Query 040528
Match_columns 86
No_of_seqs 58 out of 60
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 09:19:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040528.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040528hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00213 predicted protein; Pr 99.7 4.1E-19 8.9E-24 125.6 1.9 53 27-80 38-94 (118)
2 PF05617 Prolamin_like: Prolam 99.5 3.8E-15 8.3E-20 91.9 1.6 46 36-81 1-51 (70)
3 KOG0856 Predicted pilin-like t 40.8 15 0.00033 27.3 1.2 16 70-85 72-88 (146)
4 PLN00214 putative protein; Pro 34.2 12 0.00026 26.8 -0.2 27 45-73 45-76 (115)
5 PF04109 APG9: Autophagy prote 26.5 54 0.0012 27.0 2.3 28 42-69 329-359 (370)
6 PF08386 Abhydrolase_4: TAP-li 25.6 60 0.0013 21.0 2.0 24 43-66 78-103 (103)
7 PF00734 CBM_1: Fungal cellulo 24.3 41 0.00088 18.4 0.8 16 58-73 7-22 (29)
8 cd00578 L-fuc_L-ara-isomerases 19.3 60 0.0013 26.0 1.2 33 32-66 257-289 (452)
9 KOG3832 Predicted amino acid t 17.2 66 0.0014 26.3 1.0 20 61-80 178-205 (319)
10 COG2407 FucI L-fucose isomeras 16.3 58 0.0013 27.9 0.5 25 35-59 262-287 (470)
No 1
>PLN00213 predicted protein; Provisional
Probab=99.74 E-value=4.1e-19 Score=125.65 Aligned_cols=53 Identities=21% Similarity=0.533 Sum_probs=47.0
Q ss_pred hhhccCcchhhhhhhhcccchHHHHHHHHHhccc-ccCcccccC---CCCCchhhhhc
Q 040528 27 RLEVSGGQMECWNVLMELKSCSNEIVIFFINSQA-DIGPDCCRT---GLQCSPLSDSR 80 (86)
Q Consensus 27 rL~~~~~~~~CW~sL~~l~sCt~EIv~fflnGe~-~iGp~CC~A---~~~CWP~Mf~s 80 (86)
++.+.+++.+||+||++++||+.||.+++++||+ +||++|||| .++|||+| |.
T Consensus 38 ~~pg~pd~~kCwSSl~~vpGCv~EI~~si~~gkf~~Ig~aCCKAf~~~dnCwP~~-P~ 94 (118)
T PLN00213 38 LIPGLPDITKCFSSVMDIPGCIAEISQSIFTGKFGNLGPACCKAFLDADNCIPKI-PF 94 (118)
T ss_pred CCCCCccHHHHHHHHcCCcchHHHHHHHHHhchhcccchHHHHHHHhhhccccCC-cC
Confidence 3444568889999999999999999999999999 999999999 55999996 53
No 2
>PF05617 Prolamin_like: Prolamin-like; InterPro: IPR008502 This entry consists of several proteins of unknown function found exclusively in Arabidopsis thaliana.
Probab=99.51 E-value=3.8e-15 Score=91.87 Aligned_cols=46 Identities=30% Similarity=0.751 Sum_probs=42.3
Q ss_pred hhhhhhhcccchHHHHHHHHHhcc-cccCcccccC----CCCCchhhhhcc
Q 040528 36 ECWNVLMELKSCSNEIVIFFINSQ-ADIGPDCCRT----GLQCSPLSDSRL 81 (86)
Q Consensus 36 ~CW~sL~~l~sCt~EIv~fflnGe-~~iGp~CC~A----~~~CWP~Mf~sl 81 (86)
+||+++.++++|+.||+.+|++|+ .+||++||+| +++|||.|+..+
T Consensus 1 kc~~~~~~~~~C~~eI~~~~~~g~~~~i~~~CC~~i~~~g~~C~~~l~~~~ 51 (70)
T PF05617_consen 1 KCLSSCAKSPGCGDEIFNSFFNGNKKNIGPECCKAINKMGKDCHPALFKMF 51 (70)
T ss_pred ChHHHcCCccchHHHHHHHHHcCCCCCCChHHHHHHHHHhHhHHHHHHHHc
Confidence 699999999999999999999999 6999999999 999999955444
No 3
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=40.81 E-value=15 Score=27.29 Aligned_cols=16 Identities=19% Similarity=0.256 Sum_probs=13.8
Q ss_pred CCCC-chhhhhccccCC
Q 040528 70 GLQC-SPLSDSRLKKGT 85 (86)
Q Consensus 70 ~~~C-WP~Mf~sl~~~~ 85 (86)
+..| ||+.|..+++|.
