Query 030916
Match_columns 169
No_of_seqs 104 out of 135
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:31:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030916.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030916hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00553 CBM_2: Cellulose bind 93.0 0.72 1.6E-05 33.8 7.5 99 13-129 3-101 (101)
2 PF10563 CdCA1: Cadmium carbon 66.4 1 2.2E-05 39.0 -1.6 14 7-20 5-18 (218)
3 COG5341 Uncharacterized protei 46.8 24 0.00051 28.7 3.2 38 94-131 46-83 (132)
4 PF11837 DUF3357: Domain of un 38.2 11 0.00023 28.6 0.0 10 134-143 4-13 (106)
5 PF13850 ERGIC_N: Endoplasmic 35.0 41 0.00088 24.7 2.7 30 134-163 5-35 (96)
6 PF14927 Neurensin: Neurensin 31.7 1E+02 0.0023 24.9 4.7 13 156-168 54-66 (140)
7 PF06212 GRIM-19: GRIM-19 prot 30.0 1.1E+02 0.0024 24.4 4.5 12 130-141 8-19 (130)
8 PRK00753 psbL photosystem II r 29.9 68 0.0015 21.2 2.7 24 146-169 14-37 (39)
9 CHL00038 psbL photosystem II p 28.3 74 0.0016 21.0 2.7 23 146-168 13-35 (38)
10 PRK02542 photosystem I assembl 28.0 30 0.00064 29.6 1.1 21 103-124 99-122 (188)
11 PF11027 DUF2615: Protein of u 27.3 1.1E+02 0.0023 23.8 3.9 20 136-155 40-59 (103)
12 PF02419 PsbL: PsbL protein; 25.9 85 0.0018 20.6 2.6 22 147-168 13-34 (37)
13 PF14730 DUF4468: Domain of un 23.6 87 0.0019 22.5 2.7 25 11-36 64-88 (91)
14 PF01299 Lamp: Lysosome-associ 22.5 5.1E+02 0.011 22.4 9.4 25 8-33 157-181 (306)
15 PF15145 DUF4577: Domain of un 21.8 1E+02 0.0022 24.9 3.0 14 142-155 54-67 (128)
16 PRK05659 sulfur carrier protei 20.6 63 0.0014 21.4 1.4 14 121-134 2-15 (66)
No 1
>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=92.99 E-value=0.72 Score=33.81 Aligned_cols=99 Identities=17% Similarity=0.253 Sum_probs=61.4
Q ss_pred EEEEEeeCCCCceEEEEEEEecCCCcCCcceeEEeecCCCCCcceEEEecceecCCCCCCCcceEEEcccchhHHhhhcC
Q 030916 13 VHWHVKLNYKEYWRVKITITNFNYAMNYSLWNLVVQHPNFDNLTQLFSFYYKSLTPYEGLNDTAMLWGIKFYNDFLSEAG 92 (169)
Q Consensus 13 InWHV~~nYk~~W~vkiTi~N~~~~~ny~dW~lvvq~pn~~~~~~vySFN~t~l~~y~~~N~T~m~~Gl~~~N~ll~~~g 92 (169)
+-.-|..+.-+|+.++|||+|=. .....+|.+-++.|.-.-+++++ |++.- ...+++.+-+. .+|--|.
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 45667888999999999999966 36777999999998644444544 44421 12245555554 3443222
Q ss_pred CCCceeEEEEEEecCCCccccccccCceeeEeeCCcc
Q 030916 93 SNGNVQSELLFRKDASTFTFEKGWAFPRRIYFNGDNC 129 (169)
Q Consensus 93 ~~GkvQSeilf~K~~~~~~~~~G~~FP~rVyFNGeeC 129 (169)
+|.. ..+-|.=.. ....+-|..+-+||..|
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 234444332 12234599999999999
No 2
>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=66.41 E-value=1 Score=39.04 Aligned_cols=14 Identities=50% Similarity=1.346 Sum_probs=7.5
Q ss_pred CCCceeEEEEEeeC
Q 030916 7 HMCPIRVHWHVKLN 20 (169)
Q Consensus 7 dmCpV~InWHV~~n 20 (169)
.||||+||||+-.-
T Consensus 5 ~mc~vnvhwHlgaE 18 (218)
T PF10563_consen 5 SMCPVNVHWHLGAE 18 (218)
T ss_dssp EEEECGGG------
T ss_pred eeeeeeeecccccc
Confidence 59999999999873
No 3
>COG5341 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.81 E-value=24 Score=28.72 Aligned_cols=38 Identities=18% Similarity=0.361 Sum_probs=33.0
Q ss_pred CCceeEEEEEEecCCCccccccccCceeeEeeCCccCC
Q 030916 94 NGNVQSELLFRKDASTFTFEKGWAFPRRIYFNGDNCVM 131 (169)
Q Consensus 94 ~GkvQSeilf~K~~~~~~~~~G~~FP~rVyFNGeeC~m 131 (169)
.|++--++.++|...+|++++-+||=-+|-|.|+|-+.
