Query 013112
Match_columns 449
No_of_seqs 179 out of 381
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 00:31:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013112.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013112hhsearch_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 5.3E-45 1.1E-49 357.5 3.3 256 159-439 6-297 (351)
2 KOG3849 GDP-fucose protein O-f 96.5 0.014 3E-07 59.4 9.6 60 150-209 27-90 (386)
3 PF05830 NodZ: Nodulation prot 94.0 0.54 1.2E-05 48.6 11.1 215 152-438 2-244 (321)
4 PF14771 DUF4476: Domain of un 59.2 6.2 0.00014 33.1 1.8 40 386-440 39-78 (95)
5 PF00799 Gemini_AL1: Geminivir 45.4 22 0.00048 31.8 3.1 27 384-411 14-40 (114)
6 KOG4753 Predicted membrane pro 38.0 62 0.0013 29.7 4.8 57 32-88 12-68 (124)
7 PF10892 DUF2688: Protein of u 37.4 24 0.00051 28.6 1.8 16 383-399 42-57 (60)
8 PLN02232 ubiquinone biosynthes 37.2 1.4E+02 0.003 27.1 7.0 29 386-414 125-153 (160)
9 smart00874 B5 tRNA synthetase 30.7 41 0.00089 26.3 2.2 26 378-404 11-36 (71)
10 PF04561 RNA_pol_Rpb2_2: RNA p 27.9 19 0.00041 32.5 -0.2 17 392-408 54-70 (190)
11 PF03032 Brevenin: Brevenin/es 24.6 45 0.00098 25.6 1.4 14 78-91 7-20 (46)
12 TIGR01354 cyt_deam_tetra cytid 24.4 84 0.0018 28.0 3.3 46 387-436 80-126 (127)
13 PF13756 Stimulus_sens_1: Stim 21.9 99 0.0022 27.1 3.2 32 387-418 1-34 (112)
14 PLN00126 succinate dehydrogena 20.9 1.8E+02 0.004 26.7 4.7 12 1-12 34-45 (129)
15 KOG3111 D-ribulose-5-phosphate 20.1 3.7E+02 0.008 27.0 6.9 112 299-432 42-171 (224)
16 PF03484 B5: tRNA synthetase B 20.0 67 0.0014 25.6 1.6 27 378-405 11-37 (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=5.3e-45 Score=357.49 Aligned_cols=256 Identities=34% Similarity=0.624 Sum_probs=171.0
Q ss_pred ecCChhhHHHHHHHHHHHHHHhcceEeecccccCccccCCCC-----CCccccHHHHHHhccCceEEeccCChhhcccch
Q 013112 159 AEGGLNQQRIAICNAVAVAKIMNATLILPVLKQDQIWKDQTK-----FEDIFDVDHFIDYLKDDVRIVRDIPDWFTDKSE 233 (449)
Q Consensus 159 ~nGGLNQqR~~IcDAVaVARiLNATLViP~Ld~~s~W~D~S~-----F~dIFDvdhFI~sL~~dVrIVk~LP~~~~~~~~ 233 (449)
+.||+||||+++++||++|++||+|||||.+...+.|++.++ |+++||+++|++.++.+|++.+.+|..+.....
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 789999999999999999999999999999999999999887 999999999999999999999999876543211
Q ss_pred hh------------------------hhhhcccccCCC-CCChhhhHhhcccccccc------ceEEEccccccCCCCCC
Q 013112 234 LF------------------------SSIRRTVKNIPK-YAPAQFYIDNVLPRIKEK------KIMALKPFVDRLGYDNV 282 (449)
Q Consensus 234 ~~------------------------~~i~~~~~~~p~-~ss~~yY~~~VLP~l~k~------~VI~l~~f~~rLa~d~l 282 (449)
+. ............ |+.+.+|+++++|.+.++ +|+.|.++...+..+.+
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 00 000001112233 788889999999999886 99999999999988778
Q ss_pred CccccccceeecccccccchHHHHHHHHHHHHHHhhcCCCCCceEeeechhhhhhhhccccCCCCHHHHHHHHHHHhhcc
Q 013112 283 PPEINRLRCRVNYHALKFLPEIEQMSDLLASRMKNRTGSSNPYMALHLRFEKGMVGLSFCDFVGTREEKAKMAEYRKKEW 362 (449)
Q Consensus 283 P~eiQrLRCrvnF~ALrF~p~I~~lg~~LV~RmR~~s~~s~pfiALHLRfE~DMLAfSgC~~gg~~~E~~eL~~~R~~~w 362 (449)
+.++|| +|+|.++|+++|++++++|+. ++++|||+|||+|+|| +++|.+++ ++..|+.+|..
