Query psy1401
Match_columns 79
No_of_seqs 105 out of 198
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 17:14:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1401.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1401hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00198 60S ribosomal protein 100.0 2.2E-50 4.7E-55 278.7 8.6 78 2-79 38-115 (122)
2 PF01776 Ribosomal_L22e: Ribos 100.0 2.8E-49 6E-54 269.6 8.1 78 2-79 25-102 (112)
3 KOG3434|consensus 100.0 1.2E-44 2.6E-49 251.0 5.2 78 2-79 37-114 (125)
4 PF12970 DUF3858: Domain of Un 58.2 6.7 0.00015 27.3 1.5 32 11-44 58-89 (116)
5 PF02747 PCNA_C: Proliferating 55.7 57 0.0012 21.5 7.7 56 17-76 25-112 (128)
6 PF13543 KSR1-SAM: SAM like do 45.1 4.1 8.9E-05 28.5 -1.2 15 57-71 67-81 (129)
7 KOG2638|consensus 36.7 34 0.00074 29.0 2.7 40 11-53 107-149 (498)
8 PF08845 SymE_toxin: Toxin Sym 36.0 55 0.0012 19.7 2.9 18 20-37 40-57 (57)
9 smart00647 IBR In Between Ring 31.2 47 0.001 18.5 2.0 15 43-57 1-15 (64)
10 cd02414 jag_KH jag_K homology 30.7 1.3E+02 0.0028 18.2 5.9 50 22-73 15-74 (77)
11 PHA03383 PCNA-like protein; Pr 30.0 2.3E+02 0.005 21.4 6.0 27 40-70 212-238 (262)
12 PRK10598 lipoprotein; Provisio 29.5 33 0.00071 25.3 1.4 38 2-39 31-79 (186)
13 PHA02800 hypothetical protein; 28.7 20 0.00043 26.3 0.1 10 37-46 4-13 (161)
14 PF05481 Myco_19_kDa: Mycobact 28.4 71 0.0015 23.0 2.9 31 10-40 52-82 (160)
15 PF00838 TCTP: Translationally 28.0 42 0.0009 24.1 1.7 17 39-56 77-94 (165)
16 PHA02781 hypothetical protein; 26.9 66 0.0014 20.8 2.3 26 10-38 9-34 (78)
17 PF14651 Lipocalin_7: Lipocali 26.8 1.1E+02 0.0024 21.0 3.6 39 2-41 14-56 (128)
18 COG1088 RfbB dTDP-D-glucose 4, 26.8 29 0.00063 28.1 0.8 10 56-65 212-221 (340)
19 PF07901 DUF1672: Protein of u 25.7 55 0.0012 25.7 2.1 41 4-44 43-88 (277)
20 PF01485 IBR: IBR domain; Int 24.3 11 0.00024 21.1 -1.5 16 43-58 1-16 (64)
21 KOG4015|consensus 24.1 1.1E+02 0.0025 21.5 3.3 39 2-41 16-58 (133)
22 PF09386 ParD: Antitoxin ParD; 23.7 33 0.00072 22.5 0.5 19 2-21 48-66 (79)
23 KOG2775|consensus 23.6 48 0.001 27.2 1.4 25 37-61 330-356 (397)
24 PF04972 BON: BON domain; Int 22.7 1.6E+02 0.0034 16.5 3.3 43 8-52 5-49 (64)
25 PF03526 Microcin: Colicin E1 22.7 62 0.0013 20.0 1.5 18 39-56 20-37 (55)
26 PF08490 DUF1744: Domain of un 21.4 2.7E+02 0.0058 22.4 5.3 47 19-67 329-378 (396)
27 PF03776 MinE: Septum formatio 20.3 1.3E+02 0.0028 18.4 2.6 21 23-43 50-70 (70)
No 1
>PTZ00198 60S ribosomal protein L22; Provisional
Probab=100.00 E-value=2.2e-50 Score=278.74 Aligned_cols=78 Identities=60% Similarity=1.005 Sum_probs=77.3
Q ss_pred chHHHhhhhhccCCccCCCCCcEEEEEeCCEEEEEeccccchHHHHHHHHHHhhhccccceeEEEeecCceEEEeecC
Q psy1401 2 DMEKYLLERIKVGGKTSNFGNAVSLERQKTKVILTADVAFSKRYLKYLTKKYLKKNNLRDWLRVVANKKDSYELRYFQ 79 (79)
Q Consensus 2 ~fE~fL~erIKV~gk~gnlg~~V~v~r~k~ki~v~s~~~fsKrYlKYLtKKyLkk~~LrdwlrVva~~K~~YeLrYfn 79 (79)
+||+|||||||||||+||||+.|+|++++++|+|+|++|||||||||||||||||++|||||||||++|++|||||||
T Consensus 38 ~fekfL~erIKV~GK~gnLg~~V~v~~~k~ki~V~s~~~FSKRYLKYLTKKyLKK~~LRDwlRVVA~~K~~YELRYfn 115 (122)
T PTZ00198 38 GFEQFLQDRIKVDGKTGNLGNKVRVSREKNKITVTTTIPFSKRYLKYLTKKYLKKKQLRDFLRVVATGKGTYELKYFN 115 (122)
T ss_pred HHHHHHHHhEEECCCcCccCCcEEEEEECCEEEEEecccccHHHHHHHHHHHHhhhhhhheEEEEecCCCeEEEEEEE
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999999997
No 2
>PF01776 Ribosomal_L22e: Ribosomal L22e protein family; InterPro: IPR002671 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 [, ]. Ribosomal protein L22e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. Rattus norvegicus (Rat) L22 is related to ribosomal proteins from other eukaryotes and is identical in amino acid sequence to human EAP, the EBER 1 (Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4) encoded RNA) associated protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1D_M 4A1B_M 4A19_M 4A18_M 3IZR_W 3IZS_W.
