ~~snGYL~V~-~nGGLNQqR~~IcDaVaVARiLNATLViP~Ld---~~s~W~D~S~F~DIFDvdh------------FI~ 173 (573)
...||||+.- |-|-+-+|-..+--..|.|+.||.|||+|-.- +-.+-+--=.|+..|.|+- |+.
T Consensus 26 ~DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiEy~~pe~~n~~vpf~~yF~vepl~~YhRVitm~dFm~ 105 (386)
T KOG3849|consen 26 WDPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIEYKHPETKNLMVPFEFYFQVEPLAKYHRVITMQDFMK 105 (386)
T ss_pred CCCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchhccCCcccccccchhheeecccHhhhhhheeHHHHHH
Confidence 3468998876 99999999999999999999999999999643 2222222237888888753 444
Q ss_pred hccCceE-------Eccc-----CCccc---CCCCCCccccCCCC-------CChHHH------HHhh---hHhH-----
Q 008243 174 VLSKDVK-------IIKQ-----IPRKG---GKSLTPYHMRVPRK-------CNEKCY------QNRV---LPVL----- 217 (573)
Q Consensus 174 sL~~dVr-------IVk~-----LP~~~---~~~~~~~~~r~p~~-------~s~~yY------~~~v---LP~l----- 217 (573)
.|..+.= |--+ -|.+- .+-.+|+ =|.| ..-.|| +++. ...+
T Consensus 106 klapthwp~~~Rva~c~k~a~qr~pdkp~Ch~KeGNPF---GPfWDqfhvsFv~sE~f~~i~Fd~~~~~~~~kW~~kfp~ 182 (386)
T KOG3849|consen 106 KLAPTHWPGTPRVAICDKSAAQRSPDKPGCHSKEGNPF---GPFWDQFHVSFVGSEYFGDIGFDLNQMGSRKKWLEKFPS 182 (386)
T ss_pred HhCcccCCCCcceeeeehhhhccCCCCCCCcccCCCCC---CCchhheEeeeeccccccccccchhhcchHHHHHhhCCc
Confidence 4443321 1000 01110 0000110 0111 000111 1111 2222
Q ss_pred hhcceEEEecccccccCC-CchHHHhhhhhccccccccchHHHHHHHHHHHHHHhcCCceEEEEeecccchhhhccCCCC
Q 008243 218 LKRHAVQLSKFDYRLANK-LDTDLQKLRCRVNYHALSFTDSIQKMGEKLVHQMRMKGKHYIALHLRFEPDMLAFSGCYYG 296 (573)
Q Consensus 218 ~k~~VI~l~~fd~rLa~~-lp~eiQrLRCrvnf~ALrF~p~I~~lg~~LV~RLR~~~gpfIALHLRfE~DMLAfsgC~~g 296 (573)
++|-|+.|++.-....-. ---.|||- ||.+.+|.+.|++.+.-- ..+||+++|||--.|++-- |.+-
T Consensus 183 eeyPVLAf~gAPA~FPv~~e~~~lQkY--------l~WS~r~~e~~k~fI~a~--L~rpfvgiHLRng~DWvra--Cehi 250 (386)
T KOG3849|consen 183 EEYPVLAFSGAPAPFPVKGEVWSLQKY--------LRWSSRITEQAKKFISAN--LARPFVGIHLRNGADWVRA--CEHI 250 (386)
T ss_pred ccCceeeecCCCCCCccccccccHHHH--------HHHHHHHHHHHHHHHHHh--cCcceeEEEeecCchHHHH--HHHh
Confidence 235666666533222110 01246765 889999999999877542 2469999999999999864 7553
Q ss_pred CChHHHHHHHHHHHHhhhhcCCCc----hhhhcC-----CCCCCCHHHHHH----HHHHhCCCCcceEEEEeccccCCcc
Q 008243 297 GGDKERKELGAIRKRWKTLHISNP----DKERRH-----GKCPLTPLEVGL----MLRALGYGSDVHIYVASGEVYGGEE 363 (573)
Q Consensus 297 g~~~E~~EL~~~R~~wk~~~~~~~----~~~R~~-----G~CPLTPeEvgl----~LrALGf~~~T~IYlAaGeiyGG~~ 363 (573)
-...- | +..-+ ...+.. ..|-=.-+++-. -.+.+| .-..+|||+.. .
