Query 013199
Match_columns 448
No_of_seqs 193 out of 372
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 01:24:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013199hhsearch_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-48 1.2E-52 379.5 2.6 262 161-447 6-305 (351)
2 KOG3849 GDP-fucose protein O-f 95.5 0.035 7.6E-07 56.5 6.9 56 153-210 28-89 (386)
3 PF05830 NodZ: Nodulation prot 75.3 5.9 0.00013 41.2 5.7 213 154-436 2-242 (321)
4 PLN02232 ubiquinone biosynthes 47.8 66 0.0014 29.2 6.7 97 293-414 49-153 (160)
5 PF00799 Gemini_AL1: Geminivir 40.6 27 0.00059 31.2 2.9 27 384-411 14-40 (114)
6 PF14771 DUF4476: Domain of un 35.2 22 0.00047 29.8 1.4 36 386-436 39-74 (95)
7 KOG3111 D-ribulose-5-phosphate 31.1 2E+02 0.0043 28.8 7.3 113 299-432 42-171 (224)
8 PF10892 DUF2688: Protein of u 30.9 32 0.00068 27.8 1.6 16 383-399 42-57 (60)
9 smart00874 B5 tRNA synthetase 29.1 42 0.00091 26.3 2.1 25 379-404 12-36 (71)
10 TIGR01354 cyt_deam_tetra cytid 27.8 64 0.0014 28.8 3.2 100 325-437 21-127 (127)
11 PF05399 EVI2A: Ectropic viral 27.3 1E+02 0.0022 30.9 4.7 26 102-131 161-186 (227)
12 PF10365 DUF2436: Domain of un 26.6 20 0.00043 33.8 -0.2 25 184-211 26-50 (161)
13 PRK05578 cytidine deaminase; V 24.9 70 0.0015 29.0 3.0 99 327-438 26-131 (131)
14 PF15302 P33MONOX: P33 mono-ox 24.6 62 0.0014 33.2 2.8 21 4-26 153-173 (294)
15 PF04561 RNA_pol_Rpb2_2: RNA p 23.2 24 0.00053 31.8 -0.3 17 392-408 54-70 (190)
16 PF03484 B5: tRNA synthetase B 20.0 49 0.0011 26.4 0.9 26 379-405 12-37 (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-48 Score=379.52 Aligned_cols=262 Identities=37% Similarity=0.626 Sum_probs=175.8
Q ss_pred ecCchhHHHHHHHHHHHHHHHhcceEEeccccccccccCCCC-----CCcccChHHHHHhccccceeeccCchhHHHhhc
Q 013199 161 ANGGLNQQRISICNAVAVAGYLNATLVIPNFHYHSIWRDPSK-----FRDIYDEDYFTSVLQNDVRVVNKIPEYIMERFD 235 (448)
Q Consensus 161 ~nGGLNQqR~~IcDAVaVAriLNATLVlP~l~~~s~W~D~S~-----F~DIfDvdhFI~sL~~dVrIVk~LP~~~~~~~~ 235 (448)
|.||+||||.++++||++|++||+|||||.+.....|+|.++ |+|+||++||+++++++|.+.+.+|........
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 899999999999999999999999999999999999999988 999999999999999999999999876654221
Q ss_pred ccC-------------------------Ccceeccccc-CCChhhHHhhcccccccc------ceEEecCCCccccCC-C
Q 013199 236 HNM-------------------------SNVYNFRVKA-WSPIQFYKDEVLPKLLEE------RLIRISPFANRLSFD-A 282 (448)
Q Consensus 236 ~~~-------------------------~~~~~~~v~~-~s~~~yY~~~vlP~l~k~------~VI~l~~f~~RLa~~-l 282 (448)
... .....+.... |+.+.+|.++++|.+.++ +++.|.++..++.++ .
