Query 022412
Match_columns 297
No_of_seqs 37 out of 39
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 03:20:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022412.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022412hhsearch_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, 99.5 3.2E-14 6.9E-19 108.9 5.1 62 15-76 3-66 (77)
2 cd00122 MBD MeCP2, MBD1, MBD2, 99.3 1.6E-12 3.5E-17 94.6 4.6 60 14-73 2-62 (62)
3 smart00391 MBD Methyl-CpG bind 99.1 5.2E-11 1.1E-15 91.2 5.0 64 13-76 3-68 (77)
4 PF01429 MBD: Methyl-CpG bindi 99.1 1E-10 2.2E-15 88.3 5.1 67 11-77 4-73 (77)
5 cd01397 HAT_MBD Methyl-CpG bin 98.1 4.8E-06 1E-10 64.7 4.6 62 14-75 2-64 (73)
6 cd01395 HMT_MBD Methyl-CpG bin 96.7 0.0025 5.5E-08 48.0 4.1 58 14-72 2-59 (60)
7 KOG4161 Methyl-CpG binding tra 91.0 0.2 4.3E-06 46.6 3.1 44 19-62 20-64 (272)
8 smart00527 HMG17 domain in hig 75.5 1.7 3.7E-05 35.7 1.6 13 77-89 15-27 (88)
9 PF01101 HMG14_17: HMG14 and H 74.1 1.9 4E-05 35.4 1.5 12 77-88 17-28 (93)
10 PF07533 BRK: BRK domain; Int 60.2 3.3 7.1E-05 29.8 0.3 21 45-65 20-40 (46)
11 smart00592 BRK domain in trans 40.3 28 0.00062 24.9 2.4 23 45-67 18-40 (45)
12 COG3181 Uncharacterized protei 35.1 33 0.00072 33.2 2.8 26 39-64 124-149 (319)
13 KOG2501 Thioredoxin, nucleored 33.1 47 0.001 29.5 3.2 47 36-92 68-114 (157)
14 PRK01844 hypothetical protein; 29.8 33 0.00072 27.3 1.6 14 50-63 24-37 (72)
15 PF15297 CKAP2_C: Cytoskeleton 29.6 19 0.00042 35.6 0.3 18 77-94 302-320 (353)
16 PF03000 NPH3: NPH3 family; I 29.6 32 0.00069 32.2 1.6 12 53-64 224-235 (258)
17 PRK00523 hypothetical protein; 28.8 35 0.00077 27.2 1.5 14 50-63 25-38 (72)
18 COG3763 Uncharacterized protei 27.7 37 0.0008 27.1 1.5 14 50-63 24-37 (71)
19 cd01259 PH_Apbb1ip Apbb1ip (Am 27.5 75 0.0016 27.2 3.4 47 9-63 3-50 (114)
20 PF10952 DUF2753: Protein of u 27.3 32 0.00069 30.5 1.1 19 51-70 102-120 (140)
21 PF07624 PSD2: Protein of unkn 26.9 50 0.0011 25.0 2.0 19 44-62 1-19 (76)
22 PF03401 TctC: Tripartite tric 26.7 50 0.0011 29.8 2.3 32 38-69 79-110 (274)
23 PF13098 Thioredoxin_2: Thiore 24.1 70 0.0015 23.7 2.3 26 31-59 81-112 (112)
24 PF07122 VLPT: Variable length 24.0 43 0.00093 23.1 1.0 18 3-20 5-22 (30)
25 PRK03333 coaE dephospho-CoA ki 23.9 89 0.0019 30.1 3.5 42 21-64 304-346 (395)
26 PF03672 UPF0154: Uncharacteri 23.1 54 0.0012 25.5 1.6 13 51-63 18-30 (64)
27 COG1658 Small primase-like pro 23.0 76 0.0016 27.2 2.6 24 36-61 56-81 (127)
28 PF07419 PilM: PilM; InterPro 22.5 50 0.0011 28.0 1.4 35 52-86 38-75 (136)
29 PF06590 PerB: PerB protein; 21.0 79 0.0017 27.2 2.3 29 16-45 20-48 (129)
30 PF05939 Phage_min_tail: Phage 20.8 88 0.0019 25.3 2.5 39 34-79 41-79 (109)
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=99.49 E-value=3.2e-14 Score=108.94 Aligned_cols=62 Identities=37% Similarity=0.757 Sum_probs=58.0