Probab=100.00 E-value=2.8e-49 Score=269.63 Aligned_cols=78 Identities=72% Similarity=1.166 Sum_probs=73.5
Q ss_pred chHHHhhhhhccCCccCCCCCcEEEEEeCCEEEEEeccccchHHHHHHHHHHhhhccccceeEEEeecCceEEEeecC
Q psy1401 2 DMEKYLLERIKVGGKTSNFGNAVSLERQKTKVILTADVAFSKRYLKYLTKKYLKKNNLRDWLRVVANKKDSYELRYFQ 79 (79)
Q Consensus 2 ~fE~fL~erIKV~gk~gnlg~~V~v~r~k~ki~v~s~~~fsKrYlKYLtKKyLkk~~LrdwlrVva~~K~~YeLrYfn 79 (79)
+||+||||||||||++||||+.|+|++++++|+|+|++|||||||||||||||||++|||||||||++|++|||||||
T Consensus 25 ~fe~fL~erIKV~gk~gnlg~~V~i~~~~~ki~V~s~v~fsKrYLKYLTKKyLKK~~LRdwlrVva~~K~~YeLrYfn 102 (112)
T PF01776_consen 25 DFEKFLQERIKVNGKTGNLGNKVTISRDKNKITVTSEVPFSKRYLKYLTKKYLKKNNLRDWLRVVASSKDTYELRYFN 102 (112)
T ss_dssp HHHHHHHHHHHHHSCSSSSTTTEEEEE-SSEEEEEESSS-SHHHHHHHHHHHHTTSSSTTTEEECCSCSTCEEEEE--
T ss_pred HHHHHHHHheEeCCcccccCCeEEEEecCCEEEEEecccccHHHHHHHHHHHHhhcchhheEEEEEcCCCeEEEEEEe
Confidence 699999999999999999999999999999999999999999999999999999999999999999999999999997
No 3
>KOG3434|consensus
Probab=100.00 E-value=1.2e-44 Score=250.98 Aligned_cols=78 Identities=71% Similarity=1.149 Sum_probs=76.9
Q ss_pred chHHHhhhhhccCCccCCCCCcEEEEEeCCEEEEEeccccchHHHHHHHHHHhhhccccceeEEEeecCceEEEeecC
Q psy1401 2 DMEKYLLERIKVGGKTSNFGNAVSLERQKTKVILTADVAFSKRYLKYLTKKYLKKNNLRDWLRVVANKKDSYELRYFQ 79 (79)
Q Consensus 2 ~fE~fL~erIKV~gk~gnlg~~V~v~r~k~ki~v~s~~~fsKrYlKYLtKKyLkk~~LrdwlrVva~~K~~YeLrYfn 79 (79)
+||||||||||||||+||||+.|+|++.+++|+|+|++|||+||||||||||||+++|||||||||+++++|||||||
T Consensus 37 ~fe~fLqerIKv~GK~gnLg~vv~ie~~kskitV~s~~~Fs~rylKyltkkYLkk~~LRdwlrvva~~k~~yelryf~ 114 (125)
T KOG3434|consen 37 DLEKFLQERIKVNGKVGNLGNVVTIERSKSKITVVSTVHFSKRYLKYLTKKYLKKNNLRDWLRVVATDKNTYELRYFQ 114 (125)
T ss_pred HHHHHHHHHhhhcccccccCCeEEEecCCcEEEEEecCCccHHHHHHHHHHHHhhhhHHHHHHHhhccCceEEEEecc
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999999997
No 4
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=58.19 E-value=6.7 Score=27.32 Aligned_cols=32 Identities=16% Similarity=0.335 Sum_probs=25.3
Q ss_pred hccCCccCCCCCcEEEEEeCCEEEEEeccccchH
Q psy1401 11 IKVGGKTSNFGNAVSLERQKTKVILTADVAFSKR 44 (79)
Q Consensus 11 IKV~gk~gnlg~~V~v~r~k~ki~v~s~~~fsKr 44 (79)
.++++..|.+ .|+|..+++++.|+.++..+|+
T Consensus 58 K~I~N~~Gk~--~isv~~~~~~~~V~rsL~L~Kq 89 (116)
T PF12970_consen 58 KKIDNPVGKV--SISVKPEGNKIKVTRSLELKKQ 89 (116)
T ss_dssp EEEEETTEEE--EEEEEEETTEEEEEEEEEE--S
T ss_pred eeccCCcceE--EEEEEecCCeEEEEEEEEEeee
Confidence 4667777777 7889999999999999998885
No 5
>PF02747 PCNA_C: Proliferating cell nuclear antigen, C-terminal domain; InterPro: IPR022649 Proliferating cell nuclear antigen (PCNA), or cyclin, is a non-histone acidic nuclear protein [] that plays a key role in the control of eukaryotic DNA replication []. It acts as a co-factor for DNA polymerase delta, which is responsible for leading strand DNA replication []. The sequence of PCNA is well conserved between plants and animals, indicating a strong selective pressure for structure conservation, and suggesting that this type of DNA replication