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 0112223333 889999999999999886 999999999999876 7
Q ss_pred CchhhhhhhhhcccccccchhHHHHHHHHHHHHhhccccCCCceEEEeecchhhhHhhcccccCCchhHHHHHHHHHHhc
Q 013199 283 PPAVQRLRCLANYEALRFSSPILTMGETLVARMKERSVNHGGKYISVHLRFEEDMVAFSCCVFDGGEREKEDMKEARERG 362 (448)
Q Consensus 283 P~~iQrLRCrvnf~ALrF~p~I~~lg~~LV~Rmr~~s~~s~g~yiALHLRfE~DMlAfsgC~~~g~~~E~~eL~~~R~~~ 362 (448)
+.++|| +|+|+++|+++|++++++|+. .+++|||+|||+|+|| +++|.+++ ++..|..+|...
T Consensus 166 ~~~~~r--------~l~~~~~i~~~a~~~i~~~~~----~~~~yiavHlR~~~D~--~~~C~~~~---~~~~~~~~~~~~ 228 (351)
T PF10250_consen 166 DRDLQR--------YLRFSPEIRELADKFIKRLLA----GGGPYIAVHLRRGKDW--FSACEFKG---ERHLLASPRCWG 228 (351)
T ss_dssp GGGGGG--------G--B-HHHHHHHHHHHHHH--------SSEEEEEE--SHHH--HHHHCT-T-------TTTHHHH-
T ss_pred CccceE--------EEecCHHHHHHHHHHHHHhhc----ccCceEEEeecccCch--HhhcccCC---chHHHHHhHhhc
Confidence 888887 999999999999999999992 3689999999999999 99999955 777888877551
Q ss_pred cccccCCCCcccCchhhhcCCCCCCChHHHHHHHHhcCCCCCceEEEeeccccCccccchhHHHhCCCccccccCCCccc
Q 013199 363 WKGKFTKPGRVIRPGAIRINGKCPLTPLEVGLMLRGMGFDKNTYIFLASGKIYNAEKTMAPLIEMFPNLQTKEMLASEEE 442 (448)
Q Consensus 363 wk~k~~~~~~~i~~~~~R~~G~CPLTPeEvgl~LraLGf~~~T~IYlA~geiyGg~~~m~pL~~~FPnl~tKetLas~eE 442 (448)
. ..+++.+.+..|.||++|++++.+++++|+.+.|.||||++++|||++.|++|+++||++++|+++.+.+|
T Consensus 229 --~------~~~~~~~~~~~~~~p~~~~~~~~i~~~~~~~~~~~vYiAtd~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~ 300 (351)
T PF10250_consen 229 --K------KSINPEKKRRNGCCPSTPQEAKQILRALGKNNTTVVYIATDEIYGGERRLDPLKNMFPNVVTKDDLLSHEE 300 (351)
T ss_dssp --G------GGTT-----HHHHS--HHHHHHHHHHHHHHHT-SEEEEEESS-----------HHHHHHHHGGGT--EE--
T ss_pred --c------ccccchhhhhcCCCCChHHHHHHHHHHhccCCCCEEEEecCcccccchhHHHHHHHhhhhEeccccCCHHH
Confidence 1 14677788999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCC
Q 013199 443 LAPFK 447 (448)
Q Consensus 443 L~pF~ 447 (448)
+++|.
