Query 039928
Match_columns 675
No_of_seqs 202 out of 398
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:26:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039928.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039928hhsearch_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 3.4E-52 7.3E-57 427.3 0.5 304 108-514 6-345 (351)
2 KOG3849 GDP-fucose protein O-f 76.1 3.3 7.1E-05 44.7 4.3 175 99-294 27-249 (386)
3 PF05830 NodZ: Nodulation prot 75.6 74 0.0016 35.1 14.2 219 101-385 2-242 (321)
4 KOG3111 D-ribulose-5-phosphate 41.8 58 0.0012 34.1 5.8 110 252-381 42-171 (224)
5 PF00799 Gemini_AL1: Geminivir 33.2 40 0.00086 31.9 2.9 31 333-364 14-45 (114)
6 PF14771 DUF4476: Domain of un 30.6 34 0.00073 30.3 1.9 43 335-392 39-81 (95)
7 PF12273 RCR: Chitin synthesis 30.2 33 0.00071 32.3 1.9 19 14-32 1-19 (130)
8 KOG3849 GDP-fucose protein O-f 29.5 43 0.00092 36.6 2.8 15 114-128 115-129 (386)
9 smart00874 B5 tRNA synthetase 27.3 49 0.0011 27.4 2.2 25 328-353 12-36 (71)
10 PF10892 DUF2688: Protein of u 25.2 48 0.001 28.3 1.8 17 331-348 41-57 (60)
11 PF04561 RNA_pol_Rpb2_2: RNA p 21.6 28 0.00061 33.1 -0.3 17 341-357 54-70 (190)
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=3.4e-52 Score=427.32 Aligned_cols=304 Identities=32% Similarity=0.480 Sum_probs=203.5
Q ss_pred EcCchhhhHHHHHHHHHHHhHhcceEeccccCcccccCCCCC--CCCCCCcccChHHHHHHccCCcEEeccCchhhhhhc
Q 039928 108 IQGGFHEIRNSISDVVVVARLLNATLVIPEIQSTTSSKGISS--QFKSFAYLYNEEQFMAALAKDINIVKTLPKNLKGAR 185 (675)
Q Consensus 108 anGGLNQqR~~IcDAVaVARiLNATLVIP~Ld~ss~~~~d~s--d~S~F~DIFDvdhFI~sLk~DVrIVk~LP~~l~~~~ 185 (675)
+.||+|+||.++++||++|++||+|||||.+..... |.+.+ ..-.|+++||+++|+++++++|.+++.+|..+....
T Consensus 6 ~~GGfnNQr~~~~~a~~~A~~LnRTLVLPp~~~~~~-~~~~~~~~~ipf~~~fD~~~l~~~~~~vi~~~ef~~~~~~~~~ 84 (351)
T PF10250_consen 6 CMGGFNNQRMGFENAVVFAKALNRTLVLPPFIKHYH-WKDQSKQRHIPFSDFFDVEHLRKFLRPVITMEEFLPKHWDEVF 84 (351)
T ss_dssp -SSSHHHHHHHHHHHHHHHHHHT-EEE--EEEEESS-SS----EEEEEHHHHB-HHHHTTTS--EE-HHHHHHHHS-GGG
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCEEEcCCcccccc-ccccccccccChhhhccHHHHHHHhhCceehheeccchhcccc
Confidence 789999999999999999999999999999999864 44432 111399999999999999999999999987766543
Q ss_pred cc---------------------------CCCCcccccc-CCChhhHhhhcccccccc------eEEEEeecCCcccccC
Q 039928 186 RK---------------------------KKIPSFRVSY-SASPYFYLHHVLPVLIKH------SVVELVVSDGGCLQAS 231 (675)
Q Consensus 186 ~~---------------------------~~~~~~rvp~-~ss~~yY~~~VLP~Lkk~------~VI~l~~~d~rLa~~~ 231 (675)
.. .....+.+.. ++.+.+|+++++|++.++ +|+.|..+...+..+.
