Query psy5554
Match_columns 272
No_of_seqs 3 out of 5
Neff 1.2
Searched_HMMs 46136
Date Fri Aug 16 20:29:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5554.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5554hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK15196 secreted effector pro 82.9 5.5 0.00012 36.5 7.4 7 31-37 152-158 (350)
2 PF00681 Plectin: Plectin repe 9.6 1.6E+02 0.0035 19.4 1.0 12 237-248 9-20 (45)
3 COG3691 Uncharacterized protei 9.1 1.6E+02 0.0034 24.2 0.9 18 253-270 54-71 (98)
4 PRK00159 putative septation in 6.8 2.3E+02 0.005 22.5 0.9 29 243-271 1-29 (87)
5 TIGR00743 conserved hypothetic 6.7 2.4E+02 0.0052 22.6 1.0 18 253-270 51-68 (95)
6 KOG3381|consensus 6.2 3.8E+02 0.0083 23.6 2.0 15 258-272 74-88 (161)
7 PF07023 DUF1315: Protein of u 4.7 3.6E+02 0.0079 21.6 0.9 14 237-250 60-73 (93)
8 PF00883 Peptidase_M17: Cytoso 4.5 5.4E+02 0.012 24.0 1.9 18 254-271 55-72 (311)
9 PF06519 TolA: TolA C-terminal 4.4 6.8E+02 0.015 19.2 2.2 17 255-271 32-48 (96)
10 PF06781 UPF0233: Uncharacteri 4.3 4.1E+02 0.0088 20.8 0.9 29 243-271 1-29 (87)
No 1
>PRK15196 secreted effector protein PipB2; Provisional
Probab=82.93 E-value=5.5 Score=36.53 Aligned_cols=7 Identities=14% Similarity=0.411 Sum_probs=2.5
Q ss_pred CCCcccc
Q psy5554 31 LGLRNCN 37 (272)
Q Consensus 31 ~~LR~C~ 37 (272)
..|+...
T Consensus 152 ~~L~ga~ 158 (350)
T PRK15196 152 MNLKGAV 158 (350)
T ss_pred ccccCCc
Confidence 3333333
No 2
>PF00681 Plectin: Plectin repeat; InterPro: IPR001101 Plectin may have a role in cross-linking intermediate filaments, in inter-linking intermediate filaments with microtubules and microfilaments and in anchoring intermediate filaments to the plasma and nuclear membranes. Plectin is recruited into hemidesmosomes, multiprotein complexes that facilitate adhesion of epithelia to the basement membrane, thereby providing linkage between the intracellular keratin filaments to the laminins of the extracellular matrix. Plectin binds to hemidesmosomes through association of its actin-binding domain with the first pair of fibronectin type III repeats and a small part of the connecting segment of the integrin-beta4 subunit, the latter (integrin-alpha6,beta4) acting as a receptor for the extracellular matrix component laminin-5. The plectin repeat is also seen in the cell adhesion junction plaque proteins, desmoplakin, envoplakin, and bullous pemphigoid antigen. The domains in plakins show considerable sequence homology. The N terminus consists of a plakin domain containing a number of subdomains with high alpha-helical content, while the central coiled-coil domain is composed of heptad repeats involved in the dimerisation of plakin, and the C terminus contains one or more homologous repeat sequences referred to plectin repeats []. This entry represents the plectin repeats found in the C terminus of plakin proteins.; GO: 0005856 cytoskeleton; PDB: 1LM7_A 1LM5_A.
Probab=9.63 E-value=1.6e+02 Score=19.38 Aligned_cols=12 Identities=42% Similarity=0.803 Sum_probs=9.8
Q ss_pred CCCceeeeCCcc
Q psy5554 237 NTGGLIVPKSKR 248 (272)
Q Consensus 237 ntgglivpkskr 248 (272)
-+||+|.|+++.
