Query 007920
Match_columns 585
No_of_seqs 190 out of 399
Neff 4.0
Searched_HMMs 46136
Date Thu Mar 28 17:06:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007920.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007920hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10250 O-FucT: GDP-fucose pr 100.0 1.6E-52 3.5E-57 424.1 2.3 304 25-434 6-345 (351)
2 KOG3849 GDP-fucose protein O-f 95.8 0.03 6.5E-07 58.7 7.7 60 16-78 27-89 (386)
3 PF05830 NodZ: Nodulation prot 84.1 35 0.00077 36.9 15.0 218 18-302 2-242 (321)
4 KOG3111 D-ribulose-5-phosphate 76.8 6.2 0.00013 40.2 6.2 110 169-298 42-171 (224)
5 PF13756 Stimulus_sens_1: Stim 57.3 26 0.00056 31.9 5.6 28 253-280 1-30 (112)
6 KOG3705 Glycoprotein 6-alpha-L 48.2 44 0.00095 37.6 6.4 100 167-313 340-441 (580)
7 PF00799 Gemini_AL1: Geminivir 37.4 31 0.00067 32.0 2.9 27 250-277 14-40 (114)
8 PF14771 DUF4476: Domain of un 32.1 32 0.0007 29.8 2.0 46 252-312 39-84 (95)
9 PF10892 DUF2688: Protein of u 24.3 51 0.0011 27.6 1.7 17 248-265 41-57 (60)
10 smart00874 B5 tRNA synthetase 23.4 58 0.0012 26.5 1.9 24 245-269 12-35 (71)
11 PF04561 RNA_pol_Rpb2_2: RNA p 20.3 30 0.00066 32.3 -0.3 17 258-274 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=1.6e-52 Score=424.12 Aligned_cols=304 Identities=29% Similarity=0.454 Sum_probs=203.3
Q ss_pred EcCChhhHHHHHHHHHHHHHHhcceEeeccccccccccCCCC--CCCCCCccccHHHHHHHccccceeeccCchhHHhhc
Q 007920 25 VFGGFEKIRSSICDLVTISRLLNATLVIPEIQESLRSKGISY--KFKSFSYLYNEEQFIASLARDVIIVKSLPENLKAAR 102 (585)
Q Consensus 25 anGGLNQqR~~IcDaVaVARiLNATLVIP~Ld~~s~~~~d~s--d~s~F~DIFD~dhFI~sL~~DVrIVk~LP~~l~~~~ 102 (585)
+.||+||||.+|++||++|++||+|||||.+..... |++.+ ..-.|+++||++||++.++.+|.+++.+|..+....
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 789999999999999999999999999999999874 44432 122499999999999999999999999987776542
Q ss_pred cc---------------------------CCCCccCCCC-CCChhHHHHhhhhhhhcc------ceEEEeecCCcccccC
Q 007920 103 KR---------------------------NEFPTFKPKV-STSPNYYIQEVLPKLKRT------QVIGLILTDGGCLQSI 148 (585)
Q Consensus 103 ~~---------------------------~~i~~~~vp~-~ss~~yY~~~VlP~L~k~------~VI~l~~~d~rla~~~ 148 (585)
.. .....+.... ++.+.+|+++++|++.++ +|+.|..+...+..+.