Q ss_pred ecc-CCCCCccccccCCCCCCCcceEEEecCCchhhcchHHHHHHHHhC-CCCCCccccccCCC
Q 022412 15 ELP-APFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAH-PGGPASSEFDWGTG 76 (297)
Q Consensus 15 eLP-AP~GWkKk~~pkkgGTPkK~eIvFvAPtGEEI~~krqLe~YLKah-pGgp~~seFdWgTg 76 (297)
++| .|+||++.+.++++|+..+.+|.|++|+|..|+|+.+|.+||.+| ++++.+++|||+++
T Consensus 3 ~~~~lp~GW~r~~~~R~~gs~~k~DvyY~sP~Gkk~RS~~ev~~yL~~~~~~~~~~~~FdF~~~ 66 (77)
T cd01396 3 EDPRLPPGWKRELVPRKSGSAGKFDVYYISPTGKKFRSKVELARYLEKNGPTSLDLSDFDFTVP 66 (77)
T ss_pred CCCCCCCCCEEEEEEecCCCCCcceEEEECCCCCEEECHHHHHHHHHhCCCCCCcHhHcccCCC
Confidence 455 789999999999999999999999999999999999999999999 55799999999985
No 2
>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=99.32 E-value=1.6e-12 Score=94.56 Aligned_cols=60 Identities=28% Similarity=0.687 Sum_probs=57.0
Q ss_pred eeccCCCCCccccccCCCCCCCcceEEEecCCchhhcchHHHHHHHHhC-CCCCCcccccc
Q 022412 14 FELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAH-PGGPASSEFDW 73 (297)
Q Consensus 14 ~eLPAP~GWkKk~~pkkgGTPkK~eIvFvAPtGEEI~~krqLe~YLKah-pGgp~~seFdW 73 (297)
+.+|.|.||++.+..++.|+..+.+|.|++|+|..++|+.+|.+||..| +.++.++.|||
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 LRDPLPPGWKRELVIRKSGSAGKGDVYYYSPCGKKLRSKPEVARYLEKTGPSSLDLENFSF 62 (62)
T ss_pred CCCCCCCCeEEEEEEcCCCCCCcceEEEECCCCceecCHHHHHHHHHhCCCCCCcHHHCCC
Confidence 5789999999999999999999999999999999999999999999999 66799999997
No 3
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=99.14 E-value=5.2e-11 Score=91.20 Aligned_cols=64 Identities=27% Similarity=0.606 Sum_probs=56.8
Q ss_pred eeeccCCCCCccccccCCCC-CCCcceEEEecCCchhhcchHHHHHHHHhCCCC-CCccccccCCC
Q 022412 13 SFELPAPFGWKKKIVPRKGG-TPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGG-PASSEFDWGTG 76 (297)
Q Consensus 13 s~eLPAP~GWkKk~~pkkgG-TPkK~eIvFvAPtGEEI~~krqLe~YLKahpGg-p~~seFdWgTg 76 (297)
.+.+|.|.||++.+..++.| +..+.+|+|++|+|..++|+.+|.+||.+|+.. ..+..|||+++
T Consensus 3 ~~~~Plp~GW~R~~~~r~~g~~~~~~dV~Y~sP~GkklRs~~ev~~YL~~~~~~~~~~~~F~F~~~ 68 (77)
T smart00391 3 PLRLPLPCGWRRETKQRKSGRSAGKFDVYYISPCGKKLRSKSELARYLHKNGDLSLDLECFDFNAT 68 (77)
T ss_pred cccCCCCCCcEEEEEEecCCCCCCcccEEEECCCCCeeeCHHHHHHHHHhCCCcccccccccCcCC
Confidence 46899999999999988876 667999999999999999999999999999864 55678999875
No 4
>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=99.11 E-value=1e-10 Score=88.28 Aligned_cols=67 Identities=28% Similarity=0.634 Sum_probs=58.2
Q ss_pred eeeeeccCCCCCccccccCCCCCC-CcceEEEecCCchhhcchHHHHHHHHhCCC--CCCccccccCCCC
Q 022412 11 QVSFELPAPFGWKKKIVPRKGGTP-KKSEIVFTAPTGEEISNKKQLEQYLKAHPG--GPASSEFDWGTGE 77 (297)
Q Consensus 11 ~vs~eLPAP~GWkKk~~pkkgGTP-kK~eIvFvAPtGEEI~~krqLe~YLKahpG--gp~~seFdWgTge 77 (297)
...+.+|-|.||++.+..++.|+. .+.+|.|++|+|..++|+.++.+||..+++ .+.+..|+|.+.-
