Query 038127
Match_columns 438
No_of_seqs 118 out of 150
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 07:51:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038127hhsearch_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 4.2E-85 9.1E-90 597.4 17.7 165 49-213 1-169 (169)
2 PF00553 CBM_2: Cellulose bind 95.7 0.055 1.2E-06 45.7 7.7 56 36-94 2-57 (101)
3 PF00553 CBM_2: Cellulose bind 87.0 2.8 6E-05 35.5 7.0 99 285-401 3-101 (101)
4 smart00637 CBD_II CBD_II domai 71.3 10 0.00022 31.1 5.3 43 46-91 5-47 (92)
5 PF03128 CXCXC: CXCXC repeat; 49.5 8.3 0.00018 22.9 0.7 8 238-245 7-14 (14)
6 PF10563 CdCA1: Cadmium carbon 42.6 4.7 0.0001 39.8 -1.6 14 279-292 5-18 (218)
7 COG5341 Uncharacterized protei 30.7 52 0.0011 30.4 3.1 38 366-403 46-83 (132)
8 PF07172 GRP: Glycine rich pro 27.6 42 0.00091 29.0 1.9 9 1-9 1-9 (95)
9 TIGR03656 IsdC heme uptake pro 25.0 1.6E+02 0.0035 29.3 5.6 42 23-65 23-73 (217)
10 cd06364 PBP1_CaSR Ligand-bindi 25.0 84 0.0018 33.6 4.0 32 30-61 460-494 (510)
11 PF11153 DUF2931: Protein of u 24.6 1.2E+02 0.0027 28.8 4.7 20 37-56 28-47 (216)
12 smart00141 PDGF Platelet-deriv 22.4 56 0.0012 27.7 1.7 47 105-155 2-60 (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=4.2e-85 Score=597.39 Aligned_cols=165 Identities=67% Similarity=1.240 Sum_probs=162.3
Q ss_pred eEEEEEEecCcccccccCCCCeEEEEecCCeeEEEeccceeeecCCccccc--CCCCcccCCCCeEEeCCCCCCCCcccc
Q 038127 49 YVALVTMTNFQMYRHIMEPGWTLGWTWAKKEVIWSMVGAQATEQGDCSKFK--INIPHSCMKNPTVVDLLPGVPYNQQIA 126 (438)
Q Consensus 49 Y~A~VTi~N~q~~r~i~~pgW~L~W~W~~~EvIwsM~GA~~teqgdCs~f~--~~~ph~C~k~P~IvDLpP~~~~n~qi~ 126 (438)
|+|+|||+|||+|||||.|||+|||+|+|+||||+|+|||++|||||++|| +++||||+|+|+|||||||+++|+|++
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 999999999999999999999999999999999999999999999999998 689999999999999999999999999
Q ss_pred ccccCCeeccCCCCcccCcceEEEEEeec--CCCCccccCCcCeEEcCCCCCcccCCCeeeCCccccCCCCcceeeEeEE
Q 038127 127 NCCKGGVVGSWGQDPSAAVSSFQLSVGRS--GSSNKTVRLPKNFTLLGPGRGYTCSQAKNVLPTAFISADGRRRTQAMMT 204 (438)
Q Consensus 127 nCCrgGvl~~~~qDps~s~SsFQm~Vgk~--~~~n~tv~pP~Nf~l~~pgPgYtCg~p~~V~Pt~f~~p~g~r~tqAl~T 204 (438)
||||||||+||+|||+||+|+|||+||++ +++|++++||+||+|++|||||+||+|++|+||+|+|+||||+||||||
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 99999999999999999999999999998 7778889999999999999999999999999999999999999999999
Q ss_pred EeeEeeeec
Q 038127 205 WNVTCTYSQ 213 (438)
Q Consensus 205 WqVtC~ysq 213 (438)
|||||||||
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=95.66 E-value=0.055 Score=45.70 Aligned_cols=56 Identities=29% Similarity=0.430 Sum_probs=48.1
Q ss_pred EEEEEEEEeeCCCeEEEEEEecCcccccccCCCCeEEEEecCCeeEEEeccceeeecCC
Q 038127 36 TIKWDVMSWIPDGYVALVTMTNFQMYRHIMEPGWTLGWTWAKKEVIWSMVGAQATEQGD 94 (438)
Q Consensus 36 tI~wDV~~~~~~~Y~A~VTi~N~q~~r~i~~pgW~L~W~W~~~EvIwsM~GA~~teqgd 94 (438)
|++|.|.+--++||.++|+|.|..- ..|+ ||+|.|+-..++-|-++.+|..+..|.