mechanism is conserved throughout eukaryotes []. In Saccharomyces cerevisiae (Baker's yeast), POL30, is associated with polymerase III, the yeast analog of polymerase delta. Homologues of PCNA have also been identified in the archaea (Euryarchaeota and Crenarchaeota) and in Paramecium bursaria Chlorella virus 1 (PBCV-1) and in nuclear polyhedrosis viruses. ; GO: 0003677 DNA binding, 0030337 DNA polymerase processivity factor activity, 0006275 regulation of DNA replication, 0043626 PCNA complex; PDB: 1IZ5_A 1IZ4_A 1GE8_A 1ISQ_A 3A2F_B 1RWZ_A 3P83_A 1RXM_A 1RXZ_A 1SXJ_F ....
Probab=55.67 E-value=57 Score=21.52 Aligned_cols=56 Identities=27% Similarity=0.411 Sum_probs=34.2
Q ss_pred cCCCCCcEEEEEeCCEEEEEec----------------------------c----ccchHHHHHHHHHHhhhccccceeE
Q psy1401 17 TSNFGNAVSLERQKTKVILTAD----------------------------V----AFSKRYLKYLTKKYLKKNNLRDWLR 64 (79)
Q Consensus 17 ~gnlg~~V~v~r~k~ki~v~s~----------------------------~----~fsKrYlKYLtKKyLkk~~Lrdwlr 64 (79)
...+|+.|+|+.+++.+.+.++ - .||=+||+. |.|..+|.|-+.
T Consensus 25 l~~v~d~v~i~~~~~~~~f~~~Gd~~~~~v~~~~~~~~~~~~~~~~i~~~~~~~~~fsl~YL~~----~~Ka~~ls~~V~ 100 (128)
T PF02747_consen 25 LSSVGDTVTISADKDSVIFSAEGDIGSAEVEFKETESSEDDEELIEIEVKEPVSSSFSLDYLND----FSKAAPLSDEVT 100 (128)
T ss_dssp HHTTCSEEEEEEETTEEEEEEEESSEEEEEEEEEEEEETTCTCESEEEESSEEEEEEEHHHHHH----HGGGGGTTSEEE
T ss_pred HHhcCCEEEEEEeCCEEEEEEEeccCcEEEEEeeccccccccccceeeeccceeeEEeHHHHHh----hhccccCCceEE
Confidence 4456777777777776655333 1 255566544 566788888887
Q ss_pred EEeecCceEEEe
Q psy1401 65 VVANKKDSYELR 76 (79)
Q Consensus 65 Vva~~K~~YeLr 76 (79)
+--++.---.|+
T Consensus 101 l~l~~~~Pl~l~ 112 (128)
T PF02747_consen 101 LELGEDMPLKLE 112 (128)
T ss_dssp EEEETTSEEEEE
T ss_pred EEEcCCCCEEEE
Confidence 766665443333
No 6
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=45.06 E-value=4.1 Score=28.53 Aligned_cols=15 Identities=47% Similarity=0.924 Sum_probs=11.7
Q ss_pred ccccceeEEEeecCc
Q psy1401 57 NNLRDWLRVVANKKD 71 (79)
Q Consensus 57 ~~LrdwlrVva~~K~ 71 (79)
+.|++|||||--+++
T Consensus 67 P~l~~WL~vVgl~~~ 81 (129)
T PF13543_consen 67 PSLRQWLRVVGLRPE 81 (129)
T ss_pred CcHHHHhhhcCCCHH
Confidence 679999999965543
No 7
>KOG2638|consensus
Probab=36.72 E-value=34 Score=28.97 Aligned_cols=40 Identities=20% Similarity=0.414 Sum_probs=24.9
Q ss_pred hccCCccCCCCCcEEEEEeCCEEEEEecccc---chHHHHHHHHHH
Q psy1401 11 IKVGGKTSNFGNAVSLERQKTKVILTADVAF---SKRYLKYLTKKY 53 (79)
Q Consensus 11 IKV~gk~gnlg~~V~v~r~k~ki~v~s~~~f---sKrYlKYLtKKy 53 (79)
+|.||..|. ..-+..-|+-|.|..+..| +=|-+.||-++|
T Consensus 107 lKLNGGlGt---tmGc~gPKS~ieVR~g~tFLDL~V~QIe~LN~~Y 149 (498)
T KOG2638|consen 107 LKLNGGLGT---TMGCKGPKSVIEVRDGLTFLDLTVRQIENLNKTY 149 (498)
T ss_pred EEecCCcCC---ccccCCCceeEEEcCCCchhHHHHHHHHHHHhhc
Confidence 566766665 3334445667788777665 667777775444
No 8
