Query 019501
Match_columns 340
No_of_seqs 119 out of 154
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 09:58:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019501.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019501hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd01396 MeCP2_MBD MeCP2, MBD1, 99.9 2.1E-25 4.4E-30 175.4 7.6 76 178-256 1-76 (77)
2 cd01397 HAT_MBD Methyl-CpG bin 99.9 9.1E-24 2E-28 166.2 6.3 69 183-254 5-73 (73)
3 smart00391 MBD Methyl-CpG bind 99.9 3.6E-23 7.8E-28 162.5 7.5 73 177-253 2-75 (77)
4 cd00122 MBD MeCP2, MBD1, MBD2, 99.8 2.5E-21 5.4E-26 145.2 6.4 61 179-243 2-62 (62)
5 PF01429 MBD: Methyl-CpG bindi 99.8 4.1E-20 9E-25 143.7 6.1 69 179-249 6-75 (77)
6 KOG4161 Methyl-CpG binding tra 99.8 4.6E-20 1E-24 173.2 5.7 172 103-280 100-271 (272)
7 cd01395 HMT_MBD Methyl-CpG bin 99.4 3.2E-13 6.9E-18 103.2 4.9 55 184-243 6-60 (60)
8 PF07496 zf-CW: CW-type Zinc F 99.3 8E-13 1.7E-17 96.3 1.0 49 115-167 2-50 (50)
9 KOG4161 Methyl-CpG binding tra 99.1 6.7E-11 1.5E-15 111.7 5.4 66 180-252 15-81 (272)
10 PF07624 PSD2: Protein of unkn 41.9 7.4 0.00016 30.5 -0.4 40 210-250 1-41 (76)
11 KOG1141 Predicted histone meth 36.0 32 0.00069 39.2 3.1 100 130-246 759-861 (1262)
12 PRK00222 methionine sulfoxide 35.8 63 0.0014 29.1 4.5 92 124-215 9-117 (142)
13 PF05180 zf-DNL: DNL zinc fing 34.5 26 0.00056 27.9 1.6 19 112-130 25-43 (66)
14 KOG1141 Predicted histone meth 32.4 31 0.00066 39.3 2.3 172 60-253 480-666 (1262)
15 COG1218 CysQ 3'-Phosphoadenosi 31.5 58 0.0013 32.0 3.8 38 133-178 54-91 (276)
16 PF00397 WW: WW domain; Inter 26.7 81 0.0017 20.8 2.8 21 184-210 1-21 (31)
17 PF12528 DUF3728: Prepilin pep 26.0 1.2E+02 0.0026 24.6 4.2 37 179-215 37-74 (84)
18 cd01259 PH_Apbb1ip Apbb1ip (Am 23.4 1.2E+02 0.0025 26.8 3.8 33 186-226 14-47 (114)
19 TIGR01204 bioW 6-carboxyhexano 22.1 1.1E+02 0.0024 29.7 3.8 39 187-229 190-228 (232)
20 KOG3794 CBF1-interacting corep 21.7 51 0.0011 34.5 1.5 37 95-131 102-139 (453)
21 COG3410 Uncharacterized conser 21.6 78 0.0017 29.9 2.6 43 237-285 43-85 (191)
22 TIGR00357 methionine-R-sulfoxi 21.3 2.5E+02 0.0055 25.1 5.6 91 124-214 6-113 (134)
23 PF08358 Flexi_CP_N: Carlaviru 20.7 88 0.0019 23.9 2.3 29 286-314 19-48 (52)
24 PF09851 SHOCT: Short C-termin 20.0 77 0.0017 21.2 1.7 13 130-142 18-30 (31)
No 1
>cd01396 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1.
Probab=99.92 E-value=2.1e-25 Score=175.41 Aligned_cols=76 Identities=41% Similarity=0.725 Sum_probs=70.4
Q ss_pred CCCCCCCCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCccccccc
Q 019501 178 KPNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRK 256 (340)
Q Consensus 178 KpnIP~~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~yvkK 256 (340)
+++||.+|+||+|++++|++|+.+++||||++|+||||||++||++||..||. .+|++++|||++++++++++.++
T Consensus 1 ~~~~~~lp~GW~r~~~~R~~gs~~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~~---~~~~~~~FdF~~~k~~~~~~~~~ 76 (77)
T cd01396 1 KPEDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGP---TSLDLSDFDFTVPKKLGLGSPRR 76 (77)
T ss_pred CCCCCCCCCCCEEEEEEecCCCCCcceEEEECCCCCEEECHHHHHHHHHhCCC---CCCcHhHcccCCCcccccccCCC
Confidence 47899999999999999999977789999999999999999999999999985 47999999999999999988665
No 2
>cd01397 HAT_MBD Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity. The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog.