T Consensus 301 ~~~~~ 305 (351)
T PF10250_consen 301 LEPLN 305 (351)
T ss_dssp S----
T ss_pred hhhcc
Confidence 98764
No 2
>KOG3849 consensus GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=95.51 E-value=0.035 Score=56.54 Aligned_cols=56 Identities=23% Similarity=0.290 Sum_probs=44.2
Q ss_pred CCceEEEE-ecCchhHHHHHHHHHHHHHHHhcceEEeccccccccccCC-----CCCCcccChH
Q 013199 153 SNGYISVE-ANGGLNQQRISICNAVAVAGYLNATLVIPNFHYHSIWRDP-----SKFRDIYDED 210 (448)
Q Consensus 153 snGYL~V~-~nGGLNQqR~~IcDAVaVAriLNATLVlP~l~~~s~W~D~-----S~F~DIfDvd 210 (448)
.||||+.- |-|-..+|-...--..|.|+.||.|||+|..-. |-+-+ -.|.-.|.++
T Consensus 28 P~GYl~yCPCMGRFGNQaDhFLGsLAFAKaLnRTL~lPpwiE--y~~pe~~n~~vpf~~yF~ve 89 (386)
T KOG3849|consen 28 PAGYLLYCPCMGRFGNQADHFLGSLAFAKALNRTLVLPPWIE--YKHPETKNLMVPFEFYFQVE 89 (386)
T ss_pred CCccEEEccccccccchHHHHHHHHHHHHHhcccccCCcchh--ccCCcccccccchhheeecc
Confidence 59998775 999999999999999999999999999997543 21221 2477777765
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=75.29 E-value=5.9 Score=41.21 Aligned_cols=213 Identities=21% Similarity=0.243 Sum_probs=101.4
Q ss_pred CceEEEEecCchhHHHHHHHHHHHHHHHhcceEEeccccccccccCCC----CCCcccChHHHHHhcc--ccceeeccCc
Q 013199 154 NGYISVEANGGLNQQRISICNAVAVAGYLNATLVIPNFHYHSIWRDPS----KFRDIYDEDYFTSVLQ--NDVRVVNKIP 227 (448)
Q Consensus 154 nGYL~V~~nGGLNQqR~~IcDAVaVAriLNATLVlP~l~~~s~W~D~S----~F~DIfDvdhFI~sL~--~dVrIVk~LP 227 (448)
+.|++.+--+|+|.-=-+++-|-.+|+-.|-||||= |+++- .|...|++ |-+-.+ ..|+|+-.=+
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 578999999999999999999999999999999983 66542 35555554 434433 2344441111
Q ss_pred hhHHHhhcccCCcceecccccC-CCh---------hhH-H--hhcccccc------ccceEEecCCCccccCCCCchhhh
Q 013199 228 EYIMERFDHNMSNVYNFRVKAW-SPI---------QFY-K--DEVLPKLL------EERLIRISPFANRLSFDAPPAVQR 288 (448)
Q Consensus 228 ~~~~~~~~~~~~~~~~~~v~~~-s~~---------~yY-~--~~vlP~l~------k~~VI~l~~f~~RLa~~lP~~iQr 288 (448)
+.+. +..-++ .|+| -.| .++ . +++--++. ...||+..=+.-+ -+-+.
T Consensus 73 --i~~~-----~~~g~~-fp~~w~~p~~~~~~~pd~qi~re~d~l~~lf~~~~d~~a~~vv~d~c~~~~------c~~~a 138 (321)
T PF05830_consen 73 --INQF-----SFPGPF-FPAWWNKPSIDCVYRPDEQIFRERDELRQLFQSQEDHEANTVVCDACLMWR------CDEEA 138 (321)
T ss_dssp --GGT---------SSE-ESGGGGS-GGGGS---HHHHHHHHHHHHHHHHSSS--S-SEEEE-S--TTS------S-HHH
