Query 011800
Match_columns 477
No_of_seqs 170 out of 397
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 05:22:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011800hhsearch_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 7.8E-57 1.7E-61 453.3 3.5 308 55-417 6-349 (351)
2 KOG3849 GDP-fucose protein O-f 97.9 4.3E-05 9.3E-10 77.1 8.2 61 44-104 25-89 (386)
3 PF05830 NodZ: Nodulation prot 95.5 0.38 8.3E-06 49.9 14.3 261 48-402 2-290 (321)
4 PF00799 Gemini_AL1: Geminivir 44.5 25 0.00053 31.6 3.3 28 307-335 14-41 (114)
5 PF14771 DUF4476: Domain of un 39.9 18 0.0004 30.5 1.8 37 309-360 39-75 (95)
6 PF10892 DUF2688: Protein of u 36.4 25 0.00055 28.1 1.9 16 306-322 42-57 (60)
7 smart00874 B5 tRNA synthetase 29.6 50 0.0011 26.1 2.6 24 302-326 12-35 (71)
8 COG0859 RfaF ADP-heptose:LPS h 25.1 89 0.0019 32.2 4.2 65 313-397 198-262 (334)
9 PF07862 Nif11: Nitrogen fixat 22.7 68 0.0015 23.9 2.1 28 298-326 16-43 (49)
10 COG4878 Uncharacterized protei 22.5 88 0.0019 32.5 3.4 58 315-373 93-151 (309)
11 PLN02232 ubiquinone biosynthes 21.2 89 0.0019 28.7 3.0 29 309-337 125-153 (160)
12 PF00036 EF-hand_1: EF hand; 21.1 93 0.002 21.0 2.3 25 423-447 3-29 (29)
13 COG1747 Uncharacterized N-term 20.8 1.2E+02 0.0027 34.3 4.3 55 416-475 376-430 (711)
14 PF03484 B5: tRNA synthetase B 20.2 54 0.0012 26.3 1.1 25 303-328 13-37 (70)
15 KOG3705 Glycoprotein 6-alpha-L 20.2 5E+02 0.011 28.7 8.5 68 320-395 399-473 (580)
16 PF10365 DUF2436: Domain of un 20.0 34 0.00074 32.2 -0.0 26 77-105 25-50 (161)
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=7.8e-57 Score=453.30 Aligned_cols=308 Identities=39% Similarity=0.603 Sum_probs=210.5
Q ss_pred eCCchhHHHHHHHHHHHHHHHhcCeEeecccccCCcccCCCC-----CCcccchHHHHHhccCCceecccCchhhhhhhh
Q 011800 55 ANGGMNQQRVAICNAVVLARLLNATLVVPKFMYSSVWRDVSQ-----FSDIYQEEHFINYLTPDIRMVKELPNKLQSLDL 129 (477)
Q Consensus 55 ~nGGLnq~R~~IcdaVaVAriLNATLVlP~l~~~s~W~D~S~-----F~dIfD~dhFI~~L~~dV~IVk~LP~~~~~~~~ 129 (477)
+.||+||||+++++||++|++||+|||||.+...+.|+|.++ |+++||+++|+++++++|.+.+.+|..+.....
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 889999999999999999999999999999999999999987 999999999999999999999999877654321
Q ss_pred hhh------------------------cccccccCCCC-CCChhHHHhhhhHhHhhc------ceEEEecccCCCcCCCC
Q 011800 130 EAI------------------------GSVVTDVDIPK-ESKPSFYLKNIIPILLRN------GVVHLLGFGNRLAFDPI 178 (477)
Q Consensus 130 ~~~------------------------~~~~~~~~~~~-~s~~~~Y~~~vlP~l~k~------~Vi~l~~~~~rLa~~~l 178 (477)
... ........... ++.+.+|+++++|.+.++ +|+.|.++..++..+..
