Query psy11405
Match_columns 76
No_of_seqs 102 out of 168
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 17:36:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11405.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11405hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3037|consensus 99.9 4.6E-25 9.9E-30 167.7 7.2 61 12-72 4-66 (330)
2 PF04683 Proteasom_Rpn13: Prot 99.8 2.4E-20 5.1E-25 118.4 7.3 47 26-72 1-48 (85)
3 PF14008 Metallophos_C: Iron/z 76.7 7.6 0.00017 22.5 4.2 36 35-70 27-62 (62)
4 PF11625 DUF3253: Protein of u 51.2 7.4 0.00016 24.8 0.8 25 24-48 55-81 (83)
5 PF02870 Methyltransf_1N: 6-O- 47.3 32 0.00069 20.1 3.1 22 41-62 11-32 (77)
6 PF12101 DUF3577: Protein of u 43.9 39 0.00085 23.4 3.5 48 14-62 75-122 (137)
7 PF14795 Leucyl-specific: Leuc 39.1 35 0.00076 20.4 2.3 14 46-60 43-56 (56)
8 PF05720 Dicty_CAD: Cell-cell 36.2 52 0.0011 21.1 2.9 31 17-47 42-73 (82)
9 cd00839 MPP_PAPs purple acid p 35.0 1.4E+02 0.0031 21.0 5.4 39 34-72 254-292 (294)
10 PF01479 S4: S4 domain; Inter 34.3 13 0.00029 19.8 0.0 16 23-38 23-39 (48)
11 TIGR02588 conserved hypothetic 32.1 48 0.001 22.6 2.4 33 16-48 83-116 (122)
12 PF12043 DUF3527: Domain of un 30.5 1.1E+02 0.0024 24.2 4.5 35 37-76 2-36 (346)
13 PF09870 DUF2097: Uncharacteri 29.5 1.6E+02 0.0034 18.9 4.9 32 18-51 22-53 (86)
14 cd00712 AsnB Glutamine amidotr 29.2 1.4E+02 0.003 20.7 4.5 35 35-74 124-158 (220)
15 PF03439 Spt5-NGN: Early trans 28.8 54 0.0012 20.0 2.1 16 34-49 37-52 (84)
16 KOG4446|consensus 27.9 35 0.00077 27.8 1.4 16 34-49 122-137 (471)
17 COG1203 CRISPR-associated heli 26.8 22 0.00049 29.7 0.1 21 24-49 528-548 (733)
18 PF11773 PulG: Type II secreto 26.3 90 0.002 19.9 2.8 29 28-56 54-82 (82)
19 PF12068 DUF3548: Domain of un 25.3 96 0.0021 22.6 3.2 24 40-64 29-52 (213)
20 PF07867 DUF1654: Protein of u 25.0 1E+02 0.0023 19.2 2.9 18 44-61 53-70 (73)
21 COG3848 Phosphohistidine swive 24.8 46 0.001 22.4 1.3 23 24-46 83-105 (111)
22 PRK00807 50S ribosomal protein 23.7 1.4E+02 0.0031 17.0 3.1 28 27-57 3-30 (52)
23 cd01910 Wali7 This domain is p 23.3 2E+02 0.0044 21.2 4.6 37 34-74 131-167 (224)
24 PF10357 Kin17_mid: Domain of 22.4 83 0.0018 21.4 2.2 28 35-63 68-95 (127)
25 PF11605 Vps36_ESCRT-II: Vacuo 22.2 2.1E+02 0.0046 17.9 4.5 43 16-63 12-54 (89)
26 cd00472 Ribosomal_L24e_L24 Rib 22.0 1.8E+02 0.0038 16.9 3.3 30 25-57 3-32 (54)
27 PF14713 DUF4464: Domain of un 21.6 1.7E+02 0.0037 21.8 3.9 36 22-57 161-199 (233)
28 COG4334 Uncharacterized protei 21.5 59 0.0013 22.3 1.4 23 22-44 66-90 (131)
29 PRK14891 50S ribosomal protein 20.8 1.1E+02 0.0024 21.1 2.6 29 26-57 5-33 (131)
30 PF13511 DUF4124: Domain of un 20.6 1.1E+02 0.0024 16.9 2.2 21 42-62 13-33 (60)
31 PF10115 HlyU: Transcriptional 20.5 90 0.002 20.2 2.0 17 25-41 19-35 (91)
No 1
>KOG3037|consensus
Probab=99.91 E-value=4.6e-25 Score=167.67 Aligned_cols=61 Identities=59% Similarity=1.022 Sum_probs=57.0
Q ss_pred ccCCCcceeEEEeceeeEEcC--CEEEecCCccEEEEEeCCCCeEEEEEeeCCCCCeeeeEEE
Q psy11405 12 VSRSQSKNLVEFKAGKMTMKG--KMVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEVVWW 72 (76)
Q Consensus 12 ~~~~~~~~lieFkAGK~~~~g--~~V~Pd~rKG~i~l~~~~D~l~hf~W~~R~t~~vED~~~~ 72 (76)
++.+++..|||||||||.+.| ++|+||+|||+|||.+++|||+||||++|++++||||+|-
T Consensus 4 ss~s~~~~lVeFkAGkm~l~~gtk~v~pDprKGli~i~~sddgliHF~WkdR~~g~VEdDlIi 66 (330)
T KOG3037|consen 4 SSNSSSSTLVEFKAGKMRLVGGTKLVTPDPRKGLIYIKRSDDGLIHFCWKDRESGNVEDDLIV 66 (330)