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 57887888889888899999999999999999987544
No 4
>PF11837 DUF3357: Domain of unknown function (DUF3357); InterPro: IPR021792 This entry represents the N-terminal domain of beta-fructofuranosidase, whcih is involved in the hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides. ; GO: 0004564 beta-fructofuranosidase activity, 0004575 sucrose alpha-glucosidase activity; PDB: 3UGG_A 3UGH_B 3UGF_B.
Probab=38.21 E-value=11 Score=28.63 Aligned_cols=10 Identities=40% Similarity=0.790 Sum_probs=0.0
Q ss_pred CCCCCCCCCC
Q 030916 134 PDAYPWLPNA 143 (169)
Q Consensus 134 pd~yp~lPn~ 143 (169)
|-.|--||.+
T Consensus 4 p~sY~PLP~~ 13 (106)
T PF11837_consen 4 PYSYTPLPDS 13 (106)
T ss_dssp ----------
T ss_pred CCccCCCCCC
Confidence 4456667743
No 5
>PF13850 ERGIC_N: Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
Probab=34.96 E-value=41 Score=24.74 Aligned_cols=30 Identities=23% Similarity=0.281 Sum_probs=14.4
Q ss_pred CCCCCCCCCCC-CCcchhHHHHHHHHHHHHH
Q 030916 134 PDAYPWLPNAS-SRPVISLLRSAIIILASWV 163 (169)
Q Consensus 134 pd~yp~lPn~~-~~~~~~~~~~~l~~~~~~~ 163 (169)
-|.||..|..- .++...-.++++.++++++
T Consensus 5 ~D~F~K~~~~~~~~T~~Gg~iSi~~~~~~~~ 35 (96)
T PF13850_consen 5 FDAFPKVPEDLREKTSSGGIISIITIVLIVI 35 (96)
T ss_pred eccCCCCChHheeeccCChHHHHHHHHHHHH
Confidence 37788887552 2333333444443333333
No 6
>PF14927 Neurensin: Neurensin
Probab=31.67 E-value=1e+02 Score=24.95 Aligned_cols=13 Identities=23% Similarity=0.549 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHhc
Q 030916 156 IIILASWVLLLAY 168 (169)
Q Consensus 156 l~~~~~~~~~~~~ 168 (169)
++++..+++...|
T Consensus 54 ~Ll~Gi~~l~vgY 66 (140)
T PF14927_consen 54 LLLLGIVALTVGY 66 (140)
T ss_pred HHHHHHHHHHhhc
Confidence 4444455555544
No 7
>PF06212 GRIM-19: GRIM-19 protein; InterPro: IPR009346 This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-beta and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity [].
Probab=30.05 E-value=1.1e+02 Score=24.36 Aligned_cols=12 Identities=50% Similarity=1.021 Sum_probs=10.6
Q ss_pred CCCCCCCCCCCC
Q 030916 130 VMPPPDAYPWLP 141 (169)
Q Consensus 130 ~mP~pd~yp~lP 141 (169)
-||||-.||-++
T Consensus 8 DmPP~GGY~pv~ 19 (130)
T PF06212_consen 8 DMPPPGGYPPVQ 19 (130)
T ss_pred CCCCCCCCCCCc
Confidence 399999999888
No 8
>PRK00753 psbL photosystem II reaction center L; Provisional
Probab=29.92 E-value=68 Score=21.23 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=18.2
Q ss_pred CcchhHHHHHHHHHHHHHHHHhcC
Q 030916 146 RPVISLLRSAIIILASWVLLLAYV 169 (169)
Q Consensus 146 ~~~~~~~~~~l~~~~~~~~~~~~~ 169 (169)
-.+.|+.+.+|++.+.+++++.|.