>PF08845 SymE_toxin: Toxin SymE, type I toxin-antitoxin system; InterPro: IPR014944 This entry represents a SOS-induced gene whose product shows homology to the antitoxin MazE (SymE), the coding region contains a cis-encoded antisense RNA. The small antisense RNA and the gene have the all the hallmarks of a toxin-antitoxin module. The synthesis of the SymE is tightly repressed at multiple levels; at the transcriptional level by the LexA repressor, at the level of mRNA stability and translation by the SymR RNA and at the level of protein stability by the Lon protease. SymE co-purifies with ribosomes and overproduction of the protein leads to cell growth inhibition, decreased protein synthesis and increased RNA degradation. These properties are shared with several RNA endonuclease toxins of toxin-antitoxin modules. It seems probable that the SymE protein represents an evolutionary derivative of a toxin containing the AbrB fold, whose representatives are typically antitoxins. The SymE promoted cleavage of RNA cleavage may be important for the recycling of RNAs damaged under SOS-inducing conditions []. ; GO: 0003723 RNA binding, 0016788 hydrolase activity, acting on ester bonds, 0016070 RNA metabolic process, 0005737 cytoplasm
Probab=36.00 E-value=55 Score=19.68 Aligned_cols=18 Identities=17% Similarity=0.349 Sum_probs=15.5
Q ss_pred CCCcEEEEEeCCEEEEEe
Q psy1401 20 FGNAVSLERQKTKVILTA 37 (79)
Q Consensus 20 lg~~V~v~r~k~ki~v~s 37 (79)
-|+.|+|+...++|++++
T Consensus 40 ~G~~v~V~v~~g~lvIt~ 57 (57)
T PF08845_consen 40 IGDPVKVRVMPGCLVITP 57 (57)
T ss_pred CCCEEEEEEECCEEEEeC
Confidence 578999999999999874
No 9
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=31.17 E-value=47 Score=18.53 Aligned_cols=15 Identities=27% Similarity=0.674 Sum_probs=12.9
Q ss_pred hHHHHHHHHHHhhhc
Q psy1401 43 KRYLKYLTKKYLKKN 57 (79)
Q Consensus 43 KrYlKYLtKKyLkk~ 57 (79)
.||.++|++.|+..+
T Consensus 1 ~~y~~~~~~~~i~~~ 15 (64)
T smart00647 1 EKYERLLLESYVESN 15 (64)
T ss_pred ChHHHHHHHHHHhcC
Confidence 389999999999875
No 10
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=30.70 E-value=1.3e+02 Score=18.22 Aligned_cols=50 Identities=24% Similarity=0.424 Sum_probs=32.6
Q ss_pred CcEEEEEeCCEEEEEecccc-----chH-----HHHHHHHHHhhhccccceeEEEeecCceE
Q psy1401 22 NAVSLERQKTKVILTADVAF-----SKR-----YLKYLTKKYLKKNNLRDWLRVVANKKDSY 73 (79)
Q Consensus 22 ~~V~v~r~k~ki~v~s~~~f-----sKr-----YlKYLtKKyLkk~~LrdwlrVva~~K~~Y 73 (79)
..|.+..+...+.++-+.+= .|+ -|.||+..++.++. .++.||+..- +.|
T Consensus 15 ~~v~~~~~~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~~~~-~~~~~v~lDv-~~Y 74 (77)
T cd02414 15 ADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLNRNT-GEYVRITLDV-EGY 74 (77)
T ss_pred cEEEEEecCCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHhhcc-CCceEEEEEC-ccc
Confidence 35666665655554443332 232 48999999999875 8899998765 444
No 11
>PHA03383 PCNA-like protein; Provisional
Probab=30.02 E-value=2.3e+02 Score=21.36 Aligned_cols=27 Identities=22% Similarity=0.407 Sum_probs=17.2
Q ss_pred ccchHHHHHHHHHHhhhccccceeEEEeecC
Q psy1401 40 AFSKRYLKYLTKKYLKKNNLRDWLRVVANKK 70 (79)
Q Consensus 40 ~fsKrYlKYLtKKyLkk~~LrdwlrVva~~K 70 (79)
.||=+||+..+ |-..|.|-+.+--++.
