Query 030911
Match_columns 169
No_of_seqs 118 out of 321
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 06:26:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030911.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030911hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14299 PP2: Phloem protein 2 100.0 1.7E-61 3.7E-66 376.0 19.4 142 20-168 1-154 (154)
2 PF13464 DUF4115: Domain of un 32.8 51 0.0011 22.0 2.8 21 57-77 7-34 (77)
3 cd00063 FN3 Fibronectin type 3 31.8 1.2E+02 0.0027 18.4 5.9 16 69-84 64-79 (93)
4 KOG0418 Ubiquitin-protein liga 30.8 75 0.0016 25.8 3.7 62 53-114 28-92 (200)
5 PF05578 Peptidase_S31: Pestiv 30.6 31 0.00067 27.4 1.5 57 19-97 111-169 (211)
6 PF07353 Uroplakin_II: Uroplak 30.2 51 0.0011 26.2 2.6 18 68-85 108-125 (184)
7 PF02018 CBM_4_9: Carbohydrate 28.2 2E+02 0.0044 19.8 6.4 31 65-101 54-84 (131)
8 PF13765 PRY: SPRY-associated 26.8 82 0.0018 19.2 2.7 40 15-54 3-42 (49)
9 PF06510 DUF1102: Protein of u 26.0 3.2E+02 0.0069 21.3 10.2 30 69-100 45-77 (146)
10 COG3807 Uncharacterized protei 23.4 80 0.0017 24.9 2.6 26 65-97 42-69 (171)
No 1
>PF14299 PP2: Phloem protein 2
Probab=100.00 E-value=1.7e-61 Score=376.00 Aligned_cols=142 Identities=38% Similarity=0.720 Sum_probs=129.8
Q ss_pred CCeEEEEecccceeEeCCCCCceec---CCCCCCcceEEeeeeEEEEEEEE---EccCCCeEEEEEEEEeccCcCCCccc
Q 030911 20 ERTEATIKPRGLNIVWGNDPRYWHL---PEKRSNDPVELVQVCWLEATGSV---EVKRGKKYQIGFKISLKADAFGWSGC 93 (169)
Q Consensus 20 g~kcymlsAR~L~I~Wgd~~~yW~~---p~srf~evAeL~~VcWLeI~G~i---~LSp~t~Y~ay~v~kl~~~a~Gw~~~ 93 (169)
|+||||||||+|+|+||||++||+| |++||.|||||++||||||+|+| +|||+|+|+||||||+++++|||+.+
T Consensus 1 G~~cymlsaR~L~I~Wg~~~~yW~w~~~~~srf~evAeL~~V~WLeI~G~i~~~~Lsp~t~Y~vy~v~kl~~~~~Gw~~~ 80 (154)
T PF14299_consen 1 GKKCYMLSARALSITWGDDPRYWKWIPLPDSRFSEVAELLQVCWLEIRGKINTRMLSPGTTYAVYFVFKLKDDAYGWDSP 80 (154)
T ss_pred CCEEEEEEhhhCEEecCCCCcceeeccCCcccceeeeEEEEEEEEEEEEEEEceEcCCCCEEEEEEEEEecCCCCCCCcC
Confidence 8999999999999999999999997 78999999999999999999999 59999999999999999999999988
Q ss_pred CeEEEEEecCCCcE-EEEEEeeCCCCCCcccccCCcEEEEEccC--C---CCcEEEEEEEEEeCCeeeeeEEEEEEEEEE
Q 030911 94 PVFMMAKLGKKGKY-TWRKMKPLDHLGKEAAEIPDEKFEILVPE--Q---GENQLYFGLYEVWNGKWKGGLLIHHAFIRE 167 (169)
Q Consensus 94 pv~~~~~~g~~g~~-~~~~v~l~~~~~~~~~~~pdgW~Eie~Ge--~---~~~ev~fs~~e~~~~~wK~GLiv~GieIRP 167 (169)
||+++++++..++. ..+.+++.. .+.|||||||+|+ + ++++|+|+|+|+++++||+||||+||||||
T Consensus 81 pv~~~v~~~~~~~~~~~~~~~~~~-------~r~dgW~Eie~GeF~~~~~~~~ev~f~~~E~~~~~wK~GLiv~GieIRP 153 (154)
T PF14299_consen 81 PVEFSVKVPDGEKYEQERKVCLPK-------ERGDGWMEIELGEFFNEGGDDGEVEFSMYEVDSGHWKGGLIVEGIEIRP 153 (154)
T ss_pred CEEEEEEeCCCccccceeeEEcCC-------CCCCCEEEEEcceEEecCCCCcEEEEEEEEecCCcccCeEEEEEEEEec
Confidence 99999999543332 456677776 3569999999999 3 689999999999999999999999999999
Q ss_pred c
Q 030911 168 V 168 (169)
Q Consensus 168 ~ 168 (169)
|
T Consensus 154 K 154 (154)
T PF14299_consen 154 K 154 (154)
T ss_pred C
Confidence 7
No 2
>PF13464 DUF4115: Domain of unknown function (DUF4115)
Probab=32.84 E-value=51 Score=21.96 Aligned_cols=21 Identities=33% Similarity=0.629 Sum_probs=15.9
Q ss_pred eeeEEEEE---EEE----EccCCCeEEE
Q 030911 57 QVCWLEAT---GSV----EVKRGKKYQI 77 (169)
Q Consensus 57 ~VcWLeI~---G~i----~LSp~t~Y~a 77 (169)
.-||++|+ |+. .|.||..++.