T Consensus 14 LNRTSLy~GlLlifvl~vLFssYf 37 (39)
T PRK00753 14 LNRTSLYLGLLLVFVLGILFSSYF 37 (39)
T ss_pred echhhHHHHHHHHHHHHHHHHhhc
Confidence 356777888888888888888773
No 9
>CHL00038 psbL photosystem II protein L
Probab=28.32 E-value=74 Score=20.96 Aligned_cols=23 Identities=26% Similarity=0.275 Sum_probs=17.7
Q ss_pred CcchhHHHHHHHHHHHHHHHHhc
Q 030916 146 RPVISLLRSAIIILASWVLLLAY 168 (169)
Q Consensus 146 ~~~~~~~~~~l~~~~~~~~~~~~ 168 (169)
-.+.|+...+|++.+.+++++.|
T Consensus 13 LNRTSLy~GLLlifvl~vlfssy 35 (38)
T CHL00038 13 LNRTSLYWGLLLIFVLAVLFSNY 35 (38)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHH
Confidence 45677788888888888888776
No 10
>PRK02542 photosystem I assembly protein Ycf4; Provisional
Probab=28.03 E-value=30 Score=29.58 Aligned_cols=21 Identities=43% Similarity=0.892 Sum_probs=10.4
Q ss_pred EEecCCCccccccccCc---eeeEe
Q 030916 103 FRKDASTFTFEKGWAFP---RRIYF 124 (169)
Q Consensus 103 f~K~~~~~~~~~G~~FP---~rVyF 124 (169)
|.|++..+++-+ |||| |||.+
T Consensus 99 FdK~~g~v~ifR-wGFPGKNRrI~l 122 (188)
T PRK02542 99 FDKETGKVTIFR-WGFPGKNRRIEV 122 (188)
T ss_pred hhcCCCEEEEEe-cCCCCCceEEEE
Confidence 444444444332 6666 55554
No 11
>PF11027 DUF2615: Protein of unknown function (DUF2615); InterPro: IPR020309 This entry represents a group of uncharacterised protein from the Metazoa, including CD034 (or C4orf34) and YQF4 (or C34C12.4).
Probab=27.31 E-value=1.1e+02 Score=23.81 Aligned_cols=20 Identities=25% Similarity=0.243 Sum_probs=9.3
Q ss_pred CCCCCCCCCCCcchhHHHHH
Q 030916 136 AYPWLPNASSRPVISLLRSA 155 (169)
Q Consensus 136 ~yp~lPn~~~~~~~~~~~~~ 155 (169)
..|.+|+++.....+.++++
T Consensus 40 d~~g~p~~~~~~~~~~~~~~ 59 (103)
T PF11027_consen 40 DLPGLPQSSGDGGNSMFMMM 59 (103)
T ss_pred cCCCCCCcCCCCCccHHHHH
Confidence 34567754443334443333
No 12
>PF02419 PsbL: PsbL protein; InterPro: IPR003372 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbL found in PSII. PsbL is located in a gene cluster with PsbE, PsbF and PsbJ (PsbEFJL). Both PsbL and PsbJ (IPR002682 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbL prevent the formation of both PSII core dimers and PSII-light harvesting complex []. In addition, both PsbL and PsbJ are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_L 3A0B_l 3ARC_l 1S5L_l 2AXT_l 3BZ2_L 4FBY_L 3PRQ_L 3PRR_L 3KZI_L ....