T ss_pred ccccccceEEEEecceEEecCCcceeecccccceEEEeeCCCceEEEEecccCCCCcccceEE
Confidence 345788899999999999999 8999999999999999999999999999999999999874
No 2
>PF04683 Proteasom_Rpn13: Proteasome complex subunit Rpn13 ubiquitin receptor; InterPro: IPR006773 This family was thought originally to be involved in cell-adhesion [, ], but the members are now known to be proteasome subunit Rpn13, a novel ubiquitin receptor. The 26S proteasome is a huge macromolecular protein-degradation machine consisting of a proteolytically active 20S core, in the form of four disc-like proteins, and one or two 19S regulatory particles. The regulatory particle(s) sit on the top and or bottom of the core, de-ubiquitinate the substrate peptides, unfold them and guide them into the narrow channel through the centre of the core. Rpn13 and its homologues dock onto the regulatory particle through the N-terminal region which binds Rpn2. The C-terminal part of the domain binds de-ubiquitinating enzyme Uch37/UCHL5 and enhances its isopeptidase activity. Rpn13 binds ubiquitin via a conserved amino-terminal region called the pleckstrin-like receptor for ubiquitin, termed Pru, domain []. The domain forms two contiguous anti-parallel beta-sheets with a configuration similar to the pleckstrin-homology domain (PHD) fold []. Rpn13's ability to bind ubiquitin and the proteasome subunit Rpn2/S1 simultaneously supports evidence of its role as a ubiquitin receptor. Finally, when complexed to di-ubiquitin, via the Pru, and Uch37 via the C-terminal part, it frees up the distal ubiquitin for de-ubiquitination by the Uch37 []. ; GO: 0005634 nucleus, 0005737 cytoplasm; PDB: 2Z4D_A 2KR0_A 2Z59_A 2R2Y_A.
Probab=99.83 E-value=2.4e-20 Score=118.41 Aligned_cols=47 Identities=51% Similarity=1.036 Sum_probs=40.6
Q ss_pred eeeEEcCCEEEecCCccEEEEEeCCCCeEEEEEeeCCC-CCeeeeEEE
Q psy11405 26 GKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQS-GSVVEVVWW 72 (76)
Q Consensus 26 GK~~~~g~~V~Pd~rKG~i~l~~~~D~l~hf~W~~R~t-~~vED~~~~ 72 (76)
|||+++|++|+||+|||+|+|++++|+|+||||++|++ +.+|||+|.
T Consensus 1 Gk~~~~~~~V~pd~~KG~l~l~~~~d~l~~f~W~~r~~~~~~e~d~il 48 (85)
T PF04683_consen 1 GKMDLDGKIVTPDPRKGLLYLYKSEDGLLHFCWKPRDTTGEVEDDLIL 48 (85)
T ss_dssp EEEEEETTEEEE-SS-EEEEEEETTTS-EEEEEEETST---EEEEEEE
T ss_pred CcEEEeCCEEeECCCCEEEEEEECCCCeEEEEEEEcCcCCCcccceec
Confidence 99999999999999999999999999999999999999 999999886
No 3
>PF14008 Metallophos_C: Iron/zinc purple acid phosphatase-like protein C; PDB: 3KBP_B 1KBP_B 4KBP_C 2QFP_B 2QFR_A 1XZW_B.
Probab=76.73 E-value=7.6 Score=22.46 Aligned_cols=36 Identities=17% Similarity=0.307 Sum_probs=23.4
Q ss_pred EEecCCccEEEEEeCCCCeEEEEEeeCCCCCeeeeE
Q psy11405 35 VHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEVV 70 (76)
Q Consensus 35 V~Pd~rKG~i~l~~~~D~l~hf~W~~R~t~~vED~~ 70 (76)
..-+..-|+.+|.-.....++++|..-+++.|-|+|
T Consensus 27 a~r~~~~Gy~~l~v~N~T~l~~e~i~~~~g~v~D~f 62 (62)
T PF14008_consen 27 AFRDSEYGYGRLTVANATHLHWEFIRSDDGSVLDEF 62 (62)
T ss_dssp EEEE---EEEEEEE-SSSEEEEEEEETTS-T-CEE-
T ss_pred eeeccccCEEEEEEEcCCeEEEEEEECCCCcEecCC
Confidence 334567899998655678999999998889998875
No 4
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=51.16 E-value=7.4 Score=24.82 Aligned_cols=25 Identities=32% Similarity=0.684 Sum_probs=14.2
Q ss_pred eceeeEE--cCCEEEecCCccEEEEEe
Q psy11405 24 KAGKMTM--KGKMVHPDKRKGLVYVHQ 48 (76)
Q Consensus 24 kAGK~~~--~g~~V~Pd~rKG~i~l~~ 48 (76)
++|++.+ .|+-|.|+.-||-|+|..