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 21 1122233344 788899999999999987 9999999999887776
Q ss_pred CCCChhHhhhhhhhhcccceecchHHHHHHHHHHHHHhcCCCCeEEecccchhhhhhhcCCccccchhHHHHHHHHHHHH
Q 039928 232 LPPHLEEYQRLRCRVAFHALRFRQEVQELATRILRRLRAPGRPFIAFDPGMIRDALAYHGCAELFQDVHTELIQHKRAWM 311 (675)
Q Consensus 232 LP~~~~eiQrLRCRvnfhALrF~p~IeeLg~~LV~RLR~~g~pyIALHLRfE~DMLAfSgC~~~~~~~~~el~~~rr~~~ 311 (675)
+++ ++|| +|+|+++|+++|+++|++|+..+++|||+|||+|+|| +++|.+.. +...+..+|. +
T Consensus 165 ~~~---~~~r--------~l~~~~~i~~~a~~~i~~~~~~~~~yiavHlR~~~D~--~~~C~~~~--~~~~~~~~~~-~- 227 (351)
T PF10250_consen 165 LDR---DLQR--------YLRFSPEIRELADKFIKRLLAGGGPYIAVHLRRGKDW--FSACEFKG--ERHLLASPRC-W- 227 (351)
T ss_dssp GGG---GGGG--------G--B-HHHHHHHHHHHHHH----SSEEEEEE--SHHH--HHHHCT-T------TTTHHH-H-
T ss_pred cCc---cceE--------EEecCHHHHHHHHHHHHHhhcccCceEEEeecccCch--HhhcccCC--chHHHHHhHh-h-
Confidence 554 6777 9999999999999999999955679999999999999 99999844 2233333332 1
Q ss_pred hhhhhccCccccChhhhhcCCCCCCCHHHHHHHHHHcCCCCceeEEEecccccCcccchhhHHHhccccccccCCCCHHH
Q 039928 312 IKRRIVRGKLSVNSMELRLNGTCPLMPEEVGILLRAYGYSWDTIIYVSGGEVFGGQRTLIPLHAMFANVVDRTSLSTAWE 391 (675)
Q Consensus 312 ~k~~~~k~~~~i~s~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAaGeiYGG~~~L~pL~~~FPnl~tK~tLat~eE 391 (675)
+++.+++...|..|.||++|++++.++++||+.+.|.||||++++|||.+.|.+|+++||++++|+++.+.+|
T Consensus 228 -------~~~~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~ 300 (351)
T PF10250_consen 228 -------GKKSINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLSHEE 300 (351)
T ss_dssp --------GGGTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--EE--
T ss_pred -------ccccccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCCHHH
Confidence 3346677788889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhhccccccCCCCCCCchhHHHhhhhhcccCCCCCCCCCCCCCCCCccccccccccccCCCCCchhHHHHhhhhhhhh
Q 039928 392 LTRIYGREANLIDPKTPLSVEEEEKHESWKNVGPRPRPLPPPPARPKSYNIEGWWGWVAESDNEPESTVMELRTNAHKLL 471 (675)
Q Consensus 392 L~pf~g~~~~~~~~~~p~~~~~~~~~~~w~~~~~rp~plppp~~rp~~~~~eg~~~w~~e~~~e~~~s~~~~r~~~h~l~ 471 (675)
+++|.+ .+
T Consensus 301 ~~~~~~------------------------------------------------------------------------~~ 308 (351)
T PF10250_consen 301 LEPLND------------------------------------------------------------------------DQ 308 (351)
T ss_dssp S-----------------------------------------------------------------------------S-
T ss_pred hhhccc------------------------------------------------------------------------cc
Confidence 999862 35
Q ss_pred hhhhheeeeeccceeeeccCCCCCCCCChhhhhhccccccCCC
Q 039928 472 WEAIDYMVCVEADVFIPGFDRDGKGHPNFASLVMGHRLYQSAS 514 (675)
Q Consensus 472 ~AALDYiV~l~SDvFvpt~~~~G~g~~Nma~~v~GHR~Y~g~~ 514 (675)
+|+|||+||+.||+||.+. || .|+..|+++|.|.|..