Probab=99.89 E-value=9.1e-24 Score=166.22 Aligned_cols=69 Identities=36% Similarity=0.562 Sum_probs=64.4
Q ss_pred CCCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCccccc
Q 019501 183 QPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYV 254 (340)
Q Consensus 183 ~~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~yv 254 (340)
+++.||+|++|+|+.|++.++||||+|||||||||++||++||.+|+. .+|+++||+|++..+++++|+
T Consensus 5 Pl~~GW~Re~vir~~~~~~~~dV~Y~aPcGKklRs~~ev~~yL~~~~~---~~Lt~dnFsF~~~~~vg~f~~ 73 (73)
T cd01397 5 PLELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKNGI---SLLSRENFSFSARAPVGDFYE 73 (73)
T ss_pred CCCCCceeEEEeccCCCCccceEEEECCCCcccccHHHHHHHHHhCCc---cCccHhHccccCCcccccccC
Confidence 457999999999999977899999999999999999999999999996 489999999999999999884
No 3
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=99.88 E-value=3.6e-23 Score=162.54 Aligned_cols=73 Identities=32% Similarity=0.629 Sum_probs=66.1
Q ss_pred cCCCCCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCcccc
Q 019501 177 DKPNIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENY 253 (340)
Q Consensus 177 DKpnIP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~y 253 (340)
+..++| +|+||+|++++|+.|.+ +++||||+|||||||||++||++||.+|+++ .+++++|||.+..++...+
T Consensus 2 ~~~~~P-lp~GW~R~~~~r~~g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~~~~~---~~~~~~F~F~~~~~~~~~~ 75 (77)
T smart00391 2 DPLRLP-LPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDL---SLDLECFDFNATVPVGPKF 75 (77)
T ss_pred CcccCC-CCCCcEEEEEEecCCCCCCcccEEEECCCCCeeeCHHHHHHHHHhCCCc---ccccccccCcCCccccccc
Confidence 456788 99999999999999854 5899999999999999999999999999996 5899999999999988665
No 4
>cd00122 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family.
Probab=99.84 E-value=2.5e-21 Score=145.19 Aligned_cols=61 Identities=43% Similarity=0.748 Sum_probs=56.1
Q ss_pred CCCCCCCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCccee
Q 019501 179 PNIAQPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243 (340)
Q Consensus 179 pnIP~~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdF 243 (340)
..+|. |+||+|++++|+.|+..++||||++|+||+|||+.||++||.+|+. .+|++++|||
T Consensus 2 l~~P~-p~GW~R~~~~r~~g~~~k~dv~Y~sP~Gk~~Rs~~ev~~yL~~~~~---~~l~~~~F~F 62 (62)
T cd00122 2 LRDPL-PPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGP---SSLDLENFSF 62 (62)
T ss_pred CCCCC-CCCeEEEEEEcCCCCCCcceEEEECCCCceecCHHHHHHHHHhCCC---CCCcHHHCCC
Confidence 45777 9999999999999977789999999999999999999999999974 4799999999
No 5
>PF01429 MBD: Methyl-CpG binding domain; InterPro: IPR001739 Methylation at CpG dinucleotide, the most common DNA modification in eukaryotes, has been correlated with gene silencing associated with various phenomena such as genomic imprinting, transposon and chromosome X inactivation, differentiation, and cancer. Effects of DNA methylation are mediated through proteins which bind to symmetrically methylated CpGs. Such proteins contain a specific domain of ~70 residues, the methyl-CpG-binding domain (MBD), which is linked to additional domains associated with chromatin, such as the bromodomain, the AT hook motif,the SET domain, or the PHD finger. MBD-containing proteins appear to act as structural proteins, which recruit a variety of histone deacetylase (HDAC) complexes and chromatin remodelling factors, leading to chromatin compaction and, consequently, to transcriptional repression. The MBD of MeCP2, MBD1, MBD2, MBD4 and BAZ2 mediates binding to DNA, in case of MeCP2, MBD1 and MBD2 preferentially to methylated CpG. In case of human MBD3 and SETDB1 the MBD has been shown to mediate protein-protein interactions [, ]. The MBD folds into an alpha/beta sandwich structure comprising a layer of twisted beta sheet, backed by another layer formed by the alpha1 helix and a hairpin loop at the C terminus. These layers are both amphipathic, with the alpha1 helix and the beta sheet lying parallel and the hydrophobic faces tightly packed against each other. The beta sheet is composed of two long inner strands (beta2 and beta3) sandwiched by two shorter outer strands (beta1 and beta4) [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2KY8_A 1UB1_A 1D9N_A 1IG4_A 1QK9_A 3C2I_A.