T Consensus 166 ~~~~~r--------~l~~~~~i~~~a~~~i~~~~~---~~~~yiavHlR~~~D~--~~~C~~~~---~~~~~~~~~~~-- 227 (351)
T PF10250_consen 166 DRDLQR--------YLRFSPEIRELADKFIKRLLA---GGGPYIAVHLRRGKDW--FSACEFKG---ERHLLASPRCW-- 227 (351)
T ss_dssp GGGGGG--------G--B-HHHHHHHHHHHHHH-------SSEEEEEE--SHHH--HHHHCT-T-------TTTHHHH--
T ss_pred CccceE--------EEecCHHHHHHHHHHHHHhhc---ccCceEEEeecccCch--HhhcccCC---chHHHHHhHhh--
Confidence 889987 999999999999999999993 2579999999999999 99999955 77778777754
Q ss_pred cccccCCCcchhhhHhhhcCCCCCCChHHHHHHHHHhCCCCCceEEEeeccccCCccchhchHHhCCCcccccchhH
Q 013112 363 PRRYKNGSHLWQLALQKRKEGRCPLEPGEVAVILRAMGYPKETQIYVASGQVYGGQNRMAPLRNMFPNLVRPLNSFL 439 (449)
Q Consensus 363 ~~k~~~~~~~~~~~~~~R~~G~CPLTPeEvgl~LrALGf~~~T~IYlAsgeiyGG~~~l~pLr~~FPnl~tKe~~~~ 439 (449)
.++..+ +.+.+..|.||++|++++.+++++|+.+.|.||||++++|||++.|.+|+++||++++|+++..
T Consensus 228 ~~~~~~-------~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~ 297 (351)
T PF10250_consen 228 GKKSIN-------PEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLS 297 (351)
T ss_dssp -GGGTT------------HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--E
T ss_pred cccccc-------chhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCC
Confidence 111122 3457888999999999999999999999999999999999999999999999999999988754
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=96.54 E-value=0.014 Score=59.40 Aligned_cols=60 Identities=28% Similarity=0.413 Sum_probs=47.3
Q ss_pred CCCceEEE-EecCChhhHHHHHHHHHHHHHHhcceEeeccc---ccCccccCCCCCCccccHHH
Q 013112 150 ETNGYIFI-HAEGGLNQQRIAICNAVAVAKIMNATLILPVL---KQDQIWKDQTKFEDIFDVDH 209 (449)
Q Consensus 150 ~snGYL~V-~~nGGLNQqR~~IcDAVaVARiLNATLViP~L---d~~s~W~D~S~F~dIFDvdh 209 (449)
..||||+. -|-|-+.||-...--..|.|+.||.|||+|.. ++-.+-+---.|+..|.++-
T Consensus 27 DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiEy~~pe~~n~~vpf~~yF~vep 90 (386)
T KOG3849|consen 27 DPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIEYKHPETKNLMVPFEFYFQVEP 90 (386)
T ss_pred CCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchhccCCcccccccchhheeeccc
Confidence 46999988 69999999999999999999999999999954 33333222457888887753
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=94.04 E-value=0.54 Score=48.63 Aligned_cols=215 Identities=17% Similarity=0.310 Sum_probs=105.1
Q ss_pred CceEEEEecCChhhHHHHHHHHHHHHHHhcceEeecccccCccccC----CCCCCccccHHHHHHhcc--CceEEe-ccC
Q 013112 152 NGYIFIHAEGGLNQQRIAICNAVAVAKIMNATLILPVLKQDQIWKD----QTKFEDIFDVDHFIDYLK--DDVRIV-RDI 224 (449)
Q Consensus 152 nGYL~V~~nGGLNQqR~~IcDAVaVARiLNATLViP~Ld~~s~W~D----~S~F~dIFDvdhFI~sL~--~dVrIV-k~L 224 (449)
+.|++..--+|+|.-=-+++-|-.+|+-.|.||||= |++ ...|...|++ |-+-.+ ..|+|+ .+-
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 578999999999999999999999999999999995 665 3567777765 555544 345555 211
Q ss_pred ChhhcccchhhhhhhcccccCCCC-CCh---------hh-hHh--hcccccc------ccceEEEccccccCCCCCCCcc
Q 013112 225 PDWFTDKSELFSSIRRTVKNIPKY-APA---------QF-YID--NVLPRIK------EKKIMALKPFVDRLGYDNVPPE 285 (449)
Q Consensus 225 P~~~~~~~~~~~~i~~~~~~~p~~-ss~---------~y-Y~~--~VLP~l~------k~~VI~l~~f~~rLa~d~lP~e 285 (449)
=.+++-.. --+|.| ..+ .+ +.+ ++--+++ ...||...=+.|+= +