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 100 00001112222 678889998899999987 99999999999998888
Q ss_pred ChhhhhhcccccccccccchhHHHHHHHHHHHHhcccCCCCCCCcccCCCccchhhhhhhcccccCCceEEEeeehhhhh
Q 011800 179 PFQLQRLRCRCNFHALQFAPKIQETGALLLRRLRKHEGHSGPLDHYLVGPYADSIMKEKRGQSAKASRYLAIHLRFEIDM 258 (477)
Q Consensus 179 p~~iQrLRCrvnf~ALrF~~~I~~lg~~lV~Rlr~~~~~~~~~~~~~~g~f~~~~~~~~~~~~~~~~~yiAlHLR~E~Dm 258 (477)
+.++|| +|+|+++|+++|+++|++|+.. +++|||+|||+|+||
T Consensus 166 ~~~~~r--------~l~~~~~i~~~a~~~i~~~~~~-----------------------------~~~yiavHlR~~~D~ 208 (351)
T PF10250_consen 166 DRDLQR--------YLRFSPEIRELADKFIKRLLAG-----------------------------GGPYIAVHLRRGKDW 208 (351)
T ss_dssp GGGGGG--------G--B-HHHHHHHHHHHHHH---------------------------------SSEEEEEE--SHHH
T ss_pred CccceE--------EEecCHHHHHHHHHHHHHhhcc-----------------------------cCceEEEeecccCch
Confidence 999988 9999999999999999999932 258999999999999
Q ss_pred hhhccccCCCChhHHHHHHHHHHhhhhhhhhhhcCCCCCChHhhhcCCCCcCCHHHHHHHHHHcCCCCCcEEEEEecccc
Q 011800 259 VAHSLCEFGGGEEERQELEKYREIHFPALAHLKKTTKLPSPAEIRSEGLCPLTPEEAVLMLAALGFNRKTHVFVAGAQIY 338 (477)
Q Consensus 259 lA~sgC~~gg~~~e~~eL~~~R~~~~~~~~~~~~~~k~i~~~~~R~~G~CPLtPeEvgl~L~alGf~~~T~IYlA~geiy 338 (477)
+++|.+++ ++..|+.+|.. ..+.+.+...+..|.||++|++++.+++++|+.+.|.||||++++|
T Consensus 209 --~~~C~~~~---~~~~~~~~~~~----------~~~~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~ 273 (351)
T PF10250_consen 209 --FSACEFKG---ERHLLASPRCW----------GKKSINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIY 273 (351)
T ss_dssp --HHHHCT-T-------TTTHHHH-----------GGGTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS--
T ss_pred --HhhcccCC---chHHHHHhHhh----------ccccccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCccc
Confidence 88999955 78888888863 1234567788899999999999999999999999999999999999
Q ss_pred CccccchHHHhhCCCccccccCCCcccccccccccccchhhheeeeccCceeeecCCCCchhhhhhhhhhhccCCCCce
Q 011800 339 GGTRRLGALNSLYPYLVTKENLLSATELEPFKNFSSQLAALDFIGCTAANAFAMTDSGSQLSSLVSGYRIYYGGGKMPT 417 (477)
Q Consensus 339 Gg~~~m~~L~~~FPnl~tKetL~s~eEL~pf~~~ss~lAALDyiV~l~SDvFv~t~~G~nfa~~V~GhR~y~g~g~~kT 417 (477)
||.+.|.+|++.||++++|+++.+.+|+++|.+ .++|+||++||++||+||+|. ||+|+.+|+++|.|.|.+++||
T Consensus 274 ~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~--~~~a~vD~~i~~~s~~Figt~-~Stfs~~i~~~R~~~g~~~~~~ 349 (351)
T PF10250_consen 274 GGERRLDPLKNMFPNVVTKDDLLSHEELEPLND--DQLAMVDQEICSRSDVFIGTC-GSTFSSNIARERHYRGKPKRKS 349 (351)
T ss_dssp ---------HHHHHHHHGGGT--EE--S-------S--HHHHHHHHHHSSEEEE-T-T-HHHHHHHHHHHHSSSS---E
T ss_pred ccchhHHHHHHHhhhhEeccccCCHHHhhhccc--cchhHHHHHHHhcCCEEEecC-cchhHHHhhcccCcCCCCCCCC
Confidence 999999999999999999999999999999966 999999999999999999998 6689999999999999766555