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 1112233333 678889999999999987 9999999988877765
Q ss_pred CCCChhHHhhhhhhccccccccchHHHHHHHHHHHHHHhcCCCeEEeccchhhhhhhhhccccccchhHHHHHHHHHHHh
Q 007920 149 LPPSMSELQRLRCRVAFHALQFRPEIEILGRLMVERLRAWGQPFLAYHPGLVRETLAYHGCAELFQDVHTELIQYRRAQM 228 (585)
Q Consensus 149 LP~~~~eiQrLRCrvnf~ALrF~p~Ie~LG~~LV~RLR~~g~pyIALHLRfEkDMLAfSgC~~~~~~~~~el~~~rr~~~ 228 (585)
+++ ++|| +|+|+++|+++|+++|++|+..+++|||+|||+|+|| +++|.+.. ...+++.-|.+
T Consensus 165 ~~~---~~~r--------~l~~~~~i~~~a~~~i~~~~~~~~~yiavHlR~~~D~--~~~C~~~~---~~~~~~~~~~~- 227 (351)
T PF10250_consen 165 LDR---DLQR--------YLRFSPEIRELADKFIKRLLAGGGPYIAVHLRRGKDW--FSACEFKG---ERHLLASPRCW- 227 (351)
T ss_dssp GGG---GGGG--------G--B-HHHHHHHHHHHHHH----SSEEEEEE--SHHH--HHHHCT-T-------TTTHHHH-
T ss_pred cCc---cceE--------EEecCHHHHHHHHHHHHHhhcccCceEEEeecccCch--HhhcccCC---chHHHHHhHhh-
Confidence 553 6777 9999999999999999999965679999999999999 99999743 44444443332
Q ss_pred hhccccccccccCchhhccCCCCCCCHHHHHHHHHhcCCCCCceEEEecccccCCccchhhHHHhccCccccccCCChhh
Q 007920 229 IRQGIVNEELSVDSHLRRDNGSCPLMPEEVGILLRAMGYPPKTIIYLAGSETFGGHRVLIPLRAMFSNLVDRTSLCSQKE 308 (585)
Q Consensus 229 ~k~~~~k~~~~i~~~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAaGeIyGG~~~m~pL~~~FPnl~~k~tLat~~E 308 (585)
++..+.+...+..|.||++|++++.+++++|+.+.|.||||++++|||.+.|.+|+++||++++|++|.+.+|
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 2335667788889999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccccCCCCCCCCCCCCCCCcchhHHHHHHHhhcCCCCCCCCCCCCCccccccccccccccccCCCCCCCchhhhhhhhh
Q 007920 309 FSDLIGPETSLPQDLFQPPPAKSEKQLKEEWNKAGPRPRPLSPPPDRPIYLHEKEGWYGWITESDTEPSPSAMDLRNQAH 388 (585)
Q Consensus 309 L~~f~g~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~rp~~~~~p~~rp~y~~~~e~~~~~~~~~~~e~~~s~~~~r~~~h 388 (585)
+++|.+
T Consensus 301 ~~~~~~-------------------------------------------------------------------------- 306 (351)
T PF10250_consen 301 LEPLND-------------------------------------------------------------------------- 306 (351)
T ss_dssp S-------------------------------------------------------------------------------
T ss_pred hhhccc--------------------------------------------------------------------------
Confidence 999863
Q ss_pred hhhhhhhheeeeeccceeccccCCCCCCcCchHHhhhhccccccCC
Q 007920 389 RLLWDALDYIVSVEADAFFPGFHNDGSKWPDFASLVMGQRLYESAA 434 (585)
Q Consensus 389 ~l~~AALDYiV~l~SDvFvpt~~~~G~g~~Nma~~v~GhR~Y~g~~ 434 (585)
.++|+|||+||+.||+||.+. || .|+..|+++|.|.|..