T Consensus 73 i~~~~~~g----------~~fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~c-------~ 135 (321)
T PF05830_consen 73 INQFSFPG----------PFFPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWRC-------D 135 (321)
T ss_dssp GGT----S----------SEESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTSS--------
T ss_pred hhhhcCCC----------CcChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCcc-------h
Confidence 11111000 011222 111 11 111 1112222 34577777555542 1
Q ss_pred ccccceeecccccccchHHHHHHHHHHHHHHhhcCCCCCceEeeechh--hhhhhhccccCCCCHHHHHHHHHHHhhccc
Q 013112 286 INRLRCRVNYHALKFLPEIEQMSDLLASRMKNRTGSSNPYMALHLRFE--KGMVGLSFCDFVGTREEKAKMAEYRKKEWP 363 (449)
Q Consensus 286 iQrLRCrvnF~ALrF~p~I~~lg~~LV~RmR~~s~~s~pfiALHLRfE--~DMLAfSgC~~gg~~~E~~eL~~~R~~~w~ 363 (449)
-+..|| -|..|+-+++|++..+.+...-=. +..=|++|-|.= +|.+.+ +|++ . ++...|.+.
T Consensus 136 ~~aeR~--if~slkpR~eIqarID~iy~ehf~----g~~~IGVHVRhGngeD~~~h-~~~~--~-D~e~~L~~V------ 199 (321)
T PF05830_consen 136 EEAERE--IFSSLKPRPEIQARIDAIYREHFA----GYSVIGVHVRHGNGEDIMDH-APYW--A-DEERALRQV------ 199 (321)
T ss_dssp HHHHHH--HHHHS-B-HHHHHHHHHHHHHHTT----TSEEEEEEE------------------H-HHHHHHHHH------
T ss_pred hHHHHH--HHHhCCCCHHHHHHHHHHHHHHcC----CCceEEEEEeccCCcchhcc-Cccc--c-CchHHHHHH------
Confidence 223343 389999999999999998766422 235799999922 222222 2221 0 100011100
Q ss_pred ccccCCCcchhhhHhhhcCCCCCCChHHHHHHHHHhCCCCCceEEEeeccccCCccchhchHHhCCCcccccchh
Q 013112 364 RRYKNGSHLWQLALQKRKEGRCPLEPGEVAVILRAMGYPKETQIYVASGQVYGGQNRMAPLRNMFPNLVRPLNSF 438 (449)
Q Consensus 364 ~k~~~~~~~~~~~~~~R~~G~CPLTPeEvgl~LrALGf~~~T~IYlAsgeiyGG~~~l~pLr~~FPnl~tKe~~~ 438 (449)
......++++=.+.++.|+||+-. .+-++-+++.||.+++-+.-|
T Consensus 200 --------------------------~~ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k~F 244 (321)
T PF05830_consen 200 --------------------------CTAIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPKQF 244 (321)
T ss_dssp --------------------------HHHHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE------
T ss_pred --------------------------HHHHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEccccc
Confidence 011123456667778999999987 668999999999998875544
No 4
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=59.22 E-value=6.2 Score=33.07 Aligned_cols=40 Identities=20% Similarity=0.494 Sum_probs=35.1
Q ss_pred CCChHHHHHHHHHhCCCCCceEEEeeccccCCccchhchHHhCCCcccccchhHH
Q 013112 386 PLEPGEVAVILRAMGYPKETQIYVASGQVYGGQNRMAPLRNMFPNLVRPLNSFLM 440 (449)
Q Consensus 386 PLTPeEvgl~LrALGf~~~T~IYlAsgeiyGG~~~l~pLr~~FPnl~tKe~~~~~ 440 (449)
++|-.+++-+|+-+.|+++ +|..|+-++|++++++|-..+
T Consensus 39 ~~T~~Qv~~il~~f~fd~~---------------kl~~lk~l~p~i~D~~n~~~i 78 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDND---------------KLKALKLLYPYIVDPQNYYTI 78 (95)
T ss_pred ceeHHHHHHHHHHcCCCHH---------------HHHHHHHHhhhccCHHHHHHH
Confidence 4999999999999998753 699999999999999987654
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=45.40 E-value=22 Score=31.82 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=14.9
Q ss_pred CCCCChHHHHHHHHHhCCCCCceEEEee
Q 013112 384 RCPLEPGEVAVILRAMGYPKETQIYVAS 411 (449)
Q Consensus 384 ~CPLTPeEvgl~LrALGf~~~T~IYlAs 411 (449)
+|||||||+...|++|--+. ...||..