T Consensus 72 dsgcGWPAF~e~i~~ga 88 (146)
T KOG0856|consen 72 DSGCGWPAFFEAIGPGA 88 (146)
T ss_pred cCCCCCchhhhccCCCc
Confidence 7888 999999998773
No 4
>PLN00214 putative protein; Provisional
Probab=34.16 E-value=12 Score=26.80 Aligned_cols=27 Identities=26% Similarity=0.669 Sum_probs=21.1
Q ss_pred cchHHHHHHHHH-hcccccCcccccC----CCCC
Q 040528 45 KSCSNEIVIFFI-NSQADIGPDCCRT----GLQC 73 (86)
Q Consensus 45 ~sCt~EIv~ffl-nGe~~iGp~CC~A----~~~C 73 (86)
.-|..||+..++ ||.+ -..||+. +..|
T Consensus 45 ~KCa~EI~a~i~~N~t~--s~~CC~~LVk~GK~C 76 (115)
T PLN00214 45 PKCALDIIAVVFENGTL--IDPCCNDLVKEGKVC 76 (115)
T ss_pred HhhHHHHHHHHHcCCCC--chHHHHHHHHHhhHH
Confidence 459999999999 6655 6779887 6666
No 5
>PF04109 APG9: Autophagy protein Apg9 ; InterPro: IPR007241 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, possibly serving as a marker for a specialised compartment essential for these vesicle-mediated alternative targeting pathways [].
Probab=26.47 E-value=54 Score=26.98 Aligned_cols=28 Identities=32% Similarity=0.594 Sum_probs=24.3
Q ss_pred hcccchHHHHHHHHHhccc---ccCcccccC
Q 040528 42 MELKSCSNEIVIFFINSQA---DIGPDCCRT 69 (86)
Q Consensus 42 ~~l~sCt~EIv~fflnGe~---~iGp~CC~A 69 (86)
+.++.|+.||+-||.+=.. .+|.-|--|
T Consensus 329 f~Lp~~a~~IvdF~r~~TV~V~GvG~VCsfA 359 (370)
T PF04109_consen 329 FSLPKCADEIVDFFREFTVHVDGVGYVCSFA 359 (370)
T ss_pred hcccccHHHHHHHHHhceeecCCCCCeeeec
Confidence 6789999999999998887 688888777
No 6
>PF08386 Abhydrolase_4: TAP-like protein; InterPro: IPR013595 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 entry represents a C-terminal domain associated with putative hydrolases and bacterial peptidases that belong to MEROPS peptidase family S33 (clan SC). They are related to a tripeptidyl aminopeptidase from Streptomyces lividans (Q54410 from SWISSPROT). A member of this family (Q6E3K7 from SWISSPROT) is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterised from Propionibacterium freudenreichii []. ; GO: 0008233 peptidase activity
Probab=25.63 E-value=60 Score=21.01 Aligned_cols=24 Identities=17% Similarity=0.465 Sum_probs=16.6
Q ss_pred cccchHHHHH-HHHHhccc-ccCccc
Q 040528 43 ELKSCSNEIV-IFFINSQA-DIGPDC 66 (86)
Q Consensus 43 ~l~sCt~EIv-~fflnGe~-~iGp~C 66 (86)
.-..|+.+++ .||++|+. .-|..|
T Consensus 78 ~~s~C~~~~v~~yl~~G~lP~~~~~C 103 (103)
T PF08386_consen 78 GGSPCVDKAVDDYLLDGTLPADGTTC 103 (103)
T ss_pred CCChHHHHHHHHHHHcCCCCCCcCcC
Confidence 4557999999 56667876 445544
No 7
>PF00734 CBM_1: Fungal cellulose binding domain; InterPro: IPR000254 The microbial degradation of cellulose and xylans requires several types of enzymes 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 of a number of fungal cellulases has been shown to consist of 36 amino acid residues, and it is found either at the N-terminal or at the C-terminal extremity of the enzymes. As it is shown in the following schematic representation, there are four conserved cysteines in this type of CBD domain, all involved in disulphide bonds. +----------------+ | +-----|---------+ | | | | xxxxxxxCxxxxxxxxxxCxxxxxCxxxxxxxxxCx ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030248 cellulose binding, 0005975 carbohydrate metabolic process, 0005576 extracellular region; PDB: 1AZK_A 2CBH_A 1AZJ_A 1AZ6_A 1CBH_A 1AZH_A.