T Consensus 7 ~~sWv~V~d~dG~~~~~~~l~~G~~~~~ 34 (77)
T PF13464_consen 7 GDSWVEVTDADGKVLFSGTLKAGETKTF 34 (77)
T ss_pred CCeEEEEEeCCCcEeeeeeeCCCcEEEE
Confidence 56999998 655 4778888875
No 3
>cd00063 FN3 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.
Probab=31.81 E-value=1.2e+02 Score=18.45 Aligned_cols=16 Identities=19% Similarity=0.385 Sum_probs=12.6
Q ss_pred ccCCCeEEEEEEEEec
Q 030911 69 VKRGKKYQIGFKISLK 84 (169)
Q Consensus 69 LSp~t~Y~ay~v~kl~ 84 (169)
|.|++.|.+.++..-.
T Consensus 64 l~p~~~Y~~~v~a~~~ 79 (93)
T cd00063 64 LKPGTEYEFRVRAVNG 79 (93)
T ss_pred ccCCCEEEEEEEEECC
Confidence 8899999987665543
No 4
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.83 E-value=75 Score=25.83 Aligned_cols=62 Identities=16% Similarity=0.199 Sum_probs=43.8
Q ss_pred eEEeeeeEEEEEEEEEccCCCeEE-EEEEEEec-cCcCCCcccCeEEEEEe-cCCCcEEEEEEee
Q 030911 53 VELVQVCWLEATGSVEVKRGKKYQ-IGFKISLK-ADAFGWSGCPVFMMAKL-GKKGKYTWRKMKP 114 (169)
Q Consensus 53 AeL~~VcWLeI~G~i~LSp~t~Y~-ay~v~kl~-~~a~Gw~~~pv~~~~~~-g~~g~~~~~~v~l 114 (169)
.|+.+--+-+|+|.|.--|+|-|+ -+|++.++ .+.|=|+-.-|.|.-++ -++=+.+...+||
T Consensus 28 ve~vn~~~~~ikG~I~GP~~TPYEGG~FeldI~iPe~YPF~pPkv~F~TkIwHPnVSs~tGaICL 92 (200)
T KOG0418|consen 28 VEMVNENLKEIKGHIAGPEDTPYEGGVFELDIKIPENYPFKPPKVKFITKIWHPNVSSQTGAICL 92 (200)
T ss_pred EEEccCChhhceeEecCCCCCCCCCceEEEEEecCCCCCCCCCceeeeeeeecCCCCcccccchh
Confidence 345555677899999999999995 57777775 45688885447776555 4554555567888
No 5
>PF05578 Peptidase_S31: Pestivirus NS3 polyprotein peptidase S31; InterPro: IPR000280 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S31 (clan PA(S)). The type example is pestivirus NS3 polyprotein peptidase from bovine viral diarrhea virus, which is Type 1 pestivirus. The pestiviruses are single-stranded RNA viruses whose genomes encode one large polyprotein []. The p80 endopeptidase resides towards the middle of the polyprotein and is responsible for processing all non-structural pestivirus proteins [, ]. The p80 enzyme is similar to other proteases in the PA(S) clan and is predicted to have a fold similar to that of chymotrypsin [, ]. An HDS catalytic triad has been identified [].; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis
Probab=30.63 E-value=31 Score=27.41 Aligned_cols=57 Identities=25% Similarity=0.410 Sum_probs=33.4
Q ss_pred CCCeEEEEecccceeEeCCCCCceecCCCCCCcceEEeeeeEEEEEEEEEcc--CCCeEEEEEEEEeccCcCCCcccCeE
Q 030911 19 AERTEATIKPRGLNIVWGNDPRYWHLPEKRSNDPVELVQVCWLEATGSVEVK--RGKKYQIGFKISLKADAFGWSGCPVF 96 (169)
