Query 040209
Match_columns 388
No_of_seqs 111 out of 146
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 06:10:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040209.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040209hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04833 COBRA: COBRA-like pro 100.0 1.1E-81 2.3E-86 567.7 16.7 161 1-161 3-169 (169)
2 PF00553 CBM_2: Cellulose bind 86.2 3.3 7.2E-05 34.4 7.0 97 235-351 3-101 (101)
3 PF00553 CBM_2: Cellulose bind 50.7 39 0.00085 28.1 5.2 39 2-43 18-56 (101)
4 PF03128 CXCXC: CXCXC repeat; 48.4 8.8 0.00019 22.3 0.7 8 186-193 7-14 (14)
5 PF10563 CdCA1: Cadmium carbon 45.1 4.1 8.9E-05 39.6 -1.6 15 229-243 5-19 (218)
6 COG5341 Uncharacterized protei 37.8 44 0.00096 30.4 3.8 38 316-353 46-83 (132)
7 PF10609 ParA: ParA/MinD ATPas 22.6 42 0.00091 28.0 1.0 13 62-74 4-16 (81)
8 smart00141 PDGF Platelet-deriv 21.6 59 0.0013 27.1 1.7 49 56-108 2-62 (83)
9 cd05467 CBM20 The family 20 ca 19.2 4E+02 0.0086 21.0 6.0 52 235-288 2-66 (96)
10 cd05820 CBM20_novamyl Novamyl 16.8 4.3E+02 0.0093 22.0 5.8 52 233-288 5-71 (103)
No 1
>PF04833 COBRA: COBRA-like protein; InterPro: IPR006918 In Arabidopsis thaliana (Mouse-ear cress) members of the family are all extracellular glycosyl-phosphatidyl inositol-anchored proteins (GPI-linked) []. The type example of the family is COBRA (Q94KT8 from SWISSPROT) and the family is generally annotated as COBRA-like (COBL). COBRA is involved in determining the orientation of cell expansion, probably by playing an important role in cellulose deposition. It may act by recruiting cellulose synthesizing complexes to discrete positions on the cell surface. Some members of this family are annotated as phytochelatin synthase, but these annotations are incorrect [].
Probab=100.00 E-value=1.1e-81 Score=567.68 Aligned_cols=161 Identities=60% Similarity=1.133 Sum_probs=155.2
Q ss_pred CEEEEecCccccccCCCCCeeEEeecCCeeEEEeccceeeeeCCccccC-CCCCCcccCCCCeEEeCCCCCCCCcccccc
Q 040209 1 LRVSLFNYQLYRHIDQPGWKLNWGWQGDEVIWNMWGAEATEQGNCSKFT-GGQLPHCCEKSPVIVDLLPGAPYNQQTANC 79 (388)
Q Consensus 1 ~~VTi~N~q~~r~i~~pgW~L~W~W~~~E~IwsM~GA~~~~qgdCs~~~-~~~~ph~C~k~P~IvDL~P~~~~d~qi~nC 79 (388)
.+|||+|||+|||||.|||+|||+|+|+||||+|+||||+|||||++|+ +.++||||+|+|+|||||||+|||+|++||
T Consensus 3 A~VTi~N~~~yr~id~pgW~L~W~W~~~E~IwsM~GA~~tdqgdCs~~~~~~~~ph~C~k~P~IvDLpp~~~~n~qi~nC 82 (169)
T PF04833_consen 3 AQVTISNYQPYRHIDNPGWNLGWTWAKKEFIWSMKGAQTTDQGDCSKFYKDGDFPHCCKKRPTIVDLPPGTPYNQQIGNC 82 (169)
T ss_pred EEEEEecCCeecccCCCCceEeeEEcCCEEEEEeeCceeccCCcccccccCCCCCcccCCCCEEEeCCCCCCCccccccc
Confidence 3799999999999999999999999999999999999999999999988 445999999999999999999999999999