Probab=99.80 E-value=4.1e-20 Score=143.75 Aligned_cols=69 Identities=36% Similarity=0.627 Sum_probs=56.8
Q ss_pred CCCCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCC
Q 019501 179 PNIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPL 249 (340)
Q Consensus 179 pnIP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~ 249 (340)
+..+.+|+||+|++++|++|++ +++||||+||+|++|||+.||.+||..+++. ..+++++|+|...+.+
T Consensus 6 ~~~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~~~--~~l~~~~F~F~~~~~~ 75 (77)
T PF01429_consen 6 PLDPPLPDGWKREVVVRKSGSSAGKKDVYYYSPCGKRFRSKKEVVRYLKENPSE--HDLKPENFSFSKRLIM 75 (77)
T ss_dssp CEBTTSTTT-EEEEEESSSSTTTTSEEEEEEETTSEEESSHHHHHHHHTTSS-----SS-CTTBBTTTTB--
T ss_pred cccCCCCCCCEEEEEEecCCCcCCceEEEEECCCCCEEeCHHHHHHHHHhCCCc--ccCCHhHCCCCCCccc
Confidence 3456789999999999999976 6899999999999999999999999999853 3799999999987764
No 6
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=99.80 E-value=4.6e-20 Score=173.23 Aligned_cols=172 Identities=22% Similarity=0.182 Sum_probs=151.8
Q ss_pred CCCCccCCccceeeeecccccceeeeccHHHHHHHHhhhcCCCeeeccccccCCCCcCCCCCCCCCCCcceeeecCCCCC
Q 019501 103 NTQSRVLPSVGAFTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDKPNIA 182 (340)
Q Consensus 103 ~~~~~~~~si~~yavQC~~C~KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP~Di~~d~sR~WaIDKpnIP 182 (340)
.+..+...+|.+|+++|..|++|+.|.+..+|+++|+.+.+++|+|.+.++ +.|++++|+.+++++.|.||+++++
T Consensus 100 ~~r~~~~~~~P~~~t~~~~r~~~t~i~~~~~~~~~r~~~~~~~~~~q~~ql----~~~~~~~~l~~~s~~~e~~d~~~l~ 175 (272)
T KOG4161|consen 100 KGRGDLNLAIPIRATSCIFRRPGTKIRSHDKYEVKREPKAEDPFREQKKQL----FWLERLQDLEADSSRGESIDKLSLP 175 (272)
T ss_pred CCCcccccCCchhhhhccccccceeeccccchhhhhccccccccccccceE----EEeccccccccccccccccCccccC
Confidence 344566789999999999999999999999999999999999999999664 9999999999999999999999999
Q ss_pred CCCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCcccccccCCCCCC
Q 019501 183 QPPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENYVRKRVPKAH 262 (340)
Q Consensus 183 ~~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~yvkKrp~~~~ 262 (340)
.+|.||.|.+..++... ..++||..|+|+++++.++++.++..|+.+-.....+++|.|+.+.++++.++.|+.+...
T Consensus 176 ~~~~g~~~~~~~~s~~~--~~~~~~~~p~~~~~~~~~~~~~~~~~n~~~~~~~p~l~~~~~~~~~ir~~~~~~~~~r~~~ 253 (272)
T KOG4161|consen 176 KTPQGSGRSSAGESLLS--SVATYLETPSGKKHGESPEAVAWKNANGPSETEQPLLGDFIVTEPDIRRQESRVKNVRRSL 253 (272)
T ss_pred cCCCccCcccccccccc--ccCcccccCCCcccccchhhhhcccCCCCCcccCCCcccccccCCCcCccccchhhhhhcc
Confidence 99999999997776544 4999999999999999999999999995433346799999999999999999999988888
Q ss_pred CCCCCCCCCCCcccCCCc
Q 019501 263 TSHDTPKALEPRAVSPLS 280 (340)
Q Consensus 263 ~s~~~~~~l~~eEV~Pl~ 280 (340)
.+.+++.-+..+++..+.
T Consensus 254 ~~~l~sd~~~~~~~~~~~ 271 (272)
T KOG4161|consen 254 FSALTSDTLSKEAAKLQD 271 (272)
T ss_pred ccchhhcCcchhhhcccc
Confidence 777766667776666554
No 7
>cd01395 HMT_MBD Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins.
Probab=99.40 E-value=3.2e-13 Score=103.24 Aligned_cols=55 Identities=33% Similarity=0.510 Sum_probs=48.8
Q ss_pred CCCCceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCccee
Q 019501 184 PPPGWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSF 243 (340)
Q Consensus 184 ~P~GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdF 243 (340)
+-.||+|....|+.|+ -+.||+|.+||||+||+..||++||.++ . +.|++++|+|
T Consensus 6 ll~gw~R~~~~~~~~~-~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t-~---~~L~~d~FsF 60 (60)
T cd01395 6 LLCGFQRMKYRARVGK-VKKHVIYKAPCGRSLRNMSEVHRYLRET-C---SFLTVDNFSF 60 (60)
T ss_pred cccCeEEEEEeccCCC-cccceEEECCcchhhhcHHHHHHHHHhc-c---ccceeecccC
Confidence 3489999999998873 3688999999999999999999999999 3 3699999999
No 8
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=99.28 E-value=8e-13 Score=96.33 Aligned_cols=49 Identities=41% Similarity=0.882 Sum_probs=34.7
Q ss_pred eeeecccccceeeeccHHHHHHHHhhhcCCCeeeccccccCCCCcCCCCCCCC
Q 019501 115 FTVQCADCFKWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDIS 167 (340)
Q Consensus 115 yavQC~~C~KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP~Di~ 167 (340)
|+|||.+|.|||.|| .++..|++.+.+ +|+|.+.. |++..||+.|+|++
T Consensus 2 ~WVQCd~C~KWR~lp--~~~~~~~~~~~d-~W~C~~n~-~~~~~sC~~pee~e 50 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP--EEVDPIREELPD-PWYCSMNP-DPPFNSCDAPEEIE 50 (50)
T ss_dssp EEEE-TTT--EEEE---CCHHCTSCCSST-T--GGGSS--CCC-STTS--SS-
T ss_pred eEEECCCCCceeeCC--hhhCcccccCCC-eEEcCCCC-CCCCCCCCCcccCC
Confidence 799999999999999 778888888888 99999987 99999999999975
No 9
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=99.11 E-value=6.7e-11 Score=111.73 Aligned_cols=66 Identities=35% Similarity=0.571 Sum_probs=57.5
Q ss_pred CCCCCCCCceEEEEEeccCCC-cceEEEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCccc
Q 019501 180 NIAQPPPGWQRLLRIRGEGST-KFADVYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQEN 252 (340)
Q Consensus 180 nIP~~P~GWKRevViRksGst-~~~DVYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~ 252 (340)
.+|.+|+||.|++++|++|.. ++.||||+||.||+|||+.+++.||+.+. +++.|+|-+.+++...