Q Consensus 19 sg~kcymlsAR~L~I~Wgd~~~yW~~p~srf~evAeL~~VcWLeI~G~i~LS--p~t~Y~ay~v~kl~~~a~Gw~~~pv~ 96 (169)
.|+.||+|.|-+++|+-..+. | ..|+ .--|.|.+- .|| -|+|-.| +--||...|++
T Consensus 111 ~garcyv~npea~nisgtkga--~----------vhlq-----k~ggef~cvta~gt--paf~~~k---nlkg~s~~pif 168 (211)
T PF05578_consen 111 DGARCYVLNPEATNISGTKGA--M----------VHLQ-----KTGGEFTCVTASGT--PAFFDLK---NLKGWSGLPIF 168 (211)
T ss_pred CCcEEEEeCCcccccccCcce--E----------EEEe-----ccCCceEEEeccCC--cceeecc---ccCCCCCCcee
Confidence 369999999999999733221 1 1221 224666432 222 2444443 24599988875
Q ss_pred E
Q 030911 97 M 97 (169)
Q Consensus 97 ~ 97 (169)
-
T Consensus 169 e 169 (211)
T PF05578_consen 169 E 169 (211)
T ss_pred e
Confidence 4
No 6
>PF07353 Uroplakin_II: Uroplakin II; InterPro: IPR009952 This family contains uroplakin II, which is approximately 180 residues long and seems to be restricted to mammals. Uroplakin II is an integral membrane protein, and is one of the components of the apical plaques of mammalian urothelium formed by the asymmetric unit membrane - this is believed to play a role in strengthening the urothelial apical surface to prevent the cells from rupturing during bladder distension [].; GO: 0016044 cellular membrane organization, 0030176 integral to endoplasmic reticulum membrane
Probab=30.16 E-value=51 Score=26.25 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=14.7
Q ss_pred EccCCCeEEEEEEEEecc
Q 030911 68 EVKRGKKYQIGFKISLKA 85 (169)
Q Consensus 68 ~LSp~t~Y~ay~v~kl~~ 85 (169)
+|.|||+|.+.+.|.-..
T Consensus 108 NL~pGTkY~isY~Vtkgt 125 (184)
T PF07353_consen 108 NLQPGTKYYISYLVTKGT 125 (184)
T ss_pred ccCCCcEEEEEEEEecCc
Confidence 688999999888886653
No 7
>PF02018 CBM_4_9: Carbohydrate binding domain; InterPro: IPR003305 The 1,4-beta-glucanase CenC from Cellulomonas fimi contains two cellulose-binding domains, CBD(N1) and CBD(N2), arranged in tandem at its N terminus. These homologous CBDs are distinct in their selectivity for binding amorphous and not crystalline cellulose []. Multidimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy was used to determine the tertiary structure of the 152 amino acid N-terminal cellulose-binding domain from C. fimi 1,4-beta-glucanase CenC (CBDN1) []. The tertiary structure of CBDN1 is strikingly similar to that of the bacterial 1,3-1,4-beta-glucanases, as well as other sugar-binding proteins with jelly-roll folds.; GO: 0016798 hydrolase activity, acting on glycosyl bonds; PDB: 3OEA_B 2ZEX_B 3OEB_A 2ZEY_A 2ZEW_A 1GUI_A 2W5F_A 2WZE_A 2WYS_A 2ZEZ_B ....