T ss_pred --hhhh-----cCCCCc-ChhHHhCCCcceecCChHHHhhhhHHHHHHhhcccccccchhhhHhhcCCc------chhHH
Confidence 1000 000011 1222 111 111 1 11111121 3445555422222 12333
Q ss_pred hhhhhcccccccchhHHHHHHHHHHHHhhccccCCCceEEEeecchhhhHhhcccccCCchhHHHHHHHHHHhccccccC
Q 013199 289 LRCLANYEALRFSSPILTMGETLVARMKERSVNHGGKYISVHLRFEEDMVAFSCCVFDGGEREKEDMKEARERGWKGKFT 368 (448)
Q Consensus 289 LRCrvnf~ALrF~p~I~~lg~~LV~Rmr~~s~~s~g~yiALHLRfE~DMlAfsgC~~~g~~~E~~eL~~~R~~~wk~k~~ 368 (448)
.|| -|..|+-+++|++..+.+.+.-=. +..=|++|.|. |.|+ ..+.. .+.|...-
T Consensus 139 eR~--if~slkpR~eIqarID~iy~ehf~-----g~~~IGVHVRh------------Gnge---D~~~h--~~~~~D~e- 193 (321)
T PF05830_consen 139 ERE--IFSSLKPRPEIQARIDAIYREHFA-----GYSVIGVHVRH------------GNGE---DIMDH--APYWADEE- 193 (321)
T ss_dssp HHH--HHHHS-B-HHHHHHHHHHHHHHTT-----TSEEEEEEE--------------------------------HHHH-
T ss_pred HHH--HHHhCCCCHHHHHHHHHHHHHHcC-----CCceEEEEEec------------cCCc---chhcc--CccccCch-
Confidence 444 688999999999999998765432 44589999992 2221 11111 12232110
Q ss_pred CCCcccCchhhhcCCCCCCChH---HHHHHHHhcCCCCCceEEEeeccccCccccchhHHHhCCCcccccc
Q 013199 369 KPGRVIRPGAIRINGKCPLTPL---EVGLMLRGMGFDKNTYIFLASGKIYNAEKTMAPLIEMFPNLQTKEM 436 (448)
Q Consensus 369 ~~~~~i~~~~~R~~G~CPLTPe---Evgl~LraLGf~~~T~IYlA~geiyGg~~~m~pL~~~FPnl~tKet 436 (448)
.+=. .....++++=.+.++.|+||+-. .+-++-|++.||.+++-+.
T Consensus 194 ------------------~~L~~V~~ai~~ak~~~~~k~~~IFLATDS----aeVid~fr~~FPdiiti~k 242 (321)
T PF05830_consen 194 ------------------RALRQVCTAIDKAKALAPPKPVRIFLATDS----AEVIDQFRKKFPDIITIPK 242 (321)
T ss_dssp ------------------HHHHHHHHHHHHHHTS--SS-EEEEEEES-----HHHHHHHHHHSTTEE----
T ss_pred ------------------HHHHHHHHHHHHHHhccCCCCeeEEEecCc----HHHHHHHHHHCCCeEEccc
Confidence 0011 12224566777788999999998 6789999999999887643
No 4
>PLN02232 ubiquinone biosynthesis methyltransferase
Probab=47.82 E-value=66 Score=29.18 Aligned_cols=97 Identities=12% Similarity=-0.042 Sum_probs=55.6
Q ss_pred hcccccccchhHHHHHHHHHHHHhhccccCCCceEEEeecchhhhHhhc----ccccCCchhHHHHHHHHHHhccccccC
Q 013199 293 ANYEALRFSSPILTMGETLVARMKERSVNHGGKYISVHLRFEEDMVAFS----CCVFDGGEREKEDMKEARERGWKGKFT 368 (448)
Q Consensus 293 vnf~ALrF~p~I~~lg~~LV~Rmr~~s~~s~g~yiALHLRfE~DMlAfs----gC~~~g~~~E~~eL~~~R~~~wk~k~~ 368 (448)
++..+|++.++..+.-+.+.+.|+. +|.++-++.--+...+... -|...+... +.+.