T Consensus 309 ~a~vD~~i~~~s~~Figt~---~S---tfs~~i~~~R~~~g~~ 345 (351)
T PF10250_consen 309 LAMVDQEICSRSDVFIGTC---GS---TFSSNIARERHYRGKP 345 (351)
T ss_dssp -HHHHHHHHHHSSEEEE-T---T----HHHHHHHHHHHHSSSS
T ss_pred hhHHHHHHHhcCCEEEecC---cc---hhHHHhhcccCcCCCC
Confidence 6999999999999999865 43 7999999999999964
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=76.14 E-value=3.3 Score=44.73 Aligned_cols=175 Identities=19% Similarity=0.293 Sum_probs=96.7
Q ss_pred CCCcEEEE-EEcCchhhhHHHHHHHHHHHhHhcceEeccccCcccccCCCCCCCCCCCcccChH------------HHHH
Q 039928 99 RANGFIFV-RIQGGFHEIRNSISDVVVVARLLNATLVIPEIQSTTSSKGISSQFKSFAYLYNEE------------QFMA 165 (675)
Q Consensus 99 ~snGYL~V-~anGGLNQqR~~IcDAVaVARiLNATLVIP~Ld~ss~~~~d~sd~S~F~DIFDvd------------hFI~ 165 (675)
..||||+. -|-|-+-+|-...--..|.|+.||-|||+|-.-.-. -....+---.|...|.++ .|++
T Consensus 27 DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiEy~-~pe~~n~~vpf~~yF~vepl~~YhRVitm~dFm~ 105 (386)
T KOG3849|consen 27 DPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIEYK-HPETKNLMVPFEFYFQVEPLAKYHRVITMQDFMK 105 (386)
T ss_pred CCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchhcc-CCcccccccchhheeecccHhhhhhheeHHHHHH
Confidence 45899988 699999999999999999999999999999653210 000111112477778765 4555
Q ss_pred HccCCcEE-------eccCchhhhhhcccC-------CCC-----ccccccCCChhhH------hhhc---cccc-----
Q 039928 166 ALAKDINI-------VKTLPKNLKGARRKK-------KIP-----SFRVSYSASPYFY------LHHV---LPVL----- 212 (675)
Q Consensus 166 sLk~DVrI-------Vk~LP~~l~~~~~~~-------~~~-----~~rvp~~ss~~yY------~~~V---LP~L----- 212 (675)
.|..+.=. --+- ..+....+. +.. .+.| +-..-.|| +.+. ...+
T Consensus 106 klapthwp~~~Rva~c~k~--a~qr~pdkp~Ch~KeGNPFGPfWDqfhv-sFv~sE~f~~i~Fd~~~~~~~~kW~~kfp~ 182 (386)
T KOG3849|consen 106 KLAPTHWPGTPRVAICDKS--AAQRSPDKPGCHSKEGNPFGPFWDQFHV-SFVGSEYFGDIGFDLNQMGSRKKWLEKFPS 182 (386)
T ss_pred HhCcccCCCCcceeeeehh--hhccCCCCCCCcccCCCCCCCchhheEe-eeeccccccccccchhhcchHHHHHhhCCc
Confidence 55544211 1110 000000000 000 0000 00011111 1111 1111
Q ss_pred ccceEEEEeecCCcccccCCCCC--hhHhhhhhhhhcccceecchHHHHHHHHHHHHHhcCCCCeEEecccchhhhhhhc
Q 039928 213 IKHSVVELVVSDGGCLQASLPPH--LEEYQRLRCRVAFHALRFRQEVQELATRILRRLRAPGRPFIAFDPGMIRDALAYH 290 (675)
Q Consensus 213 kk~~VI~l~~~d~rLa~~~LP~~--~~eiQrLRCRvnfhALrF~p~IeeLg~~LV~RLR~~g~pyIALHLRfE~DMLAfS 290 (675)
++|-|+.|++. ...+|.. .-.|||- ||.+.+|.+.|++.+.-- ..+||+++|||---|++--
T Consensus 183 eeyPVLAf~gA-----PA~FPv~~e~~~lQkY--------l~WS~r~~e~~k~fI~a~--L~rpfvgiHLRng~DWvra- 246 (386)
T KOG3849|consen 183 EEYPVLAFSGA-----PAPFPVKGEVWSLQKY--------LRWSSRITEQAKKFISAN--LARPFVGIHLRNGADWVRA- 246 (386)
T ss_pred ccCceeeecCC-----CCCCccccccccHHHH--------HHHHHHHHHHHHHHHHHh--cCcceeEEEeecCchHHHH-
Confidence 34567766643 2223431 1126654 899999999999877642 2359999999999998854
Q ss_pred CCcc
Q 039928 291 GCAE 294 (675)
Q Consensus 291 gC~~ 294 (675)
|.+
T Consensus 247 -Ceh 249 (386)
T KOG3849|consen 247 -CEH 249 (386)
T ss_pred -HHH
Confidence 754