T Consensus 15 ~c~~lp~GW~~~~~~r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~~-------~~s~~~~v~~k~~~~~ 81 (272)
T KOG4161|consen 15 DCPALPPGWTREEVQRSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKVG-------DLSLFDFVTGKMSPSE 81 (272)
T ss_pred cCCCCCCCcchhhhcccCCCcccccceEEeCCcccccccccHHHHHhcccc-------ccccCccccccccccc
Confidence 466789999999999999865 68999999999999999999999998754 5778888888877653
No 10
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=41.88 E-value=7.4 Score=30.46 Aligned_cols=40 Identities=20% Similarity=0.559 Sum_probs=32.9
Q ss_pred CCCCccccHHHHHHHHHhC-cccccCCcccCcceecCCcCCc
Q 019501 210 PSGKKLRSMVEIQKYFLEH-PEYARAGVKMSQFSFQIPKPLQ 250 (340)
Q Consensus 210 PtGKKLRSk~EVarYL~~N-pey~~~gLtLe~FdFstPK~~~ 250 (340)
|+|..|....||.++|.++ +++. ..+.-.-+.|..+..+.
T Consensus 1 pdG~~f~~~~eLk~~L~~~~~~~~-~~~~~kl~~YAlGR~~~ 41 (76)
T PF07624_consen 1 PDGTSFEGAAELKQYLAERKDQFA-RCFAEKLLTYALGRPLE 41 (76)
T ss_pred CCCCccCCHHHHHHHHHHCHHHHH-HHHHHHHHHHHcCCCCC
Confidence 8999999999999999999 5543 46677777888887775
No 11
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=35.96 E-value=32 Score=39.20 Aligned_cols=100 Identities=23% Similarity=0.345 Sum_probs=66.5
Q ss_pred cHHHHHHHHhhhcCCCeeeccccccCCCCcCCCC---CCCCCCCcceeeecCCCCCCCCCCceEEEEEeccCCCcceEEE
Q 019501 130 TKEKYEEIREHVLENPFTCEKAREWRPDVSCDDP---TDISQDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFADVY 206 (340)
Q Consensus 130 Tke~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP---~Di~~d~sR~WaIDKpnIP~~P~GWKRevViRksGst~~~DVY 206 (340)
+--+|..+-|.+...|+.|.+++ -|+-| .-+.|+|--+.+.--.-+ -.||.|.-.--..| +-.-
T Consensus 759 ~gykyKRl~e~~ptg~yEc~k~c------kc~~~~C~nrmvqhg~qvRlq~fkt~---~kGWg~rclddi~~----g~fV 825 (1262)
T KOG1141|consen 759 NGYKYKRLIEIRPTGPYECLKAC------KCCGPDCLNRMVQHGYQVRLQRFKTI---HKGWGRRCLDDITG----GNFV 825 (1262)
T ss_pred cchhhHHHHHhcCCCHHHHHHhh------ccCcHHHHHHHhhcCceeEeeecccc---ccccceEeeeecCC----ceEE
Confidence 34588899999999999999865 55544 124566633222111112 35998765543333 3456
Q ss_pred EECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCC
Q 019501 207 YEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIP 246 (340)
Q Consensus 207 Y~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstP 246 (340)
|+.|+|--++...+...|..-.. | -++|..|+|..+
T Consensus 826 ciy~g~~l~~~~sdks~~~~~~~-~---~~~id~~~f~~~ 861 (1262)
T KOG1141|consen 826 CIYPGGALLHQISDKSEYIHVTR-S---LLTIDCFSFDAR 861 (1262)
T ss_pred EEecchhhhhhhchhhhhcccch-h---hhcccccchhcc
Confidence 77899999999999998876533 3 268999999754
No 12
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=35.79 E-value=63 Score=29.11 Aligned_cols=92 Identities=26% Similarity=0.458 Sum_probs=58.8
Q ss_pred ceeeeccHHHHHHHHhhhcCCCeeeccccccCCCC----cCCCC---CCCCCCCcceee-----ecCCCCCCC---CCCc
Q 019501 124 KWRLIPTKEKYEEIREHVLENPFTCEKAREWRPDV----SCDDP---TDISQDGSRLWA-----IDKPNIAQP---PPGW 188 (340)
Q Consensus 124 KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~wrp~~----sCddP---~Di~~d~sR~Wa-----IDKpnIP~~---P~GW 188 (340)
.||.+=|.++|.-+|++-.|.||.=+......+++ -|..| .+-.+|++-=|- |+.-+|-.. -.|.