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 69999999999999997653 5667643
No 6
>KOG4753 consensus Predicted membrane protein [Function unknown]
Probab=37.97 E-value=62 Score=29.70 Aligned_cols=57 Identities=12% Similarity=0.154 Sum_probs=35.1
Q ss_pred CCCCCCCCCcccCCcccccccccCCCCCCCCCcccccccchHHHHHHHHHHHHHHhh
Q 013112 32 QHADDDDDGRSRHLFRDRVRSIWSYFPFVSDDPRVSQQNSRISLCLALFVVVAGLIS 88 (449)
Q Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (449)
.+.+.++-.+.+|.+++.|-.+--...+-..+||.+-...+...+|+++..++-.++
T Consensus 12 ~dss~~~~~y~~~~~s~~Dsd~~~~~~~~~s~tr~P~k~i~lavvL~~fg~Lli~lg 68 (124)
T KOG4753|consen 12 RDSSRTSMAYSDHAFSISDSDIQIDYSYKVSNTRHPVKEIALAVVLLVFGLLLIGLG 68 (124)
T ss_pred cCCCccchhhcccccccccccceeecccccCCCCCchHHHHHHHHHHHHHHHHHHHH
Confidence 334445567788888887766665566667778888776666555554443333333
No 7
>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=37.42 E-value=24 Score=28.55 Aligned_cols=16 Identities=44% Similarity=0.744 Sum_probs=14.2
Q ss_pred CCCCCChHHHHHHHHHh
Q 013112 383 GRCPLEPGEVAVILRAM 399 (449)
Q Consensus 383 G~CPLTPeEvgl~LrAL 399 (449)
|-| +||||-+-+++++
T Consensus 42 ~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDC-ITPEEDREILEAT 57 (60)
T ss_pred hcc-CCHHHHHHHHHHH
Confidence 578 9999999999875
No 8
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=37.15 E-value=1.4e+02 Score=27.11 Aligned_cols=29 Identities=14% Similarity=0.257 Sum_probs=25.6
Q ss_pred CCChHHHHHHHHHhCCCCCceEEEeeccc
Q 013112 386 PLEPGEVAVILRAMGYPKETQIYVASGQV 414 (449)
Q Consensus 386 PLTPeEvgl~LrALGf~~~T~IYlAsgei 414 (449)
+++|+|..-+|+.-||.+-+.-+++.|-+
T Consensus 125 f~~~~el~~ll~~aGF~~~~~~~~~~g~~ 153 (160)
T PLN02232 125 YLTGEELETLALEAGFSSACHYEISGGFM 153 (160)
T ss_pred CcCHHHHHHHHHHcCCCcceEEECcchHh
Confidence 58999999999999999998888887754
No 9
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=30.69 E-value=41 Score=26.32 Aligned_cols=26 Identities=31% Similarity=0.442 Sum_probs=21.3
Q ss_pred hhhcCCCCCCChHHHHHHHHHhCCCCC
Q 013112 378 QKRKEGRCPLEPGEVAVILRAMGYPKE 404 (449)
Q Consensus 378 ~~R~~G~CPLTPeEvgl~LrALGf~~~ 404 (449)
-.+..|.. ++++|+.-+|+.|||.-+
T Consensus 11 i~~llG~~-i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 11 INRLLGLD-LSAEEIEEILKRLGFEVE 36 (71)
T ss_pred HHHHHCCC-CCHHHHHHHHHHCCCeEE
Confidence 35666765 999999999999999753
No 10
>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=27.92 E-value=19 Score=32.48 Aligned_cols=17 Identities=29% Similarity=0.712 Sum_probs=12.9
Q ss_pred HHHHHHHhCCCCCceEE
Q 013112 392 VAVILRAMGYPKETQIY 408 (449)
Q Consensus 392 vgl~LrALGf~~~T~IY 408 (449)