T Consensus 4 ~~~~~~~Lp~GW~re~~~R~~g~~~~~~dv~Y~sP~Gk~~RS~~eV~~yL~~~~~~~~l~~~~F~F~~~~ 73 (77)
T PF01429_consen 4 ISPLDPPLPDGWKREVVVRKSGSSAGKKDVYYYSPCGKRFRSKKEVVRYLKENPSEHDLKPENFSFSKRL 73 (77)
T ss_dssp SECEBTTSTTT-EEEEEESSSSTTTTSEEEEEEETTSEEESSHHHHHHHHTTSS---SS-CTTBBTTTTB
T ss_pred cccccCCCCCCCEEEEEEecCCCcCCceEEEEECCCCCEEeCHHHHHHHHHhCCCcccCCHhHCCCCCCc
Confidence 455778999999999999998766 799999999999999999999999999998 9999999998763
No 5
>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=98.08 E-value=4.8e-06 Score=64.65 Aligned_cols=62 Identities=19% Similarity=0.475 Sum_probs=55.5
Q ss_pred eeccCCCCCccccccCCCCCCCcceEEEecCCchhhcchHHHHHHHHhCC-CCCCccccccCC
Q 022412 14 FELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHP-GGPASSEFDWGT 75 (297)
Q Consensus 14 ~eLPAP~GWkKk~~pkkgGTPkK~eIvFvAPtGEEI~~krqLe~YLKahp-Ggp~~seFdWgT 75 (297)
+-+|-|.||++...-++.|.-.+.+|.|.||.|--+++.-++.+||..|+ .++.+..|+..+
T Consensus 2 ~r~Pl~~GW~Re~vir~~~~~~~~dV~Y~aPcGKklRs~~ev~~yL~~~~~~~Lt~dnFsF~~ 64 (73)
T cd01397 2 LRVPLELGWRRETRIRGLGGRIQGEVAYYAPCGKKLRQYPEVIKYLSKNGISLLSRENFSFSA 64 (73)
T ss_pred ccCCCCCCceeEEEeccCCCCccceEEEECCCCcccccHHHHHHHHHhCCccCccHhHccccC
Confidence 45788999999998888777789999999999999999999999999887 478899998865
No 6
>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=96.68 E-value=0.0025 Score=48.04 Aligned_cols=58 Identities=19% Similarity=0.410 Sum_probs=49.5
Q ss_pred eeccCCCCCccccccCCCCCCCcceEEEecCCchhhcchHHHHHHHHhCCCCCCccccc
Q 022412 14 FELPAPFGWKKKIVPRKGGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFD 72 (297)
Q Consensus 14 ~eLPAP~GWkKk~~pkkgGTPkK~eIvFvAPtGEEI~~krqLe~YLKahpGgp~~seFd 72 (297)
+-+|--.||.+...-.+.| -.+..|+|-||.|.-++|-.++.+||..+.-.+.+..|+
T Consensus 2 L~~Pll~gw~R~~~~~~~~-~~k~~V~Y~aPCGr~Lr~~~EV~~YL~~t~~~L~~d~Fs 59 (60)
T cd01395 2 LHTPLLCGFQRMKYRARVG-KVKKHVIYKAPCGRSLRNMSEVHRYLRETCSFLTVDNFS 59 (60)
T ss_pred cccccccCeEEEEEeccCC-CcccceEEECCcchhhhcHHHHHHHHHhccccceeeccc
Confidence 4577779999998877766 457779999999999999999999999997677777775
No 7
>KOG4161 consensus Methyl-CpG binding transcription regulators [Transcription; Chromatin structure and dynamics]
Probab=91.04 E-value=0.2 Score=46.61 Aligned_cols=44 Identities=34% Similarity=0.708 Sum_probs=39.3
Q ss_pred CCCCccccccCCCCCC-CcceEEEecCCchhhcchHHHHHHHHhC
Q 022412 19 PFGWKKKIVPRKGGTP-KKSEIVFTAPTGEEISNKKQLEQYLKAH 62 (297)
Q Consensus 19 P~GWkKk~~pkkgGTP-kK~eIvFvAPtGEEI~~krqLe~YLKah 62 (297)
|+||++...++++|-+ -+.+|+|+.|.|--.+|+-+|-.||--.
T Consensus 20 p~GW~~~~~~r~~~~~~g~~dv~~~sp~g~~frsk~~l~~~~~~~ 64 (272)
T KOG4161|consen 20 PPGWTREEVQRSSGLSAGKSDVYYISPSGKKFRSKPQLARYLGKV 64 (272)
T ss_pred CCCcchhhhcccCCCcccccceEEeCCcccccccccHHHHHhccc
Confidence 7999999999997644 5899999999999999999999999654
No 8
>smart00527 HMG17 domain in high mobilty group proteins HMG14 and HMG 17.