Probab=24.34 E-value=41 Score=18.43 Aligned_cols=16 Identities=38% Similarity=1.028 Sum_probs=9.1
Q ss_pred cccccCcccccCCCCC
Q 040528 58 SQADIGPDCCRTGLQC 73 (86)
Q Consensus 58 Ge~~iGp~CC~A~~~C 73 (86)
|+.+-||.||.+...|
T Consensus 7 G~~~~G~t~C~~g~~C 22 (29)
T PF00734_consen 7 GIGWTGPTCCASGYTC 22 (29)
T ss_dssp CTT-SS---BSSSSCE
T ss_pred CCCcccCCcCCCcCEe
Confidence 5668999999986666
No 8
>cd00578 L-fuc_L-ara-isomerases L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose in glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in various oligo- and polysaccharides in mammals, bacteria and plants. AI catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion to D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute.
Probab=19.31 E-value=60 Score=26.02 Aligned_cols=33 Identities=18% Similarity=0.292 Sum_probs=26.7
Q ss_pred CcchhhhhhhhcccchHHHHHHHHHhcccccCccc
Q 040528 32 GGQMECWNVLMELKSCSNEIVIFFINSQADIGPDC 66 (86)
Q Consensus 32 ~~~~~CW~sL~~l~sCt~EIv~fflnGe~~iGp~C 66 (86)
.-..+||..|.++ +++.=+..++||.+. |+.+|
T Consensus 257 a~a~~C~~~l~~~-~~~pcla~s~L~~~g-ip~ac 289 (452)
T cd00578 257 AFTIQCFEDLTDL-GQLPCLAEQRLNAEG-IPFAC 289 (452)
T ss_pred EEEecchhhhccc-CcchhHHHHHhccCC-ceeEE
Confidence 3457899999999 899999999999885 54444
No 9
>KOG3832 consensus Predicted amino acid transporter [General function prediction only]
Probab=17.20 E-value=66 Score=26.26 Aligned_cols=20 Identities=30% Similarity=0.414 Sum_probs=14.2
Q ss_pred ccCcccccC--------CCCCchhhhhc
Q 040528 61 DIGPDCCRT--------GLQCSPLSDSR 80 (86)
Q Consensus 61 ~iGp~CC~A--------~~~CWP~Mf~s 80 (86)
.||.+=|+. +++|||.++..
T Consensus 178 a~g~dscgvead~~~~dtdrcwg~ilrr 205 (319)
T KOG3832|consen 178 AIGADSCGVEADPCHEDTDRCWGEILRR 205 (319)
T ss_pred hcCCccccccCCcccccccccchHHHhh
Confidence 466666663 89999987654
No 10
>COG2407 FucI L-fucose isomerase and related proteins [Carbohydrate transport and metabolism]
Probab=16.27 E-value=58 Score=27.95 Aligned_cols=25 Identities=16% Similarity=0.255 Sum_probs=23.0
Q ss_pred hhhhhhhhcccchHHHHHHHHHh-cc
Q 040528 35 MECWNVLMELKSCSNEIVIFFIN-SQ 59 (86)
Q Consensus 35 ~~CW~sL~~l~sCt~EIv~ffln-Ge 59 (86)
..||..|...-+++.-++.+||| |+
T Consensus 262 ~~C~~~l~~~~~~~~C~~~a~LNDg~ 287 (470)
T COG2407 262 AGCWPQLQWTLGIPPCTIEAVLNDGR 287 (470)
T ss_pred hhcchHHHHhcCCCchhhhhhcccCC
Confidence 56999999999999999999999 66
Done!