T Consensus 212 ~ysl~YL~~~~----Ka~~ls~~V~i~l~~d 238 (262)
T PHA03383 212 KFSLKYLTSFT----KASGMSSSVEIYLKES 238 (262)
T ss_pred EEeHHHHHHhh----ccccCCCeEEEEEcCC
Confidence 46777776555 4567777766655544
No 12
>PRK10598 lipoprotein; Provisional
Probab=29.53 E-value=33 Score=25.30 Aligned_cols=38 Identities=26% Similarity=0.429 Sum_probs=26.6
Q ss_pred chHHHhhhhhccCCccCCCC---------C-cEEEEEeC-CEEEEEecc
Q psy1401 2 DMEKYLLERIKVGGKTSNFG---------N-AVSLERQK-TKVILTADV 39 (79)
Q Consensus 2 ~fE~fL~erIKV~gk~gnlg---------~-~V~v~r~k-~ki~v~s~~ 39 (79)
+.++||++++.+.-+.|--| + .++|.|+. ++|+|++..
T Consensus 31 Ein~yL~k~~~~~k~~G~~gl~~a~i~l~~l~~~IGr~~~~~v~l~g~a 79 (186)
T PRK10598 31 EINQYLAKHNNFEKQIGLPGVADAHIVLTNLTSQIGREEPNKVTLTGDA 79 (186)
T ss_pred HHHHHHHHhccHHHhcCCCceeeeEEEeeeceeecCCCCCCEEEEecee
Confidence 35789999988877777222 1 46777765 788888744
No 13
>PHA02800 hypothetical protein; Provisional
Probab=28.72 E-value=20 Score=26.34 Aligned_cols=10 Identities=50% Similarity=0.982 Sum_probs=8.3
Q ss_pred eccccchHHH
Q psy1401 37 ADVAFSKRYL 46 (79)
Q Consensus 37 s~~~fsKrYl 46 (79)
.+.||||||+
T Consensus 4 ~~~~~~~~~~ 13 (161)
T PHA02800 4 NTLPFSKRYI 13 (161)
T ss_pred CCCCcchhhc
Confidence 4579999987
No 14
>PF05481 Myco_19_kDa: Mycobacterium 19 kDa lipoprotein antigen; InterPro: IPR008691 Most of the antigens of Mycobacterium leprae and Mycobacterium tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18 kDa M. leprae antigen and the 19 kDa M. tuberculosis antigen are strongly cross-reactive between these two species and are coded within very similar genes [, ].; GO: 0016020 membrane
Probab=28.38 E-value=71 Score=22.99 Aligned_cols=31 Identities=23% Similarity=0.331 Sum_probs=26.3
Q ss_pred hhccCCccCCCCCcEEEEEeCCEEEEEeccc
Q psy1401 10 RIKVGGKTSNFGNAVSLERQKTKVILTADVA 40 (79)
Q Consensus 10 rIKV~gk~gnlg~~V~v~r~k~ki~v~s~~~ 40 (79)
++.|||+.-+..+.|+.+.....++|...-.
T Consensus 52 ~VtVdG~~~~~~~~V~C~~~~g~~~I~ig~~ 82 (160)
T PF05481_consen 52 KVTVDGKDQNVTGPVTCSQTGGKTTIAIGDA 82 (160)
T ss_pred EEEECCCccCCCcCeEEeecCCEEEEEeCCC
Confidence 6899999999888999999999988876543
No 15
>PF00838 TCTP: Translationally controlled tumour protein; InterPro: IPR018105 Mammalian translationally controlled tumour protein (TCTP) (or P23) is a protein which has been found to be preferentially synthesised in cells during the early growth phase of some types of tumour [, ], but which is also expressed in normal cells. The physiological function of TCTP is still not known. It was first identified as a histamine-releasing factor, acting in IgE +-dependent allergic reactions. In addition, TCTP has been shown to bind to tubulin in the cytoskeleton, has a high affinity for calcium, is the binding target for the antimalarial compound artemisinin, and is induced in vitamin D-dependent apoptosis. TCTP production is thought to be controlled at the translational as well as the transcriptional level []. TCTP is a hydrophilic protein of 18 to 20 kD. TCTPs do not share significant sequence similarity with any other class of proteins. Recently, the structure of TCTP was determined and exhibited significant structural similarity to the human protein Mss4, which is a guanine nucleotide-free chaperone of the Rab protein []. Close homologues have been found in plants [], earthworm [], Caenorhabditis elegans (F52H2.11), Hydra, Saccharomyces cerevisiae (YKL056c) [] and Schizosaccharomyces pombe (SpAC1F12.02c).; PDB: 2KWB_A 2LOY_A 1TXJ_A 1H6Q_A 1H7Y_A 3P3K_A 1YZ1_C 3EBM_D 2HR9_A.