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=97.87 E-value=4.3e-05 Score=77.06 Aligned_cols=61 Identities=26% Similarity=0.363 Sum_probs=47.3
Q ss_pred CCCCCcEEEE-EeCCchhHHHHHHHHHHHHHHHhcCeEeecccc---cCCcccCCCCCCcccchH
Q 011800 44 SGGNNGYILV-TANGGMNQQRVAICNAVVLARLLNATLVVPKFM---YSSVWRDVSQFSDIYQEE 104 (477)
Q Consensus 44 ~~~snGyl~V-~~nGGLnq~R~~IcdaVaVAriLNATLVlP~l~---~~s~W~D~S~F~dIfD~d 104 (477)
....||||+. .|-|-+.+|-....-..|.|+.||.|||||-.- +-.+-.---.|...|.++
T Consensus 25 ~~DP~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiEy~~pe~~n~~vpf~~yF~ve 89 (386)
T KOG3849|consen 25 SWDPAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIEYKHPETKNLMVPFEFYFQVE 89 (386)
T ss_pred CCCCCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchhccCCcccccccchhheeecc
Confidence 4578999998 699999999999999999999999999999642 111111114788888875
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=95.46 E-value=0.38 Score=49.87 Aligned_cols=261 Identities=16% Similarity=0.271 Sum_probs=121.8
Q ss_pred CcEEEEEeCCchhHHHHHHHHHHHHHHHhcCeEeecccccCCcccCC----CCCCcccchHHHHHhccC--CceecccCc
Q 011800 48 NGYILVTANGGMNQQRVAICNAVVLARLLNATLVVPKFMYSSVWRDV----SQFSDIYQEEHFINYLTP--DIRMVKELP 121 (477)
Q Consensus 48 nGyl~V~~nGGLnq~R~~IcdaVaVAriLNATLVlP~l~~~s~W~D~----S~F~dIfD~dhFI~~L~~--dV~IVk~LP 121 (477)
+.|++..--+|++.-=-+++-|-.+|+-.|.||||- |+++ ..|...|++ |-+-.++ .|+|+-+-+
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 468888899999999999999999999999999984 7776 577777765 5555542 455552211
Q ss_pred hhhhhhhhhhhccccc------ccCCCCCCChhHHH--hhhhHhHhh------cceEEEecccCCCcCCCCChhhhhhcc
Q 011800 122 NKLQSLDLEAIGSVVT------DVDIPKESKPSFYL--KNIIPILLR------NGVVHLLGFGNRLAFDPIPFQLQRLRC 187 (477)
Q Consensus 122 ~~~~~~~~~~~~~~~~------~~~~~~~s~~~~Y~--~~vlP~l~k------~~Vi~l~~~~~rLa~~~lp~~iQrLRC 187 (477)
+.... .-++.+| .++......+.-+. +++--+++. ..||+-.=...| -..++.|
T Consensus 73 --i~~~~--~~g~~fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~-----c~~~aeR--- 140 (321)
T PF05830_consen 73 --INQFS--FPGPFFPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWR-----CDEEAER--- 140 (321)
T ss_dssp --GGT------SSEESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTS-----S-HHHHH---
T ss_pred --hhhhc--CCCCcChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCc-----chhHHHH---
Confidence 11100 0011111 11111111111111 233333333 345554433332 1234443
Q ss_pred cccccccccchhHHHHHHHHHHHHhcccCCCCCCCcccCCCccchhhhhhhcccccCCceEEEeeehh--hhhhhhcccc
Q 011800 188 RCNFHALQFAPKIQETGALLLRRLRKHEGHSGPLDHYLVGPYADSIMKEKRGQSAKASRYLAIHLRFE--IDMVAHSLCE 265 (477)
Q Consensus 188 rvnf~ALrF~~~I~~lg~~lV~Rlr~~~~~~~~~~~~~~g~f~~~~~~~~~~~~~~~~~yiAlHLR~E--~DmlA~sgC~ 265 (477)
.-|..|+-+++|++..+.+.+.-=. | ..=|++|.|.= +|-+.+ +|.