T Consensus 49 ~~~~~l~~~~d~~~~l~ei~rvLkp-----GG~l~i~d~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~ 109 (160)
T PLN02232 49 TMGYGLRNVVDRLRAMKEMYRVLKP-----GSRVSILDFNKSNQSVTTFMQGWMIDNVVVPV--------------ATVY 109 (160)
T ss_pred EecchhhcCCCHHHHHHHHHHHcCc-----CeEEEEEECCCCChHHHHHHHHHHccchHhhh--------------hHHh
Confidence 3445677777778877888888874 7888877765432211100 000000000 0000
Q ss_pred CCCcccCchhhh----cCCCCCCChHHHHHHHHhcCCCCCceEEEeeccc
Q 013199 369 KPGRVIRPGAIR----INGKCPLTPLEVGLMLRGMGFDKNTYIFLASGKI 414 (448)
Q Consensus 369 ~~~~~i~~~~~R----~~G~CPLTPeEvgl~LraLGf~~~T~IYlA~gei 414 (448)
-..++.+ .... +++|+|..-+|+.-||.+-+.-+++.|-+
T Consensus 110 -----~~~~~y~yl~~si~~-f~~~~el~~ll~~aGF~~~~~~~~~~g~~ 153 (160)
T PLN02232 110 -----DLAKEYEYLKYSING-YLTGEELETLALEAGFSSACHYEISGGFM 153 (160)
T ss_pred -----CChHHHHhHHHHHHH-CcCHHHHHHHHHHcCCCcceEEECcchHh
Confidence 0000101 1122 58999999999999999998888887754
No 5
>PF00799 Gemini_AL1: Geminivirus Rep catalytic domain; InterPro: IPR022690 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome []. For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer []. It is found in association with PF08283 from PFAM. ; GO: 0006260 DNA replication; PDB: 1L5I_A 1L2M_A.
Probab=40.55 E-value=27 Score=31.24 Aligned_cols=27 Identities=19% Similarity=0.225 Sum_probs=14.9
Q ss_pred CCCCChHHHHHHHHhcCCCCCceEEEee
Q 013199 384 KCPLTPLEVGLMLRGMGFDKNTYIFLAS 411 (448)
Q Consensus 384 ~CPLTPeEvgl~LraLGf~~~T~IYlA~ 411 (448)
+||||+||+...|++|--+ ....||..
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 6999999999999999764 35667644
No 6
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=35.19 E-value=22 Score=29.78 Aligned_cols=36 Identities=19% Similarity=0.303 Sum_probs=32.4
Q ss_pred CCChHHHHHHHHhcCCCCCceEEEeeccccCccccchhHHHhCCCcccccc
Q 013199 386 PLTPLEVGLMLRGMGFDKNTYIFLASGKIYNAEKTMAPLIEMFPNLQTKEM 436 (448)
Q Consensus 386 PLTPeEvgl~LraLGf~~~T~IYlA~geiyGg~~~m~pL~~~FPnl~tKet 436 (448)
++|-.+++-+|+-..|++ .+|+.|+-++|++++++.
T Consensus 39 ~~T~~Qv~~il~~f~fd~---------------~kl~~lk~l~p~i~D~~n 74 (95)
T PF14771_consen 39 CFTCAQVKQILSLFSFDN---------------DKLKALKLLYPYIVDPQN 74 (95)
T ss_pred ceeHHHHHHHHHHcCCCH---------------HHHHHHHHHhhhccCHHH
Confidence 499999999999999985 379999999999999974
No 7
>KOG3111 consensus D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism]
Probab=31.06 E-value=2e+02 Score=28.79 Aligned_cols=113 Identities=25% Similarity=0.376 Sum_probs=68.6
Q ss_pred ccchhHHHHHHHHHHHHhhccccCCCceEEEeecchh-----hhHhhccc----ccCCc-hhHHHHHHHHHHhccccccC
Q 013199 299 RFSSPILTMGETLVARMKERSVNHGGKYISVHLRFEE-----DMVAFSCC----VFDGG-EREKEDMKEARERGWKGKFT 368 (448)
Q Consensus 299 rF~p~I~~lg~~LV~Rmr~~s~~s~g~yiALHLRfE~-----DMlAfsgC----~~~g~-~~E~~eL~~~R~~~wk~k~~ 368 (448)
+|+|.| +.|.-+|++||+... .-+|.-+||=.|. |=+|-.|- .|--. ++-.+-.+++|++.-|.