T Consensus 251 kd~~~-------~------hlfASpQClGy~~~~gaLt~e~C~Psk~~I~rqik~~v~si~--dakSVfVAsDs-----~ 310 (386)
T KOG3849|consen 251 KDTTN-------R------HLFASPQCLGYGHHLGALTKEICSPSKQQILRQIKEKVGSIG--DAKSVFVASDS-----D 310 (386)
T ss_pred cccCC-------C------ccccChhhccccccccccchhhhCccHHHHHHHHHHHHhhhc--ccceEEEeccc-----h
Confidence 21000 0 00000 011122 234323333322 222334 23469999876 3
Q ss_pred cccc-hH-hhcCCccccccccccccCCCCCcccccchhheeeecCCceeeeCCCCchhhhhhhhccccC
Q 008243 364 TLAP-LK-ALFPNFYSKETIASKELEPFSSFSSRMAALDFIVCDESDIFVTNNNGNMAKILAGRRKYFG 430 (573)
Q Consensus 364 ~l~p-L~-~~FPnl~tKetLas~EL~pF~~~ss~~AALDY~Vc~~SDVFVpt~~GNma~~V~GhR~y~G 430 (573)
.|.+ |. +++|- .+..-.|+| --+-+|..|--+||-||.|--..|..+|.-.|--.|
T Consensus 311 hmi~Eln~aL~~~-----~i~vh~l~p------dd~y~dLaIlGqadhFiGNCvSsfsafvKRERD~~G 368 (386)
T KOG3849|consen 311 HMIDELNEALKPY-----EIEVHRLEP------DDMYTDLAILGQADHFIGNCVSSFSAFVKRERDHAG 368 (386)
T ss_pred hhhHHHHHhhccc-----ceeEEecCc------ccchhhhhhhcccchhhhhhHHHHHHHHhhhhcccC
Confidence 3433 33 23331 111013333 246789999999999999999999999999998877
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=91.73 E-value=3.8 Score=43.81 Aligned_cols=249 Identities=18% Similarity=0.233 Sum_probs=118.8
Q ss_pred CcEEEEEecCCchhhHHHHHHHHHHHHHhCCeEEeeccCCCcccCCCC----CCCccccHHHHHHhcc--CceEEcccCC
Q 008243 113 NRYLAIVTSGGLNQQRTGIIDAVVAARILNATLVIPKLDQKSFWKDAS----DFSEIFDVDRFISVLS--KDVKIIKQIP 186 (573)
Q Consensus 113 nGYL~V~~nGGLNQqR~~IcDaVaVARiLNATLViP~Ld~~s~W~D~S----~F~DIFDvdhFI~sL~--~dVrIVk~LP 186 (573)
+.|++.+--+|++.-=-+++-|-..|+-.|.||||= |+++= .|...|++ |-+-.. ..|+|+-.=+
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 579999999999999999999999999999999994 55543 56665554 333332 3344441111
Q ss_pred -cccCCCCCCccccCCCCCC-h---------HHHH---HhhhHhHhh------cceEEEecccccccCCCchHHHhhhhh
Q 008243 187 -RKGGKSLTPYHMRVPRKCN-E---------KCYQ---NRVLPVLLK------RHAVQLSKFDYRLANKLDTDLQKLRCR 246 (573)
Q Consensus 187 -~~~~~~~~~~~~r~p~~~s-~---------~yY~---~~vLP~l~k------~~VI~l~~fd~rLa~~lp~eiQrLRCr 246 (573)
.++. .+-.+ .|.||. | .++. +++--++.- .-||+.. .|--.- +-+..||-
T Consensus 73 i~~~~---~~g~~-fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~----c~~~~c--~~~aeR~i 142 (321)