T Consensus 9 ew~~~Lt~~qy~V~r~~gTE~pftg~~~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~V~~~~D~s~gm 88 (142)
T PRK00222 9 EWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKPIDEEAIRELRDTSHGM 88 (142)
T ss_pred HHHhhCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcccCCCceEEeeccCCCc
Confidence 59999999999999999999999766555556654 56665 455677777674 333333332 3699
Q ss_pred eEEEEEeccCCCcceEEEEE--CCCCCcc
Q 019501 189 QRLLRIRGEGSTKFADVYYE--APSGKKL 215 (340)
Q Consensus 189 KRevViRksGst~~~DVYY~--SPtGKKL 215 (340)
.|..|+=+.+....+-||-= .|+|+|.
T Consensus 89 ~RtEv~C~~Cg~HLGHVF~DGP~ptg~Ry 117 (142)
T PRK00222 89 VRTEVRCANCDSHLGHVFPDGPKPTGLRY 117 (142)
T ss_pred eEEEEEeCCCCCccCcccCCCCCCCCCEe
Confidence 99766633333223444432 5666553
No 13
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=34.50 E-value=26 Score=27.90 Aligned_cols=19 Identities=37% Similarity=0.681 Sum_probs=12.5
Q ss_pred cceeeeecccccceeeecc
Q 019501 112 VGAFTVQCADCFKWRLIPT 130 (340)
Q Consensus 112 i~~yavQC~~C~KWR~IpT 130 (340)
=|+.-|||..|..|.+|-.
T Consensus 25 ~GvViv~C~gC~~~HlIaD 43 (66)
T PF05180_consen 25 KGVVIVQCPGCKNRHLIAD 43 (66)
T ss_dssp TSEEEEE-TTS--EEES--
T ss_pred CCeEEEECCCCcceeeehh
Confidence 4788999999999999864
No 14
>KOG1141 consensus Predicted histone methyl transferase [Chromatin structure and dynamics]
Probab=32.41 E-value=31 Score=39.32 Aligned_cols=172 Identities=20% Similarity=0.231 Sum_probs=95.5
Q ss_pred CCCcccccceEEeccCCCCCCcccCCCCcccccCC---CCC---CCCC-CCCCCc----cCCccceeeeecccccceeee
Q 019501 60 QINGDASKQLVLYDPTANGTSEIEPVPESFQYNRA---PFG---RYSG-PNTQSR----VLPSVGAFTVQCADCFKWRLI 128 (340)
Q Consensus 60 ~~~e~~s~q~v~y~~~~~~~~e~~~~~~p~q~~~~---~~~---~~~~-~~~~~~----~~~si~~yavQC~~C~KWR~I 128 (340)
++...++..--.|+|+.++.|...+..+-.|-..+ |.. -+.. ...-++ .++.-|+=++-= --..
T Consensus 480 ~ir~~~~~k~~s~~p~~~~sgd~~p~~~~~qen~S~~fp~~~~t~~a~~~~~as~p~~~~f~~~g~~~~~s-----le~~ 554 (1262)
T KOG1141|consen 480 NIRDLAMTKQGSYDPSLNTSGDVGPRVACRQENSSSQFPKKTLTGTAAGRRRASRPDFLIFFDNGTDAYVS-----LETM 554 (1262)
T ss_pred hhhhhhhhcccccCcccccCCCccccchhhhhccccCCCccccccccccccccCCCCcccccCCCCCceee-----cccC
Confidence 45556667777899999998888776544443221 111 0000 000001 111222211111 2234
Q ss_pred ccHHHHHHHHhhhcCCCeeeccccccCCCCcCCCCCCCC----CCCcceeeecCCCCCCCCCCceEEEEEeccCCCcceE
Q 019501 129 PTKEKYEEIREHVLENPFTCEKAREWRPDVSCDDPTDIS----QDGSRLWAIDKPNIAQPPPGWQRLLRIRGEGSTKFAD 204 (340)
Q Consensus 129 pTke~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP~Di~----~d~sR~WaIDKpnIP~~P~GWKRevViRksGst~~~D 204 (340)
|-.=-||.--|++.--+.+|.-| |-.-+-|- |-| .+|..-+.-.-|+|.---|++.-....-
T Consensus 555 p~ep~y~~~seklsy~sh~cs~a--------cl~~~~~~~~~~~~g------~npl~lp~~~~F~r~~a~~rs~~~~~fh 620 (1262)
T KOG1141|consen 555 PGEPGYEVASEKLSYFSHKCSIA--------CLNAAQIAIMVGQPG------GNPLNLPYFLTFHRIRASHRSAYIRDFH 620 (1262)
T ss_pred CCCcccccccccccccchhhHHH--------HHhccchhhhccCCC------CCccccceEEEeeehhhhhhhhhhhcce
Confidence 44456777777788888888863 43333332 222 1222211124555543333332223467
Q ss_pred EEEECCCCCccccHHHHHHHHHhCcccccCCcccCcceecCCcCCcccc
Q 019501 205 VYYEAPSGKKLRSMVEIQKYFLEHPEYARAGVKMSQFSFQIPKPLQENY 253 (340)
Q Consensus 205 VYY~SPtGKKLRSk~EVarYL~~Npey~~~gLtLe~FdFstPK~~~e~y 253 (340)
|-|-+|||.-||-+.||-|||-+..-- =|.++.|+|..-..+...|
T Consensus 621 v~yktpcg~~lr~~~el~ryL~et~c~---flf~~~f~~~~yV~~~r~~ 666 (1262)
T KOG1141|consen 621 VEYKTPCGMPLRMRIELYRYLVETRCK---FLFVIGFDRAFYVVRHRAP 666 (1262)