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--ADPFFDVHMMVENPEQWVDQMAKAGASLFTFHYEATQKPAELVEKIREKGMKV--- 115 (224)
T ss_pred cccCCc-ccchHHHHHHHhccC--CCcceeEEEeecCHHHHHHHHHhcCcceEEEEEeeccCHHHHHHHHHHcCCee---
Confidence 678876 689999999998421 2359999997653 11222221 11001 11123344556554332
Q ss_pred CCCcccCchhhhcCCCCCCChHHHHHHHHhcCCCCCceEEEeeccccCccccch-------hHHHhCCCcc
Q 013199 369 KPGRVIRPGAIRINGKCPLTPLEVGLMLRGMGFDKNTYIFLASGKIYNAEKTMA-------PLIEMFPNLQ 432 (448)
Q Consensus 369 ~~~~~i~~~~~R~~G~CPLTPeEvgl~LraLGf~~~T~IYlA~geiyGg~~~m~-------pL~~~FPnl~ 432 (448)
|-.++ |=||-|....+.. .-|--+-.+----|||++.|. -||+-|||+.
T Consensus 116 --G~alk----------PgT~Ve~~~~~~~---~~D~vLvMtVePGFGGQkFme~mm~KV~~lR~kyp~l~ 171 (224)
T KOG3111|consen 116 --GLALK----------PGTPVEDLEPLAE---HVDMVLVMTVEPGFGGQKFMEDMMPKVEWLREKYPNLD 171 (224)
T ss_pred --eEEeC----------CCCcHHHHHHhhc---cccEEEEEEecCCCchhhhHHHHHHHHHHHHHhCCCce
Confidence 22232 5688888877766 335555556666699999985 5899999984
No 8
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=30.92 E-value=32 Score=27.79 Aligned_cols=16 Identities=38% Similarity=0.675 Sum_probs=13.8
Q ss_pred CCCCCChHHHHHHHHhc
Q 013199 383 GKCPLTPLEVGLMLRGM 399 (448)
Q Consensus 383 G~CPLTPeEvgl~LraL 399 (448)
|-| +||||-+-+++++
T Consensus 42 ~~C-itpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDC-ITPEEDREILEAT 57 (60)
T ss_pred hcc-CCHHHHHHHHHHH
Confidence 668 9999999998875
No 9
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=29.12 E-value=42 Score=26.26 Aligned_cols=25 Identities=28% Similarity=0.476 Sum_probs=20.6
Q ss_pred hhcCCCCCCChHHHHHHHHhcCCCCC
Q 013199 379 IRINGKCPLTPLEVGLMLRGMGFDKN 404 (448)
Q Consensus 379 ~R~~G~CPLTPeEvgl~LraLGf~~~ 404 (448)
.+..|.. ++++|+.-+|+.|||+-+
T Consensus 12 ~~llG~~-i~~~ei~~~L~~lg~~~~ 36 (71)
T smart00874 12 NRLLGLD-LSAEEIEEILKRLGFEVE 36 (71)
T ss_pred HHHHCCC-CCHHHHHHHHHHCCCeEE
Confidence 3556764 999999999999999753
No 10
>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=27.80 E-value=64 Score=28.78 Aligned_cols=100 Identities=15% Similarity=0.210 Sum_probs=58.3
Q ss_pred ceEEEeecchhhhHhhcccccC------CchhHHHHHHHHHHhccccccCCCCcccCchhhhcCCCCCCChHH-HHHHHH
Q 013199 325 KYISVHLRFEEDMVAFSCCVFD------GGEREKEDMKEARERGWKGKFTKPGRVIRPGAIRINGKCPLTPLE-VGLMLR 397 (448)
Q Consensus 325 ~yiALHLRfE~DMlAfsgC~~~------g~~~E~~eL~~~R~~~wk~k~~~~~~~i~~~~~R~~G~CPLTPeE-vgl~Lr 397 (448)
..++..++-+.+ --|+||.-. +...|+..|.++-...-+ ++. ..++.. ..+. +++|-- .--+|.