T Consensus 55 ~~G~i~I~qkG~~Vdp~~~rGpiRirl 81 (83)
T PF11625_consen 55 RAGRIEITQKGKPVDPETFRGPIRIRL 81 (83)
T ss_dssp HTTSEEEEETTEE--TTT--S--EEEE
T ss_pred HCCcEEEEECCEecCcccCcCCeEeec
Confidence 4677764 588899999999999854
No 5
>PF02870 Methyltransf_1N: 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; InterPro: IPR008332 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources []. This group of proteins are characterised by having an N-terminal ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity (IPR001497 from INTERPRO).; GO: 0003908 methylated-DNA-[protein]-cysteine S-methyltransferase activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A.
Probab=47.26 E-value=32 Score=20.05 Aligned_cols=22 Identities=18% Similarity=0.335 Sum_probs=17.3
Q ss_pred ccEEEEEeCCCCeEEEEEeeCC
Q psy11405 41 KGLVYVHQSDDSLMHFCWKDRQ 62 (76)
Q Consensus 41 KG~i~l~~~~D~l~hf~W~~R~ 62 (76)
=|.|.|.-++.||.++.|.+..
T Consensus 11 lG~l~l~a~e~gL~~i~f~~~~ 32 (77)
T PF02870_consen 11 LGPLLLAASEKGLCGIDFEDQD 32 (77)
T ss_dssp TEEEEEEEETTCEEEEEEEC-H
T ss_pred CeEEEEEEECCeEEEEEECCCc
Confidence 4888888889999999996543
No 6
>PF12101 DUF3577: Protein of unknown function (DUF3577); InterPro: IPR021960 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length.
Probab=43.89 E-value=39 Score=23.40 Aligned_cols=48 Identities=17% Similarity=0.253 Sum_probs=38.8
Q ss_pred CCCcceeEEEeceeeEEcCCEEEecCCccEEEEEeCCCCeEEEEEeeCC
Q psy11405 14 RSQSKNLVEFKAGKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQ 62 (76)
Q Consensus 14 ~~~~~~lieFkAGK~~~~g~~V~Pd~rKG~i~l~~~~D~l~hf~W~~R~ 62 (76)
...++.||.|+.|-+..+.-+.+--.++|.--+.. .--|+++.|...+
T Consensus 75 ~~~~KVli~FrlgDl~~d~f~~~~G~~~Ge~g~sL-KgRLl~i~~iKVd 122 (137)
T PF12101_consen 75 DEDKKVLIGFRLGDLWADTFTYKKGERAGEPGASL-KGRLLKIKWIKVD 122 (137)
T ss_pred ccCCcEEEEEEecCCceeeEEeccCCcCCccceee-EEEEEEEEEEEEC
Confidence 46789999999999999988888888999876655 3468999996544
No 7
>PF14795 Leucyl-specific: Leucine-tRNA synthetase-specific domain; PDB: 1OBC_A 2BTE_A 2V0G_A 2BYT_A 1OBH_A 1H3N_A 2V0C_A.
Probab=39.08 E-value=35 Score=20.38 Aligned_cols=14 Identities=36% Similarity=0.976 Sum_probs=9.3
Q ss_pred EEeCCCCeEEEEEee
Q psy11405 46 VHQSDDSLMHFCWKD 60 (76)
Q Consensus 46 l~~~~D~l~hf~W~~ 60 (76)
+..-+||-+|| ||+
T Consensus 43 LR~hedG~~h~-WKP 56 (56)
T PF14795_consen 43 LRPHEDGTLHF-WKP 56 (56)
T ss_dssp EEE-TTSSEEE-EEE
T ss_pred cccCCCCeEee-cCC
Confidence 44448999987 664
No 8
>PF05720 Dicty_CAD: Cell-cell adhesion domain; InterPro: IPR008601 This family is based on a group of Dictyostelium discoideum (Slime mould) proteins that are essential in early development []. P16642 from SWISSPROT and P16643 from SWISSPROT are located on the cell surface and mediate cell-cell adhesion.; GO: 0007155 cell adhesion
Probab=36.20 E-value=52 Score=21.05 Aligned_cols=31 Identities=19% Similarity=0.252 Sum_probs=24.0
Q ss_pred cceeEEEeceeeEEcCCEE-EecCCccEEEEE
Q psy11405 17 SKNLVEFKAGKMTMKGKMV-HPDKRKGLVYVH 47 (76)
Q Consensus 17 ~~~lieFkAGK~~~~g~~V-~Pd~rKG~i~l~ 47 (76)
+..=++++-||++++|+.+ -|..+.+.....