Q ss_pred ccCCeeccCccCccCCceeEEEEEeec--CCC-CCcCCCcCeEecC--CceecCCCeeeCCCcccCCCCceeeeEeEEEe
Q 040209 80 CKGGVLSSLTQDPSKFVAGFQMNVGGS--ADY-TGFQMPENFTLGI--PGYTCGNATEVPPSKFYSDGGRRRTQALRTWN 154 (388)
Q Consensus 80 Cr~G~l~~~~~Dps~s~S~FQm~Vg~~--~~~-~~~~~P~nf~l~~--pgYtCg~p~~V~Pt~f~~p~g~r~t~Al~TWq 154 (388)
||||||+||+|||+||+|+|||+||++ +++ ++++||+||+|++ |||+||+|++|+||+|+|+||||+||||||||
T Consensus 83 CrgG~l~~~~~Dps~s~S~FQm~Vg~~pp~~~~~~~~~P~nf~l~~~~pgYtCg~~~~V~pT~f~~~~g~r~t~A~~TWq 162 (169)
T PF04833_consen 83 CRGGVLSSWAQDPSKSVSAFQMSVGKAPPGTNNTTVKPPQNFTLGGPGPGYTCGPPKRVSPTVFPDPDGRRTTQALMTWQ 162 (169)
T ss_pred cCCCEECCcccChhhCceEEEEEEeEeeccCCCceecCCcceEEcCCCCCcCCCCcceeCCceeeCCCCCEEEEEEEEEe
Confidence 999999999999999999999999999 556 9999999999999 56999999999999999999999999999999
Q ss_pred eEeeeec
Q 040209 155 VTCIYSQ 161 (388)
Q Consensus 155 VtC~ysq 161 (388)
|||||||
T Consensus 163 vtC~ysq 169 (169)
T PF04833_consen 163 VTCNYSQ 169 (169)
T ss_pred EEEEeeC
Confidence 9999997
No 2
>PF00553 CBM_2: Cellulose binding domain; InterPro: IPR001919 The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (3.2.1.4 from EC), cellobiohydrolases (3.2.1.91 from EC) (exoglucanases), or xylanases (3.2.1.8 from EC) []. Structurally, cellulases and xylanases generally consist of a catalytic domain joined to a cellulose-binding domain (CBD) by a short linker sequence rich in proline and/or hydroxy-amino acids. The CBD domain is found either at the N-terminal or at the C-terminal extremity of these enzymes. As it is shown in the following schematic representation, there are two conserved cysteines in this CBD domain - one at each extremity of the domain - which have been shown [] to be involved in a disulphide bond. There are also four conserved tryptophan, two are involved in cellulose binding. The CBD of a number of bacterial cellulases has been shown to consist of about 105 amino acid residues [, ]. +-------------------------------------------------+ | | xCxxxxWxxxxxNxxxWxxxxxxxWxxxxxxxxWNxxxxxGxxxxxxxxxxCx 'C': conserved cysteine involved in a disulphide bond. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 2CZN_A 2CWR_A 1HEH_C 1HEJ_C 3NDZ_E 3NDY_E 2XBD_A 1E5C_A 1XBD_A 1E5B_A ....
Probab=86.22 E-value=3.3 Score=34.41 Aligned_cols=97 Identities=20% Similarity=0.268 Sum_probs=61.9
Q ss_pred EeEEEeeCCCCceEEEEEEEecCCccCcccceEEeecCCCCCceeEEEecceeCCCCCcccceEEEEccchhhHHHhhcC
Q 040209 235 VHWHVKQSYTQYWRVKITITNLNVVQNYSQWNLVALHPNLQSVTQVFSFNYKPLNQYGYINDTGMFWGIEFYNDMLLQAG 314 (388)
Q Consensus 235 IhWHVk~nYk~~WrvkiTi~N~~~~~ny~dW~lvvqhpn~~~~~~vySFN~t~l~~y~~~NdT~m~~Gl~~yN~ll~e~g 314 (388)
+-.-|..+.-+++.+.|||+|=. .....+|.+-++.|.-.-+++++ |++.- ...+++.+-+. .||-.|.