T Consensus 307 -~~~a~vD~~i~~~s~~Figt~---~S---tfs~~i~~~R~~~g~~ 345 (351)
T PF10250_consen 307 -DQLAMVDQEICSRSDVFIGTC---GS---TFSSNIARERHYRGKP 345 (351)
T ss_dssp -S--HHHHHHHHHHSSEEEE-T---T----HHHHHHHHHHHHSSSS
T ss_pred -cchhHHHHHHHhcCCEEEecC---cc---hhHHHhhcccCcCCCC
Confidence 235999999999999999874 43 8999999999999974
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=95.77 E-value=0.03 Score=58.72 Aligned_cols=60 Identities=22% Similarity=0.388 Sum_probs=45.6
Q ss_pred CCCceEEE-EEcCChhhHHHHHHHHHHHHHHhcceEeeccccccccccCCC--CCCCCCCccccHH
Q 007920 16 ENNGFIYA-KVFGGFEKIRSSICDLVTISRLLNATLVIPEIQESLRSKGIS--YKFKSFSYLYNEE 78 (585)
Q Consensus 16 ~snGYL~V-~anGGLNQqR~~IcDaVaVARiLNATLVIP~Ld~~s~~~~d~--sd~s~F~DIFD~d 78 (585)
..||||+. -|-|-+.+|-...--..|.|+.||.|||||-.-. ++..+ +---.|...|.++
T Consensus 27 DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiE---y~~pe~~n~~vpf~~yF~ve 89 (386)
T KOG3849|consen 27 DPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIE---YKHPETKNLMVPFEFYFQVE 89 (386)
T ss_pred CCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchh---ccCCcccccccchhheeecc
Confidence 46999987 8999999999999999999999999999996532 11111 1123577788765
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=84.14 E-value=35 Score=36.88 Aligned_cols=218 Identities=17% Similarity=0.134 Sum_probs=101.7
Q ss_pred CceEEEEEcCChhhHHHHHHHHHHHHHHhcceEeeccccccccccCCCCCCCCCCccccHHHHHHHcc--ccceeeccCc
Q 007920 18 NGFIYAKVFGGFEKIRSSICDLVTISRLLNATLVIPEIQESLRSKGISYKFKSFSYLYNEEQFIASLA--RDVIIVKSLP 95 (585)
Q Consensus 18 nGYL~V~anGGLNQqR~~IcDaVaVARiLNATLVIP~Ld~~s~~~~d~sd~s~F~DIFD~dhFI~sL~--~DVrIVk~LP 95 (585)
..|++.+--+||+.-=-+++-|-.+|+-.|-||||=-=. + .+-+ ..|...|++ |-+-.+ ..|+|+-.=+
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-CYLD-----QPFTNAFPV--FFEPVEDIAGVRVICDDR 72 (321)
T ss_dssp --EEEEE--S-HHHHHHHHHHHHHHHHHHT-EEEEE-BT---TT-S-----STTSBSHHH--HB---SEETTEEEE-SGG
T ss_pred CceEEEeccCCchhHHHHHHHHHHHHHHhCCeEEEEcCC-c-eecC-----CcccccCCc--ccchhhhhcCceeEecch
Confidence 568999999999999999999999999999999984211 1 1222 247776654 545444 2455542211
Q ss_pred hhHHhhcccCCCCccCCCCCC-ChhH---------H---HHhhhhhhh------ccceEEEeecCCcccccCCCCChhHH
Q 007920 96 ENLKAARKRNEFPTFKPKVST-SPNY---------Y---IQEVLPKLK------RTQVIGLILTDGGCLQSILPPSMSEL 156 (585)
Q Consensus 96 ~~l~~~~~~~~i~~~~vp~~s-s~~y---------Y---~~~VlP~L~------k~~VI~l~~~d~rla~~~LP~~~~ei 156 (585)
+... ...-++- |.|+ .|.- . .+++--++. ...||+..-.--++ +-
T Consensus 73 --i~~~---~~~g~~f-p~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~c----------~~ 136 (321)
T PF05830_consen 73 --INQF---SFPGPFF-PAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWRC----------DE 136 (321)
T ss_dssp --GGT-------SSEE-SGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTSS-----------H
T ss_pred --hhhh---cCCCCcC-hhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCcc----------hh
Confidence 1000 0000111 2222 2211 1 112222222 33566665332221 23
Q ss_pred hhhhhhccccccccchHHHHHHHHHHHHHHhcCCCeEEeccchh--hhhhhhhccccccchhHHHHHHHHHHHhhhcccc
Q 007920 157 QRLRCRVAFHALQFRPEIEILGRLMVERLRAWGQPFLAYHPGLV--RETLAYHGCAELFQDVHTELIQYRRAQMIRQGIV 234 (585)
Q Consensus 157 QrLRCrvnf~ALrF~p~Ie~LG~~LV~RLR~~g~pyIALHLRfE--kDMLAfSgC~~~~~~~~~el~~~rr~~~~k~~~~ 234 (585)
+..||. |..|+-+++|++..+.+-+.-= .|..=|++|-|.= +|.... +|. +.|.+.-|-+...
