Query 018866
Match_columns 349
No_of_seqs 118 out of 166
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 04:41:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018866.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018866hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05022 SRP40_C: SRP40, C-ter 100.0 6.7E-34 1.5E-38 222.6 4.8 72 269-343 1-72 (72)
2 KOG2992 Nucleolar GTPase/ATPas 99.7 1.2E-17 2.7E-22 165.6 4.4 80 264-346 367-446 (446)
3 PF14975 DUF4512: Domain of un 19.0 76 0.0017 26.7 1.8 21 3-23 8-29 (88)
4 PF02395 Peptidase_S6: Immunog 14.5 78 0.0017 35.0 1.0 17 329-345 453-469 (769)
5 PF08694 UFC1: Ubiquitin-fold 13.7 77 0.0017 29.3 0.6 12 328-339 106-117 (161)
6 PF13074 DUF3938: Protein of u 13.4 1.2E+02 0.0027 25.7 1.7 27 6-32 72-100 (102)
7 KOG2992 Nucleolar GTPase/ATPas 12.8 1.4E+02 0.0031 31.3 2.3 21 261-281 361-381 (446)
8 COG0292 RplT Ribosomal protein 11.7 1.3E+02 0.0028 26.8 1.4 12 5-16 58-69 (118)
9 PF01102 Glycophorin_A: Glycop 11.0 1.2E+02 0.0025 26.7 0.8 8 34-41 109-116 (122)
10 PHA03049 IMV membrane protein; 8.3 2.5E+02 0.0053 23.0 1.7 15 1-17 1-15 (68)
No 1
>PF05022 SRP40_C: SRP40, C-terminal domain; InterPro: IPR007718 This presumed domain is found at the C terminus of the Saccharomyces cerevisiae SRP40 protein P32583 from SWISSPROT and its homologues. SRP40/nopp40 is a chaperone involved in nucleocytoplasmic transport. SRP40 is also a suppressor of mutant AC40 subunit of RNA polymerase I and III.
Probab=100.00 E-value=6.7e-34 Score=222.63 Aligned_cols=72 Identities=65% Similarity=0.927 Sum_probs=69.7
Q ss_pred CCCccccCCceeeccccccCCcccccCCCCcchHHHHHhHhccccCCcccccccccccccccCceeecccceeeC
Q 018866 269 KAFQRVKVDEVEFTDERLKDNSYWAKDGAEIGYGAKAQEVLGQVRGRDFRHEKTKKKRGSYRGGQIDLQSHSVKF 343 (349)
Q Consensus 269 ~PFqRV~~eev~f~DerL~DNSYeAK~Ga~d~wGeKAnedL~~TRGKgFRKEKnKKKRGSYRGG~ID~svnSIKF 343 (349)
.|||||++++|+|+|++|+||||+++. ++||++||++|++||||+|||||||||||||+||+||++||||||
T Consensus 1 ~pF~RV~~~~v~~~d~~l~dNsy~~~~---~~~G~kA~~~L~~trGK~FrkEK~KkKRgsy~GG~Id~~v~SiKF 72 (72)
T PF05022_consen 1 KPFQRVDEEKVEFVDERLKDNSYEAKF---DGWGEKANEDLIVTRGKGFRKEKNKKKRGSYRGGQIDTSVNSIKF 72 (72)
T ss_pred CCCcccChhheeecCcccccCCCcccc---ChHHHHHHhhhccccCCCccccccccccccccCCeecCccceeeC
Confidence 499999999999999999999999975 689999999999999999999999999999999999999999999
No 2
>KOG2992 consensus Nucleolar GTPase/ATPase p130 [Nuclear structure]
Probab=99.69 E-value=1.2e-17 Score=165.63 Aligned_cols=80 Identities=48% Similarity=0.691 Sum_probs=68.1
Q ss_pred CCCCCCCCccccCCceeeccccccCCcccccCCCCcchHHHHHhHhccccCCcccccccccccccccCceeecccceeeC
Q 018866 264 EPKSVKAFQRVKVDEVEFTDERLKDNSYWAKDGAEIGYGAKAQEVLGQVRGRDFRHEKTKKKRGSYRGGQIDLQSHSVKF 343 (349)