T Consensus 3 v~~~v~~~W~~Gf~~~v~v~N~~-~~~i~~W~v~~~~~~~~~i~~~W--na~~s----~~g~~~~v~~~-~wn~~i~--- 71 (101)
T PF00553_consen 3 VTYTVTNSWGGGFQGEVTVTNNG-SSPINGWTVTFTFPSGQTITSSW--NATVS----QSGNTVTVTNP-SWNGTIA--- 71 (101)
T ss_dssp EEEEEEEESSSEEEEEEEEEESS-SSTEESEEEEEEESTTEEEEEEE--SCEEE----EETTEEEEEES-STCSEEE---
T ss_pred EEEEEecccCCCeEEEEEEEECC-CCccCCEEEEEEeCCCCEEeeee--ccEEE----ecCCEEEEEcC-CcCcccC---
Confidence 45567888999999999999966 46777999999998644455544 44421 12346666654 3443322
Q ss_pred CCCceeEEEEEeecCCCeeeeccCC--CceeeEeeCCcc
Q 040209 315 ESGNVQTEMLLHKDSGIFTFREGWG--FPRRILFNGDEC 351 (388)
Q Consensus 315 ~~G~vQSeilf~K~~~~ft~~~Gw~--FP~rVyFNGeeC 351 (388)
+|.- ..+ +|...+.-. -|..+-|||..|
T Consensus 72 -~G~s-~~~-------Gf~~~~~~~~~~p~~~t~ng~~C 101 (101)
T PF00553_consen 72 -PGGS-VTF-------GFQASGSGSSAAPSTCTVNGAPC 101 (101)
T ss_dssp -ESEE-EEE-------EEEEEESSS--SESEEEETTEEE
T ss_pred -CCCe-EEE-------EEEEeCCCCCCCCcEEEEcCeeC
Confidence 1222 223 333333333 499999999998
No 3
>PF00553 CBM_2: Cellulose binding domain; InterPro: IPR001919 The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (3.2.1.4 from EC), cellobiohydrolases (3.2.1.91 from EC) (exoglucanases), or xylanases (3.2.1.8 from EC) []. Structurally, cellulases and xylanases generally consist of a catalytic domain joined to a cellulose-binding domain (CBD) by a short linker sequence rich in proline and/or hydroxy-amino acids. The CBD domain is found either at the N-terminal or at the C-terminal extremity of these enzymes. As it is shown in the following schematic representation, there are two conserved cysteines in this CBD domain - one at each extremity of the domain - which have been shown [] to be involved in a disulphide bond. There are also four conserved tryptophan, two are involved in cellulose binding. The CBD of a number of bacterial cellulases has been shown to consist of about 105 amino acid residues [, ]. +-------------------------------------------------+ | | xCxxxxWxxxxxNxxxWxxxxxxxWxxxxxxxxWNxxxxxGxxxxxxxxxxCx 'C': conserved cysteine involved in a disulphide bond. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 2CZN_A 2CWR_A 1HEH_C 1HEJ_C 3NDZ_E 3NDY_E 2XBD_A 1E5C_A 1XBD_A 1E5B_A ....
Probab=50.75 E-value=39 Score=28.05 Aligned_cols=39 Identities=23% Similarity=0.577 Sum_probs=31.6
Q ss_pred EEEEecCccccccCCCCCeeEEeecCCeeEEEeccceeeeeC
Q 040209 2 RVSLFNYQLYRHIDQPGWKLNWGWQGDEVIWNMWGAEATEQG 43 (388)
Q Consensus 2 ~VTi~N~q~~r~i~~pgW~L~W~W~~~E~IwsM~GA~~~~qg 43 (388)
+|+|.|..- ..|+ ||+|.|+-..++-|-++.+|..+..|
T Consensus 18 ~v~v~N~~~-~~i~--~W~v~~~~~~~~~i~~~Wna~~s~~g 56 (101)
T PF00553_consen 18 EVTVTNNGS-SPIN--GWTVTFTFPSGQTITSSWNATVSQSG 56 (101)
T ss_dssp EEEEEESSS-STEE--SEEEEEEESTTEEEEEEESCEEEEET
T ss_pred EEEEEECCC-CccC--CEEEEEEeCCCCEEeeeeccEEEecC
Confidence 578888766 4554 89999999989999999999877643
No 4
>PF03128 CXCXC: CXCXC repeat; InterPro: IPR004153 This repeat contains the conserved pattern CXCXC where X can be any amino acid. The repeat is found in up to five copies in Vascular endothelial growth factor C []. In the salivary glands of the dipteran Chironomus tentans, a specific messenger ribonucleoprotein (mRNP) particle, the Balbiani ring (BR) granule, can be visualized during its assembly on the gene and during its nucleocytoplasmic transport. This repeat is found over 70 copies in the balbiani ring protein 3 (Q03376 from SWISSPROT). It is also found in some silk proteins [].