T Consensus 2 tv~~~v~~~W~~Gf~~~v~v~N~~~-~~i~--~W~v~~~~~~~~~i~~~Wna~~s~~g~ 57 (101)
T PF00553_consen 2 TVTYTVTNSWGGGFQGEVTVTNNGS-SPIN--GWTVTFTFPSGQTITSSWNATVSQSGN 57 (101)
T ss_dssp EEEEEEEEESSSEEEEEEEEEESSS-STEE--SEEEEEEESTTEEEEEEESCEEEEETT
T ss_pred EEEEEEecccCCCeEEEEEEEECCC-CccC--CEEEEEEeCCCCEEeeeeccEEEecCC
Confidence 6889999888999999999999885 4565 899999999889988999998866443
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=87.03 E-value=2.8 Score=35.46 Aligned_cols=99 Identities=18% Similarity=0.258 Sum_probs=62.5
Q ss_pred EeEEEeeccccceEEEEEEEecccccCccceeeEeecCCCCCcceEEeeecccCCCCCCCCceeEEEecchhhhHhhhcC
Q 038127 285 VHWHVKLNYKKYWRVKMSITNFNYQVNYTEWTLVVQHPNLNNVTEVFSFNYKPLIPYDSTNDTGMFYGIKFFNDILLQSG 364 (438)
Q Consensus 285 IhWHvk~nYk~~WrvkiTi~N~~~~~ny~~W~lvVqhpn~~~~t~vySFN~t~L~~y~~~NdT~m~~Gl~~yN~ll~~~g 364 (438)
+-.-|-.+.-+++.+.|+|+|=. .....+|.+-++.|.-.-+++++ |++.- ...+++.+-+. .||--|.
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 55667889999999999999966 36667999999999644455554 44421 12346666664 3443332
Q ss_pred CCCceeEEEEEeecCCCcccccCCCCceeeEeeCCcc
Q 038127 365 PEGNVQSELILQKDMNTFTYKQGWAFPRKIYFNGDEC 401 (438)
Q Consensus 365 ~~G~vQSeilf~Kd~~~ft~~~GwaFP~rVyFNGeEC 401 (438)
+|.- ..+-|.-.. ....+-|..+-|||..|
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 1322 334444221 22334599999999998
No 4
>smart00637 CBD_II CBD_II domain.
Probab=71.30 E-value=10 Score=31.11 Aligned_cols=43 Identities=26% Similarity=0.370 Sum_probs=34.0
Q ss_pred CCCeEEEEEEecCcccccccCCCCeEEEEecCCeeEEEeccceeee
Q 038127 46 PDGYVALVTMTNFQMYRHIMEPGWTLGWTWAKKEVIWSMVGAQATE 91 (438)
Q Consensus 46 ~~~Y~A~VTi~N~q~~r~i~~pgW~L~W~W~~~EvIwsM~GA~~te 91 (438)
.+||.+.|+|.|..-. .|+ +|.+.|+-..++-|-++..|..+.