Probab=28.02 E-value=42 Score=24.05 Aligned_cols=17 Identities=47% Similarity=0.944 Sum_probs=12.8
Q ss_pred cccch-HHHHHHHHHHhhh
Q psy1401 39 VAFSK-RYLKYLTKKYLKK 56 (79)
Q Consensus 39 ~~fsK-rYlKYLtKKyLkk 56 (79)
.+|+| .|.+|+ |.|+|+
T Consensus 77 t~f~Kk~y~~yi-K~Y~K~ 94 (165)
T PF00838_consen 77 TSFDKKSYKAYI-KDYMKK 94 (165)
T ss_dssp ECCHHHHHHHHH-HHHHHH
T ss_pred ecccHHHHHHHH-HHHHHH
Confidence 37977 588887 778875
No 16
>PHA02781 hypothetical protein; Provisional
Probab=26.90 E-value=66 Score=20.78 Aligned_cols=26 Identities=23% Similarity=0.396 Sum_probs=18.9
Q ss_pred hhccCCccCCCCCcEEEEEeCCEEEEEec
Q psy1401 10 RIKVGGKTSNFGNAVSLERQKTKVILTAD 38 (79)
Q Consensus 10 rIKV~gk~gnlg~~V~v~r~k~ki~v~s~ 38 (79)
+|.|+.|.|| .|+|+-+-.+|++...
T Consensus 9 kitvdskign---vvtisynlekitidvt 34 (78)
T PHA02781 9 KITVDSKIGN---VVTISYNLEKITIDVT 34 (78)
T ss_pred EEEeecccCc---EEEEEeeeEEEEEecC
Confidence 3456777666 7899888778887764
No 17
>PF14651 Lipocalin_7: Lipocalin / cytosolic fatty-acid binding protein family; PDB: 2F73_A 3B2L_A 3B2J_A 3STN_A 3STK_A 3STM_X 3VG6_A 3VG4_A 3VG5_A 3B2K_A ....
Probab=26.80 E-value=1.1e+02 Score=21.03 Aligned_cols=39 Identities=13% Similarity=0.169 Sum_probs=23.3
Q ss_pred chHHHhhhhhccC----CccCCCCCcEEEEEeCCEEEEEecccc
Q psy1401 2 DMEKYLLERIKVG----GKTSNFGNAVSLERQKTKVILTADVAF 41 (79)
Q Consensus 2 ~fE~fL~erIKV~----gk~gnlg~~V~v~r~k~ki~v~s~~~f 41 (79)
|||.||. .|-|. .+.-+..-.+.|+.+++..+++...|-
T Consensus 14 N~e~fmk-aiGvp~d~i~k~k~~k~v~Ei~q~Gd~ft~t~~~~g 56 (128)
T PF14651_consen 14 NFEEFMK-AIGVPEDKIQKGKDAKPVTEISQNGDDFTWTTTTPG 56 (128)
T ss_dssp SHHHHHH-HCT--HHHHHHHTTS-EEEEEEEETTEEEEEEEETT
T ss_pred CHHHHHH-HhCCCHHHHHhhhCCCceEEEEEeCCeEEEEEEecC
Confidence 6888873 23321 133344446889999998888765553
No 18
>COG1088 RfbB dTDP-D-glucose 4,6-dehydratase [Cell envelope biogenesis, outer membrane]
Probab=26.75 E-value=29 Score=28.10 Aligned_cols=10 Identities=50% Similarity=0.953 Sum_probs=8.2
Q ss_pred hccccceeEE
Q psy1401 56 KNNLRDWLRV 65 (79)
Q Consensus 56 k~~LrdwlrV 65 (79)
-.|.||||+|
T Consensus 212 G~~iRDWl~V 221 (340)
T COG1088 212 GLQIRDWLYV 221 (340)
T ss_pred CcceeeeEEe
Confidence 3689999987
No 19
>PF07901 DUF1672: Protein of unknown function (DUF1672); InterPro: IPR012873 This family is composed of hypothetical bacterial proteins of unknown function.
Probab=25.69 E-value=55 Score=25.73 Aligned_cols=41 Identities=24% Similarity=0.396 Sum_probs=28.8
Q ss_pred HHHhhhhhccCCccCCC-----CCcEEEEEeCCEEEEEeccccchH
Q psy1401 4 EKYLLERIKVGGKTSNF-----GNAVSLERQKTKVILTADVAFSKR 44 (79)
Q Consensus 4 E~fL~erIKV~gk~gnl-----g~~V~v~r~k~ki~v~s~~~fsKr 44 (79)
++|+++.-+.+=|+.|. |-.|-|++++.-|.-++.|||.+-
T Consensus 43 ~~yfkd~y~t~VKv~NVVga~dga~V~Veced~~I~F~aSv~~~~~ 88 (277)
T PF07901_consen 43 IQYFKDNYKTDVKVTNVVGARDGAVVYVECEDHPIVFNASVPVDKD 88 (277)
T ss_pred HHHHHHhcCceeEEEEEEccCCcEEEEEEecCCCceEEEEEEechh
Confidence 56777766555565553 225677887667999999999874
No 20
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=24.34 E-value=11 Score=21.12 Aligned_cols=16 Identities=38% Similarity=0.862 Sum_probs=8.7
Q ss_pred hHHHHHHHHHHhhhcc
Q psy1401 43 KRYLKYLTKKYLKKNN 58 (79)
Q Consensus 43 KrYlKYLtKKyLkk~~ 58 (79)
+||.+++.++||..+.