T ss_pred eeccCCCccchHHHHHHHHHHHHhcCc---EEEEeecccchheeecccC
Confidence 999999999999999999999986521 3789999998665555444
No 15
>COG1218 CysQ 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase [Inorganic ion transport and metabolism]
Probab=31.47 E-value=58 Score=32.01 Aligned_cols=38 Identities=18% Similarity=0.243 Sum_probs=28.7
Q ss_pred HHHHHHhhhcCCCeeeccccccCCCCcCCCCCCCCCCCcceeeecC
Q 019501 133 KYEEIREHVLENPFTCEKAREWRPDVSCDDPTDISQDGSRLWAIDK 178 (340)
Q Consensus 133 ~yEeIRe~~~e~Pf~C~~a~~wrp~~sCddP~Di~~d~sR~WaIDK 178 (340)
=++.|+..+.+.|++|+- +|...--....+.|.|.||-
T Consensus 54 I~~~L~a~~P~ipvv~EE--------~~~~~~~~~~~~~rfWLiDP 91 (276)
T COG1218 54 ILEGLRALFPDIPVVSEE--------EEAIDWEERLHWDRFWLVDP 91 (276)
T ss_pred HHHHHHHhCCCCCEEEec--------cccCCCCCcccCceEEEECC
Confidence 478999999999999996 34443333455689999993
No 16
>PF00397 WW: WW domain; InterPro: IPR001202 Synonym(s): Rsp5 or WWP domain The WW domain is a short conserved region in a number of unrelated proteins, which folds as a stable, triple stranded beta-sheet. This short domain of approximately 40 amino acids, may be repeated up to four times in some proteins [, , , ]. The name WW or WWP derives from the presence of two signature tryptophan residues that are spaced 20-23 amino acids apart and are present in most WW domains known to date, as well as that of a conserved Pro. The WW domain binds to proteins with particular proline-motifs, [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs [, ]. It is frequently associated with other domains typical for proteins in signal transduction processes. A large variety of proteins containing the WW domain are known. These include; dystrophin, a multidomain cytoskeletal protein; utrophin, a dystrophin-like protein of unknown function; vertebrate YAP protein, substrate of an unknown serine kinase; Mus musculus (Mouse) NEDD-4, involved in the embryonic development and differentiation of the central nervous system; Saccharomyces cerevisiae (Baker's yeast) RSP5, similar to NEDD-4 in its molecular organisation; Rattus norvegicus (Rat) FE65, a transcription-factor activator expressed preferentially in liver; Nicotiana tabacum (Common tobacco) DB10 protein, amongst others.; GO: 0005515 protein binding; PDB: 2JXW_A 2DK1_A 2JOC_A 2JO9_A 1YIU_A 1O6W_A 2JMF_A 1TK7_A 2KYK_A 2L5F_A ....
Probab=26.75 E-value=81 Score=20.76 Aligned_cols=21 Identities=29% Similarity=0.793 Sum_probs=12.0
Q ss_pred CCCCceEEEEEeccCCCcceEEEEECC
Q 019501 184 PPPGWQRLLRIRGEGSTKFADVYYEAP 210 (340)
Q Consensus 184 ~P~GWKRevViRksGst~~~DVYY~SP 210 (340)
+|.||++..- .+ + +.+||+-.
T Consensus 1 LP~gW~~~~~--~~--~--g~~YY~N~ 21 (31)
T PF00397_consen 1 LPPGWEEYFD--PD--S--GRPYYYNH 21 (31)
T ss_dssp SSTTEEEEEE--TT--T--SEEEEEET
T ss_pred CCcCCEEEEc--CC--C--CCEEEEeC
Confidence 5899963222 22 2 56788743
No 17
>PF12528 DUF3728: Prepilin peptidase dependent protein C (DUF3728); InterPro: IPR022204 This family of proteins is found in bacteria. Proteins in this family are typically between 106 and 121 amino acids in length. The family is found in association with PF07963 from PFAM. There are two completely conserved C residues that may be functionally important. This family is frequently annotated as prepilin peptidase dependent protein C however there is little accompanying literature to confirm this.