Probab=48.43 E-value=8.8 Score=22.34 Aligned_cols=8 Identities=38% Similarity=1.427 Sum_probs=6.2
Q ss_pred CCCccCCC
Q 040209 186 PKCSCHCQ 193 (388)
Q Consensus 186 ~tCaCGC~ 193 (388)
.||+|+|+
T Consensus 7 ~tC~C~Cp 14 (14)
T PF03128_consen 7 DTCQCECP 14 (14)
T ss_pred CCcCccCC
Confidence 46999994
No 5
>PF10563 CdCA1: Cadmium carbonic anhydrase repeat; InterPro: IPR018883 This entry represents the cadmium-binding carbonic anhydrase domain of marine diatoms []. The prevalence of carbonic anhydrase in diatoms that contain Cd at their active site probably reflects the very low concentration of Zn in the marine environment and the difficulty in acquiring inorganic carbon for photosynthesis. Compared with alpha- and gamma-carbonic anhydrases that use three histidines to coordinate the zinc-atom, this beta-carbonic anhydrase has two cysteines and one histidine, and rapidly binds cadmium []. ; PDB: 3BOH_A 3BOJ_A 3BOC_A 3BOE_A 3BOB_A.
Probab=45.08 E-value=4.1 Score=39.60 Aligned_cols=15 Identities=53% Similarity=1.221 Sum_probs=7.7
Q ss_pred CCCceEEeEEEeeCC
Q 040209 229 HMCPVRVHWHVKQSY 243 (388)
Q Consensus 229 ~mCpV~IhWHVk~nY 243 (388)
.||||+||||+-.-.
T Consensus 5 ~mc~vnvhwHlgaEh 19 (218)
T PF10563_consen 5 SMCPVNVHWHLGAEH 19 (218)
T ss_dssp EEEECGGG------C
T ss_pred eeeeeeeecccccch
Confidence 499999999998733
No 6
>COG5341 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.76 E-value=44 Score=30.39 Aligned_cols=38 Identities=24% Similarity=0.422 Sum_probs=33.3
Q ss_pred CCceeEEEEEeecCCCeeeeccCCCceeeEeeCCccCC
Q 040209 316 SGNVQTEMLLHKDSGIFTFREGWGFPRRILFNGDECVM 353 (388)
Q Consensus 316 ~G~vQSeilf~K~~~~ft~~~Gw~FP~rVyFNGeeC~m 353 (388)
.|++=-++.++|...+|++++-+||=-+|-|.|+|=+.
T Consensus 46 ~Gk~~r~i~l~Kg~~t~~v~~~~g~~n~vev~g~~IRV 83 (132)
T COG5341 46 DGKVIRTIPLTKGNETFDVKENGGFYNKVEVKGNRIRV 83 (132)
T ss_pred CCEEEEEEEcccCCccEEEEcCCCceEEEEEcCCEEEE
Confidence 57888888899888899999999999999999987544
No 7
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=22.59 E-value=42 Score=27.96 Aligned_cols=13 Identities=38% Similarity=0.713 Sum_probs=8.4
Q ss_pred eEEeCCCCCCCCc
Q 040209 62 VIVDLLPGAPYNQ 74 (388)
Q Consensus 62 ~IvDL~P~~~~d~ 74 (388)
.|||||||+-+..
T Consensus 4 LiiD~PPGTgD~~ 16 (81)
T PF10609_consen 4 LIIDLPPGTGDEH 16 (81)
T ss_dssp EEEE--SCSSSHH
T ss_pred EEEeCCCCCCcHH
Confidence 5899999996543
No 8
>smart00141 PDGF Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family. Platelet-derived growth factor is a potent activator for cells of mesenchymal origin. PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer. Members of the VEGF family are homologues of PDGF.
Probab=21.62 E-value=59 Score=27.06 Aligned_cols=49 Identities=16% Similarity=0.274 Sum_probs=32.7
Q ss_pred ccCCCCeEEeCCCCCCCCcc------------ccccccCCeeccCccCccCCceeEEEEEeecCC
Q 040209 56 CCEKSPVIVDLLPGAPYNQQ------------TANCCKGGVLSSLTQDPSKFVAGFQMNVGGSAD 108 (388)
Q Consensus 56 ~C~k~P~IvDL~P~~~~d~q------------i~nCCr~G~l~~~~~Dps~s~S~FQm~Vg~~~~ 108 (388)
.|+.|++||||.++-|.+.. -.=||-.-.| +=-.++.+..+|+|.+...