T PF05830_consen 73 INQFS---FPGPF-FPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDA----CLMWRC--DEEAEREI 142 (321)
T ss_dssp GGT-------SSE-ESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S------TTSS---HHHHHHH
T ss_pred hhhhc---CCCCc-ChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHh----hcCCcc--hhHHHHHH
Confidence 1110 00000 122321 1 1211 122222222 2344433 221111 23333433
Q ss_pred ccccccccchHHHHHHHHHHHHHHhcCCceEEEEeecc--cchhhhccCCCCCChHHHHHHHHHHHHhhhhcCCCchhhh
Q 008243 247 VNYHALSFTDSIQKMGEKLVHQMRMKGKHYIALHLRFE--PDMLAFSGCYYGGGDKERKELGAIRKRWKTLHISNPDKER 324 (573)
Q Consensus 247 vnf~ALrF~p~I~~lg~~LV~RLR~~~gpfIALHLRfE--~DMLAfsgC~~gg~~~E~~EL~~~R~~wk~~~~~~~~~~R 324 (573)
|..|+-+++|++..+.+.+.-=. +..-|.+|.|.= +|.+.+ +| +|...+
T Consensus 143 --f~slkpR~eIqarID~iy~ehf~-g~~~IGVHVRhGngeD~~~h-~~-----------------~~~D~e-------- 193 (321)
T PF05830_consen 143 --FSSLKPRPEIQARIDAIYREHFA-GYSVIGVHVRHGNGEDIMDH-AP-----------------YWADEE-------- 193 (321)
T ss_dssp --HHHS-B-HHHHHHHHHHHHHHTT-TSEEEEEEE---------------------------------HHHH--------
T ss_pred --HHhCCCCHHHHHHHHHHHHHHcC-CCceEEEEEeccCCcchhcc-Cc-----------------cccCch--------
Confidence 99999999999999998766422 346899999931 122221 12 232211
Q ss_pred cCCCCCCCHH---HHHHHHHHhCCCCcceEEEEeccccCCcccccchHhhcCCcccccccccc-ccCCCCCc-----ccc
Q 008243 325 RHGKCPLTPL---EVGLMLRALGYGSDVHIYVASGEVYGGEETLAPLKALFPNFYSKETIASK-ELEPFSSF-----SSR 395 (573)
Q Consensus 325 ~~G~CPLTPe---Evgl~LrALGf~~~T~IYlAaGeiyGG~~~l~pL~~~FPnl~tKetLas~-EL~pF~~~-----ss~ 395 (573)
.+=. .....++++-...++.|+||+-. .+-++-|++.||.+++-++=-.+ .-.+.-+. +-.
T Consensus 194 ------~~L~~V~~ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k~F~~~~~g~Lhs~~~g~~gg~ 263 (321)
T PF05830_consen 194 ------RALRQVCTAIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPKQFPASQAGPLHSAAVGIEGGE 263 (321)
T ss_dssp ------HHHHHHHHHHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE----------------HHHHHHHHH
T ss_pred ------HHHHHHHHHHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEcccccCCCCCCcCcccccccchHH
Confidence 0011 11223455666678999999988 57899999999998876543322 21222111 112
Q ss_pred cchhheeeecCCceee-eCCCCchh
Q 008243 396 MAALDFIVCDESDIFV-TNNNGNMA 419 (573)
Q Consensus 396 ~AALDY~Vc~~SDVFV-pt~~GNma 419 (573)
.|-+|-+.-..+|+.| .+...-|.