Probab=25.95 E-value=1.2e+02 Score=24.63 Aligned_cols=37 Identities=27% Similarity=0.617 Sum_probs=27.1
Q ss_pred CCCCCCCCCceEEEEEec-cCCCcceEEEEECCCCCcc
Q 019501 179 PNIAQPPPGWQRLLRIRG-EGSTKFADVYYEAPSGKKL 215 (340)
Q Consensus 179 pnIP~~P~GWKRevViRk-sGst~~~DVYY~SPtGKKL 215 (340)
+.+..+|.||+....... .+.=...-|-..+|.|+..
T Consensus 37 ~~~~~~~~gWq~~~~~~~~~~~C~~itvtv~tP~~~~a 74 (84)
T PF12528_consen 37 PALSGPPPGWQYSRQQTSIQGGCRSITVTVTTPQNQQA 74 (84)
T ss_pred ccccCCCCCceeeeeeeccCCCeEEEEEEEecCCCccc
Confidence 556788999999998877 4332346677789988764
No 18
>cd01259 PH_Apbb1ip Apbb1ip (Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein) pleckstrin homology (PH) domain. Apbb1ip (Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein) pleckstrin homology (PH) domain. Apbb1ip consists of a Ras-associated domain and a PH domain. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=23.35 E-value=1.2e+02 Score=26.77 Aligned_cols=33 Identities=21% Similarity=0.495 Sum_probs=23.8
Q ss_pred CCceE-EEEEeccCCCcceEEEEECCCCCccccHHHHHHHHH
Q 019501 186 PGWQR-LLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFL 226 (340)
Q Consensus 186 ~GWKR-evViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~ 226 (340)
..||| -.++|++| -||+|-| +.++..+|+.+..
T Consensus 14 KsWKk~~f~LR~SG-------LYy~~Kg-ksk~srdL~cl~~ 47 (114)
T cd01259 14 KSWKKYYFVLRSSG-------LYYFPKE-KTKNTRDLACLNL 47 (114)
T ss_pred ccceEEEEEEeCCe-------eEEccCC-CcCCHHHHHHHHh
Confidence 56776 46778776 3788999 5567778877764
No 19
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase. Alternate name: pimeloyl-CoA synthase.
Probab=22.07 E-value=1.1e+02 Score=29.67 Aligned_cols=39 Identities=15% Similarity=0.388 Sum_probs=34.6
Q ss_pred CceEEEEEeccCCCcceEEEEECCCCCccccHHHHHHHHHhCc
Q 019501 187 GWQRLLRIRGEGSTKFADVYYEAPSGKKLRSMVEIQKYFLEHP 229 (340)
Q Consensus 187 GWKRevViRksGst~~~DVYY~SPtGKKLRSk~EVarYL~~Np 229 (340)
|+.|.-.++..|+...+-|||+.++ . ...++..||.+.|
T Consensus 190 gY~RI~~lK~~G~~~GGRvffv~~~-~---~l~~~i~yLE~~p 228 (232)
T TIGR01204 190 GYVRITPLKEKGDELGGRVFFVSRK-N---ELSEYIHCLEQKP 228 (232)
T ss_pred CeEeCccccccCCCCCCEEEEEeCC-C---CHHHHHHHHhcCc
Confidence 8999999999998878999999986 2 8899999999766
No 20
>KOG3794 consensus CBF1-interacting corepressor CIR and related proteins [Transcription]
Probab=21.73 E-value=51 Score=34.53 Aligned_cols=37 Identities=30% Similarity=0.573 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCCccCC-ccceeeeecccccceeeeccH
Q 019501 95 PFGRYSGPNTQSRVLP-SVGAFTVQCADCFKWRLIPTK 131 (340)
Q Consensus 95 ~~~~~~~~~~~~~~~~-si~~yavQC~~C~KWR~IpTk 131 (340)
|+-.+....+..|++| -|..=.|+|++|.||--|-|-
T Consensus 102 pRE~~ak~~~~irdqPFGiqVRNVrC~kChkwGH~n~D 139 (453)
T KOG3794|consen 102 PREKLAKAPTEIRDQPFGIQVRNVRCLKCHKWGHINTD 139 (453)
T ss_pred cHHHHhcCCccccccccceEeeeeeEEeecccccccCC
Confidence 3333444445556654 588889999999999988764
No 21
>COG3410 Uncharacterized conserved protein [Function unknown]
Probab=21.63 E-value=78 Score=29.92 Aligned_cols=43 Identities=23% Similarity=0.320 Sum_probs=34.7
Q ss_pred ccCcceecCCcCCcccccccCCCCCCCCCCCCCCCCCcccCCCcccCCC
Q 019501 237 KMSQFSFQIPKPLQENYVRKRVPKAHTSHDTPKALEPRAVSPLSWVSPD 285 (340)
Q Consensus 237 tLe~FdFstPK~~~e~yvkKrp~~~~~s~~~~~~l~~eEV~Pl~wA~p~ 285 (340)
.++.|+|..+.++++.|+-+.+---. -|-.-++-||.| |++..