Probab=75.45 E-value=1.7 Score=35.70 Aligned_cols=13 Identities=62% Similarity=0.777 Sum_probs=10.5
Q ss_pred CCCcchhhhhccc
Q 022412 77 ETPRRSARISEKA 89 (297)
Q Consensus 77 eTPRRSaRiseK~ 89 (297)
+-.|||||||-|.
T Consensus 15 EP~RRSARLSAkP 27 (88)
T smart00527 15 EPKRRSARLSAKP 27 (88)
T ss_pred cccchhhhhccCC
Confidence 4569999999775
No 9
>PF01101 HMG14_17: HMG14 and HMG17; InterPro: IPR000079 High mobility group (HMG) proteins constitute a family of relatively low molecular weight non-histone components in chromatin. HMG14 and HMG17 are highly-similar proteins of about 100 amino acid residues; the sequence of chicken HMG14 is almost as similar to chicken HMG17 as it is to mammalian HMG14 polypeptides []. The proteins bind to the inner side of the nucleosomal DNA, altering the interaction between the DNA and the histone octamer. It is thought that they may be involved in the process that confers specific chromatin conformations to transcribable regions in the genome []. The SMART signature describes a nucleosomal binding domain, which facilitates binding of proteins to nucleosomes in chromatin. The domain is most commonly found in the high mobility group (HMG) proteins, HMG14 and HMG17, however, it is also found in other proteins which bind to nucleosomes, e.g. NBP-45. NBP-45 is a nucleosomal binding protein, first identified in mice [], which is related to HMG14 and HMG17. NBP-45 binds specifically to nucleosome core particles, and can function as a transcriptional activator. These findings led to the suggestion that this domain, common to NBP-45, HMG14 and HMG17 is responsible for binding of the proteins to nucleosomes in chromatin.; GO: 0003677 DNA binding, 0000785 chromatin, 0005634 nucleus
Probab=74.15 E-value=1.9 Score=35.45 Aligned_cols=12 Identities=67% Similarity=0.844 Sum_probs=10.1
Q ss_pred CCCcchhhhhcc
Q 022412 77 ETPRRSARISEK 88 (297)
Q Consensus 77 eTPRRSaRiseK 88 (297)
+..|||+|||-|
T Consensus 17 EP~RRSaRLSAk 28 (93)
T PF01101_consen 17 EPQRRSARLSAK 28 (93)
T ss_pred CCCcccccccCC
Confidence 456999999987
No 10
>PF07533 BRK: BRK domain; InterPro: IPR006576 BRK is a domain of unknown function found only in the metazoa and in association with CHROMO domain (IPR000953 from INTERPRO) and DEAD/DEAH box helicase domain (IPR011545 from INTERPRO).; GO: 0005515 protein binding, 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2DL6_A 2CKA_A 2V0F_A 2V0E_A 2CKC_A.
Probab=60.18 E-value=3.3 Score=29.82 Aligned_cols=21 Identities=48% Similarity=0.847 Sum_probs=15.5
Q ss_pred CchhhcchHHHHHHHHhCCCC
Q 022412 45 TGEEISNKKQLEQYLKAHPGG 65 (297)
Q Consensus 45 tGEEI~~krqLe~YLKahpGg 65 (297)
+|.+-...++|.+||..|||-
T Consensus 20 ~G~~AP~~~~L~~WL~~~P~y 40 (46)
T PF07533_consen 20 TGDEAPKLKELEEWLEEHPGY 40 (46)
T ss_dssp -CCCS-BCCCHHHHHHH-TTE
T ss_pred ccccCcCHHHHHHHHHHCcCc
Confidence 466777889999999999974
No 11
>smart00592 BRK domain in transcription and CHROMO domain helicases.
Probab=40.26 E-value=28 Score=24.93 Aligned_cols=23 Identities=30% Similarity=0.589 Sum_probs=17.9
Q ss_pred CchhhcchHHHHHHHHhCCCCCC
Q 022412 45 TGEEISNKKQLEQYLKAHPGGPA 67 (297)
Q Consensus 45 tGEEI~~krqLe~YLKahpGgp~ 67 (297)
+|..-...++|..||..|||--.