T Consensus 264 ~ALIDM~LLSrCD~LIr~~ptS~Fs 288 (321)
T PF05830_consen 264 SALIDMYLLSRCDYLIRFPPTSAFS 288 (321)
T ss_dssp HHHHHHHHHTTSSEEEEESTT-GGG
T ss_pred HHHHHHHHHHhCCeEEEcCCCchhh
Confidence 4778999999999999 44444443
No 4
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=43.84 E-value=7.3 Score=33.75 Aligned_cols=54 Identities=24% Similarity=0.333 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHhCCCCcceEEEEeccccCCcccccchHhhcCCcccccccccc-ccCCCCCcccccchhh
Q 008243 330 PLTPLEVGLMLRALGYGSDVHIYVASGEVYGGEETLAPLKALFPNFYSKETIASK-ELEPFSSFSSRMAALD 400 (573)
Q Consensus 330 PLTPeEvgl~LrALGf~~~T~IYlAaGeiyGG~~~l~pL~~~FPnl~tKetLas~-EL~pF~~~ss~~AALD 400 (573)
++|-.+++-+|+-+.|+++ +|..|+-++|++++++.-..- +.-.|. +++..|-+
T Consensus 39 ~~T~~Qv~~il~~f~fd~~---------------kl~~lk~l~p~i~D~~n~~~i~~~f~f~--s~k~~~~~ 93 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDND---------------KLKALKLLYPYIVDPQNYYTIIDAFSFS--SDKDKARE 93 (95)
T ss_pred ceeHHHHHHHHHHcCCCHH---------------HHHHHHHHhhhccCHHHHHHHHHHhcCc--ccHHHHHH
Confidence 4999999999999999764 799999999999999744433 433443 34444433
No 5
>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=40.00 E-value=32 Score=31.83 Aligned_cols=28 Identities=29% Similarity=0.243 Sum_probs=15.5
Q ss_pred CCCCCHHHHHHHHHHhCCCCcceEEEEec
Q 008243 328 KCPLTPLEVGLMLRALGYGSDVHIYVASG 356 (573)
Q Consensus 328 ~CPLTPeEvgl~LrALGf~~~T~IYlAaG 356 (573)
+|||||||+...|++|--+. ...||...
T Consensus 14 qC~l~ke~~l~~L~~l~~~~-~~~yI~v~ 41 (114)
T PF00799_consen 14 QCSLTKEEALEQLKNLLTPS-NKKYIRVC 41 (114)
T ss_dssp T----HHHHHHHHHH---SS--EEEEEEE
T ss_pred CCCCCHHHHHHHHHHhCCcc-CceEEEee
Confidence 69999999999999997653 56676443
No 6
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=38.39 E-value=33 Score=32.17 Aligned_cols=98 Identities=10% Similarity=-0.019 Sum_probs=56.6
Q ss_pred ccccccccchHHHHHHHHHHHHHHhcCCceEEEEeecccchhh-----hccCCCCCChHHH--HHHHHHHHHhhhhcCCC
Q 008243 247 VNYHALSFTDSIQKMGEKLVHQMRMKGKHYIALHLRFEPDMLA-----FSGCYYGGGDKER--KELGAIRKRWKTLHISN 319 (573)
Q Consensus 247 vnf~ALrF~p~I~~lg~~LV~RLR~~~gpfIALHLRfE~DMLA-----fsgC~~gg~~~E~--~EL~~~R~~wk~~~~~~ 319 (573)
++..+|++.++..+.-+.+.+.|+. +|.++.++..-+...+. +. |...+..-+. ....++++-|..