Q Consensus 264 ~pk~n~PFqRV~~eev~f~DerL~DNSYeAK~Ga~d~wGeKAnedL~~TRGKgFRKEKnKKKRGSYRGG~ID~svnSIKF 343 (349)
..++..|||||++.++.++-.. |+|..+.|+.++||.+|+++|++|||++|||+|||||||+||||.|++.+++|+|
T Consensus 367 ~~t~~~~~r~~~~~kd~~~~~~---~~~~~~~~~~~~wG~~An~~l~~~rGk~fr~eKtkkkRgsy~gG~I~~~~~s~kF 443 (446)
T KOG2992|consen 367 SETKKSPFRRVDPVKDSRVEDI---LSDNKKDGAAGGWGKRANKDLGPGRGKDFRHEKTKKKRGSYRGGSITLDVNSIKF 443 (446)
T ss_pred cccCCCCccccccccccccccc---cccccccccccccccccccccccccccccccccccccCccccCCccccccccccc
Confidence 3455579999977766654333 6666666788999999999999999999999999999999999999999999999
Q ss_pred CCC
Q 018866 344 NYS 346 (349)
Q Consensus 344 dDS 346 (349)
+++
T Consensus 444 ~~~ 446 (446)
T KOG2992|consen 444 DLS 446 (446)
T ss_pred CCC
Confidence 975
No 3
>PF14975 DUF4512: Domain of unknown function (DUF4512)
Probab=19.00 E-value=76 Score=26.68 Aligned_cols=21 Identities=24% Similarity=0.428 Sum_probs=15.0
Q ss_pred hhhHHHHH-HHhhhhhhhcccc
Q 018866 3 SVIALWIW-RICAASILRLDSQ 23 (349)
Q Consensus 3 ~~~~~~~~-~~~~~~~~~~~~~ 23 (349)
.-|.|||| |+..--|+||=+.
T Consensus 8 IPvLLwIykkFlqP~i~~~~sp 29 (88)
T PF14975_consen 8 IPVLLWIYKKFLQPYIYPFWSP 29 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHhCc
Confidence 34689999 5666677788764
No 4
>PF02395 Peptidase_S6: Immunoglobulin A1 protease Serine protease Prosite pattern; InterPro: IPR000710 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 group of serine peptidases belong to the MEROPS peptidase family S6 (clan PA(S)). The type sample being the IgA1-specific serine endopeptidase from Neisseria gonorrhoeae []. These cleave prolyl bonds in the hinge regions of immunoglobulin A heavy chains. Similar specificity is shown by the unrelated family of M26 metalloendopeptidases.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 3SZE_A 3H09_B 3SYJ_A 1WXR_A 3AK5_B.
Probab=14.46 E-value=78 Score=34.95 Aligned_cols=17 Identities=35% Similarity=0.915 Sum_probs=11.5
Q ss_pred ccCceeecccceeeCCC
Q 018866 329 YRGGQIDLQSHSVKFNY 345 (349)
Q Consensus 329 YRGG~ID~svnSIKFdD 345 (349)
||||.+|+..|++.|..
T Consensus 453 frGG~LDlNGn~ltF~~ 469 (769)
T PF02395_consen 453 FRGGRLDLNGNDLTFKR 469 (769)
T ss_dssp TT-EEEE-TT--EEESS
T ss_pred ecCceeeccCccchhhh
Confidence 78999999999999963
No 5
>PF08694 UFC1: Ubiquitin-fold modifier-conjugating enzyme 1; InterPro: IPR014806 Ubiquitin-like (UBL) post-translational modifiers are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. Ubiquitin-fold modifier 1 (Ufm1) a ubiquitin-like protein is activated by a novel E1-like enzyme, Uba5, by forming a high-energy thioester bond. Activated Ufm1 is then transferred to its cognate E2-like enzyme, Ufc1, in a similar thioester linkage. This family represents the E2-like enzyme [].; PDB: 2Z6P_A 2K07_A 2Z6O_A 3EVX_D 3KPA_A.