T Consensus 42 ~~~~F~v~S~kiE~~Gq~ydiPss~~~~~~~~ 73 (82)
T PF05720_consen 42 NNNEFKVNSGKIERNGQEYDIPSSRGSSWRDD 73 (82)
T ss_pred cccceEeeeeeEEECCEEeeCCcccCceeecc
Confidence 3445789999999999987 588887776654
No 9
>cd00839 MPP_PAPs purple acid phosphatases of the metallophosphatase superfamily, metallophosphatase domain. Purple acid phosphatases (PAPs) belong to a diverse family of binuclear metallohydrolases that have been identified and characterized in plants, animals, and fungi. PAPs contain a binuclear metal center and their characteristic pink or purple color derives from a charge-transfer transition between a tyrosine residue and a chromophoric ferric ion within the binuclear center. PAPs catalyze the hydrolysis of a wide range of activated phosphoric acid mono- and di-esters and anhydrides. PAPs are distinguished from the other phosphatases by their insensitivity to L-(+) tartrate inhibition and are therefore also known as tartrate resistant acid phosphatases (TRAPs). While only a few copies of PAP-like genes are present in mammalian and fungal genomes, multiple copies are present in plant genomes. PAPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diver
Probab=35.00 E-value=1.4e+02 Score=21.03 Aligned_cols=39 Identities=18% Similarity=0.482 Sum_probs=30.4
Q ss_pred EEEecCCccEEEEEeCCCCeEEEEEeeCCCCCeeeeEEE
Q psy11405 34 MVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEVVWW 72 (76)
Q Consensus 34 ~V~Pd~rKG~i~l~~~~D~l~hf~W~~R~t~~vED~~~~ 72 (76)
++..+..-|.+.|.-..+..+.|+|.+-.++++-|.|..
T Consensus 254 ~~~~~~~~g~~~~~~~~~t~l~~~~~~~~~g~v~D~f~i 292 (294)
T cd00839 254 SAFRESDYGFGRLTVHNSTHLHFEWIRNDDGVVIDSFWI 292 (294)
T ss_pred eEEEeccCCEEEEEEEecCeEEEEEEECCCCeEEEEEEE
Confidence 355677889999886555588899998888899888753
No 10
>PF01479 S4: S4 domain; InterPro: IPR002942 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterised, small proteins that may be involved in translation regulation []. The S4 domain probably mediates binding to RNA.; GO: 0003723 RNA binding; PDB: 3BBU_A 1DM9_B 2K6P_A 3U5G_E 3U5C_E 3IZB_D 2XZM_D 2XZN_D 3O30_E 3O2Z_E ....
Probab=34.31 E-value=13 Score=19.82 Aligned_cols=16 Identities=38% Similarity=0.852 Sum_probs=13.3
Q ss_pred EeceeeEEcCCEEE-ec
Q psy11405 23 FKAGKMTMKGKMVH-PD 38 (76)
Q Consensus 23 FkAGK~~~~g~~V~-Pd 38 (76)
+++|++.++|+.|+ |.
T Consensus 23 I~~g~V~VNg~~v~~~~ 39 (48)
T PF01479_consen 23 IKQGRVKVNGKVVKDPS 39 (48)
T ss_dssp HHTTTEEETTEEESSTT
T ss_pred cCCCEEEECCEEEcCCC
Confidence 57899999999887 54
No 11
>TIGR02588 conserved hypothetical protein TIGR02588. The function of this protein is unknown. It is always found as part of a two-gene operon with TIGR02587, a protein that appears to span the membrane seven times. It is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus, so far, all of which are bacterial.
Probab=32.12 E-value=48 Score=22.56 Aligned_cols=33 Identities=15% Similarity=0.341 Sum_probs=25.1
Q ss_pred CcceeEEEeceeeEEcCCE-EEecCCccEEEEEe
Q psy11405 16 QSKNLVEFKAGKMTMKGKM-VHPDKRKGLVYVHQ 48 (76)
Q Consensus 16 ~~~~lieFkAGK~~~~g~~-V~Pd~rKG~i~l~~ 48 (76)
....-|.|-+|+-..+|.- .+.||++|.|.|.-
T Consensus 83 ~~e~tiDfl~g~e~~~G~~IF~~dP~~g~L~irv 116 (122)
T TIGR02588 83 NAEVTIDYLASGSKENGTLIFRSDPRNGQLRLRV 116 (122)
T ss_pred EeeEEEEEcCCCCeEeEEEEEccCcccCeEEEEE
Confidence 4455677888888887775 59999999887754
No 12
>PF12043 DUF3527: Domain of unknown function (DUF3527); InterPro: IPR021916 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain has a conserved CDCGGWD sequence motif.