T Consensus 49 ~~~~~l~~~~d~~~~l~ei~rvLkp-GG~l~i~d~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~y~yl~~s----- 121 (160)
T PLN02232 49 TMGYGLRNVVDRLRAMKEMYRVLKP-GSRVSILDFNKSNQSVTTFMQGWM-IDNVVVPVATVYDLAKEYEYLKYS----- 121 (160)
T ss_pred EecchhhcCCCHHHHHHHHHHHcCc-CeEEEEEECCCCChHHHHHHHHHH-ccchHhhhhHHhCChHHHHhHHHH-----
Confidence 4455677777777888888888866 57888777654322111 00 1110100000 000112221111
Q ss_pred chhhhcCCCCCCCHHHHHHHHHHhCCCCcceEEEEeccc
Q 008243 320 PDKERRHGKCPLTPLEVGLMLRALGYGSDVHIYVASGEV 358 (573)
Q Consensus 320 ~~~~R~~G~CPLTPeEvgl~LrALGf~~~T~IYlAaGei 358 (573)
-.. +++|+|+..+|+..||.+-+.-+++.|-+
T Consensus 122 ------i~~-f~~~~el~~ll~~aGF~~~~~~~~~~g~~ 153 (160)
T PLN02232 122 ------ING-YLTGEELETLALEAGFSSACHYEISGGFM 153 (160)
T ss_pred ------HHH-CcCHHHHHHHHHHcCCCcceEEECcchHh
Confidence 012 58999999999999999998888887763
No 7
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=34.12 E-value=26 Score=42.69 Aligned_cols=13 Identities=8% Similarity=0.082 Sum_probs=7.4
Q ss_pred HHHHHhccCCCCc
Q 008243 461 VRSYQRGFMGEPN 473 (573)
Q Consensus 461 Vr~~h~~~~g~p~ 473 (573)
|-.+|..++..|-
T Consensus 1326 ~sdvh~~r~k~p~ 1338 (1516)
T KOG1832|consen 1326 MSDVHTRRVKHPL 1338 (1516)
T ss_pred hhhhcccccccch
Confidence 4456666665553
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=29.48 E-value=40 Score=28.17 Aligned_cols=16 Identities=44% Similarity=0.700 Sum_probs=13.7
Q ss_pred CCCCCCHHHHHHHHHHh
Q 008243 327 GKCPLTPLEVGLMLRAL 343 (573)
Q Consensus 327 G~CPLTPeEvgl~LrAL 343 (573)
|-| +||||-+.+++++
T Consensus 42 ~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDC-ITPEEDREILEAT 57 (60)
T ss_pred hcc-CCHHHHHHHHHHH
Confidence 457 9999999999875
No 9
>COG1312 UxuA D-mannonate dehydratase [Carbohydrate transport and metabolism]
Probab=27.32 E-value=77 Score=34.77 Aligned_cols=66 Identities=18% Similarity=0.193 Sum_probs=46.9
Q ss_pred CCChHHHHHhhhHhHhhcce-EEEecccccccC-CCc------hHHHhhh------------hhccccccccchHHHHHH
Q 008243 203 KCNEKCYQNRVLPVLLKRHA-VQLSKFDYRLAN-KLD------TDLQKLR------------CRVNYHALSFTDSIQKMG 262 (573)
Q Consensus 203 ~~s~~yY~~~vLP~l~k~~V-I~l~~fd~rLa~-~lp------~eiQrLR------------Crvnf~ALrF~p~I~~lg 262 (573)
|-.-.|++++|.|+-.+.|| +.+.|-|+-+.- +|| .++|++. |.-+|.+.-. ..|-++.
T Consensus 187 ~~nL~yFL~~ViPVAEe~gVkmaiHPDDPP~pi~GLpRIvst~ed~~~ll~~vdSp~NGiTlCtGS~G~~~d-nDl~~mi 265 (362)
T COG1312 187 WENLAYFLKEVIPVAEEVGVKMAIHPDDPPWPIFGLPRIVSTIEDYQRLLEMVDSPYNGITLCTGSLGARAD-NDLPEMI 265 (362)
T ss_pred HHHHHHHHHhhcchHHhcCceEEeCCCCCCccccCcchhcCCHHHHHHHHHhccCccCCEEEeccccccCcc-ccHHHHH
Confidence 44567999999999999999 888888887763 565 4888875 6666665433 4555555
Q ss_pred HHHHHHH
Q 008243 263 EKLVHQM 269 (573)
Q Consensus 263 ~~LV~RL 269 (573)
....+|+
T Consensus 266 r~F~~rI 272 (362)
T COG1312 266 REFASRI 272 (362)
T ss_pred HHHhhhc
Confidence 5555554
No 10
>TIGR03006 pepcterm_polyde polysaccharide deactylase family protein, PEP-CTERM locus subfamily. Members of this protein family belong to the family of polysaccharide deacetylases (pfam01522). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. The highest scoring homologs below the trusted cutoff for this model are found in several species of Methanosarcina, an archaeal genus.