T Consensus 137 ~aeR~i--f~slkpR~eIqarID~iy~ehf-~g~~~IGVHVRhGngeD~~~h-~~~--~~D~e~~L~~V~~--------- 201 (321)
T PF05830_consen 137 EAEREI--FSSLKPRPEIQARIDAIYREHF-AGYSVIGVHVRHGNGEDIMDH-APY--WADEERALRQVCT--------- 201 (321)
T ss_dssp HHHHHH--HHHS-B-HHHHHHHHHHHHHHT-TTSEEEEEEE------------------HHHHHHHHHHHH---------
T ss_pred HHHHHH--HHhCCCCHHHHHHHHHHHHHHc-CCCceEEEEEeccCCcchhcc-Ccc--ccCchHHHHHHHH---------
Confidence 444444 8999999999987777665532 2335799999942 122222 222 2222111111111
Q ss_pred ccccccCchhhccCCCCCCCHHHHHHHHHhcCCCCCceEEEecccccCCccchhhHHHhccCcccccc
Q 007920 235 NEELSVDSHLRRDNGSCPLMPEEVGILLRAMGYPPKTIIYLAGSETFGGHRVLIPLRAMFSNLVDRTS 302 (585)
Q Consensus 235 k~~~~i~~~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAaGeIyGG~~~m~pL~~~FPnl~~k~t 302 (585)
....++++=.+.++.|+||+-. +.-++-|++.||.+++-+.
T Consensus 202 -----------------------ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k 242 (321)
T PF05830_consen 202 -----------------------AIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPK 242 (321)
T ss_dssp -----------------------HHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE----
T ss_pred -----------------------HHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEccc
Confidence 1112355666778999999998 6779999999999876643
No 4
>KOG3111 consensus D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=76.77 E-value=6.2 Score=40.18 Aligned_cols=110 Identities=29% Similarity=0.447 Sum_probs=69.8
Q ss_pred ccchHHHHHHHHHHHHHHhc-C-CCeEEeccchhh-----hhhhhhccc------cccchhHHHHHHHHHHHhhhccccc
Q 007920 169 QFRPEIEILGRLMVERLRAW-G-QPFLAYHPGLVR-----ETLAYHGCA------ELFQDVHTELIQYRRAQMIRQGIVN 235 (585)
Q Consensus 169 rF~p~Ie~LG~~LV~RLR~~-g-~pyIALHLRfEk-----DMLAfSgC~------~~~~~~~~el~~~rr~~~~k~~~~k 235 (585)
+|+|.| .+|.-+|++||.+ + .+|.-+||=.|. |=+|-.|-. |..|+ ..+++++-|+.-.|-+
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 677877 6899999999995 2 259999996553 223333322 22233 4567665554222222
Q ss_pred cccccCchhhccCCCCCCCHHHHHHHHHhcCCCCCceEEEecccccCCccchh-------hHHHhccCcc
Q 007920 236 EELSVDSHLRRDNGSCPLMPEEVGILLRAMGYPPKTIIYLAGSETFGGHRVLI-------PLRAMFSNLV 298 (585)
Q Consensus 236 ~~~~i~~~~~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAaGeIyGG~~~m~-------pL~~~FPnl~ 298 (585)
+.++ |=||-|....+.. .-+-.+-.+---=||||+.|. -||+.|||+.