Probab=30.53 E-value=1.1e+02 Score=24.18 Aligned_cols=35 Identities=23% Similarity=0.376 Sum_probs=25.7
Q ss_pred ecCCccEEEEEeCCCCeEEEEEeeCCCCCeeeeEEEeecC
Q psy11405 37 PDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEVVWWSTLW 76 (76)
Q Consensus 37 Pd~rKG~i~l~~~~D~l~hf~W~~R~t~~vED~~~~~~~~ 76 (76)
|....|+|++.. .+|+.||...--+. .++|-|++|
T Consensus 2 ~s~~qalLq~t~-KNG~P~F~Fsvd~~----~~VlaAt~~ 36 (346)
T PF12043_consen 2 PSHLQALLQCTW-KNGLPLFEFSVDNP----EEVLAATMW 36 (346)
T ss_pred CcceeEEEEEEE-eCCeEEEEEEeCCc----ccEEEEEEe
Confidence 566788998876 58999998854332 277888876
No 13
>PF09870 DUF2097: Uncharacterized protein conserved in archaea (DUF2097); InterPro: IPR019208 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=29.52 E-value=1.6e+02 Score=18.88 Aligned_cols=32 Identities=13% Similarity=0.438 Sum_probs=25.0
Q ss_pred ceeEEEeceeeEEcCCEEEecCCccEEEEEeCCC
Q psy11405 18 KNLVEFKAGKMTMKGKMVHPDKRKGLVYVHQSDD 51 (76)
Q Consensus 18 ~~lieFkAGK~~~~g~~V~Pd~rKG~i~l~~~~D 51 (76)
.-.++.--|||...|+.+.-+. |.+.+....+
T Consensus 22 ~D~lEisygRv~vpG~V~~~~~--~~~~l~~~~~ 53 (86)
T PF09870_consen 22 GDYLEISYGRVHVPGEVLSIED--GFLRLQLDGE 53 (86)
T ss_pred CCEEEEEeeEEEeeeEEEEeee--eEEEEEEcCc
Confidence 3468888999999999877766 7777776555
No 14
>cd00712 AsnB Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a synthetase domain. The N-terminal glutaminase domain hydrolyzes glutamine to glutamic acid and ammonia.
Probab=29.24 E-value=1.4e+02 Score=20.66 Aligned_cols=35 Identities=11% Similarity=0.121 Sum_probs=26.1
Q ss_pred EEecCCccEEEEEeCCCCeEEEEEeeCCCCCeeeeEEEee
Q psy11405 35 VHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEVVWWST 74 (76)
Q Consensus 35 V~Pd~rKG~i~l~~~~D~l~hf~W~~R~t~~vED~~~~~~ 74 (76)
|-=|++++.+++..+.-|..-+.|... ++.++|||
T Consensus 124 vi~d~~~~~l~~~rD~~G~~pLy~~~~-----~~~~~~aS 158 (220)
T cd00712 124 ALWDKRKRRLFLARDRFGIKPLYYGRD-----GGGLAFAS 158 (220)
T ss_pred EEEECCCCEEEEEECCCCCEeeEEEEE-----CCEEEEEc
Confidence 555788899999997778877777432 25688876
No 15
>PF03439 Spt5-NGN: Early transcription elongation factor of RNA pol II, NGN section; InterPro: IPR005100 Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4 []. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit []. ; PDB: 3H7H_B 3QQC_D 3P8B_B 2EXU_A.
Probab=28.81 E-value=54 Score=20.02 Aligned_cols=16 Identities=38% Similarity=0.760 Sum_probs=12.5
Q ss_pred EEEecCCccEEEEEeC
Q psy11405 34 MVHPDKRKGLVYVHQS 49 (76)
Q Consensus 34 ~V~Pd~rKG~i~l~~~ 49 (76)
.+.|+.-||+||+.-.
T Consensus 37 i~~~~~lkGyIyVEA~ 52 (84)
T PF03439_consen 37 IFAPDSLKGYIYVEAE 52 (84)
T ss_dssp EEE-TTSTSEEEEEES
T ss_pred EEEeCCCceEEEEEeC
Confidence 3789999999999753
No 16
>KOG4446|consensus
Probab=27.91 E-value=35 Score=27.80 Aligned_cols=16 Identities=31% Similarity=0.627 Sum_probs=14.3
Q ss_pred EEEecCCccEEEEEeC
Q psy11405 34 MVHPDKRKGLVYVHQS 49 (76)
Q Consensus 34 ~V~Pd~rKG~i~l~~~ 49 (76)
.+.|++.||+|||+.+
T Consensus 122 ~~r~~~~~g~lyV~pd 137 (471)
T KOG4446|consen 122 ASRPTIKKGYLYVFPD 137 (471)
T ss_pred cccCCcccceEEEecC
Confidence 4899999999999985
No 17
>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]
Probab=26.81 E-value=22 Score=29.71 Aligned_cols=21 Identities=33% Similarity=0.680 Sum_probs=16.6
Q ss_pred eceeeEEcCCEEEecCCccEEEEEeC
Q psy11405 24 KAGKMTMKGKMVHPDKRKGLVYVHQS 49 (76)
Q Consensus 24 kAGK~~~~g~~V~Pd~rKG~i~l~~~ 49 (76)
|||||.+.|+. .+|.++++..