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=75.63 E-value=74 Score=35.13 Aligned_cols=219 Identities=16% Similarity=0.139 Sum_probs=102.6
Q ss_pred CcEEEEEEcCchhhhHHHHHHHHHHHhHhcceEeccccCcccccCCCCCCCCCCCcccChHHHHHHcc--CCcEEeccCc
Q 039928 101 NGFIFVRIQGGFHEIRNSISDVVVVARLLNATLVIPEIQSTTSSKGISSQFKSFAYLYNEEQFMAALA--KDINIVKTLP 178 (675)
Q Consensus 101 nGYL~V~anGGLNQqR~~IcDAVaVARiLNATLVIP~Ld~ss~~~~d~sd~S~F~DIFDvdhFI~sLk--~DVrIVk~LP 178 (675)
+.|++.+--+||+.-=-+++-|-..|+-.|-||||=-=. + .+-++ .|...|++ |-+-.. .-|+|+-.=+
T Consensus 2 ~r~~~~r~r~g~gd~l~~la~aw~~a~~~~r~l~idw~~-s-~~~~~-----~f~n~f~~--ffepv~~i~~~~~~~~d~ 72 (321)
T PF05830_consen 2 QRFVVSRRRTGLGDCLWSLAAAWRYAKRTGRTLVIDWRG-S-CYLDQ-----PFTNAFPV--FFEPVEDIAGVRVICDDR 72 (321)
T ss_dssp --EEEEE--S-HHHHHHHHHHHHHHHHHHT-EEEEE-BT---TT-SS-----TTSBSHHH--HB---SEETTEEEE-SGG
T ss_pred CceEEEeccCCchhHHHHHHHHHHHHHHhCCeEEEEcCC-c-eecCC-----cccccCCc--ccchhhhhcCceeEecch
Confidence 568999999999999999999999999999999994211 1 12232 26666654 444443 3455542211
Q ss_pred hhhhhhcccCCCCccccccCCChhh---------Hh---hhcccccc------cceEEEEeecCCcccccCCCCChhHhh
Q 039928 179 KNLKGARRKKKIPSFRVSYSASPYF---------YL---HHVLPVLI------KHSVVELVVSDGGCLQASLPPHLEEYQ 240 (675)
Q Consensus 179 ~~l~~~~~~~~~~~~rvp~~ss~~y---------Y~---~~VLP~Lk------k~~VI~l~~~d~rLa~~~LP~~~~eiQ 240 (675)
+... ...-++-+..|-.|+- +. +++--++. ..-||+..=...++ +-+
T Consensus 73 --i~~~---~~~g~~fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~c----------~~~ 137 (321)
T PF05830_consen 73 --INQF---SFPGPFFPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWRC----------DEE 137 (321)
T ss_dssp --GGT-------SSEESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTSS-----------HH
T ss_pred --hhhh---cCCCCcChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCcc----------hhH
Confidence 1100 0001111111112211 10 11112222 34677776433332 233
Q ss_pred hhhhhhcccceecchHHHHHHHHHHHHHhcCCCCeEEecccchh--hhhhhcCCccccchhHHHHHHHHHHHHhhhhhcc
Q 039928 241 RLRCRVAFHALRFRQEVQELATRILRRLRAPGRPFIAFDPGMIR--DALAYHGCAELFQDVHTELIQHKRAWMIKRRIVR 318 (675)
Q Consensus 241 rLRCRvnfhALrF~p~IeeLg~~LV~RLR~~g~pyIALHLRfE~--DMLAfSgC~~~~~~~~~el~~~rr~~~~k~~~~k 318 (675)
..||. |..|+-+++|++..+.+-++-=. |..=|.+|-|.-- |.... +|+ +.|...-|.+..
T Consensus 138 aeR~i--f~slkpR~eIqarID~iy~ehf~-g~~~IGVHVRhGngeD~~~h-~~~--~~D~e~~L~~V~----------- 200 (321)
T PF05830_consen 138 AEREI--FSSLKPRPEIQARIDAIYREHFA-GYSVIGVHVRHGNGEDIMDH-APY--WADEERALRQVC----------- 200 (321)
T ss_dssp HHHHH--HHHS-B-HHHHHHHHHHHHHHTT-TSEEEEEEE------------------HHHHHHHHHHH-----------
T ss_pred HHHHH--HHhCCCCHHHHHHHHHHHHHHcC-CCceEEEEEeccCCcchhcc-Ccc--ccCchHHHHHHH-----------
Confidence 44444 99999999999999998777433 4458999999521 11111 111 111111111100
Q ss_pred CccccChhhhhcCCCCCCCHHHHHHHHHHcCCCCceeEEEecccccCcccchhhHHHhccccccccC
Q 039928 319 GKLSVNSMELRLNGTCPLMPEEVGILLRAYGYSWDTIIYVSGGEVFGGQRTLIPLHAMFANVVDRTS 385 (675)
Q Consensus 319 ~~~~i~s~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAaGeiYGG~~~L~pL~~~FPnl~tK~t 385 (675)
.....++++=.+.++.|+||+-. +.-++-|++.||.+++.+.