T Consensus 43 ~~st~d~~~~~d~ks~yv~~~t~l~v----~W~m~ektevt~--Wree~ 85 (191)
T COG3410 43 NVSTFDYRIGYDLKSYYVYDETGLNV----PWLMTEKTEVTP--WREEL 85 (191)
T ss_pred CCcccceeccCCCCceeEEeCCCccc----eeecCCCccCCc--cccCC
Confidence 56699999999999999998875433 267778889999 88876
No 22
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=21.33 E-value=2.5e+02 Score=25.12 Aligned_cols=91 Identities=21% Similarity=0.311 Sum_probs=58.6
Q ss_pred ceeeeccHHHHHHHHhhhcCCCeeeccccccCCC----CcCCCC---CCCCCCCcceee-----ecCCCCCC---CCCCc
Q 019501 124 KWRLIPTKEKYEEIREHVLENPFTCEKAREWRPD----VSCDDP---TDISQDGSRLWA-----IDKPNIAQ---PPPGW 188 (340)
Q Consensus 124 KWR~IpTke~yEeIRe~~~e~Pf~C~~a~~wrp~----~sCddP---~Di~~d~sR~Wa-----IDKpnIP~---~P~GW 188 (340)
.||.+=|.++|.-+|++-.|.||.=+......++ +-|..| .+..+|++-=|- |+.-.|-. .-.|.
T Consensus 6 ewr~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D~s~gm 85 (134)
T TIGR00357 6 ELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDESHGM 85 (134)
T ss_pred HHHHhCCHHHHHHHHHhCCCCCCCCCCCCCCCCeEEEccCCCCccccccchhcCCCCCcCcCcccCCCceEEeecCCCCc
Confidence 5898889999999999999999987766666666 356666 466677766663 32222322 23688
Q ss_pred eEEEEEeccCCCcceEEEEE--CCCCCc
Q 019501 189 QRLLRIRGEGSTKFADVYYE--APSGKK 214 (340)
Q Consensus 189 KRevViRksGst~~~DVYY~--SPtGKK 214 (340)
.|..|.=+......+-||-= .|+|+|
T Consensus 86 ~RtEv~C~~Cg~HLGHVF~DGP~ptg~R 113 (134)
T TIGR00357 86 IRTEVRCRNCDAHLGHVFDDGPEPTGLR 113 (134)
T ss_pred EEEEEEecCCCCccCcccCCCCCCCCce
Confidence 88666544333223444422 566665
No 23
>PF08358 Flexi_CP_N: Carlavirus coat; InterPro: IPR013569 This domain is found together with the viral coat protein domain (IPR000052 from INTERPRO) in coat/capsid proteins of the plant infecting Carlavirus. It is required for genome encapsidation by forming ribonucleoprotein complexes along with TGB1 helicase and viral RNA. The N- and the C terminus of this coat protein can be exposed on the surface of the virus particle. The central core sequence may be important in maintaining correct tertiary structure of the coat protein and/or play a role in the interaction with the viral RNA. Coat proteins are often used to distinguish between Carlavirus isolates. In the coat protein amino acid sequences of definitive and tentative species of carlaviruses, there is a region of seven amino acids (GLGVPTE) that are conserved []. The complete coat protein (CP) sequences of 29 Indian Chrysanthemum virus B (CVB) isolates were highly heterogeneous, sharing nucleotide sequence identities of 74-98% [, ].
Probab=20.68 E-value=88 Score=23.93 Aligned_cols=29 Identities=24% Similarity=0.564 Sum_probs=22.7
Q ss_pred CccccccCCCCCCCC-CCCCCCCCCCCchh
Q 019501 286 NFTDLQLGRPALPAP-PVEAPISDPNPRPA 314 (340)
Q Consensus 286 ~~~~lql~~~~l~~p-~~~s~~~~~~~rp~ 314 (340)
+-..+..|+|.|-++ -|..-..|++.||+
T Consensus 19 ~N~~fE~GRP~l~~~~~mr~d~tN~y~RpS 48 (52)
T PF08358_consen 19 TNPGFEIGRPKLEPSDDMRGDPTNPYSRPS 48 (52)
T ss_pred cccccccCCcCCcCchhhCCCcCcccCCcc
Confidence 344577899998554 88888899999986
No 24
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=20.03 E-value=77 Score=21.24 Aligned_cols=13 Identities=31% Similarity=0.708 Sum_probs=11.5
Q ss_pred cHHHHHHHHhhhc
Q 019501 130 TKEKYEEIREHVL 142 (340)
Q Consensus 130 Tke~yEeIRe~~~ 142 (340)
|.+||+..|.+++
T Consensus 18 seeEy~~~k~~ll 30 (31)
T PF09851_consen 18 SEEEYEQKKARLL 30 (31)
T ss_pred CHHHHHHHHHHHh
Confidence 7899999999876
Done!