T Consensus 9 ~~gGiidp~tg~ 20 (45)
T PF00681_consen 9 ATGGIIDPETGE 20 (45)
T ss_dssp TTTSEEETTTTE
T ss_pred eeeeEEeCCCCe
Confidence 378999999875
No 3
>COG3691 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=9.15 E-value=1.6e+02 Score=24.20 Aligned_cols=18 Identities=33% Similarity=0.619 Sum_probs=14.2
Q ss_pred hccccCCCceeEEEeecc
Q psy5554 253 NASRSENEPCLVKIKFTP 270 (272)
Q Consensus 253 nasrsenepclvkikftp 270 (272)
-|..-|.|||.|+-++++
T Consensus 54 kAr~veSepc~I~~ei~~ 71 (98)
T COG3691 54 KARAVESEPCEIEYEITD 71 (98)
T ss_pred HHHhhccCcceeeeeeEe
Confidence 455667899999988875
No 4
>PRK00159 putative septation inhibitor protein; Reviewed
Probab=6.81 E-value=2.3e+02 Score=22.47 Aligned_cols=29 Identities=31% Similarity=0.356 Sum_probs=14.0
Q ss_pred eeCCccchhhhccccCCCceeEEEeeccC
Q psy5554 243 VPKSKRGAQENASRSENEPCLVKIKFTPN 271 (272)
Q Consensus 243 vpkskrgaqenasrsenepclvkikftpn 271 (272)
.||||.-.++....+..+.=-||+|-.|+
T Consensus 1 MPkSK~RKk~~~t~~~~~rtpvk~~~~~s 29 (87)
T PRK00159 1 MPKSKVRKKNDFTVSSVSRTPVKVKAGPS 29 (87)
T ss_pred CCCccccCCCCCCCCCccCCCccccCCCC
Confidence 48888765433222221111277775543
No 5
>TIGR00743 conserved hypothetical protein. These small proteins are approximately 100 amino acids in length and appear to be found only in gamma proteobacteria. The function of this protein family is unknown.
Probab=6.74 E-value=2.4e+02 Score=22.58 Aligned_cols=18 Identities=33% Similarity=0.569 Sum_probs=13.7
Q ss_pred hccccCCCceeEEEeecc
Q psy5554 253 NASRSENEPCLVKIKFTP 270 (272)
Q Consensus 253 nasrsenepclvkikftp 270 (272)
-|..-|.|||.|+-+++|
T Consensus 51 kAk~vesepc~I~~~i~~ 68 (95)
T TIGR00743 51 KARAVESEPCEIASEITD 68 (95)
T ss_pred HHHHhhcCCceeEEEEEE
Confidence 455667899999887765
No 6
>KOG3381|consensus
Probab=6.16 E-value=3.8e+02 Score=23.61 Aligned_cols=15 Identities=40% Similarity=0.782 Sum_probs=11.1
Q ss_pred CCCceeEEEeeccCC
Q psy5554 258 ENEPCLVKIKFTPNL 272 (272)
Q Consensus 258 enepclvkikftpnl 272 (272)
++|--.|+|+|||-+
T Consensus 74 ~~~~s~V~i~ftPTi 88 (161)
T KOG3381|consen 74 GDEESYVRITFTPTI 88 (161)
T ss_pred CCcceEEEEEeccCC
Confidence 444468999999953
No 7
>PF07023 DUF1315: Protein of unknown function (DUF1315); InterPro: IPR009749 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=4.74 E-value=3.6e+02 Score=21.62 Aligned_cols=14 Identities=36% Similarity=0.297 Sum_probs=11.8
Q ss_pred CCCceeeeCCccch
Q psy5554 237 NTGGLIVPKSKRGA 250 (272)
Q Consensus 237 ntgglivpkskrga 250 (272)
.++|.|+.|||...