Probab=25.55 E-value=3.3e+02 Score=28.30 Aligned_cols=118 Identities=17% Similarity=0.124 Sum_probs=62.4
Q ss_pred HHHHhhhHhHhhcceEEEeccc-ccccCCCchHHHhhhhhccccccccchHHHHHHHHHHHHHHhcCCceEEEEeecccc
Q 008243 208 CYQNRVLPVLLKRHAVQLSKFD-YRLANKLDTDLQKLRCRVNYHALSFTDSIQKMGEKLVHQMRMKGKHYIALHLRFEPD 286 (573)
Q Consensus 208 yY~~~vLP~l~k~~VI~l~~fd-~rLa~~lp~eiQrLRCrvnf~ALrF~p~I~~lg~~LV~RLR~~~gpfIALHLRfE~D 286 (573)
....+||++|++++|- .|=|- ...+.+. -.++++|.+. |+=||.|=--=.+
T Consensus 28 ~nt~riL~lL~~~gik-ATFFv~g~~~e~~--------------------------p~lir~i~~~-GhEIgsHg~sH~~ 79 (265)
T TIGR03006 28 RNTDRILDLLDRHGVK-ATFFTLGWVAERY--------------------------PELVRRIVAA-GHELASHGYGHER 79 (265)
T ss_pred HhHHHHHHHHHHcCCc-EEEEEeccchhhC--------------------------HHHHHHHHHc-CCEeeeccccCcC
Confidence 3578999999999983 22111 1111111 2457788876 6899998432211
Q ss_pred hhhhccCCCCCC-hHHHHHHHHHHHHhhhhcCCCchhhhcCCCCCCCHH--HHHHHHHHhCCCCcceEEEEeccccCC
Q 008243 287 MLAFSGCYYGGG-DKERKELGAIRKRWKTLHISNPDKERRHGKCPLTPL--EVGLMLRALGYGSDVHIYVASGEVYGG 361 (573)
Q Consensus 287 MLAfsgC~~gg~-~~E~~EL~~~R~~wk~~~~~~~~~~R~~G~CPLTPe--Evgl~LrALGf~~~T~IYlAaGeiyGG 361 (573)
+ ...+ ++++++|.+.+..-.......+.--|.-+.+ .++. .+--+|+..||.-+..+|=...+-||.
T Consensus 80 l-------~~ls~ee~~~eI~~s~~~Le~itG~~~~gfRaP~~s-~~~~t~~a~~iL~e~Gy~YdsS~~p~~~d~~g~ 149 (265)
T TIGR03006 80 V-------TTQTPEAFRADIRRSKALLEDLSGQPVRGYRAPSFS-IGKKNLWALDVLAEAGYRYSSSIYPVRHDHYGM 149 (265)
T ss_pred c-------hhCCHHHHHHHHHHHHHHHHHHhCCCceEEECCCCC-CCCCcHHHHHHHHHCCCEEEEeeccCcCCcCCC
Confidence 1 1222 3346666655543221111112223333322 2332 234689999999888887544566663
No 11
>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=24.78 E-value=86 Score=28.95 Aligned_cols=47 Identities=19% Similarity=0.424 Sum_probs=35.3
Q ss_pred CCHHHH-HHHHHHhCCCCcceEEEEeccccCCcccccchHhhcCCccccccc
Q 008243 331 LTPLEV-GLMLRALGYGSDVHIYVASGEVYGGEETLAPLKALFPNFYSKETI 381 (573)
Q Consensus 331 LTPeEv-gl~LrALGf~~~T~IYlAaGeiyGG~~~l~pL~~~FPnl~tKetL 381 (573)
++|--+ -.+|..++ +.++.|++...+ |.....+|+++.|.-+.+++|
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 455442 44788887 679999999887 666678999999998877654
No 12
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=23.72 E-value=63 Score=26.15 Aligned_cols=24 Identities=29% Similarity=0.472 Sum_probs=20.0