T Consensus 18 ~g~~aP~~~~l~~WL~~~p~yev 40 (45)
T smart00592 18 TGDDAPKAKDLERWLEENPEYEV 40 (45)
T ss_pred ccccCCcHHHHHHHHhcCCCccc
Confidence 45555778999999999997533
No 12
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.06 E-value=33 Score=33.21 Aligned_cols=26 Identities=31% Similarity=0.400 Sum_probs=24.0
Q ss_pred EEEecCCchhhcchHHHHHHHHhCCC
Q 022412 39 IVFTAPTGEEISNKKQLEQYLKAHPG 64 (297)
Q Consensus 39 IvFvAPtGEEI~~krqLe~YLKahpG 64 (297)
-+|+.+.....+|-..|-.|+|+|||
T Consensus 124 ~~l~v~~~s~~~t~~dlv~~~k~~p~ 149 (319)
T COG3181 124 GVLVVRADSPYKTLKDLVAYAKADPG 149 (319)
T ss_pred ceEEEeCCCCcccHHHHHHHHHhCCC
Confidence 36888899999999999999999998
No 13
>KOG2501 consensus Thioredoxin, nucleoredoxin and related proteins [General function prediction only]
Probab=33.13 E-value=47 Score=29.54 Aligned_cols=47 Identities=26% Similarity=0.463 Sum_probs=31.2
Q ss_pred cceEEEecCCchhhcchHHHHHHHHhCCCCCCccccccCCCCCCcchhhhhccccCC
Q 022412 36 KSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETPRRSARISEKAKIS 92 (297)
Q Consensus 36 K~eIvFvAPtGEEI~~krqLe~YLKahpGgp~~seFdWgTgeTPRRSaRiseK~Kat 92 (297)
-.|||||+-+. +..+|..|+..|+|.=.+--| | -.+...|+.|-...
T Consensus 68 ~fEVvfVS~D~----~~~~~~~y~~~~~~~W~~iPf----~--d~~~~~l~~ky~v~ 114 (157)
T KOG2501|consen 68 PFEVVFVSSDR----DEESLDEYMLEHHGDWLAIPF----G--DDLIQKLSEKYEVK 114 (157)
T ss_pred ceEEEEEecCC----CHHHHHHHHHhcCCCeEEecC----C--CHHHHHHHHhcccC
Confidence 57999999985 568999999999874333222 1 23444555555544
No 14
>PRK01844 hypothetical protein; Provisional
Probab=29.82 E-value=33 Score=27.32 Aligned_cols=14 Identities=29% Similarity=0.603 Sum_probs=12.5
Q ss_pred cchHHHHHHHHhCC
Q 022412 50 SNKKQLEQYLKAHP 63 (297)
Q Consensus 50 ~~krqLe~YLKahp 63 (297)
-.|+++++||+.||
T Consensus 24 ~ark~~~k~lk~NP 37 (72)
T PRK01844 24 IARKYMMNYLQKNP 37 (72)
T ss_pred HHHHHHHHHHHHCC
Confidence 36899999999997
No 15
>PF15297 CKAP2_C: Cytoskeleton-associated protein 2 C-terminus
Probab=29.60 E-value=19 Score=35.57 Aligned_cols=18 Identities=56% Similarity=0.696 Sum_probs=14.2
Q ss_pred CCC-cchhhhhccccCCCC
Q 022412 77 ETP-RRSARISEKAKISPA 94 (297)
Q Consensus 77 eTP-RRSaRiseK~Kat~~ 94 (297)
-|| |||+||.+|.-.-|.
