Query 043271
Match_columns 385
No_of_seqs 117 out of 141
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:14:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043271.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043271hhsearch_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 2.8E-85 6.1E-90 590.0 17.5 164 25-188 1-169 (169)
2 PF00553 CBM_2: Cellulose bind 95.9 0.04 8.8E-07 45.7 7.6 55 12-69 2-56 (101)
3 PF00553 CBM_2: Cellulose bind 82.4 7.6 0.00017 32.2 7.5 99 246-364 3-101 (101)
4 smart00637 CBD_II CBD_II domai 73.4 8.8 0.00019 30.9 5.3 43 22-67 5-47 (92)
5 PF03128 CXCXC: CXCXC repeat; 48.0 9.1 0.0002 22.3 0.7 8 213-220 7-14 (14)
6 PF10563 CdCA1: Cadmium carbon 43.1 4.1 8.8E-05 39.6 -2.0 15 240-254 5-19 (218)
7 COG5341 Uncharacterized protei 30.7 63 0.0014 29.4 3.6 37 329-365 46-82 (132)
8 PF14903 WG_beta_rep: WG conta 24.8 70 0.0015 20.8 2.2 27 5-32 4-32 (35)
9 PF10609 ParA: ParA/MinD ATPas 22.4 43 0.00093 27.9 1.0 12 87-98 4-15 (81)
10 smart00141 PDGF Platelet-deriv 19.6 71 0.0015 26.6 1.7 49 81-133 2-62 (83)
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=2.8e-85 Score=589.99 Aligned_cols=164 Identities=52% Similarity=0.971 Sum_probs=160.5
Q ss_pred eEEEEEEecCccccccCCCCCeeeEEEcCCeeEEeecCceeeeecCccccC--CCCCccccCCCeEEecCCCCCCCCccc
Q 043271 25 YVARVTIQNYHQYRHVDQPGWKIGWTWADNEIILSMSGAFATEQGNCSDFK--FQSPHSCEKDPVIVDLGPDASPQNMTD 102 (385)
Q Consensus 25 Y~A~VTi~N~q~~r~i~~pgW~L~W~W~~~E~IwsM~GA~~~eqgdC~~~k--~~~ph~C~k~P~IvDLpP~~~~d~qi~ 102 (385)
|+|+|||+|||+|||||.|||+|||+|+++||||+|+|||++|||||++|+ +++||||+|+|+|||||||+++|+||+
T Consensus 1 Y~A~VTi~N~~~yr~id~pgW~L~W~W~~~E~IwsM~GA~~tdqgdCs~~~~~~~~ph~C~k~P~IvDLpp~~~~n~qi~ 80 (169)
T PF04833_consen 1 YVAQVTISNYQPYRHIDNPGWNLGWTWAKKEFIWSMKGAQTTDQGDCSKFYKDGDFPHCCKKRPTIVDLPPGTPYNQQIG 80 (169)
T ss_pred CEEEEEEecCCeecccCCCCceEeeEEcCCEEEEEeeCceeccCCcccccccCCCCCcccCCCCEEEeCCCCCCCccccc
Confidence 899999999999999999999999999999999999999999999999998 889999999999999999999999999
Q ss_pred ccccCCeeccCccCcCCccceEEEEEeecCC--C-CCCcCCcCeEeecCCCCcccCCceecCCCcccCCCCceeeeEEEE
Q 043271 103 ACCRGGVLSSYTINPANSFSFFEVTVGNLGM--N-ASGYAPQNLTLWAPGPGYTCGLLEDVDPTVSLEIGGRRQVQVFRT 179 (385)
Q Consensus 103 nCCr~Gvl~~~~~Dps~s~S~FQm~Vg~~~~--n-~t~~~P~nf~l~~pgPgYtCg~~~~V~Pt~f~~~~g~r~tqAl~T 179 (385)
||||||||+||+|||+||+|+|||+||++|+ | ++++||+||+|++|||||+||+|++|+||+|+|+||||.||||||
T Consensus 81 nCCrgG~l~~~~~Dps~s~S~FQm~Vg~~pp~~~~~~~~~P~nf~l~~~~pgYtCg~~~~V~pT~f~~~~g~r~t~A~~T 160 (169)
T PF04833_consen 81 NCCRGGVLSSWAQDPSKSVSAFQMSVGKAPPGTNNTTVKPPQNFTLGGPGPGYTCGPPKRVSPTVFPDPDGRRTTQALMT 160 (169)
T ss_pred cccCCCEECCcccChhhCceEEEEEEeEeeccCCCceecCCcceEEcCCCCCcCCCCcceeCCceeeCCCCCEEEEEEEE
Confidence 9999999999999999999999999999966 4 459999999999999999999999999999999999999999999
Q ss_pred Eeeeeeeec