T Consensus 1 eky~~~~~~~~~~~~~ 16 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDP 16 (64)
T ss_dssp HCHHHCCCHS---S--
T ss_pred ChHHHHHHHHHHHCCC
Confidence 4788888888885443
No 21
>KOG4015|consensus
Probab=24.10 E-value=1.1e+02 Score=21.46 Aligned_cols=39 Identities=15% Similarity=0.251 Sum_probs=25.4
Q ss_pred chHHHhhhhhccC----CccCCCCCcEEEEEeCCEEEEEecccc
Q psy1401 2 DMEKYLLERIKVG----GKTSNFGNAVSLERQKTKVILTADVAF 41 (79)
Q Consensus 2 ~fE~fL~erIKV~----gk~gnlg~~V~v~r~k~ki~v~s~~~f 41 (79)
+|+.||.+- =|+ -.+..+...++|+.++++.++....-|
T Consensus 16 NFdeymk~l-GV~~~~Rk~a~~~kp~~~i~~~G~~~~~~t~Stf 58 (133)
T KOG4015|consen 16 NFDEYLKAL-GVGWATRKIAKLAKPVLEITQDGDKFTIKTLSTF 58 (133)
T ss_pred CHHHHHHhc-CCcHhHHHHHhhcCCeEEEEEcCCEEEEEEeecc
Confidence 689998771 111 122333457889999999998875544
No 22
>PF09386 ParD: Antitoxin ParD; InterPro: IPR018985 ParD is a plasmid anti-toxin than forms a ribbon-helix-helix DNA binding structure []. It stabilises plasmids by inhibiting ParE toxicity in cells that express ParD and ParE. ParD forms a dimer and also regulates its own promoter (parDE). ; PDB: 2AN7_A.
Probab=23.68 E-value=33 Score=22.54 Aligned_cols=19 Identities=26% Similarity=0.415 Sum_probs=9.5
Q ss_pred chHHHhhhhhccCCccCCCC
Q psy1401 2 DMEKYLLERIKVGGKTSNFG 21 (79)
Q Consensus 2 ~fE~fL~erIKV~gk~gnlg 21 (79)
+++.||.+||. +|.+|++.
T Consensus 48 eL~~lL~~Ri~-~g~~G~vs 66 (79)
T PF09386_consen 48 ELKALLGERIA-QGLAGKVS 66 (79)
T ss_dssp HHCHHS-S----SS-SS--S
T ss_pred HHHHHHHHHHH-HHHcCCCc
Confidence 46789999998 78888875
No 23
>KOG2775|consensus
Probab=23.65 E-value=48 Score=27.25 Aligned_cols=25 Identities=44% Similarity=0.711 Sum_probs=16.7
Q ss_pred eccccchHHHHHHH-HHHhhh-ccccc
Q psy1401 37 ADVAFSKRYLKYLT-KKYLKK-NNLRD 61 (79)
Q Consensus 37 s~~~fsKrYlKYLt-KKyLkk-~~Lrd 61 (79)
++.||++|||-+|. -|||.. ++|.|
T Consensus 330 gTLaFcrR~lDrlGetKyLmAlk~Lc~ 356 (397)
T KOG2775|consen 330 GTLAFCRRWLDRLGETKYLMALKNLCD 356 (397)
T ss_pred ccccccHHHHHHhhhHHHHHHHHhhhh
Confidence 46799999998874 246643 44444
No 24
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=22.70 E-value=1.6e+02 Score=16.53 Aligned_cols=43 Identities=12% Similarity=0.181 Sum_probs=22.5
Q ss_pred hhhhccCCccCCCCCcEEEEEeCCEEEEEecccc--chHHHHHHHHH
Q psy1401 8 LERIKVGGKTSNFGNAVSLERQKTKVILTADVAF--SKRYLKYLTKK 52 (79)
Q Consensus 8 ~erIKV~gk~gnlg~~V~v~r~k~ki~v~s~~~f--sKrYlKYLtKK 52 (79)
+++|.-++...+ ..|.|+..++.|+++..+|= .++.+.-+...