T Consensus 302 ~TPVRrS~Ri~~k~~~~p~ 320 (353)
T PF15297_consen 302 LTPVRRSARIERKTSKLPD 320 (353)
T ss_pred ecchhhHHHHHHhhhhcch
Confidence 478 999999999665553
No 16
>PF03000 NPH3: NPH3 family; InterPro: IPR004249 The RPT2 protein is a signal transducer of the phototropic response in Arabidopsis thaliana. The RPT2 gene is light inducible; encodes a novel protein with putative phosphorylation sites, a nuclear localization signal, a BTB/POZ domain (IPR000210 from INTERPRO), and a coiled-coil domain. RPT2 belongs to a large gene family that includes the recently isolated NPH3 gene []. The NPH3 protein is a NPH1 photoreceptor-interacting protein that is essential for phototropism. Phototropism of A. thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase []. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay []. Many of the proteins in this group also contain the BTB/POZ domain (IPR000210 from INTERPRO) at the N-terminal.; GO: 0004871 signal transducer activity, 0009416 response to light stimulus
Probab=29.59 E-value=32 Score=32.20 Aligned_cols=12 Identities=58% Similarity=1.212 Sum_probs=10.3
Q ss_pred HHHHHHHHhCCC
Q 022412 53 KQLEQYLKAHPG 64 (297)
Q Consensus 53 rqLe~YLKahpG 64 (297)
|.++-|||+||+
T Consensus 224 rAID~YLk~Hp~ 235 (258)
T PF03000_consen 224 RAIDIYLKAHPG 235 (258)
T ss_pred HHHHHHHHHccc
Confidence 678899999994
No 17
>PRK00523 hypothetical protein; Provisional
Probab=28.80 E-value=35 Score=27.19 Aligned_cols=14 Identities=21% Similarity=0.539 Sum_probs=12.5
Q ss_pred cchHHHHHHHHhCC
Q 022412 50 SNKKQLEQYLKAHP 63 (297)
Q Consensus 50 ~~krqLe~YLKahp 63 (297)
-.|+++++||+.||
T Consensus 25 iark~~~k~l~~NP 38 (72)
T PRK00523 25 VSKKMFKKQIRENP 38 (72)
T ss_pred HHHHHHHHHHHHCc
Confidence 36899999999998
No 18
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.66 E-value=37 Score=27.14 Aligned_cols=14 Identities=36% Similarity=0.619 Sum_probs=12.6
Q ss_pred cchHHHHHHHHhCC
Q 022412 50 SNKKQLEQYLKAHP 63 (297)
Q Consensus 50 ~~krqLe~YLKahp 63 (297)
-++|++.+|||.||
T Consensus 24 iark~~~k~lk~NP 37 (71)
T COG3763 24 IARKQMKKQLKDNP 37 (71)
T ss_pred HHHHHHHHHHhhCC
Confidence 46999999999998
No 19
>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=27.55 E-value=75 Score=27.23 Aligned_cols=47 Identities=19% Similarity=0.299 Sum_probs=36.9
Q ss_pred cceeeeeccCCCCCccccccCC-CCCCCcceEEEecCCchhhcchHHHHHHHHhCC
Q 022412 9 EEQVSFELPAPFGWKKKIVPRK-GGTPKKSEIVFTAPTGEEISNKKQLEQYLKAHP 63 (297)
Q Consensus 9 ee~vs~eLPAP~GWkKk~~pkk-gGTPkK~eIvFvAPtGEEI~~krqLe~YLKahp 63 (297)
++.+.+.-|.=-+|||.||--| +| +|..|-| ..++.|||.++..-+.
T Consensus 3 ~g~LylK~~gkKsWKk~~f~LR~SG-------LYy~~Kg-ksk~srdL~cl~~f~~ 50 (114)
T cd01259 3 EGPLYLKADGKKSWKKYYFVLRSSG-------LYYFPKE-KTKNTRDLACLNLLHG 50 (114)
T ss_pred cceEEEccCCCccceEEEEEEeCCe-------eEEccCC-CcCCHHHHHHHHhccc
Confidence 4566677777789999877654 45 7888888 8999999999987764
No 20
>PF10952 DUF2753: Protein of unknown function (DUF2753); InterPro: IPR020206 This entry represents a group of uncharacterised proteins.
Probab=27.27 E-value=32 Score=30.47 Aligned_cols=19 Identities=37% Similarity=0.672 Sum_probs=15.7
Q ss_pred chHHHHHHHHhCCCCCCccc
Q 022412 51 NKKQLEQYLKAHPGGPASSE 70 (297)
Q Consensus 51 ~krqLe~YLKahpGgp~~se 70 (297)
-+..|..|||.|| +|.|..
T Consensus 102 Ck~ALl~F~KRHP-NP~iA~ 120 (140)
T PF10952_consen 102 CKKALLDFMKRHP-NPEIAR 120 (140)
T ss_pred cHHHHHHHHHhCC-CHHHHH
Confidence 4788999999999 887753
No 21
>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=26.88 E-value=50 Score=25.01 Aligned_cols=19 Identities=32% Similarity=0.644 Sum_probs=18.3
Q ss_pred CCchhhcchHHHHHHHHhC
Q 022412 44 PTGEEISNKKQLEQYLKAH 62 (297)
Q Consensus 44 PtGEEI~~krqLe~YLKah 62 (297)
|+|.++.+-..|.+||..+
T Consensus 1 pdG~~f~~~~eLk~~L~~~ 19 (76)
T PF07624_consen 1 PDGTSFEGAAELKQYLAER 19 (76)
T ss_pred CCCCccCCHHHHHHHHHHC
Confidence 8999999999999999988
No 22
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=26.66 E-value=50 Score=29.82 Aligned_cols=32 Identities=22% Similarity=0.291 Sum_probs=23.5
Q ss_pred eEEEecCCchhhcchHHHHHHHHhCCCCCCcc
Q 022412 38 EIVFTAPTGEEISNKKQLEQYLKAHPGGPASS 69 (297)
Q Consensus 38 eIvFvAPtGEEI~~krqLe~YLKahpGgp~~s 69 (297)
-.+++++..-.++|-..|..|+|+|||...+.