T Consensus 528 R~GRv~R~g~~-----~~~~~~v~~~ 548 (733)
T COG1203 528 RAGRVNRHGKK-----ENGKIYVYND 548 (733)
T ss_pred HHHHHhhcccc-----cCCceeEeec
Confidence 89999999966 6777777664
No 18
>PF11773 PulG: Type II secretory pathway pseudopilin ; InterPro: IPR021749 The secreton (type II secretion) and type IV pilus biogenesis branches of the general secretory pathway in Gram-negative bacteria share many features that suggest a common evolutionary origin. Five components of the secreton, the pseudopilins, are similar to subunits of type IV pili. Pseudopilin PulG is one of the secreton pseudopilins, and is found to assemble into pilus-like bundles []. PulG interacts with proteins H, I and J within the multi-protein complex as well as blocking extracellular secretion and reducing the amount of PulE protein as well as the amounts of PulL, PulM, PulC and PulD when G is over-expressed []. In Klebsiella the pilus-like structure is composed largely of PulG [].
Probab=26.25 E-value=90 Score=19.89 Aligned_cols=29 Identities=14% Similarity=0.381 Sum_probs=23.4
Q ss_pred eEEcCCEEEecCCccEEEEEeCCCCeEEE
Q psy11405 28 MTMKGKMVHPDKRKGLVYVHQSDDSLMHF 56 (76)
Q Consensus 28 ~~~~g~~V~Pd~rKG~i~l~~~~D~l~hf 56 (76)
+.++|-.|+=...++.|++|.++..++|+
T Consensus 54 L~lNGv~V~v~~~~~~i~V~~~~keil~v 82 (82)
T PF11773_consen 54 LSLNGVEVQVERTQKGIIVYEGGKEILHV 82 (82)
T ss_pred EEEcCeEEEEEEcCCeEEEEeCCEEEeeC
Confidence 45788889999999999999876667763
No 19
>PF12068 DUF3548: Domain of unknown function (DUF3548); InterPro: IPR021935 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes and is typically between 184 to 216 amino acids in length. The domain is found associated with PF00566 from PFAM and at the N terminus of GYP7 proteins.
Probab=25.34 E-value=96 Score=22.63 Aligned_cols=24 Identities=17% Similarity=0.386 Sum_probs=18.1
Q ss_pred CccEEEEEeCCCCeEEEEEeeCCCC
Q psy11405 40 RKGLVYVHQSDDSLMHFCWKDRQSG 64 (76)
Q Consensus 40 rKG~i~l~~~~D~l~hf~W~~R~t~ 64 (76)
-.|.|.|.+ .++-+-++|+|.+..
T Consensus 29 IpGfL~Ive-k~~~~~l~w~P~e~~ 52 (213)
T PF12068_consen 29 IPGFLRIVE-KDSEVLLEWSPSEDS 52 (213)
T ss_pred CCeEEEEEE-eCCCcccccCCcccc
Confidence 349999996 456666999988763
No 20
>PF07867 DUF1654: Protein of unknown function (DUF1654); InterPro: IPR012449 This entry is represented by Bacteriophage F116 (Pseudomonas phage F116), Orf28. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of proteins from the Pseudomonadaceae.
Probab=25.03 E-value=1e+02 Score=19.16 Aligned_cols=18 Identities=28% Similarity=0.464 Sum_probs=13.7
Q ss_pred EEEEeCCCCeEEEEEeeC
Q psy11405 44 VYVHQSDDSLMHFCWKDR 61 (76)
Q Consensus 44 i~l~~~~D~l~hf~W~~R 61 (76)
|.|...+||-++++|..-
T Consensus 53 v~v~~~dDGsv~i~W~~~ 70 (73)
T PF07867_consen 53 VEVTFNDDGSVRIRWERP 70 (73)
T ss_pred eEEEEcCCCeEEEEEEcc
Confidence 356566899999999653
No 21
>COG3848 Phosphohistidine swiveling domain [Signal transduction mechanisms]
Probab=24.77 E-value=46 Score=22.43 Aligned_cols=23 Identities=35% Similarity=0.626 Sum_probs=18.2
Q ss_pred eceeeEEcCCEEEecCCccEEEE
Q psy11405 24 KAGKMTMKGKMVHPDKRKGLVYV 46 (76)
Q Consensus 24 kAGK~~~~g~~V~Pd~rKG~i~l 46 (76)
+|=+...+|..|+=|.++|.||=
T Consensus 83 ~at~~i~dG~~vTvD~~rG~VY~ 105 (111)
T COG3848 83 KATQLIRDGAIVTVDAQRGVVYE 105 (111)
T ss_pred chhhhccCCCEEEEecccceEEe
Confidence 44555667889999999999884
No 22
>PRK00807 50S ribosomal protein L24e; Validated
Probab=23.66 E-value=1.4e+02 Score=17.00 Aligned_cols=28 Identities=32% Similarity=0.788 Sum_probs=17.4
Q ss_pred eeEEcCCEEEecCCccEEEEEeCCCCeEEEE
Q psy11405 27 KMTMKGKMVHPDKRKGLVYVHQSDDSLMHFC 57 (76)
Q Consensus 27 K~~~~g~~V~Pd~rKG~i~l~~~~D~l~hf~ 57 (76)
+|.+-|..|.|.. |..++.. |--.+.||
T Consensus 3 ~C~fcG~~I~pg~--G~~~vr~-Dgkv~~Fc 30 (52)
T PRK00807 3 TCSFCGKEIEPGT--GKMYVKK-DGTILYFC 30 (52)
T ss_pred ccCCCCCeEcCCC--CeEEEEe-CCcEEEEe
Confidence 3556677887765 7777754 23355666
No 23
>cd01910 Wali7 This domain is present in Wali7, a protein of unknown function, expressed in wheat and induced by aluminum. Wali7 has a single domain similar to the glutamine amidotransferase domain of glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). The Wali7 domain is also somewhat similar to the Ntn hydrolase fold of the proteasomal alph and beta subunits.