Probab=25.89 E-value=85 Score=20.59 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=15.9
Q ss_pred cchhHHHHHHHHHHHHHHHHhc
Q 030916 147 PVISLLRSAIIILASWVLLLAY 168 (169)
Q Consensus 147 ~~~~~~~~~l~~~~~~~~~~~~ 168 (169)
.+.|+.+.+|++.+..+++++|
T Consensus 13 NRTSLY~GLllifvl~vLFssy 34 (37)
T PF02419_consen 13 NRTSLYWGLLLIFVLAVLFSSY 34 (37)
T ss_dssp -CCHHHHHHHHHHHHHHHHHHH
T ss_pred hHHhHHHHHHHHHHHHHHhhhh
Confidence 4567777777787877777776
No 13
>PF14730 DUF4468: Domain of unknown function (DUF4468) with TBP-like fold
Probab=23.59 E-value=87 Score=22.49 Aligned_cols=25 Identities=28% Similarity=0.639 Sum_probs=22.5
Q ss_pred eeEEEEEeeCCCCceEEEEEEEecCC
Q 030916 11 IRVHWHVKLNYKEYWRVKITITNFNY 36 (169)
Q Consensus 11 V~InWHV~~nYk~~W~vkiTi~N~~~ 36 (169)
.+|+..++.+-|+| ++|+|++|..|
T Consensus 64 ~~i~y~l~i~~kDg-k~r~~~~~i~y 88 (91)
T PF14730_consen 64 TRINYTLIIDCKDG-KYRLTITNISY 88 (91)
T ss_pred eEEEEEEEEEEECC-EEEEEEEEEEE
Confidence 78999999999999 89999998876
No 14
>PF01299 Lamp: Lysosome-associated membrane glycoprotein (Lamp); InterPro: IPR002000 Lysosome-associated membrane glycoproteins (lamp) [] are integral membrane proteins, specific to lysosomes, and whose exact biological function is not yet clear. Structurally, the lamp proteins consist of two internally homologous lysosome-luminal domains separated by a proline-rich hinge region; at the C-terminal extremity there is a transmembrane region (TM) followed by a very short cytoplasmic tail (C). In each of the duplicated domains, there are two conserved disulphide bonds. This structure is schematically represented in the figure below. +-----+ +-----+ +-----+ +-----+ | | | | | | | | xCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxxxCxxxxxCxxxxxxxxxxxxCxxxxxCxxxxxxxx +--------------------------++Hinge++--------------------------++TM++C+ In mammals, there are two closely related types of lamp: lamp-1 and lamp-2, which form major components of the lysosome membrane. In chicken lamp-1 is known as LEP100. Also included in this entry is the macrophage protein CD68 (or macrosialin) [] is a heavily glycosylated integral membrane protein whose structure consists of a mucin-like domain followed by a proline-rich hinge; a single lamp-like domain; a transmembrane region and a short cytoplasmic tail. Similar to CD68, mammalian lamp-3, which is expressed in lymphoid organs, dendritic cells and in lung, contains all the C-terminal regions but lacks the N-terminal lamp-like region []. In a lamp-family protein from nematodes [] only the part C-terminal to the hinge is conserved. ; GO: 0016020 membrane
Probab=22.51 E-value=5.1e+02 Score=22.41 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=16.2
Q ss_pred CCceeEEEEEeeCCCCceEEEEEEEe
Q 030916 8 MCPIRVHWHVKLNYKEYWRVKITITN 33 (169)
Q Consensus 8 mCpV~InWHV~~nYk~~W~vkiTi~N 33 (169)
.|+-. +=++..+++++|.+.++..-
T Consensus 157 ~C~~~-~~~L~L~~~~~~~L~f~F~~ 181 (306)
T PF01299_consen 157 SCGSN-SSTLTLSFPGGWNLTFTFTK 181 (306)
T ss_pred EcCCC-ccEEEEeeCCccEEEEEEEe
Confidence 35444 44566688888888776653
No 15
>PF15145 DUF4577: Domain of unknown function (DUF4577)
Probab=21.84 E-value=1e+02 Score=24.89 Aligned_cols=14 Identities=7% Similarity=0.024 Sum_probs=5.3
Q ss_pred CCCCCcchhHHHHH
Q 030916 142 NASSRPVISLLRSA 155 (169)
Q Consensus 142 n~~~~~~~~~~~~~ 155 (169)
+++...+.-.++.+
T Consensus 54 ~sg~g~~~lffvgl 67 (128)
T PF15145_consen 54 NSGNGSRSLFFVGL 67 (128)
T ss_pred CCCCCceeehHHHH
Confidence 44443333333333
No 16
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=20.62 E-value=63 Score=21.42 Aligned_cols=14 Identities=29% Similarity=0.496 Sum_probs=11.9
Q ss_pred eeEeeCCccCCCCC
Q 030916 121 RIYFNGDNCVMPPP 134 (169)
Q Consensus 121 rVyFNGeeC~mP~p 134 (169)
+|++||+++.+|.+
T Consensus 2 ~i~vNG~~~~~~~~ 15 (66)
T PRK05659 2 NIQLNGEPRELPDG 15 (66)
T ss_pred EEEECCeEEEcCCC
Confidence 68999999988873
Done!