T Consensus 79 ~~vl~v~~dsp~~t~~eli~~ak~~p~~~~~g 110 (274)
T PF03401_consen 79 PNVLVVRADSPYKTLEELIEYAKANPGKLTFG 110 (274)
T ss_dssp EEEEEEETTSS-SSHHHHHHHHHCSCCC-EEE
T ss_pred ceEEEEeCCCccccHHHHHHHHHhCCCCeEEE
Confidence 34555555678999999999999999876554
No 23
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=24.15 E-value=70 Score=23.69 Aligned_cols=26 Identities=35% Similarity=0.583 Sum_probs=17.4
Q ss_pred CCCCCcceEEEecCCchhhc------chHHHHHHH
Q 022412 31 GGTPKKSEIVFTAPTGEEIS------NKKQLEQYL 59 (297)
Q Consensus 31 gGTPkK~eIvFvAPtGEEI~------~krqLe~YL 59 (297)
.|||. |+|+.++|..|. +..+|.++|
T Consensus 81 ~gtPt---~~~~d~~G~~v~~~~G~~~~~~l~~~L 112 (112)
T PF13098_consen 81 NGTPT---IVFLDKDGKIVYRIPGYLSPEELLKML 112 (112)
T ss_dssp -SSSE---EEECTTTSCEEEEEESS--HHHHHHHH
T ss_pred CccCE---EEEEcCCCCEEEEecCCCCHHHHHhhC
Confidence 47776 889989999774 445555554
No 24
>PF07122 VLPT: Variable length PCR target protein (VLPT); InterPro: IPR009805 This entry represents a 29 residue repeated sequence which seem to be specific to the Ehrlichia chaffeensis variable length PCR target (VLPT) protein. E. chaffeensis is a tick-transmitted rickettsial agent and is responsible for human monocytic ehrlichiosis (HME). The function of this family is unknown [].
Probab=24.02 E-value=43 Score=23.09 Aligned_cols=18 Identities=50% Similarity=0.529 Sum_probs=15.5
Q ss_pred CCcccccceeeeeccCCC
Q 022412 3 SSDSVKEEQVSFELPAPF 20 (297)
Q Consensus 3 ~~d~a~ee~vs~eLPAP~ 20 (297)
|+|...-+..++|||.|+
T Consensus 5 sSdsdlh~ss~vELp~ps 22 (30)
T PF07122_consen 5 SSDSDLHGSSSVELPSPS 22 (30)
T ss_pred cccccccCccceecCCch
Confidence 677778889999999985
No 25
>PRK03333 coaE dephospho-CoA kinase/protein folding accessory domain-containing protein; Provisional
Probab=23.92 E-value=89 Score=30.15 Aligned_cols=42 Identities=14% Similarity=0.279 Sum_probs=28.2
Q ss_pred CCccccccCCCCCC-CcceEEEecCCchhhcchHHHHHHHHhCCC
Q 022412 21 GWKKKIVPRKGGTP-KKSEIVFTAPTGEEISNKKQLEQYLKAHPG 64 (297)
Q Consensus 21 GWkKk~~pkkgGTP-kK~eIvFvAPtGEEI~~krqLe~YLKahpG 64 (297)
+|-+.|+.+ +.| +-.-|-.+.+++..+.+.-.+-.||.+||.
T Consensus 304 ~~~~~~~~~--~~~~r~~~lHv~~~~~~~~~~~l~FRDyLr~~p~ 346 (395)
T PRK03333 304 LWGKRLHAS--ADPGRPVNLHVRVDGWPGQRFALLFRDWLRADPA 346 (395)
T ss_pred ccceeeecc--CCCCCcEEEEEecCCCHHHHHHHHHHHHHhcCHH
Confidence 555555554 333 334444455667779999999999999983
No 26
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=23.09 E-value=54 Score=25.53 Aligned_cols=13 Identities=38% Similarity=0.669 Sum_probs=12.0
Q ss_pred chHHHHHHHHhCC
Q 022412 51 NKKQLEQYLKAHP 63 (297)
Q Consensus 51 ~krqLe~YLKahp 63 (297)
.|+++++||+.||
T Consensus 18 ar~~~~k~l~~NP 30 (64)
T PF03672_consen 18 ARKYMEKQLKENP 30 (64)
T ss_pred HHHHHHHHHHHCC
Confidence 6899999999997
No 27
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=23.04 E-value=76 Score=27.18 Aligned_cols=24 Identities=46% Similarity=0.850 Sum_probs=20.1
Q ss_pred cceEEEecCC--chhhcchHHHHHHHHh
Q 022412 36 KSEIVFTAPT--GEEISNKKQLEQYLKA 61 (297)
Q Consensus 36 K~eIvFvAPt--GEEI~~krqLe~YLKa 61 (297)
|.-|+|+.|+ |+.| +++|.+||..