Probab=23.30 E-value=2e+02 Score=21.22 Aligned_cols=37 Identities=24% Similarity=0.332 Sum_probs=28.9
Q ss_pred EEEecCCccEEEEEeCCCCeEEEEEeeCCCCCeeeeEEEee
Q psy11405 34 MVHPDKRKGLVYVHQSDDSLMHFCWKDRQSGSVVEVVWWST 74 (76)
Q Consensus 34 ~V~Pd~rKG~i~l~~~~D~l~hf~W~~R~t~~vED~~~~~~ 74 (76)
.|-=|++++.+++-++..|..-+.|.-.. ++.++|||
T Consensus 131 Fvi~D~~~~~l~lARD~~Gi~PLYyg~~~----dG~l~FAS 167 (224)
T cd01910 131 FVLYDKKTSTVFVASDADGSVPLYWGIAA----DGSVVFSD 167 (224)
T ss_pred EEEEECCCCEEEEEEcCCCCcceEEEEeC----CCEEEEEe
Confidence 37779999999999988999999995322 34677775
No 24
>PF10357 Kin17_mid: Domain of Kin17 curved DNA-binding protein; InterPro: IPR019447 This entry represents the conserved central 169 residue region of the Kin17 DNA/RNA-binding proteins. The N-terminal region of Kin17 contains a zinc-finger domain, while in the human and mouse proteins there is a RecA-like domain found in the C-terminal region. In humans, Kin17 protein forms intra-nuclear foci during cell proliferation and is re-distributed in the nucleoplasm during the cell cycle []. ; PDB: 2V1N_A.
Probab=22.44 E-value=83 Score=21.44 Aligned_cols=28 Identities=21% Similarity=0.343 Sum_probs=19.4
Q ss_pred EEecCCccEEEEEeCCCCeEEEEEeeCCC
Q psy11405 35 VHPDKRKGLVYVHQSDDSLMHFCWKDRQS 63 (76)
Q Consensus 35 V~Pd~rKG~i~l~~~~D~l~hf~W~~R~t 63 (76)
|+=..+.|++.+...+.|+. +.|.||+.
T Consensus 68 vkyLgr~G~~~Vdetekg~~-I~yID~~p 95 (127)
T PF10357_consen 68 VKYLGREGKCKVDETEKGWF-ISYIDRSP 95 (127)
T ss_dssp HHHHTTTTSEEEEEETTEEE-EEE--SSH
T ss_pred HHHHhhCCeeEeecCCCceE-EEeeCCCH
Confidence 44456789999988777765 99999864
No 25
>PF11605 Vps36_ESCRT-II: Vacuolar protein sorting protein 36 Vps36; InterPro: IPR021648 Vps36 is a subunit of ESCRT-II, a protein involved in driving protein sorting from endosomes to lysosomes. The GLUE domain of Vps36 allows for a tight interaction to occur between the protein and Vps28, a subunit of ESCRT-I. This interaction is critical for ubiquitinated cargo progression from early to late endosomes []. ; PDB: 2HTH_B 2DX5_A 2CAY_B.
Probab=22.22 E-value=2.1e+02 Score=17.90 Aligned_cols=43 Identities=19% Similarity=0.399 Sum_probs=32.4
Q ss_pred CcceeEEEeceeeEEcCCEEEecCCccEEEEEeCCCCeEEEEEeeCCC
Q psy11405 16 QSKNLVEFKAGKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFCWKDRQS 63 (76)
Q Consensus 16 ~~~~lieFkAGK~~~~g~~V~Pd~rKG~i~l~~~~D~l~hf~W~~R~t 63 (76)
.++.++...-|-..++|+.=+|+-..|.++|.. =+++|.+...