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 4699999999997542 354 999999998887777777777654
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=49.53 E-value=8.3 Score=22.88 Aligned_cols=8 Identities=38% Similarity=1.435 Sum_probs=6.4
Q ss_pred CCCccCCC
Q 038127 238 PSCSCGCQ 245 (438)
Q Consensus 238 ~tCaCGC~ 245 (438)
.||+|+|+
T Consensus 7 ~tC~C~Cp 14 (14)
T PF03128_consen 7 DTCQCECP 14 (14)
T ss_pred CCcCccCC
Confidence 47999995
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=42.60 E-value=4.7 Score=39.77 Aligned_cols=14 Identities=50% Similarity=1.346 Sum_probs=7.3
Q ss_pred CCCceeEeEEEeec
Q 038127 279 HMCPIRVHWHVKLN 292 (438)
Q Consensus 279 hmCpV~IhWHvk~n 292 (438)
.||||+||||+-.-
T Consensus 5 ~mc~vnvhwHlgaE 18 (218)
T PF10563_consen 5 SMCPVNVHWHLGAE 18 (218)
T ss_dssp EEEECGGG------
T ss_pred eeeeeeeecccccc
Confidence 49999999999873
No 7
>COG5341 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.70 E-value=52 Score=30.42 Aligned_cols=38 Identities=26% Similarity=0.404 Sum_probs=32.7
Q ss_pred CCceeEEEEEeecCCCcccccCCCCceeeEeeCCccCC
Q 038127 366 EGNVQSELILQKDMNTFTYKQGWAFPRKIYFNGDECSM 403 (438)
Q Consensus 366 ~G~vQSeilf~Kd~~~ft~~~GwaFP~rVyFNGeEC~m 403 (438)
.|++=-++.++|...+|++++-+||=-+|-|.|+|=+.
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 57777788888888899999999999999999987543
No 8
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=27.63 E-value=42 Score=29.02 Aligned_cols=9 Identities=44% Similarity=0.578 Sum_probs=6.2
Q ss_pred CcchhhHHH
Q 038127 1 MVSKRYACL 9 (438)
Q Consensus 1 ~~~~~~~~~ 9 (438)
|-|+.+..|
T Consensus 1 MaSK~~llL 9 (95)
T PF07172_consen 1 MASKAFLLL 9 (95)
T ss_pred CchhHHHHH
Confidence 778876654
No 9
>TIGR03656 IsdC heme uptake protein IsdC. Isd proteins are iron-regulated surface proteins found in Bacillus, Staphylococcus and Listeria species and are responsible for heme scavenging from hemoproteins. The IsdC protein consists of an N-terminal hydrophobic signal sequence, a central NEAT (NEAr Transporter, pfam05031) domain which confers the ability to bind heme and a C-terminal SrtB processing signal which targets the protein to the cell wall. IsdC is believed to make a direct contact with, and transfer heme to, the heme-binding component (IsdE) of an ABC transporter in the cytoplasmic membrane, and to receive heme from other NEAT-containing heme-binding proteins also localized in the cell wall.
Probab=25.03 E-value=1.6e+02 Score=29.29 Aligned_cols=42 Identities=26% Similarity=0.262 Sum_probs=33.2
Q ss_pred cccccCCCCCCCEEEEEEEEEeeCC------CeE---EEEEEecCccccccc
Q 038127 23 AVAYDTLDPTGNITIKWDVMSWIPD------GYV---ALVTMTNFQMYRHIM 65 (438)
Q Consensus 23 ~~aydPldp~GnitI~wDV~~~~~~------~Y~---A~VTi~N~q~~r~i~ 65 (438)
..+=.-| .+|--+|.|.|+....| +|+ |.|++.|-+.|=++.