T Consensus 21 ~~vgAa~~~~~G-~i~~G~n~e~~~~~~s~~AE~~Ai~~a~~~g~~-~i~--~i~vv~----~~~~-~~sPCG~Crq~l~ 91 (127)
T TIGR01354 21 FKVGAALLTKDG-RIFTGVNVENASYPLTICAERSAIGKAISAGYR-KFV--AIAVAD----SADD-PVSPCGACRQVLA 91 (127)
T ss_pred CeEEEEEEeCCC-CEEEEEeecccCCCCCcCHHHHHHHHHHHcCCC-CeE--EEEEEe----CCCC-CcCccHHHHHHHH
Confidence 457777776533 344466432 235787777766543211 110 001111 1111 245543 234788
Q ss_pred hcCCCCCceEEEeeccccCccccchhHHHhCCCccccccC
Q 013199 398 GMGFDKNTYIFLASGKIYNAEKTMAPLIEMFPNLQTKEML 437 (448)
Q Consensus 398 aLGf~~~T~IYlA~geiyGg~~~m~pL~~~FPnl~tKetL 437 (448)
.++ +.+|.|++...+ |+....+|+++.|.-+.+++|
T Consensus 92 e~~-~~~~~v~~~~~~---~~~~~~~l~eLLP~~f~~~~l 127 (127)
T TIGR01354 92 EFA-GPDTPIYMTNND---GTYKVYTVGELLPFGFGPSDL 127 (127)
T ss_pred HhC-CCCcEEEEECCC---CCEEEEEHHHhCcCcCCcCcC
Confidence 887 679999999877 555678999999998887764
No 11
>PF05399 EVI2A: Ectropic viral integration site 2A protein (EVI2A); InterPro: IPR008608 This family contains several mammalian ectropic viral integration site 2A (EVI2A) proteins. The function of this protein is unknown although it is thought to be a membrane protein and may function as an oncogene in retrovirus induced myeloid tumours [, ].; GO: 0016021 integral to membrane
Probab=27.28 E-value=1e+02 Score=30.87 Aligned_cols=26 Identities=31% Similarity=0.317 Sum_probs=12.3
Q ss_pred cccChHHHhhhccccccCCCCccccccccc
Q 013199 102 VYRSPQVYAKLKPEMDADNSSSDAISTIWK 131 (448)
Q Consensus 102 ~~rs~~~~~~l~~~~~~~~~~~~~~~~lW~ 131 (448)
.-|+.|+..| .+.+|+..-+.+.||-
T Consensus 161 LKrskQ~gKR----qpRSNGDFLASSgLWP 186 (227)
T PF05399_consen 161 LKRSKQVGKR----QPRSNGDFLASSGLWP 186 (227)
T ss_pred HHHHHHhhcc----CCCcccceeeccccCc
Confidence 3455555443 1334433334556884
No 12
>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=26.60 E-value=20 Score=33.79 Aligned_cols=25 Identities=28% Similarity=0.658 Sum_probs=21.0
Q ss_pred ceEEeccccccccccCCCCCCcccChHH
Q 013199 184 ATLVIPNFHYHSIWRDPSKFRDIYDEDY 211 (448)
Q Consensus 184 ATLVlP~l~~~s~W~D~S~F~DIfDvdh 211 (448)
|++| |..+.+|+|.|.|.-++|.||
T Consensus 26 A~II---Leah~vW~DgsGyQ~LlDaDH 50 (161)
T PF10365_consen 26 ARII---LEAHNVWGDGSGYQMLLDADH 50 (161)
T ss_pred eEEE---EeccccccCCcceEEEEcCCc
Confidence 5555 456789999999999999998
No 13
>PRK05578 cytidine deaminase; Validated
Probab=24.92 E-value=70 Score=29.02 Aligned_cols=99 Identities=17% Similarity=0.195 Sum_probs=57.8
Q ss_pred EEEeecchhhhHhhccccc------CCchhHHHHHHHHHHhccccccCCCCcccCchhhhcCCCCCCChHHH-HHHHHhc