T Consensus 12 ~~E~~~~~q~~V~LYdG~~K~~~~q~G~l~LTs-----HRliw~d~~~ 54 (89)
T PF11605_consen 12 PNETIVYQQDGVGLYDGDQKTPNFQNGRLYLTS-----HRLIWVDDSD 54 (89)
T ss_dssp TT--EEEEEEEEEEEETTECSTT-SCEEEEEES-----SEEEEEESSG
T ss_pred CCceEEEEecCeeeEcCCccCccccCCEEEEEe-----eEEEEEcCCC
Confidence 356678888888899999888899999999974 4789976654
No 26
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=21.97 E-value=1.8e+02 Score=16.91 Aligned_cols=30 Identities=30% Similarity=0.675 Sum_probs=20.7
Q ss_pred ceeeEEcCCEEEecCCccEEEEEeCCCCeEEEE
Q psy11405 25 AGKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFC 57 (76)
Q Consensus 25 AGK~~~~g~~V~Pd~rKG~i~l~~~~D~l~hf~ 57 (76)
...|.+-|..+.|-. |..|+.. |--.++||
T Consensus 3 ~~~C~f~g~~I~PG~--G~~~Vr~-Dgkv~~F~ 32 (54)
T cd00472 3 TEKCSFCGYKIYPGH--GKMYVRN-DGKVFRFC 32 (54)
T ss_pred EEEecCcCCeecCCC--ccEEEec-CCCEEEEE
Confidence 456777788888765 8888865 33456776
No 27
>PF14713 DUF4464: Domain of unknown function (DUF4464)
Probab=21.59 E-value=1.7e+02 Score=21.83 Aligned_cols=36 Identities=17% Similarity=0.391 Sum_probs=26.5
Q ss_pred EEeceeeEEcC---CEEEecCCccEEEEEeCCCCeEEEE
Q psy11405 22 EFKAGKMTMKG---KMVHPDKRKGLVYVHQSDDSLMHFC 57 (76)
Q Consensus 22 eFkAGK~~~~g---~~V~Pd~rKG~i~l~~~~D~l~hf~ 57 (76)
--+-|++..+. -.|.+|+..|+|+.++.|--.+.+.
T Consensus 161 nW~t~~~~~N~S~NfqVi~d~~~GLlFkhk~D~K~I~Vd 199 (233)
T PF14713_consen 161 NWHTNTVCSNDSDNFQVIADNEHGLLFKHKGDRKIINVD 199 (233)
T ss_pred ecCCCeEEecCCCCeEEecCCCceEEEEECCCCCEEeeC
Confidence 34567777764 4799999999999998655555543
No 28
>COG4334 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.52 E-value=59 Score=22.31 Aligned_cols=23 Identities=30% Similarity=0.449 Sum_probs=18.1
Q ss_pred EEeceeeEEcCCE--EEecCCccEE
Q psy11405 22 EFKAGKMTMKGKM--VHPDKRKGLV 44 (76)
Q Consensus 22 eFkAGK~~~~g~~--V~Pd~rKG~i 44 (76)
.=|||+++.+|++ |+-.|.-|.|
T Consensus 66 ~qraGrItaaG~t~~V~FEPVtgai 90 (131)
T COG4334 66 IQRAGRITAAGKTYQVEFEPVTGAI 90 (131)
T ss_pred HhhCCeEEecceEEEEEEeecccch
Confidence 3489999999976 8888888754
No 29
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=20.84 E-value=1.1e+02 Score=21.14 Aligned_cols=29 Identities=24% Similarity=0.651 Sum_probs=20.6
Q ss_pred eeeEEcCCEEEecCCccEEEEEeCCCCeEEEE
Q psy11405 26 GKMTMKGKMVHPDKRKGLVYVHQSDDSLMHFC 57 (76)
Q Consensus 26 GK~~~~g~~V~Pd~rKG~i~l~~~~D~l~hf~ 57 (76)
-+|.+-|..|-|-. |..||.. +-..++||
T Consensus 5 e~CsFcG~kIyPG~--G~~fVR~-DGkvf~Fc 33 (131)
T PRK14891 5 RTCDYTGEEIEPGT--GTMFVRK-DGTVLHFV 33 (131)
T ss_pred eeecCcCCcccCCC--CcEEEec-CCCEEEEe
Confidence 36777788888765 8888865 33466777
No 30
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=20.59 E-value=1.1e+02 Score=16.90 Aligned_cols=21 Identities=14% Similarity=0.294 Sum_probs=15.8
Q ss_pred cEEEEEeCCCCeEEEEEeeCC
Q psy11405 42 GLVYVHQSDDSLMHFCWKDRQ 62 (76)
Q Consensus 42 G~i~l~~~~D~l~hf~W~~R~ 62 (76)
+.||=+.+++|-+||.=.+-.
T Consensus 13 a~vYk~~D~~G~v~ysd~P~~ 33 (60)
T PF13511_consen 13 AEVYKWVDENGVVHYSDTPPP 33 (60)
T ss_pred ccEEEEECCCCCEEECccCCC
Confidence 578888888999998655443
No 31
>PF10115 HlyU: Transcriptional activator HlyU; InterPro: IPR018772 This is a family of hypothetical prokaryotic proteins, with no known function. One of the proteins in this entry corresponds to the transcriptional activator HlyU, indicating a possible similar role in other members.
Probab=20.51 E-value=90 Score=20.22 Aligned_cols=17 Identities=24% Similarity=0.405 Sum_probs=10.8
Q ss_pred ceeeEEcCCEEEecCCc
Q psy11405 25 AGKMTMKGKMVHPDKRK 41 (76)
Q Consensus 25 AGK~~~~g~~V~Pd~rK 41 (76)
+--..++|..+.|.|.+
T Consensus 19 ~ep~eYkgf~I~~~P~~ 35 (91)
T PF10115_consen 19 AEPVEYKGFLIYPEPMS 35 (91)
T ss_pred cCCeEeCCEEEEeCccc
Confidence 33446778887766654
Done!