T Consensus 141 -~if~slkpR~eIqarID~iy~ehf~-------------g-----------------~~~IGVHVRhGngeD~~~h-~~~ 188 (321)
T PF05830_consen 141 -EIFSSLKPRPEIQARIDAIYREHFA-------------G-----------------YSVIGVHVRHGNGEDIMDH-APY 188 (321)
T ss_dssp -HHHHHS-B-HHHHHHHHHHHHHHTT-------------T-----------------SEEEEEEE---------------
T ss_pred -HHHHhCCCCHHHHHHHHHHHHHHcC-------------C-----------------CceEEEEEeccCCcchhcc-Ccc
Confidence 2478999999999998887665322 2 45799999931 222222 222
Q ss_pred CCCChhHHHHHHHHHHhhhhhhhhhhcCCCCCChHhhhcCCCCcCCHHHHHHHHHHcCCCCCcEEEEEeccccCccccch
Q 011800 266 FGGGEEERQELEKYREIHFPALAHLKKTTKLPSPAEIRSEGLCPLTPEEAVLMLAALGFNRKTHVFVAGAQIYGGTRRLG 345 (477)
Q Consensus 266 ~gg~~~e~~eL~~~R~~~~~~~~~~~~~~k~i~~~~~R~~G~CPLtPeEvgl~L~alGf~~~T~IYlA~geiyGg~~~m~ 345 (477)
+ .+++..|.+.. .....++++=...++.|+||+-.- ..++
T Consensus 189 ~---~D~e~~L~~V~---------------------------------~ai~~ak~~~~~k~~~IFLATDSa----eVid 228 (321)
T PF05830_consen 189 W---ADEERALRQVC---------------------------------TAIDKAKALAPPKPVRIFLATDSA----EVID 228 (321)
T ss_dssp ----HHHHHHHHHHH---------------------------------HHHHHHHTS--SS-EEEEEEES-H----HHHH
T ss_pred c---cCchHHHHHHH---------------------------------HHHHHHHhccCCCCeeEEEecCcH----HHHH
Confidence 1 01111111100 011223555566789999998643 4588
Q ss_pred HHHhhCCCccccccCCCccccccccccc-----ccchhhheeeeccCceee-ecCCCCchhhh
Q 011800 346 ALNSLYPYLVTKENLLSATELEPFKNFS-----SQLAALDFIGCTAANAFA-MTDSGSQLSSL 402 (477)
Q Consensus 346 ~L~~~FPnl~tKetL~s~eEL~pf~~~s-----s~lAALDyiV~l~SDvFv-~t~~G~nfa~~ 402 (477)
-+++.||.+++.+.=..+..-.+..+.. -..|-+|-+....+|+-| ++-.+ .|+..