Q 043271 180 WKSTCTYST 188 (385)
Q Consensus 180 WqVtC~ysq 188 (385)
|||||||||
T Consensus 161 WqvtC~ysq 169 (169)
T PF04833_consen 161 WQVTCNYSQ 169 (169)
T ss_pred EeEEEEeeC
Confidence 999999997
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=95.89 E-value=0.04 Score=45.68 Aligned_cols=55 Identities=25% Similarity=0.497 Sum_probs=47.5
Q ss_pred EEEEEEEEeeCCCeEEEEEEecCccccccCCCCCeeeEEEcCCeeEEeecCceeeeec
Q 043271 12 TVTFDIHQWTNDGYVARVTIQNYHQYRHVDQPGWKIGWTWADNEIILSMSGAFATEQG 69 (385)
Q Consensus 12 tI~wDV~~~~~~~Y~A~VTi~N~q~~r~i~~pgW~L~W~W~~~E~IwsM~GA~~~eqg 69 (385)
+++|.|.+--++||.++|+|.|..- ..|+ ||+|.|+-..++-|-++.+|..+..|
T Consensus 2 tv~~~v~~~W~~Gf~~~v~v~N~~~-~~i~--~W~v~~~~~~~~~i~~~Wna~~s~~g 56 (101)
T PF00553_consen 2 TVTYTVTNSWGGGFQGEVTVTNNGS-SPIN--GWTVTFTFPSGQTITSSWNATVSQSG 56 (101)
T ss_dssp EEEEEEEEESSSEEEEEEEEEESSS-STEE--SEEEEEEESTTEEEEEEESCEEEEET
T ss_pred EEEEEEecccCCCeEEEEEEEECCC-CccC--CEEEEEEeCCCCEEeeeeccEEEecC
Confidence 6899999888999999999999885 4564 89999999988998899999877643
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=82.37 E-value=7.6 Score=32.19 Aligned_cols=99 Identities=23% Similarity=0.368 Sum_probs=61.6
Q ss_pred EEEEEeeCCCCceEEEEEEEeccCccCcccceEEEecCCCCCcceEEeeccccCCCCCCCcceEEEecccchhHHHHHcC
Q 043271 246 VHWHVQNNYVGHWRVKVTVSNYNYKRNYSNWNVVVQHPGFSQKATAYSFNSSVLPSAGFSEKVALFWGISYYNEELLQAG 325 (385)
Q Consensus 246 IhWHVk~nYk~~WrvkiTi~N~~~~~ny~~W~lvvqhpn~~~~~~~ySFN~t~l~~y~~~N~T~m~~Gl~~yN~ll~~~g 325 (385)
+-.-|..+.-+++.+.|+|+|=. .....+|.+-++.|.-.-+++++ |++.- . ..+++.+-++. ||-.|.
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-Q---SGNTVTVTNPS-WNGTIA--- 71 (101)
T ss_dssp EEEEEEEESSSEEEEEEEEEESS-SSTEESEEEEEEESTTEEEEEEE--SCEEE-E---ETTEEEEEESS-TCSEEE---
T ss_pred EEEEEecccCCCeEEEEEEEECC-CCccCCEEEEEEeCCCCEEeeee--ccEEE-e---cCCEEEEEcCC-cCcccC---
Confidence 45667888999999999999966 36777999999998645555555 44421 1 22456666553 443222
Q ss_pred CCCCCceeEEEEEEecCCCceecCCCCCceeeEeeCCcc
Q 043271 326 ENQVGSVTTQILLEKDSESFTLSNGWALPRRIYFNGENC 364 (385)
Q Consensus 326 ~~~~G~vQSeilf~K~~~~ft~~~Gw~FP~rVyFNGeeC 364 (385)
+|.. ..+-|.=.. ....+-|..+-|||..|
T Consensus 72 ---~G~s-~~~Gf~~~~-----~~~~~~p~~~t~ng~~C 101 (101)
T PF00553_consen 72 ---PGGS-VTFGFQASG-----SGSSAAPSTCTVNGAPC 101 (101)
T ss_dssp ---ESEE-EEEEEEEEE-----SSS--SESEEEETTEEE
T ss_pred ---CCCe-EEEEEEEeC-----CCCCCCCcEEEEcCeeC
Confidence 2322 234444321 22234599999999998
No 4
>smart00637 CBD_II CBD_II domain.
Probab=73.41 E-value=8.8 Score=30.94 Aligned_cols=43 Identities=19% Similarity=0.444 Sum_probs=34.2
Q ss_pred CCCeEEEEEEecCccccccCCCCCeeeEEEcCCeeEEeecCceeee
Q 043271 22 NDGYVARVTIQNYHQYRHVDQPGWKIGWTWADNEIILSMSGAFATE 67 (385)
Q Consensus 22 ~~~Y~A~VTi~N~q~~r~i~~pgW~L~W~W~~~E~IwsM~GA~~~e 67 (385)
.+||.+.|+|.|-.-. .|+ +|.|.|+-..++-|-++..|..+.