T Consensus 117 --~alk----------PgT~Ve~~~~~~~---~~D~vLvMtVePGFGGQkFme~mm~KV~~lR~kyp~l~ 171 (224)
T KOG3111|consen 117 --LALK----------PGTPVEDLEPLAE---HVDMVLVMTVEPGFGGQKFMEDMMPKVEWLREKYPNLD 171 (224)
T ss_pred --EEeC----------CCCcHHHHHHhhc---cccEEEEEEecCCCchhhhHHHHHHHHHHHHHhCCCce
Confidence 2332 5688898877766 234445555555799999986 5899999984
No 5
>PF13756 Stimulus_sens_1: Stimulus-sensing domain
Probab=57.31 E-value=26 Score=31.94 Aligned_cols=28 Identities=32% Similarity=0.428 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHhcCCCCCce--EEEecccc
Q 007920 253 LMPEEVGILLRAMGYPPKTI--IYLAGSET 280 (585)
Q Consensus 253 LTPeEVgl~LrALGf~~~T~--IYlAaGeI 280 (585)
|.|+-|+-||+-|.-+.+|+ ||=+.|.+
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 55566654
No 6
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=48.16 E-value=44 Score=37.59 Aligned_cols=100 Identities=15% Similarity=0.267 Sum_probs=57.3
Q ss_pred ccccchHHHHHHHHHHHHHHhcC--CCeEEeccchhhhhhhhhccccccchhHHHHHHHHHHHhhhccccccccccCchh
Q 007920 167 ALQFRPEIEILGRLMVERLRAWG--QPFLAYHPGLVRETLAYHGCAELFQDVHTELIQYRRAQMIRQGIVNEELSVDSHL 244 (585)
Q Consensus 167 ALrF~p~Ie~LG~~LV~RLR~~g--~pyIALHLRfEkDMLAfSgC~~~~~~~~~el~~~rr~~~~k~~~~k~~~~i~~~~ 244 (585)
-+||.|-.++ +|-+-|++.| +|-|+||.|-..-.=.-..|. . -+|-+.+-..|+ +
T Consensus 340 L~Rpqp~t~~---~l~~a~k~lg~~~PivGvhvRRTDKVGTEAAfH----~-~eEYM~~vE~~f------~--------- 396 (580)
T KOG3705|consen 340 LMRPQPATQE---KLDKALKSLGLDKPIVGVHVRRTDKVGTEAAFH----A-LEEYMEWVEIWF------K--------- 396 (580)
T ss_pred HhCCChhhHH---HHHHHHHhCCCCCceeeEEEEecccccchhhhh----h-HHHHHHHHHHHH------H---------
Confidence 4788888876 6777777754 699999998742211111121 0 122222222231 0
Q ss_pred hccCCCCCCCHHHHHHHHHhcCCCCCceEEEecccccCCccchhhHHHhccCccccccCCChhhhcccc
Q 007920 245 RRDNGSCPLMPEEVGILLRAMGYPPKTIIYLAGSETFGGHRVLIPLRAMFSNLVDRTSLCSQKEFSDLI 313 (585)
Q Consensus 245 ~R~~G~CPLTPeEVgl~LrALGf~~~T~IYlAaGeIyGG~~~m~pL~~~FPnl~~k~tLat~~EL~~f~ 313 (585)
+|..=|=+-.-+||||+... .-+.--+.-|||. .+.+.-|.+...
T Consensus 397 ----------------~le~rg~~~~rRiflAsDDp----~vv~EAk~kYPnY----e~igd~eia~~A 441 (580)
T KOG3705|consen 397 ----------------VLEKRGKPLERRIFLASDDP----TVVPEAKNKYPNY----EVIGDTEIAKTA 441 (580)
T ss_pred ----------------HHHHhCCchhheEEEecCCc----hhchHhhccCCCc----EEeccHHHHHHh
Confidence 11122334456899999984 4566778889997 344555555544
No 7
>PF00799 Gemini_AL1: Geminivirus Rep catalytic domain; InterPro: IPR022690 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome []. For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer []. It is found in association with PF08283 from PFAM. ; GO: 0006260 DNA replication; PDB: 1L5I_A 1L2M_A.