Q ss_pred hhcCCCCCCCHHHHHHHHHHhCCCC
Q 008243 323 ERRHGKCPLTPLEVGLMLRALGYGS 347 (573)
Q Consensus 323 ~R~~G~CPLTPeEvgl~LrALGf~~ 347 (573)
.+.-|. .++++|+.-+|+.|||.-
T Consensus 12 ~~llG~-~i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 12 NRLLGL-DLSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHHCC-CCCHHHHHHHHHHCCCeE
Confidence 355665 599999999999999975
No 13
>PRK05578 cytidine deaminase; Validated
Probab=22.35 E-value=93 Score=29.19 Aligned_cols=96 Identities=18% Similarity=0.296 Sum_probs=57.0
Q ss_pred eEEEEeecccchhhhccCCCC------CChHHHHHHHHHHHH----hhhhcCCCchhhhcCCCCCCCHHHH-HHHHHHhC
Q 008243 276 YIALHLRFEPDMLAFSGCYYG------GGDKERKELGAIRKR----WKTLHISNPDKERRHGKCPLTPLEV-GLMLRALG 344 (573)
Q Consensus 276 fIALHLRfE~DMLAfsgC~~g------g~~~E~~EL~~~R~~----wk~~~~~~~~~~R~~G~CPLTPeEv-gl~LrALG 344 (573)
-++-.+|-+ |=-.|.||.-. +.-.|+..+.++=.. .+...++. +.. -+++|==. -.+|.-++
T Consensus 25 ~Vgaa~~~~-~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G~~~i~~i~vv~----~~~--~~~sPCG~CRQ~l~e~~ 97 (131)
T PRK05578 25 PVGAALLTD-DGRIYTGCNIENASYGLTNCAERTAIFKAISEGGGRLVAIACVG----ETG--EPLSPCGRCRQVLAEFG 97 (131)
T ss_pred ceEEEEEeC-CCCEEEEEEeeCccccCCcCHHHHHHHHHHHcCCCceEEEEEEe----cCC--CccCccHHHHHHHHHhC
Confidence 367777775 45555665422 224677777665321 22111211 111 23444322 24566564
Q ss_pred CCCcceEEEEeccccCCcccccchHhhcCCcccccccc
Q 008243 345 YGSDVHIYVASGEVYGGEETLAPLKALFPNFYSKETIA 382 (573)
Q Consensus 345 f~~~T~IYlAaGeiyGG~~~l~pL~~~FPnl~tKetLa 382 (573)
+.+|.||+...+ |+.....|+++.|.-+++++|+
T Consensus 98 -~~~~~v~l~~~~---~~~~~~~l~eLLP~~f~~~~l~ 131 (131)
T PRK05578 98 -GPDLLVTLVAKD---GPTGEMTLGELLPYAFTPDDLG 131 (131)
T ss_pred -CCCcEEEEEcCC---CCEEEEEHHHhCcCcCChhhcC
Confidence 579999999877 5566789999999999988774
No 14
>COG2241 CobL Precorrin-6B methylase 1 [Coenzyme metabolism]
Probab=21.52 E-value=3e+02 Score=28.10 Aligned_cols=116 Identities=20% Similarity=0.223 Sum_probs=63.1
Q ss_pred HHhhhHhHhhcceEEEecccccccCCCchHHHhhhhhccccccccchHHHHHHHHHHHHHHhc--CCceEEEEeecccch
Q 008243 210 QNRVLPVLLKRHAVQLSKFDYRLANKLDTDLQKLRCRVNYHALSFTDSIQKMGEKLVHQMRMK--GKHYIALHLRFEPDM 287 (573)
Q Consensus 210 ~~~vLP~l~k~~VI~l~~fd~rLa~~lp~eiQrLRCrvnf~ALrF~p~I~~lg~~LV~RLR~~--~gpfIALHLRfE~DM 287 (573)
++.++...+.+.|+.|+.=|+....-.....-+..| +=++.-|-|..+ +....||.-. .-.++.+|-|-.