T Consensus 229 ~fr~~FPdiiti~k~F~~~~~g~Lhs~~~g~~gg~~ALIDM~LLSrCD~LIr~~ptS-~Fsr~ 290 (321)
T PF05830_consen 229 QFRKKFPDIITIPKQFPASQAGPLHSAAVGIEGGESALIDMYLLSRCDYLIRFPPTS-AFSRY 290 (321)
T ss_dssp HHHHHSTTEE----------------HHHHHHHHHHHHHHHHHHTTSSEEEEESTT--GGGHH
T ss_pred HHHHHCCCeEEcccccCCCCCCcCcccccccchHHHHHHHHHHHHhCCeEEEcCCCc-hhhhH
Confidence 9999999998875544332222332211 124889999999999999 55333 36544
No 4
>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=44.53 E-value=25 Score=31.64 Aligned_cols=28 Identities=29% Similarity=0.333 Sum_probs=15.9
Q ss_pred CCcCCHHHHHHHHHHcCCCCCcEEEEEec
Q 011800 307 LCPLTPEEAVLMLAALGFNRKTHVFVAGA 335 (477)
Q Consensus 307 ~CPLtPeEvgl~L~alGf~~~T~IYlA~g 335 (477)
.|||||||+...|++|--+ ....||..+
T Consensus 14 qC~l~ke~~l~~L~~l~~~-~~~~yI~v~ 41 (114)
T PF00799_consen 14 QCSLTKEEALEQLKNLLTP-SNKKYIRVC 41 (114)
T ss_dssp T----HHHHHHHHHH---S-S-EEEEEEE
T ss_pred CCCCCHHHHHHHHHHhCCc-cCceEEEee
Confidence 6999999999999999754 467787554
No 5
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=39.95 E-value=18 Score=30.52 Aligned_cols=37 Identities=32% Similarity=0.575 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHcCCCCCcEEEEEeccccCccccchHHHhhCCCccccccC
Q 011800 309 PLTPEEAVLMLAALGFNRKTHVFVAGAQIYGGTRRLGALNSLYPYLVTKENL 360 (477)
Q Consensus 309 PLtPeEvgl~L~alGf~~~T~IYlA~geiyGg~~~m~~L~~~FPnl~tKetL 360 (477)
++|-.+++-+|+-..|++ .+|..|+-++|++++++.-
T Consensus 39 ~~T~~Qv~~il~~f~fd~---------------~kl~~lk~l~p~i~D~~n~ 75 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDN---------------DKLKALKLLYPYIVDPQNY 75 (95)
T ss_pred ceeHHHHHHHHHHcCCCH---------------HHHHHHHHHhhhccCHHHH
Confidence 499999999999999987 4699999999999999643
No 6
>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=36.45 E-value=25 Score=28.10 Aligned_cols=16 Identities=50% Similarity=0.765 Sum_probs=13.9
Q ss_pred CCCcCCHHHHHHHHHHc
Q 011800 306 GLCPLTPEEAVLMLAAL 322 (477)
Q Consensus 306 G~CPLtPeEvgl~L~al 322 (477)
|-| +||||-+.+++++
T Consensus 42 ~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDC-ITPEEDREILEAT 57 (60)
T ss_pred hcc-CCHHHHHHHHHHH
Confidence 568 9999999999875
No 7
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=29.64 E-value=50 Score=26.07 Aligned_cols=24 Identities=42% Similarity=0.506 Sum_probs=20.0
Q ss_pred hhcCCCCcCCHHHHHHHHHHcCCCC
Q 011800 302 IRSEGLCPLTPEEAVLMLAALGFNR 326 (477)
Q Consensus 302 ~R~~G~CPLtPeEvgl~L~alGf~~ 326 (477)
.+..|. .++++|+.-+|+.|||+-
T Consensus 12 ~~llG~-~i~~~ei~~~L~~lg~~~ 35 (71)
T smart00874 12 NRLLGL-DLSAEEIEEILKRLGFEV 35 (71)
T ss_pred HHHHCC-CCCHHHHHHHHHHCCCeE
Confidence 355565 499999999999999975
No 8
>COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=25.06 E-value=89 Score=32.15 Aligned_cols=65 Identities=32% Similarity=0.342 Sum_probs=42.0
Q ss_pred HHHHHHHHHcCCCCCcEEEEEeccccCccccchHHHhhCCCccccccCCCcccccccccccccchhhheeeeccCceeee
Q 011800 313 EEAVLMLAALGFNRKTHVFVAGAQIYGGTRRLGALNSLYPYLVTKENLLSATELEPFKNFSSQLAALDFIGCTAANAFAM 392 (477)
Q Consensus 313 eEvgl~L~alGf~~~T~IYlA~geiyGg~~~m~~L~~~FPnl~tKetL~s~eEL~pf~~~ss~lAALDyiV~l~SDvFv~ 392 (477)
.|++..|.+-| .+|.|.+|. .-..+.+.+.+..++.+. |+....|.. ++||- ..||.||+
T Consensus 198 ~~l~~~l~~~~----~~Vvl~g~~--~e~e~~~~i~~~~~~~~~---l~~k~sL~e-------~~~li----~~a~l~I~ 257 (334)
T COG0859 198 AELAELLIAKG----YQVVLFGGP--DEEERAEEIAKGLPNAVI---LAGKTSLEE-------LAALI----AGADLVIG 257 (334)
T ss_pred HHHHHHHHHCC----CEEEEecCh--HHHHHHHHHHHhcCCccc---cCCCCCHHH-------HHHHH----hcCCEEEc
Confidence 57788888888 779999987 333445667777776554 332222222 23333 68999999
Q ss_pred cCCCC
Q 011800 393 TDSGS 397 (477)
Q Consensus 393 t~~G~ 397 (477)
+++|.