+.++|||||+.++.-||
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 68899999998887766
No 11
>PF03032 Brevenin: Brevenin/esculentin/gaegurin/rugosin family; InterPro: IPR004275 In addition to the highly specific cell-mediated immune system, vertebrates possess an efficient host-defence mechanism against invading microorganisms which involves the synthesis of highly potent antimicrobial peptides with a large spectrum of activity. This entry represents a number of these defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins.; GO: 0006952 defense response, 0042742 defense response to bacterium, 0005576 extracellular region
Probab=24.62 E-value=45 Score=25.63 Aligned_cols=14 Identities=29% Similarity=0.375 Sum_probs=10.5
Q ss_pred HHHHHHHHHhhhcc
Q 013112 78 ALFVVVAGLISILS 91 (449)
Q Consensus 78 ~~~~~~~~~~~~~~ 91 (449)
+|+||++|+|+++-
T Consensus 7 llLlfflG~ISlSl 20 (46)
T PF03032_consen 7 LLLLFFLGTISLSL 20 (46)
T ss_pred HHHHHHHHHcccch
Confidence 67788888887654
No 12
>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=24.44 E-value=84 Score=28.04 Aligned_cols=46 Identities=17% Similarity=0.386 Sum_probs=34.6
Q ss_pred CChHH-HHHHHHHhCCCCCceEEEeeccccCCccchhchHHhCCCcccccc
Q 013112 387 LEPGE-VAVILRAMGYPKETQIYVASGQVYGGQNRMAPLRNMFPNLVRPLN 436 (449)
Q Consensus 387 LTPeE-vgl~LrALGf~~~T~IYlAsgeiyGG~~~l~pLr~~FPnl~tKe~ 436 (449)
++|-- ---+|..++ +.+|.|++...+ |+....+|+++.|.-+.+++
T Consensus 80 ~sPCG~Crq~l~e~~-~~~~~v~~~~~~---~~~~~~~l~eLLP~~f~~~~ 126 (127)
T TIGR01354 80 VSPCGACRQVLAEFA-GPDTPIYMTNND---GTYKVYTVGELLPFGFGPSD 126 (127)
T ss_pred cCccHHHHHHHHHhC-CCCcEEEEECCC---CCEEEEEHHHhCcCcCCcCc
Confidence 44543 234788887 679999999877 55567899999999887765
No 13
>PF13756 Stimulus_sens_1: Stimulus-sensing domain
Probab=21.87 E-value=99 Score=27.14 Aligned_cols=32 Identities=25% Similarity=0.497 Sum_probs=25.0
Q ss_pred CChHHHHHHHHHhCCCCCce--EEEeeccccCCc
Q 013112 387 LEPGEVAVILRAMGYPKETQ--IYVASGQVYGGQ 418 (449)
Q Consensus 387 LTPeEvgl~LrALGf~~~T~--IYlAsgeiyGG~ 418 (449)
|+||.|+-||+-|.-+.+|+ ||=+.|.+-.-.
T Consensus 1 l~pe~a~plLrrL~~Pt~~RARlyd~dG~Ll~DS 34 (112)
T PF13756_consen 1 LNPERARPLLRRLISPTRTRARLYDPDGNLLADS 34 (112)
T ss_pred CCHHHHHHHHHHhCCCCCceEEEECCCCCEEeec
Confidence 68999999999999999996 665666554433
No 14
>PLN00126 succinate dehydrogenase, cytochrome b subunit family; Provisional
Probab=20.86 E-value=1.8e+02 Score=26.72 Aligned_cols=12 Identities=42% Similarity=0.589 Sum_probs=9.1
Q ss_pred Cccccccccccc
Q 013112 1 MAELRHSSSLGS 12 (449)
Q Consensus 1 ~~~~~~~~~~~~ 12 (449)
|..||||+.++.