T Consensus 23 ~~~~~~L-~DGtYsV~fkVlK~~tde~Smmn~Y~~kPAkv~VknGK~~Vt~T 73 (217)
T TIGR03656 23 FSNSANL-ADGTYTINYTVYKADNDSASMANDYFEKPAKLIVKNGKMTVQIT 73 (217)
T ss_pred ccccccc-cCceEEEEEEEEeCCCCchhhHHhhccCCcEEEEECCEEEEEEE
Confidence 3434556 89999999999988665 477 789999999888875
No 10
>cd06364 PBP1_CaSR Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. CaSR provides feedback control of extracellular calcium homeostasis by responding sensitively to acute fluctuations in extracellular ionized Ca2+ concentration. This ligand-binding domain has homology to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). CaSR is widely expressed in mammalian tissues and is active in tissues that are not directly involved in extracellular calcium homeostasis. Moreover, CaSR responds to aromatic, aliphatic, and polar amino acids, but not to positively charged or branched chain amino acids, which suggests that changes in plasma amino acid levels are likely to modulate whole body calci
Probab=25.02 E-value=84 Score=33.58 Aligned_cols=32 Identities=25% Similarity=0.720 Sum_probs=27.2
Q ss_pred CCCCCEEEEEEEEEee--C-CCeEEEEEEecCccc
Q 038127 30 DPTGNITIKWDVMSWI--P-DGYVALVTMTNFQMY 61 (438)
Q Consensus 30 dp~GnitI~wDV~~~~--~-~~Y~A~VTi~N~q~~ 61 (438)
|++||..-.|||++|. + +|...-|.|--+.++
T Consensus 460 d~~Gd~~~~YdI~n~q~~~~~~~~~~v~VG~~~~~ 494 (510)
T cd06364 460 DEGGDLVGNYSIINWHLSPEDGSVVFKEVGYYNVY 494 (510)
T ss_pred ecCCCCccceeEEEeeecCCCCcEEEEEEEEEcCC
Confidence 6899999999999998 3 788888888888764
No 11
>PF11153 DUF2931: Protein of unknown function (DUF2931); InterPro: IPR021326 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently, there is no known function.
Probab=24.61 E-value=1.2e+02 Score=28.76 Aligned_cols=20 Identities=25% Similarity=0.429 Sum_probs=17.4
Q ss_pred EEEEEEEeeCCCeEEEEEEe
Q 038127 37 IKWDVMSWIPDGYVALVTMT 56 (438)
Q Consensus 37 I~wDV~~~~~~~Y~A~VTi~ 56 (438)
..|.+.-.+|.+|-|.||.-
T Consensus 28 ~~W~~~~~~P~~ypv~V~~~ 47 (216)
T PF11153_consen 28 FEWRFGVAAPKHYPVWVTYA 47 (216)
T ss_pred CccEEEEecCCCCEEEEEEE
Confidence 46999999999999999754
No 12
>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=22.42 E-value=56 Score=27.67 Aligned_cols=47 Identities=13% Similarity=0.276 Sum_probs=31.3
Q ss_pred ccCCCCeEEeCCCCCCCCcc------------ccccccCCeeccCCCCcccCcceEEEEEeec
Q 038127 105 SCMKNPTVVDLLPGVPYNQQ------------IANCCKGGVVGSWGQDPSAAVSSFQLSVGRS 155 (438)
Q Consensus 105 ~C~k~P~IvDLpP~~~~n~q------------i~nCCrgGvl~~~~qDps~s~SsFQm~Vgk~ 155 (438)
.|+.|++||||.++-|.+.. -.=||-.-.|. =-.++.+..+|+|.+.
T Consensus 2 ~C~pre~~V~i~~e~~~~~~~~y~P~Cv~v~RCgGCCn~e~l~----C~pt~t~~v~~~v~~~ 60 (83)
T smart00141 2 ECKPREVVVEVSREYPDETNFLFKPPCVTVQRCGGCCNDEGLE----CVPTETHNVTMQLLEI 60 (83)
T ss_pred CCceeeEEEECchhcCCccCcEEecCcEEeceecCCCCCCCCE----EEccEEEEEEEEEEEE
Confidence 49999999999998877654 14567322221 1225666788888874
Done!