T Consensus 201 ---------------------~ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k 242 (321)
T PF05830_consen 201 ---------------------TAIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPK 242 (321)
T ss_dssp ---------------------HHHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE----
T ss_pred ---------------------HHHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEccc
Confidence 11123455566778999999986 3578999999999887644
No 4
>KOG3111 consensus D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=41.84 E-value=58 Score=34.08 Aligned_cols=110 Identities=25% Similarity=0.314 Sum_probs=65.9
Q ss_pred ecchHHHHHHHHHHHHHhcC-C-CCeEEecccchh-----hhhhhcCCc------cccchhHHHHHHHHHHHHhhhhhcc
Q 039928 252 RFRQEVQELATRILRRLRAP-G-RPFIAFDPGMIR-----DALAYHGCA------ELFQDVHTELIQHKRAWMIKRRIVR 318 (675)
Q Consensus 252 rF~p~IeeLg~~LV~RLR~~-g-~pyIALHLRfE~-----DMLAfSgC~------~~~~~~~~el~~~rr~~~~k~~~~k 318 (675)
+|+|.| .+|.-+|++||.. + .+|.-+||=.|. |=+|-.|-. +..|+ ..+++++-|+.-.|.+
T Consensus 42 ~FVpNi-T~G~pvV~slR~~~~~~~ffD~HmMV~~Peq~V~~~a~agas~~tfH~E~~q~-~~~lv~~ir~~Gmk~G--- 116 (224)
T KOG3111|consen 42 HFVPNI-TFGPPVVESLRKHTGADPFFDVHMMVENPEQWVDQMAKAGASLFTFHYEATQK-PAELVEKIREKGMKVG--- 116 (224)
T ss_pred cccCCc-ccchHHHHHHHhccCCCcceeEEEeecCHHHHHHHHHhcCcceEEEEEeeccC-HHHHHHHHHHcCCeee---
Confidence 455655 5888999999984 2 269999995442 223444432 11222 4566654433211211
Q ss_pred CccccChhhhhcCCCCCCCHHHHHHHHHHcCCCCceeEEEecccccCcccchh-------hHHHhccccc
Q 039928 319 GKLSVNSMELRLNGTCPLMPEEVGILLRAYGYSWDTIIYVSGGEVFGGQRTLI-------PLHAMFANVV 381 (675)
Q Consensus 319 ~~~~i~s~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAaGeiYGG~~~L~-------pL~~~FPnl~ 381 (675)
+. .=|=||-|....+.. .-+--+-.+---=||||+.|. -||+-|||+.
T Consensus 117 --~a----------lkPgT~Ve~~~~~~~---~~D~vLvMtVePGFGGQkFme~mm~KV~~lR~kyp~l~ 171 (224)
T KOG3111|consen 117 --LA----------LKPGTPVEDLEPLAE---HVDMVLVMTVEPGFGGQKFMEDMMPKVEWLREKYPNLD 171 (224)
T ss_pred --EE----------eCCCCcHHHHHHhhc---cccEEEEEEecCCCchhhhHHHHHHHHHHHHHhCCCce
Confidence 11 235688888777765 334455555556699999886 5888888873
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=33.23 E-value=40 Score=31.88 Aligned_cols=31 Identities=23% Similarity=0.201 Sum_probs=16.4
Q ss_pred CCCCCHHHHHHHHHHcCCCCceeEEEec-cccc
Q 039928 333 TCPLMPEEVGILLRAYGYSWDTIIYVSG-GEVF 364 (675)
Q Consensus 333 ~CPLTPeEVgl~LrALGf~~~T~IYlAa-GeiY 364 (675)
+|||||||+...|++|--+. ...||.. -|..