T Consensus 258 ~DSg~ 262 (334)
T COG0859 258 NDSGP 262 (334)
T ss_pred cCChH
Confidence 98884
No 9
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=22.71 E-value=68 Score=23.89 Aligned_cols=28 Identities=25% Similarity=0.434 Sum_probs=23.5
Q ss_pred ChHhhhcCCCCcCCHHHHHHHHHHcCCCC
Q 011800 298 SPAEIRSEGLCPLTPEEAVLMLAALGFNR 326 (477)
Q Consensus 298 ~~~~~R~~G~CPLtPeEvgl~L~alGf~~ 326 (477)
|++.+.....| -+|+|+.-+.+..||.=
T Consensus 16 d~~l~~~l~~~-~~~~e~~~lA~~~Gy~f 43 (49)
T PF07862_consen 16 DPELREQLKAC-QNPEEVVALAREAGYDF 43 (49)
T ss_pred CHHHHHHHHhc-CCHHHHHHHHHHcCCCC
Confidence 66677777788 49999999999999974
No 10
>COG4878 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.52 E-value=88 Score=32.55 Aligned_cols=58 Identities=24% Similarity=0.148 Sum_probs=47.1
Q ss_pred HHHHHHHcCCC-CCcEEEEEeccccCccccchHHHhhCCCccccccCCCccccccccccc
Q 011800 315 AVLMLAALGFN-RKTHVFVAGAQIYGGTRRLGALNSLYPYLVTKENLLSATELEPFKNFS 373 (477)
Q Consensus 315 vgl~L~alGf~-~~T~IYlA~geiyGg~~~m~~L~~~FPnl~tKetL~s~eEL~pf~~~s 373 (477)
++.++..|--. -+|.||++-+.| +-++.-..|.+.||++-|-.++.+.+|+.+|..-+
T Consensus 93 L~~y~~~ls~~~y~~~vfVppSni-l~q~gk~alvk~~p~lktissiy~~deykd~~se~ 151 (309)
T COG4878 93 LADYGDILSITGYDTFVFVPPSNI-LLQKGKFALVKQAPSLKTISSIYNTDEYKDFNSES 151 (309)
T ss_pred HHHHHHHHhccccceEEEeCcccc-cchhHHHHHHHhCCCcceeeeEecccccCcccchh
Confidence 44555555444 578999999999 66777899999999999999999999999995443
No 11
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=21.17 E-value=89 Score=28.66 Aligned_cols=29 Identities=28% Similarity=0.339 Sum_probs=25.6
Q ss_pred cCCHHHHHHHHHHcCCCCCcEEEEEeccc
Q 011800 309 PLTPEEAVLMLAALGFNRKTHVFVAGAQI 337 (477)
Q Consensus 309 PLtPeEvgl~L~alGf~~~T~IYlA~gei 337 (477)
+++|+|...+|+..||.+-+.-+++.|-+
T Consensus 125 f~~~~el~~ll~~aGF~~~~~~~~~~g~~ 153 (160)
T PLN02232 125 YLTGEELETLALEAGFSSACHYEISGGFM 153 (160)
T ss_pred CcCHHHHHHHHHHcCCCcceEEECcchHh
Confidence 48999999999999999998888887743
No 12
>PF00036 EF-hand_1: EF hand; InterPro: IPR018248 Many calcium-binding proteins belong to the same evolutionary family and share a type of calcium-binding domain known as the EF-hand. This type of domain consists of a twelve residue loop flanked on both sides by a twelve residue alpha-helical domain. In an EF-hand loop the calcium ion is coordinated in a pentagonal bipyramidal configuration. The six residues involved in the binding are in positions 1, 3, 5, 7, 9 and 12; these residues are denoted by X, Y, Z, -Y, -X and -Z. The invariant Glu or Asp at position 12 provides two oxygens for liganding Ca (bidentate ligand).; PDB: 1BJF_A 1XFW_R 1XFV_O 2K0J_A 2F3Z_A 3BYA_A 1XFU_Q 2R28_B 1ZOT_B 3G43_D ....