Q 013199 327 ISVHLRFEEDMVAFSCCVF------DGGEREKEDMKEARERGWKGKFTKPGRVIRPGAIRINGKCPLTPLEV-GLMLRGM 399 (448)
Q Consensus 327 iALHLRfE~DMlAfsgC~~------~g~~~E~~eL~~~R~~~wk~k~~~~~~~i~~~~~R~~G~CPLTPeEv-gl~LraL 399 (448)
|+-.+|-+ |=-.|.||.- .+..+|+-.+..+-...=+ ++. ..++.... .-+++|-=. --+|..+
T Consensus 26 Vgaa~~~~-~G~i~~G~nvEna~~~~~~CAE~~Ai~~av~~G~~-~i~--~i~vv~~~-----~~~~sPCG~CRQ~l~e~ 96 (131)
T PRK05578 26 VGAALLTD-DGRIYTGCNIENASYGLTNCAERTAIFKAISEGGG-RLV--AIACVGET-----GEPLSPCGRCRQVLAEF 96 (131)
T ss_pred eEEEEEeC-CCCEEEEEEeeCccccCCcCHHHHHHHHHHHcCCC-ceE--EEEEEecC-----CCccCccHHHHHHHHHh
Confidence 67777765 4455555532 2335788888776432111 110 00122111 123455322 2456666
Q ss_pred CCCCCceEEEeeccccCccccchhHHHhCCCccccccCC
Q 013199 400 GFDKNTYIFLASGKIYNAEKTMAPLIEMFPNLQTKEMLA 438 (448)
Q Consensus 400 Gf~~~T~IYlA~geiyGg~~~m~pL~~~FPnl~tKetLa 438 (448)
+ +.+|.||+...+ |+.....|+++.|+-+++++|+
T Consensus 97 ~-~~~~~v~l~~~~---~~~~~~~l~eLLP~~f~~~~l~ 131 (131)
T PRK05578 97 G-GPDLLVTLVAKD---GPTGEMTLGELLPYAFTPDDLG 131 (131)
T ss_pred C-CCCcEEEEEcCC---CCEEEEEHHHhCcCcCChhhcC
Confidence 4 679999999876 5556689999999999998874
No 14
>PF15302 P33MONOX: P33 mono-oxygenase
Probab=24.56 E-value=62 Score=33.23 Aligned_cols=21 Identities=43% Similarity=0.678 Sum_probs=16.1
Q ss_pred cCCCCCCCCCCCCCCCCCCCccc
Q 013199 4 NRLPSSGHTTPSPPASPRRSPRY 26 (448)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~ 26 (448)
.|+++|.++|||-+|+ +||..
T Consensus 153 erq~sSaQSTPssTP~--ssPkq 173 (294)
T PF15302_consen 153 ERQPSSAQSTPSSTPH--SSPKQ 173 (294)
T ss_pred hcCccccccCCCCCCC--CCccc
Confidence 4788999999888776 66653
No 15
>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=23.18 E-value=24 Score=31.79 Aligned_cols=17 Identities=24% Similarity=0.636 Sum_probs=12.9
Q ss_pred HHHHHHhcCCCCCceEE
Q 013199 392 VGLMLRGMGFDKNTYIF 408 (448)
Q Consensus 392 vgl~LraLGf~~~T~IY 408 (448)
+.++|||||+.++.-||
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 78999999998887766
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=20.04 E-value=49 Score=26.38 Aligned_cols=26 Identities=23% Similarity=0.445 Sum_probs=17.7
Q ss_pred hhcCCCCCCChHHHHHHHHhcCCCCCc
Q 013199 379 IRINGKCPLTPLEVGLMLRGMGFDKNT 405 (448)
Q Consensus 379 ~R~~G~CPLTPeEvgl~LraLGf~~~T 405 (448)
.+..|.. ++++|+.-+|+.|||.-+-
T Consensus 12 ~~~lG~~-i~~~~i~~~L~~lg~~~~~ 37 (70)
T PF03484_consen 12 NKLLGID-ISPEEIIKILKRLGFKVEK 37 (70)
T ss_dssp HHHHTS----HHHHHHHHHHTT-EEEE
T ss_pred HHHhCCC-CCHHHHHHHHHHCCCEEEE
Confidence 3555765 9999999999999997554
Done!