Probab=28.18 E-value=2e+02 Score=19.78 Aligned_cols=31 Identities=19% Similarity=0.353 Sum_probs=22.8
Q ss_pred EEEEccCCCeEEEEEEEEeccCcCCCcccCeEEEEEe
Q 030911 65 GSVEVKRGKKYQIGFKISLKADAFGWSGCPVFMMAKL 101 (169)
Q Consensus 65 G~i~LSp~t~Y~ay~v~kl~~~a~Gw~~~pv~~~~~~ 101 (169)
..+.|.||.+|.+.|-++.... .++.+.+..
T Consensus 54 ~~~~l~~G~~Y~~s~~vk~~~~------~~~~~~~~~ 84 (131)
T PF02018_consen 54 QTISLKPGKTYTVSFWVKADSG------GTVSVSLRD 84 (131)
T ss_dssp EEEEE-TTSEEEEEEEEEESSS------EEEEEEEEE
T ss_pred cceEecCCCEEEEEEEEEeCCC------CEEEEEEEE
Confidence 3367899999999999999763 466666555
No 8
>PF13765 PRY: SPRY-associated domain; PDB: 3KB5_A 2VOK_A 2VOL_B 2FBE_B 2WL1_A 2IWG_E.
Probab=26.77 E-value=82 Score=19.22 Aligned_cols=40 Identities=10% Similarity=0.214 Sum_probs=25.5
Q ss_pred EEeeCCCeEEEEecccceeEeCCCCCceecCCCCCCcceE
Q 030911 15 MEWNAERTEATIKPRGLNIVWGNDPRYWHLPEKRSNDPVE 54 (169)
Q Consensus 15 ld~~sg~kcymlsAR~L~I~Wgd~~~yW~~p~srf~evAe 54 (169)
||.+|...+..||.-.-++.+++..+-.--...||...+-
T Consensus 3 lDp~TAh~~L~lS~d~k~v~~~~~~~~~p~~peRF~~~~~ 42 (49)
T PF13765_consen 3 LDPNTAHPSLVLSEDGKSVRYSEQPQNYPDNPERFDHWPQ 42 (49)
T ss_dssp B-TTTS-TTEEEETTSSEEEE-SST-S--S-TTS-SSSSE
T ss_pred ECcccCCCCeEECCCCeEEEEccCCccCCCCCCccCCcCe
Confidence 7889999999999999999998887654444568874443
No 9
>PF06510 DUF1102: Protein of unknown function (DUF1102); InterPro: IPR009482 This family consists of several hypothetical archaeal proteins of unknown function.
Probab=26.04 E-value=3.2e+02 Score=21.26 Aligned_cols=30 Identities=10% Similarity=0.298 Sum_probs=23.4
Q ss_pred ccCCCeEEEEEEEEeccCcCCCcc---cCeEEEEE
Q 030911 69 VKRGKKYQIGFKISLKADAFGWSG---CPVFMMAK 100 (169)
Q Consensus 69 LSp~t~Y~ay~v~kl~~~a~Gw~~---~pv~~~~~ 100 (169)
|||++.|.-==||.+.. ..|++ .|+-+.++
T Consensus 45 lSp~S~Y~Fd~VF~VsN--~lwEn~~~~~IcV~I~ 77 (146)
T PF06510_consen 45 LSPNSTYVFDEVFEVSN--HLWENGADVPICVTIS 77 (146)
T ss_pred cCCCceEeeeeEEEeec--ccccccCCceEEEEEe
Confidence 89999999777888865 68997 67766554
No 10
>COG3807 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.38 E-value=80 Score=24.94 Aligned_cols=26 Identities=23% Similarity=0.422 Sum_probs=19.7
Q ss_pred EEEEcc--CCCeEEEEEEEEeccCcCCCcccCeEE
Q 030911 65 GSVEVK--RGKKYQIGFKISLKADAFGWSGCPVFM 97 (169)
Q Consensus 65 G~i~LS--p~t~Y~ay~v~kl~~~a~Gw~~~pv~~ 97 (169)
++.++. |+|.|++.++|.-+- .||++
T Consensus 42 ~~VN~R~GP~~~yav~W~y~k~G-------lPVEI 69 (171)
T COG3807 42 AEVNARVGPGTDYAVEWVYLKKG-------LPVEI 69 (171)
T ss_pred cceecccCCCccceeEEeeeccC-------Cceeh
Confidence 444544 999999999998764 56766
Done!