Probab=21.10 E-value=93 Score=21.02 Aligned_cols=25 Identities=20% Similarity=0.406 Sum_probs=18.8
Q ss_pred HHHHHHHhc--CCCcchHHHHHHHHHH
Q 011800 423 RRLAAIFVK--NSTIEWKVFEQRVRKA 447 (477)
Q Consensus 423 k~l~~lf~~--~~~~~w~~f~~~v~~~ 447 (477)
+.+-+.||. ++.|+.+||...++++
T Consensus 3 ~~~F~~~D~d~dG~I~~~Ef~~~~~~L 29 (29)
T PF00036_consen 3 KEAFREFDKDGDGKIDFEEFKEMMKKL 29 (29)
T ss_dssp HHHHHHHSTTSSSEEEHHHHHHHHHHT
T ss_pred HHHHHHHCCCCCCcCCHHHHHHHHHhC
Confidence 345567775 6678999999988764
No 13
>COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]
Probab=20.83 E-value=1.2e+02 Score=34.28 Aligned_cols=55 Identities=13% Similarity=0.399 Sum_probs=42.5
Q ss_pred ceeccchHHHHHHHhcCCCcchHHHHHHHHHHHHhccccCCCCCCCCcccCCCCCCCCCC
Q 011800 416 PTIRPNKRRLAAIFVKNSTIEWKVFEQRVRKAVRQTKHIQSRSKGRSVYRYPRCKECMCP 475 (477)
Q Consensus 416 kTI~Pdrk~l~~lf~~~~~~~w~~f~~~v~~~~~~~~~~~~~~~~~s~y~~P~~peC~C~ 475 (477)
++..-=|+.||+++. +.-+|+.|+...|+.+++..+.-..+.+-++|.+- +|-|.
T Consensus 376 ~nlKeIK~ELVpsli--~e~dWnsWsqkAK~ilKk~t~f~a~~s~~D~Yv~~---~~~~s 430 (711)
T COG1747 376 KNLKEIKQELVPSLI--PEGDWNSWSQKAKKILKKSTRFAAPPSNKDPYVVR---SCGVS 430 (711)
T ss_pred ccHHHHHHHHHHhhC--ChhhhhHHHHHHHHHHhcCCcccCCCCCCCCeEeC---CCCcC
Confidence 444455789999996 55689999999999999888876666667888776 66664
No 14
>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=20.21 E-value=54 Score=26.32 Aligned_cols=25 Identities=32% Similarity=0.620 Sum_probs=17.0
Q ss_pred hcCCCCcCCHHHHHHHHHHcCCCCCc
Q 011800 303 RSEGLCPLTPEEAVLMLAALGFNRKT 328 (477)
Q Consensus 303 R~~G~CPLtPeEvgl~L~alGf~~~T 328 (477)
+..|.. ++++|+.-+|+.|||.-..