Probab=37.38 E-value=31 Score=32.01 Aligned_cols=27 Identities=26% Similarity=0.336 Sum_probs=15.2
Q ss_pred CCCCCHHHHHHHHHhcCCCCCceEEEec
Q 007920 250 SCPLMPEEVGILLRAMGYPPKTIIYLAG 277 (585)
Q Consensus 250 ~CPLTPeEVgl~LrALGf~~~T~IYlAa 277 (585)
+||||+||+...|++|--+ ....||..
T Consensus 14 qC~l~ke~~l~~L~~l~~~-~~~~yI~v 40 (114)
T PF00799_consen 14 QCSLTKEEALEQLKNLLTP-SNKKYIRV 40 (114)
T ss_dssp T----HHHHHHHHHH---S-S-EEEEEE
T ss_pred CCCCCHHHHHHHHHHhCCc-cCceEEEe
Confidence 7999999999999999765 36667644
No 8
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=32.09 E-value=32 Score=29.85 Aligned_cols=46 Identities=13% Similarity=0.210 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHhcCCCCCceEEEecccccCCccchhhHHHhccCccccccCCChhhhccc
Q 007920 252 PLMPEEVGILLRAMGYPPKTIIYLAGSETFGGHRVLIPLRAMFSNLVDRTSLCSQKEFSDL 312 (585)
Q Consensus 252 PLTPeEVgl~LrALGf~~~T~IYlAaGeIyGG~~~m~pL~~~FPnl~~k~tLat~~EL~~f 312 (585)
++|-.+|+-+|+-+.|++ .+|..|+-++|+++|++.--+-.+...|
T Consensus 39 ~~T~~Qv~~il~~f~fd~---------------~kl~~lk~l~p~i~D~~n~~~i~~~f~f 84 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDN---------------DKLKALKLLYPYIVDPQNYYTIIDAFSF 84 (95)
T ss_pred ceeHHHHHHHHHHcCCCH---------------HHHHHHHHHhhhccCHHHHHHHHHHhcC
Confidence 499999999999998874 4699999999999999754444444333
No 9
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=24.33 E-value=51 Score=27.61 Aligned_cols=17 Identities=41% Similarity=0.710 Sum_probs=14.5
Q ss_pred CCCCCCCHHHHHHHHHhc
Q 007920 248 NGSCPLMPEEVGILLRAM 265 (585)
Q Consensus 248 ~G~CPLTPeEVgl~LrAL 265 (585)
-|-| +||||-+-+|+++
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 10
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=23.44 E-value=58 Score=26.46 Aligned_cols=24 Identities=29% Similarity=0.419 Sum_probs=20.0
Q ss_pred hccCCCCCCCHHHHHHHHHhcCCCC
Q 007920 245 RRDNGSCPLMPEEVGILLRAMGYPP 269 (585)
Q Consensus 245 ~R~~G~CPLTPeEVgl~LrALGf~~ 269 (585)
.+..|.. ++++|+.-+|+.|||.-
T Consensus 12 ~~llG~~-i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 12 NRLLGLD-LSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHHCCC-CCHHHHHHHHHHCCCeE
Confidence 4556654 99999999999999975
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=20.30 E-value=30 Score=32.32 Aligned_cols=17 Identities=41% Similarity=0.563 Sum_probs=12.6
Q ss_pred HHHHHHhcCCCCCceEE
Q 007920 258 VGILLRAMGYPPKTIIY 274 (585)
Q Consensus 258 Vgl~LrALGf~~~T~IY 274 (585)
+.++|||||+.++.-||
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 78999999998877665
Done!