T Consensus 2 ~C~pre~~V~i~~e~~~~~~~~y~P~Cv~v~RCgGCCn~e~l----~C~pt~t~~v~~~v~~~~~ 62 (83)
T smart00141 2 ECKPREVVVEVSREYPDETNFLFKPPCVTVQRCGGCCNDEGL----ECVPTETHNVTMQLLEIVR 62 (83)
T ss_pred CCceeeEEEECchhcCCccCcEEecCcEEeceecCCCCCCCC----EEEccEEEEEEEEEEEEeC
Confidence 49999999999998887753 1456632211 1123666778888887644
No 9
>cd05467 CBM20 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch.
Probab=19.23 E-value=4e+02 Score=20.99 Aligned_cols=52 Identities=21% Similarity=0.309 Sum_probs=31.1
Q ss_pred EeEEEeeCCCCceEEEEE-----EEecCC----ccC----cccceEEeecCCCCCceeEEEecceeC
Q 040209 235 VHWHVKQSYTQYWRVKIT-----ITNLNV----VQN----YSQWNLVALHPNLQSVTQVFSFNYKPL 288 (388)
Q Consensus 235 IhWHVk~nYk~~WrvkiT-----i~N~~~----~~n----y~dW~lvvqhpn~~~~~~vySFN~t~l 288 (388)
|+++|...-.-|.++.|+ +-||+. .|. ...|.+.+..|.=.+ ..+.|.|...
T Consensus 2 v~f~i~~~t~~Ge~l~v~G~~~~LG~W~~~~a~~m~~~~~~~~W~~~v~~~~~~~--~~~~yKy~~~ 66 (96)
T cd05467 2 VRFQVRCTTQFGQSVYVVGSHPELGNWDPAKALRLNTSNSYPLWTGEIPLPAPEG--QVIEYKYVIV 66 (96)
T ss_pred EEEEEEEECCCCCEEEEEeCcHHhCCcChhcCccccCCCCCCcEEEEEEecCCCC--CeEEEEEEEE
Confidence 556666555566677765 457773 223 455999998886222 3455555533
No 10
>cd05820 CBM20_novamyl Novamyl (also known as acarviose transferase, ATase, maltogenic alpha-amylase, glucan 1,4-alpha-maltohydrolase, and AcbD), C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Novamyl has a five-domain structure similar to that of cyclodextrin glucanotransferase (CGTase). Novamyl has a substrate-binding surface with an open groove which can accommodate both cyclodextrins and linear substrates. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific reco
Probab=16.77 E-value=4.3e+02 Score=21.97 Aligned_cols=52 Identities=17% Similarity=0.192 Sum_probs=29.6
Q ss_pred eEEeEEEeeCCCCceEEEEE-----EEecCCc----------cCcccceEEeecCCCCCceeEEEecceeC
Q 040209 233 VRVHWHVKQSYTQYWRVKIT-----ITNLNVV----------QNYSQWNLVALHPNLQSVTQVFSFNYKPL 288 (388)
Q Consensus 233 V~IhWHVk~nYk~~WrvkiT-----i~N~~~~----------~ny~dW~lvvqhpn~~~~~~vySFN~t~l 288 (388)
|++|-+....-.-|.++.|+ +-||+.. .+|..|...+..|... .++|.|-.+
T Consensus 5 v~f~~~~~~~t~~Ge~l~vvGs~~~LG~W~~~~~~a~~~l~~~~~~~W~~~~~lp~~~----~veyK~v~~ 71 (103)
T cd05820 5 VIFTVQNTPETAPGEFLYLTGSVPELGNWSTSTDQAVGPLLCPNWPDWFVVASVPAGT----YIEFKFLKA 71 (103)
T ss_pred EEEEEeCCcCcCCCCEEEEEECcHHhCCCChhccccccccccCCCCCEEEEEEcCCCC----cEEEEEEEE
Confidence 44443332333455565553 3467641 3678899999998742 466665544
Done!