T Consensus 13 ~~lG~~-i~~~~i~~~L~~lg~~~~~ 37 (70)
T PF03484_consen 13 KLLGID-ISPEEIIKILKRLGFKVEK 37 (70)
T ss_dssp HHHTS----HHHHHHHHHHTT-EEEE
T ss_pred HHhCCC-CCHHHHHHHHHHCCCEEEE
Confidence 455654 9999999999999998644
No 15
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=20.17 E-value=5e+02 Score=28.73 Aligned_cols=68 Identities=18% Similarity=0.182 Sum_probs=39.4
Q ss_pred HHcCCCCCcEEEEEeccccCccccchHHHhhCCCccccccCCCccccccccccc------cc-chhhheeeeccCceeee
Q 011800 320 AALGFNRKTHVFVAGAQIYGGTRRLGALNSLYPYLVTKENLLSATELEPFKNFS------SQ-LAALDFIGCTAANAFAM 392 (477)
Q Consensus 320 ~alGf~~~T~IYlA~geiyGg~~~m~~L~~~FPnl~tKetL~s~eEL~pf~~~s------s~-lAALDyiV~l~SDvFv~ 392 (477)
..=|=+-.-+||||+-+. ..+.--+.-|||. .+.+..|.+.-.... |. ---+|..+.+.+|..|.
T Consensus 399 e~rg~~~~rRiflAsDDp----~vv~EAk~kYPnY----e~igd~eia~~A~l~nRYTd~sL~GvIlDIh~LS~~d~LVC 470 (580)
T KOG3705|consen 399 EKRGKPLERRIFLASDDP----TVVPEAKNKYPNY----EVIGDTEIAKTAQLNNRYTDASLMGVILDIHILSKVDYLVC 470 (580)
T ss_pred HHhCCchhheEEEecCCc----hhchHhhccCCCc----EEeccHHHHHHhhccccchhhhhhheeeeeeeecccceEEE
Confidence 333445566799999865 3355568889986 344455555433222 11 13456666666666666
Q ss_pred cCC
Q 011800 393 TDS 395 (477)
Q Consensus 393 t~~ 395 (477)
|.+
T Consensus 471 TFS 473 (580)
T KOG3705|consen 471 TFS 473 (580)
T ss_pred ech
Confidence 543
No 16
>PF10365 DUF2436: Domain of unknown function (DUF2436); InterPro: IPR018832 Gingipains R and K are endopeptidases with specificity for arginyl and lysyl bonds, respectively. Like other cysteine peptidases, they require reducing conditions for activity. They are maximally active at approximately neutral pH. Gingipains R and K are secreted by the bacterium Porphyromonas gingivalis (Bacteroides gingivalis). The bacterium is a major pathogen in periodontal disease, and the many ways in which the activities of the gingipains may contribute to the disease processes have been reviewed []. These enzymes are also involved in the hemagglutinating activity of the organisms. This entry represents a central region found in gingipain K peptidases, active on lysyl bonds; they belong to the MEROPS peptidase family C25 (gingipain family, clan CD).
Probab=20.02 E-value=34 Score=32.16 Aligned_cols=26 Identities=23% Similarity=0.489 Sum_probs=21.4
Q ss_pred cCeEeecccccCCcccCCCCCCcccchHH
Q 011800 77 NATLVVPKFMYSSVWRDVSQFSDIYQEEH 105 (477)
Q Consensus 77 NATLVlP~l~~~s~W~D~S~F~dIfD~dh 105 (477)
-||+|| ..+.+|+|.|+|.-++|.||
T Consensus 25 ~A~IIL---eah~vW~DgsGyQ~LlDaDH 50 (161)
T PF10365_consen 25 MARIIL---EAHNVWGDGSGYQMLLDADH 50 (161)
T ss_pred ceEEEE---eccccccCCcceEEEEcCCc
Confidence 355654 45789999999999999999
Done!