T Consensus 34 ~~~~~~~~~~~~ 45 (129)
T PLN00126 34 IDHLRQSSNLEQ 45 (129)
T ss_pred cccccccchHHH
Confidence 557899988874
No 15
>KOG3111 consensus D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=20.10 E-value=3.7e+02 Score=27.00 Aligned_cols=112 Identities=24% Similarity=0.384 Sum_probs=64.9
Q ss_pred ccchHHHHHHHHHHHHHHhhcCCCCCceEeeechhh------hhhhhcccc---CC--CCHHHHHHHHHHHhhccccccc
Q 013112 299 KFLPEIEQMSDLLASRMKNRTGSSNPYMALHLRFEK------GMVGLSFCD---FV--GTREEKAKMAEYRKKEWPRRYK 367 (449)
Q Consensus 299 rF~p~I~~lg~~LV~RmR~~s~~s~pfiALHLRfE~------DMLAfSgC~---~g--g~~~E~~eL~~~R~~~w~~k~~ 367 (449)
+|+|.| ..|.-+|++||+..+ -.+|.-+||=.|. +| |-.|-. +. -+++-.+-..++|++..+-
T Consensus 42 ~FVpNi-T~G~pvV~slR~~~~-~~~ffD~HmMV~~Peq~V~~~-a~agas~~tfH~E~~q~~~~lv~~ir~~Gmk~--- 115 (224)
T KOG3111|consen 42 HFVPNI-TFGPPVVESLRKHTG-ADPFFDVHMMVENPEQWVDQM-AKAGASLFTFHYEATQKPAELVEKIREKGMKV--- 115 (224)
T ss_pred cccCCc-ccchHHHHHHHhccC-CCcceeEEEeecCHHHHHHHH-HhcCcceEEEEEeeccCHHHHHHHHHHcCCee---
Confidence 466666 478889999998532 2469999996652 22 222211 11 1111122233455544321
Q ss_pred CCCcchhhhHhhhcCCCCCCChHHHHHHHHHhCCCCCceEEEeeccccCCccchh-------chHHhCCCcc
Q 013112 368 NGSHLWQLALQKRKEGRCPLEPGEVAVILRAMGYPKETQIYVASGQVYGGQNRMA-------PLRNMFPNLV 432 (449)
Q Consensus 368 ~~~~~~~~~~~~R~~G~CPLTPeEvgl~LrALGf~~~T~IYlAsgeiyGG~~~l~-------pLr~~FPnl~ 432 (449)
|. -.=|=||-|....+.. .-|--+-.+---=|||++-|. -||+-|||+.
T Consensus 116 -G~------------alkPgT~Ve~~~~~~~---~~D~vLvMtVePGFGGQkFme~mm~KV~~lR~kyp~l~ 171 (224)
T KOG3111|consen 116 -GL------------ALKPGTPVEDLEPLAE---HVDMVLVMTVEPGFGGQKFMEDMMPKVEWLREKYPNLD 171 (224)
T ss_pred -eE------------EeCCCCcHHHHHHhhc---cccEEEEEEecCCCchhhhHHHHHHHHHHHHHhCCCce
Confidence 11 1236678887777665 234455555555599998875 5899999984
No 16
>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=20.00 E-value=67 Score=25.64 Aligned_cols=27 Identities=26% Similarity=0.466 Sum_probs=18.4
Q ss_pred hhhcCCCCCCChHHHHHHHHHhCCCCCc
Q 013112 378 QKRKEGRCPLEPGEVAVILRAMGYPKET 405 (449)
Q Consensus 378 ~~R~~G~CPLTPeEvgl~LrALGf~~~T 405 (449)
-.+..|.. ++++|+.-+|+.|||.-+.
T Consensus 11 i~~~lG~~-i~~~~i~~~L~~lg~~~~~ 37 (70)
T PF03484_consen 11 INKLLGID-ISPEEIIKILKRLGFKVEK 37 (70)
T ss_dssp HHHHHTS----HHHHHHHHHHTT-EEEE
T ss_pred HHHHhCCC-CCHHHHHHHHHHCCCEEEE
Confidence 34666765 9999999999999997554
Done!