T Consensus 59 l~~i~~~~~g~~v~VLasGDP~f~G~g~~l~~~~~~----~~v~iIPgiSS~-q~a~ARlg~~~~~~~~islHgr~~--- 130 (210)
T COG2241 59 LEEILAERKGRDVVVLASGDPLFSGVGRLLRRKFSC----EEVEIIPGISSV-QLAAARLGWPLQDTEVISLHGRPV--- 130 (210)
T ss_pred HHHHHHHhCCCCeEEEecCCcchhhhHHHHHHhcCc----cceEEecChhHH-HHHHHHhCCChHHeEEEEecCCCH---
Confidence 456666666688888888787665422223333333 235566666554 3344455321 037888883332
Q ss_pred hhhccCCCCCChHHHHHHHHHHHHhhhhcCCCchhhhcCCCCC--CCHHHHHHHHHHhCCCCcceEEEEecccc
Q 008243 288 LAFSGCYYGGGDKERKELGAIRKRWKTLHISNPDKERRHGKCP--LTPLEVGLMLRALGYGSDVHIYVASGEVY 359 (573)
Q Consensus 288 LAfsgC~~gg~~~E~~EL~~~R~~wk~~~~~~~~~~R~~G~CP--LTPeEvgl~LrALGf~~~T~IYlAaGeiy 359 (573)
+. |..+... ....++ .|| .+|.+++.+|...||. +++++|---=-|
T Consensus 131 -------------~~--l~~~~~~-~~~~vi---------l~~~~~~P~~IA~~L~~~G~~-~~~~~VlE~L~~ 178 (210)
T COG2241 131 -------------EL--LRPLLEN-GRRLVI---------LTPDDFGPAEIAKLLTENGIG-DSRVTVLENLGY 178 (210)
T ss_pred -------------HH--HHHHHhC-CceEEE---------eCCCCCCHHHHHHHHHhCCCC-CceEEEEcccCC
Confidence 11 1111100 000111 122 5799999999999999 888887543333
No 15
>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.
Probab=20.04 E-value=75 Score=28.39 Aligned_cols=71 Identities=23% Similarity=0.274 Sum_probs=41.0
Q ss_pred cccchhhhccCCCCCChHHHHHHHHHHHHhhhhcCCCchhhhcCCCC-CCCHHHHHHHHHHhCCCCcceEEEEeccccCC
Q 008243 283 FEPDMLAFSGCYYGGGDKERKELGAIRKRWKTLHISNPDKERRHGKC-PLTPLEVGLMLRALGYGSDVHIYVASGEVYGG 361 (573)
Q Consensus 283 fE~DMLAfsgC~~gg~~~E~~EL~~~R~~wk~~~~~~~~~~R~~G~C-PLTPeEvgl~LrALGf~~~T~IYlAaGeiyGG 361 (573)
..+|+++|| |.+..-..-.+..+.+|+.+....++ .-|-+ -+.|+++ |...++ =|+.-|| |
T Consensus 38 ~~pdiv~~S-~~~~~~~~~~~~~~~ik~~~p~~~iv------~GG~~~t~~p~~~---~~~~~~-----D~vv~GE---g 99 (127)
T cd02068 38 LKPDVVGIS-LMTSAIYEALELAKIAKEVLPNVIVV------VGGPHATFFPEEI---LEEPGV-----DFVVIGE---G 99 (127)
T ss_pred cCCCEEEEe-eccccHHHHHHHHHHHHHHCCCCEEE------ECCcchhhCHHHH---hcCCCC-----CEEEECC---c
Confidence 345888888 55544333344455666665433222 23433 3478876 333333 3888999 8
Q ss_pred cccccchHhh
Q 008243 362 EETLAPLKAL 371 (573)
Q Consensus 362 ~~~l~pL~~~ 371 (573)
+..+..|-+.
T Consensus 100 E~~~~~l~~~ 109 (127)
T cd02068 100 EETFLKLLEE 109 (127)
T ss_pred HHHHHHHHHH
Confidence 8877777654
Done!