Probab=13.68 E-value=77 Score=29.31 Aligned_cols=12 Identities=58% Similarity=1.030 Sum_probs=7.4
Q ss_pred cccCceeecccc
Q 018866 328 SYRGGQIDLQSH 339 (349)
Q Consensus 328 SYRGG~ID~svn 339 (349)
-||||.|.+++|
T Consensus 106 MYRGGkIClt~H 117 (161)
T PF08694_consen 106 MYRGGKICLTDH 117 (161)
T ss_dssp BCCCCBB---TT
T ss_pred hhcCceEeeecc
Confidence 499999998865
No 6
>PF13074 DUF3938: Protein of unknown function (DUF3938)
Probab=13.37 E-value=1.2e+02 Score=25.71 Aligned_cols=27 Identities=37% Similarity=0.776 Sum_probs=18.7
Q ss_pred HHHHHHH--hhhhhhhcccccCCCCccch
Q 018866 6 ALWIWRI--CAASILRLDSQKDGDSKRGK 32 (349)
Q Consensus 6 ~~~~~~~--~~~~~~~~~~~~~~~s~~~~ 32 (349)
.||.|-| |.|-++.|-.....||-|..
T Consensus 72 glwtwfiafcladvfnllqdneedsgrqi 100 (102)
T PF13074_consen 72 GLWTWFIAFCLADVFNLLQDNEEDSGRQI 100 (102)
T ss_pred hHHHHHHHHHHHHHHHHhcCchhhccCcC
Confidence 5788865 88888887665555665543
No 7
>KOG2992 consensus Nucleolar GTPase/ATPase p130 [Nuclear structure]
Probab=12.83 E-value=1.4e+02 Score=31.31 Aligned_cols=21 Identities=5% Similarity=-0.179 Sum_probs=15.0
Q ss_pred CCCCCCCCCCCccccCCceee
Q 018866 261 GSAEPKSVKAFQRVKVDEVEF 281 (349)
Q Consensus 261 gs~~pk~n~PFqRV~~eev~f 281 (349)
+....+...+|.+++...+.+
T Consensus 361 ~~g~~~~~t~~~~~r~~~~~k 381 (446)
T KOG2992|consen 361 SGGGEGSETKKSPFRRVDPVK 381 (446)
T ss_pred CCCccccccCCCCcccccccc
Confidence 445677777999998876554
No 8
>COG0292 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]
Probab=11.74 E-value=1.3e+02 Score=26.77 Aligned_cols=12 Identities=58% Similarity=0.794 Sum_probs=10.1
Q ss_pred hHHHHHHHhhhh
Q 018866 5 IALWIWRICAAS 16 (349)
Q Consensus 5 ~~~~~~~~~~~~ 16 (349)
=.|||-||-||.
T Consensus 58 R~LWI~RINAA~ 69 (118)
T COG0292 58 RKLWIARINAAA 69 (118)
T ss_pred HHHHHHHHHHHH
Confidence 369999999885
No 9
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=10.99 E-value=1.2e+02 Score=26.65 Aligned_cols=8 Identities=25% Similarity=0.231 Sum_probs=0.0
Q ss_pred HHHhhhHH
Q 018866 34 AESAAGVE 41 (349)
Q Consensus 34 ~~~~~~~e 41 (349)
+.-+--||
T Consensus 109 ~~p~~~~~ 116 (122)
T PF01102_consen 109 DVPLSSVE 116 (122)
T ss_dssp --------
T ss_pred CCCcceee
Confidence 33344444
No 10
>PHA03049 IMV membrane protein; Provisional
Probab=8.32 E-value=2.5e+02 Score=23.00 Aligned_cols=15 Identities=53% Similarity=0.718 Sum_probs=9.6
Q ss_pred CchhhHHHHHHHhhhhh
Q 018866 1 MISVIALWIWRICAASI 17 (349)
Q Consensus 1 ~~~~~~~~~~~~~~~~~ 17 (349)
||+-++|.| ||.|-|
T Consensus 1 MI~d~~l~i--ICVaIi 15 (68)
T PHA03049 1 MIGDIILVI--ICVVII 15 (68)
T ss_pred ChHHHHHHH--HHHHHH
Confidence 677666655 677654
Done!