T Consensus 5 ~~G~~~~v~vtN~~~~-~~~--~W~v~~~~~~~~~i~~~Wn~~~~~ 47 (92)
T smart00637 5 GSGFTANVTVTNTGSS-AIN--GWTVTFDLPGGQTVTNSWNATVSQ 47 (92)
T ss_pred CCCEEEEEEEEeCCCC-ccc--CeEEEEEcCCCcEEeeeEEEEEEe
Confidence 5699999999997542 354 999999998888777777776654
No 5
>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=48.04 E-value=9.1 Score=22.33 Aligned_cols=8 Identities=38% Similarity=1.344 Sum_probs=6.3
Q ss_pred CCCccCCC
Q 043271 213 PVCSCGCR 220 (385)
Q Consensus 213 ~tCaCGC~ 220 (385)
.||+|+|+
T Consensus 7 ~tC~C~Cp 14 (14)
T PF03128_consen 7 DTCQCECP 14 (14)
T ss_pred CCcCccCC
Confidence 47999985
No 6
>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=43.14 E-value=4.1 Score=39.60 Aligned_cols=15 Identities=53% Similarity=1.236 Sum_probs=7.6
Q ss_pred CCCceEEEEEEeeCC
Q 043271 240 HMCPVRVHWHVQNNY 254 (385)
Q Consensus 240 hmCpV~IhWHVk~nY 254 (385)
.||||+||||+-.-.
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 7
>COG5341 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.71 E-value=63 Score=29.43 Aligned_cols=37 Identities=22% Similarity=0.346 Sum_probs=32.6
Q ss_pred CCceeEEEEEEecCCCceecCCCCCceeeEeeCCccC
Q 043271 329 VGSVTTQILLEKDSESFTLSNGWALPRRIYFNGENCE 365 (385)
Q Consensus 329 ~G~vQSeilf~K~~~~ft~~~Gw~FP~rVyFNGeeC~ 365 (385)
.|++=-++.++|...+|++++-+||=-+|-|.|+|=+
T Consensus 46 ~Gk~~r~i~l~Kg~~t~~v~~~~g~~n~vev~g~~IR 82 (132)
T COG5341 46 DGKVIRTIPLTKGNETFDVKENGGFYNKVEVKGNRIR 82 (132)
T ss_pred CCEEEEEEEcccCCccEEEEcCCCceEEEEEcCCEEE
Confidence 5788888889988899999999999999999998743
No 8
>PF14903 WG_beta_rep: WG containing repeat
Probab=24.75 E-value=70 Score=20.79 Aligned_cols=27 Identities=30% Similarity=0.444 Sum_probs=19.6
Q ss_pred CCCCCCEEE--EEEEEEeeCCCeEEEEEEe
Q 043271 5 LDPYGNITV--TFDIHQWTNDGYVARVTIQ 32 (385)
Q Consensus 5 ldp~GnitI--~wDV~~~~~~~Y~A~VTi~ 32 (385)
+|.+|++.| +||-+....+|| |.|...
T Consensus 4 id~~G~~vi~~~yd~i~~~~~g~-~~v~~~ 32 (35)
T PF14903_consen 4 IDKNGKIVIPPKYDEIYPFSNGY-AIVKKD 32 (35)
T ss_pred EeCCCCEEEEccccCccccCCCE-EEEEEC
Confidence 588999877 588887787776 556543
No 9
>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=22.39 E-value=43 Score=27.90 Aligned_cols=12 Identities=33% Similarity=0.714 Sum_probs=7.8
Q ss_pred eEEecCCCCCCC
Q 043271 87 VIVDLGPDASPQ 98 (385)
Q Consensus 87 ~IvDLpP~~~~d 98 (385)
.|||||||+-+.
T Consensus 4 LiiD~PPGTgD~ 15 (81)
T PF10609_consen 4 LIIDLPPGTGDE 15 (81)
T ss_dssp EEEE--SCSSSH
T ss_pred EEEeCCCCCCcH
Confidence 589999999643
No 10
>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=19.63 E-value=71 Score=26.57 Aligned_cols=49 Identities=12% Similarity=0.246 Sum_probs=33.0
Q ss_pred cccCCCeEEecCCCCCCCCc------------ccccccCCeeccCccCcCCccceEEEEEeecCC
Q 043271 81 SCEKDPVIVDLGPDASPQNM------------TDACCRGGVLSSYTINPANSFSFFEVTVGNLGM 133 (385)
Q Consensus 81 ~C~k~P~IvDLpP~~~~d~q------------i~nCCr~Gvl~~~~~Dps~s~S~FQm~Vg~~~~ 133 (385)
.|+.|++||||.++-+.+.. -.=||-.-.| +=-.++.+..+|+|.+...
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 59999999999998887653 2556732222 1123666778888887754
Done!