T Consensus 60 ~~~G~I~~ksK~~l 73 (93)
T PF07023_consen 60 GADGYIDMKSKAEL 73 (93)
T ss_pred CCCCEEccccHHHH
Confidence 57899999999854
No 8
>PF00883 Peptidase_M17: Cytosol aminopeptidase family, catalytic domain; InterPro: IPR000819 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF), the type example being leucyl aminopeptidase from Bos taurus (Bovine). Aminopeptidases are exopeptidases involved in the processing and regular turnover of intracellular proteins, although their precise role in cellular metabolism is unclear [, ]. Leucine aminopeptidases cleave leucine residues from the N-terminal of polypeptide chains, but substantial rates are evident for all amino acids []. The enzymes exist as homo-hexamers, comprising 2 trimers stacked on top of one another []. Each monomer binds 2 zinc ions and folds into 2 alpha/beta-type quasi-spherical globular domains, producing a comma-like shape []. The N-terminal 150 residues form a 5-stranded beta-sheet with 4 parallel and 1 anti-parallel strand sandwiched between 4 alpha-helices []. An alpha-helix extends into the C-terminal domain, which comprises a central 8-stranded saddle-shaped beta-sheet sandwiched between groups of helices, forming the monomer hydrophobic core []. A 3-stranded beta-sheet resides on the surface of the monomer, where it interacts with other members of the hexamer []. The 2 zinc ions and the active site are entirely located in the C-terminal catalytic domain [].; GO: 0004177 aminopeptidase activity, 0006508 proteolysis, 0005622 intracellular; PDB: 3KZW_L 3KQX_C 3KQZ_L 3KR4_I 3KR5_J 3T8W_C 3H8F_D 3H8G_A 3H8E_B 3IJ3_A ....
Probab=4.51 E-value=5.4e+02 Score=23.98 Aligned_cols=18 Identities=28% Similarity=0.466 Sum_probs=13.0
Q ss_pred ccccCCCceeEEEeeccC
Q psy5554 254 ASRSENEPCLVKIKFTPN 271 (272)
Q Consensus 254 asrsenepclvkikftpn 271 (272)
..-|+++|.+|.++|.|+
T Consensus 55 g~gS~~~P~lv~l~Y~g~ 72 (311)
T PF00883_consen 55 GRGSRHPPRLVVLEYKGN 72 (311)
T ss_dssp HTTSSS--EEEEEEEETS
T ss_pred cccCCCCCEEEEEEECCC
Confidence 345789999999999885
No 9
>PF06519 TolA: TolA C-terminal; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2X9A_D 3QDP_A 3QDR_A 1TOL_A 1S62_A.
Probab=4.44 E-value=6.8e+02 Score=19.23 Aligned_cols=17 Identities=24% Similarity=0.684 Sum_probs=11.5
Q ss_pred cccCCCceeEEEeeccC
Q psy5554 255 SRSENEPCLVKIKFTPN 271 (272)
Q Consensus 255 srsenepclvkikftpn 271 (272)
+.-...-|.|+|++.|+
T Consensus 32 ~~y~GK~C~v~i~l~~d 48 (96)
T PF06519_consen 32 ESYKGKECRVRIRLAPD 48 (96)
T ss_dssp GGGTT--EEEEEEEETT
T ss_pred cccCCCEEEEEEEECCC
Confidence 34456789999999875
No 10
>PF06781 UPF0233: Uncharacterised protein family (UPF0233); InterPro: IPR009619 This is a group of proteins of unknown function.
Probab=4.31 E-value=4.1e+02 Score=20.84 Aligned_cols=29 Identities=28% Similarity=0.338 Sum_probs=0.0
Q ss_pred eeCCccchhhhccccCCCceeEEEeeccC
Q psy5554 243 VPKSKRGAQENASRSENEPCLVKIKFTPN 271 (272)
Q Consensus 243 vpkskrgaqenasrsenepclvkikftpn 271 (272)
.||||...+......+.+.=-+|+|-.||
T Consensus 1 MPkSk~rKk~~~~~~~~~r~~~~~~~~~s 29 (87)
T PF06781_consen 1 MPKSKVRKKAAYTPPPASRTPVKVKAKPS 29 (87)
T ss_pred CCCccccccccCCCCCcccCCccccCCCC
Done!