T Consensus 14 qC~l~ke~~l~~L~~l~~~~-~~~yI~v~rE~H 45 (114)
T PF00799_consen 14 QCSLTKEEALEQLKNLLTPS-NKKYIRVCRELH 45 (114)
T ss_dssp T----HHHHHHHHHH---SS--EEEEEEEEEE-
T ss_pred CCCCCHHHHHHHHHHhCCcc-CceEEEeecccC
Confidence 79999999999999998654 5667643 3443
No 6
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=30.55 E-value=34 Score=30.29 Aligned_cols=43 Identities=19% Similarity=0.297 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHcCCCCceeEEEecccccCcccchhhHHHhccccccccCCCCHHHH
Q 039928 335 PLMPEEVGILLRAYGYSWDTIIYVSGGEVFGGQRTLIPLHAMFANVVDRTSLSTAWEL 392 (675)
Q Consensus 335 PLTPeEVgl~LrALGf~~~T~IYlAaGeiYGG~~~L~pL~~~FPnl~tK~tLat~eEL 392 (675)
++|-.+|+-+|+-+.|+++ +|..|+-++|++++++.-.+-.+.
T Consensus 39 ~~T~~Qv~~il~~f~fd~~---------------kl~~lk~l~p~i~D~~n~~~i~~~ 81 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDND---------------KLKALKLLYPYIVDPQNYYTIIDA 81 (95)
T ss_pred ceeHHHHHHHHHHcCCCHH---------------HHHHHHHHhhhccCHHHHHHHHHH
Confidence 4999999999999998763 699999999999999754333333
No 7
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=30.21 E-value=33 Score=32.28 Aligned_cols=19 Identities=21% Similarity=0.471 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 039928 14 KWVGLIGLILSTFSLLVHI 32 (675)
Q Consensus 14 ~~v~~~~l~ls~~sll~~~ 32 (675)
+||+++|||+..|.+|+-+
T Consensus 1 RW~l~~iii~~i~l~~~~~ 19 (130)
T PF12273_consen 1 RWVLFAIIIVAILLFLFLF 19 (130)
T ss_pred CeeeHHHHHHHHHHHHHHH
Confidence 4777777666666665444
No 8
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=29.53 E-value=43 Score=36.63 Aligned_cols=15 Identities=27% Similarity=0.215 Sum_probs=11.0
Q ss_pred hhHHHHHHHHHHHhH
Q 039928 114 EIRNSISDVVVVARL 128 (675)
Q Consensus 114 QqR~~IcDAVaVARi 128 (675)
.-|.+|||-++.-|-
T Consensus 115 ~~Rva~c~k~a~qr~ 129 (386)
T KOG3849|consen 115 TPRVAICDKSAAQRS 129 (386)
T ss_pred CcceeeeehhhhccC
Confidence 357889999866654
No 9
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=27.32 E-value=49 Score=27.41 Aligned_cols=25 Identities=32% Similarity=0.473 Sum_probs=20.5
Q ss_pred hhcCCCCCCCHHHHHHHHHHcCCCCc
Q 039928 328 LRLNGTCPLMPEEVGILLRAYGYSWD 353 (675)
Q Consensus 328 ~R~~G~CPLTPeEVgl~LrALGf~~~ 353 (675)
.+..|.. ++++|+.-+|+.|||.-+
T Consensus 12 ~~llG~~-i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 12 NRLLGLD-LSAEEIEEILKRLGFEVE 36 (71)
T ss_pred HHHHCCC-CCHHHHHHHHHHCCCeEE
Confidence 4556764 999999999999999753
No 10
>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=25.21 E-value=48 Score=28.32 Aligned_cols=17 Identities=41% Similarity=0.675 Sum_probs=14.6
Q ss_pred CCCCCCCHHHHHHHHHHc
Q 039928 331 NGTCPLMPEEVGILLRAY 348 (675)
Q Consensus 331 ~G~CPLTPeEVgl~LrAL 348 (675)
-|-| +||||-+-+|+++
T Consensus 41 C~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 41 CGDC-ITPEEDREILEAT 57 (60)
T ss_pred hhcc-CCHHHHHHHHHHH
Confidence 4678 9999999999875
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=21.63 E-value=28 Score=33.14 Aligned_cols=17 Identities=47% Similarity=0.532 Sum_probs=12.5
Q ss_pred HHHHHHHcCCCCceeEE
Q 039928 341 VGILLRAYGYSWDTIIY 357 (675)
Q Consensus 341 Vgl~LrALGf~~~T~IY 357 (675)
+.++|||||+.++.-||
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 78999999998877555
Done!