T Consensus 5 ~~~L~~~~~~~~--~~i~v~v~~g~v~L~G~v~s~~~~~~a~~~a~~ 49 (64)
T PF04972_consen 5 RAALRADPWLPD--SNISVSVENGVVTLSGEVPSQEQRDAAERLARS 49 (64)
T ss_dssp --------CTT---TTEEEEEECTEEEEEEEESSCHHHHHHHHHHHC
T ss_pred ccccccccccCC--CeEEEEEECCEEEEEeeCcHHHHHHhHHhhhcc
Confidence 344444442222 37899999999999998873 34444444433
No 25
>PF03526 Microcin: Colicin E1 (microcin) immunity protein; InterPro: IPR003061 The structural and functional relationships among independently cloned segments of the plasmid ColE1 region that regulates and codes for colicin E1 (cea), immunity (imm) and the mitomycin C-induced lethality function (lys) have been analysed []. A model for the structure and expression of the colicin E1 operon has been proposed in which the cea and lys genes are expressed from a single inducible promoter that is controlled by the lexA repressor in response to the SOS system of Escherichia coli []. The imm gene lies between the cea and lys genes and is expressed by transcription in the opposite direction from a promoter located within the lys gene []. This arrangement indicates that the transcriptional units for all three genes overlap. It is proposed that the formation of anti-sense RNA may be an important element in the coordinate regulation of gene expression in this system []. Hydropathy analysis of the imm gene products suggests that they have hydrophobic domains characteristic of membrane-associated proteins []. The microcin E1 immunity protein is able to protect a cell that harbours the plasmid ColE1 encoding colicin E1 against colicin E1; it is thus essential both for autonomous replication and colicin E1 immunity []. ; GO: 0015643 toxin binding, 0030153 bacteriocin immunity
Probab=22.67 E-value=62 Score=19.96 Aligned_cols=18 Identities=33% Similarity=0.475 Sum_probs=12.2
Q ss_pred cccchHHHHHHHHHHhhh
Q psy1401 39 VAFSKRYLKYLTKKYLKK 56 (79)
Q Consensus 39 ~~fsKrYlKYLtKKyLkk 56 (79)
-||||+++....=||-++
T Consensus 20 ~PfSk~aIE~ialkft~k 37 (55)
T PF03526_consen 20 FPFSKWAIEKIALKFTKK 37 (55)
T ss_pred hhhHHHHHHHHHHHhccH
Confidence 389999876655555544
No 26
>PF08490 DUF1744: Domain of unknown function (DUF1744); InterPro: IPR013697 This domain is found on the catalytic subunit of DNA polymerase epsilon. It is found C-terminal to IPR006133 from INTERPRO and IPR006134 from INTERPRO. ; GO: 0003887 DNA-directed DNA polymerase activity, 0008270 zinc ion binding, 0006260 DNA replication, 0005634 nucleus
Probab=21.42 E-value=2.7e+02 Score=22.43 Aligned_cols=47 Identities=21% Similarity=0.481 Sum_probs=36.0
Q ss_pred CCCCcEEEEEeCCEEEEEeccc---cchHHHHHHHHHHhhhccccceeEEEe
Q psy1401 19 NFGNAVSLERQKTKVILTADVA---FSKRYLKYLTKKYLKKNNLRDWLRVVA 67 (79)
Q Consensus 19 nlg~~V~v~r~k~ki~v~s~~~---fsKrYlKYLtKKyLkk~~LrdwlrVva 67 (79)
.||-.| |-.+-++|.|.+..+ =..-|..|+.+. ++.+.|-.||.+-.
T Consensus 329 rlG~~V-VyA~~~riil~T~K~~~~~A~ay~~yi~~~-i~~~~lF~~l~l~~ 378 (396)
T PF08490_consen 329 RLGSKV-VYADFNRIILCTGKTSLENAYAYVQYILKS-IRSRELFSWLDLKP 378 (396)
T ss_pred HcCCEE-EEEcCCEEEEECCCCCHHHHHHHHHHHHHH-HhcccccccEEeEH
Confidence 456555 667789999998765 378999999985 66788999887643
No 27
>PF03776 MinE: Septum formation topological specificity factor MinE; InterPro: IPR005527 Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerisation, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD []. MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for `topological specificity' - that is, the ability of MinE to antagonise MinCD inhibition of Z rings at the midcell position but not at the poles.; GO: 0032955 regulation of barrier septum formation, 0051301 cell division; PDB: 2KXO_A 3MCD_B 3KU7_A 3R9J_C 3R9I_E 1EV0_B.
Probab=20.33 E-value=1.3e+02 Score=18.44 Aligned_cols=21 Identities=29% Similarity=0.556 Sum_probs=16.0
Q ss_pred cEEEEEeCCEEEEEeccccch
Q psy1401 23 AVSLERQKTKVILTADVAFSK 43 (79)
Q Consensus 23 ~V~v~r~k~ki~v~s~~~fsK 43 (79)
.|.++++++--.+.+++|+.+
T Consensus 50 ~v~l~~~~~~~~L~~nIpl~~ 70 (70)
T PF03776_consen 50 EVQLERDDDMSVLEANIPLPR 70 (70)
T ss_dssp EEEEEECTTEEEEEEEEEE--
T ss_pred EEEEEECCCceEEEEEEEcCC
Confidence 677888888888889999863
Done!