T Consensus 56 k~VIILTD~D~~Ge~I--rk~l~~~l~~ 81 (127)
T COG1658 56 KGVIILTDPDRKGERI--RKKLKEYLPG 81 (127)
T ss_pred CCEEEEeCCCcchHHH--HHHHHHHhcc
Confidence 5579999997 8888 5789999976
No 28
>PF07419 PilM: PilM; InterPro: IPR009987 This entry contains the bacterial protein PilM (approximately 150 residues long). PilM is an inner membrane protein that has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body [].; PDB: 3EOI_A 3HG9_A.
Probab=22.55 E-value=50 Score=27.95 Aligned_cols=35 Identities=31% Similarity=0.492 Sum_probs=22.3
Q ss_pred hHHHHHHHHhCC---CCCCccccccCCCCCCcchhhhh
Q 022412 52 KKQLEQYLKAHP---GGPASSEFDWGTGETPRRSARIS 86 (297)
Q Consensus 52 krqLe~YLKahp---Ggp~~seFdWgTgeTPRRSaRis 86 (297)
+-.|..|+.+|| |.+..+-|.|-....||=+.+|+
T Consensus 38 ~nav~~y~~~~p~~~G~v~~~~L~lp~~~~~~i~~~i~ 75 (136)
T PF07419_consen 38 RNAVNDYAYAHPGASGTVPDSQLGLPPNPDPRISNVIS 75 (136)
T ss_dssp HHHHHHHHCCSGCGGC---CCCCTS-S-SSTTEEEEEC
T ss_pred HHHHHHHHHhCCCCCcccCHHHcCCCCCCchhhheeee
Confidence 456889999999 88889999887744445555554
No 29
>PF06590 PerB: PerB protein; InterPro: IPR009513 This family consists of several PerB or BfpV proteins found specifically in Escherichia coli. PerB is thought to play a role in regulating the expression of BfpA [].
Probab=21.03 E-value=79 Score=27.18 Aligned_cols=29 Identities=31% Similarity=0.655 Sum_probs=15.6
Q ss_pred ccCCCCCccccccCCCCCCCcceEEEecCC
Q 022412 16 LPAPFGWKKKIVPRKGGTPKKSEIVFTAPT 45 (297)
Q Consensus 16 LPAP~GWkKk~~pkkgGTPkK~eIvFvAPt 45 (297)
|.-|+|||- ..|+|...-.---|.||-|.
T Consensus 20 lslps~wka-itpkknn~tseiiv~fippk 48 (129)
T PF06590_consen 20 LSLPSEWKA-ITPKKNNVTSEIIVFFIPPK 48 (129)
T ss_pred eecCCccee-cccCCCCccceEEEEEeCCC
Confidence 677999974 45555433222233455553
No 30
>PF05939 Phage_min_tail: Phage minor tail protein; InterPro: IPR010265 This entry is represented by Bacteriophage lambda, GpM, the minor tail protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of a series of phage minor tail proteins and related sequences from several bacterial species.
Probab=20.85 E-value=88 Score=25.33 Aligned_cols=39 Identities=26% Similarity=0.472 Sum_probs=27.7
Q ss_pred CCcceEEEecCCchhhcchHHHHHHHHhCCCCCCccccccCCCCCC
Q 022412 34 PKKSEIVFTAPTGEEISNKKQLEQYLKAHPGGPASSEFDWGTGETP 79 (297)
Q Consensus 34 PkK~eIvFvAPtGEEI~~krqLe~YLKahpGgp~~seFdWgTgeTP 79 (297)
++...|+|.... .+|. .|..||.+|-| +.-|.|......
T Consensus 41 ~~~~~ltf~~~~-~~~~---~I~~FL~~h~G---~~sF~WtpP~~~ 79 (109)
T PF05939_consen 41 LRSWSLTFTGTE-AEIR---AIEAFLDRHGG---VKSFLWTPPGGE 79 (109)
T ss_pred ccEEEEEEEECH-HHHH---HHHHHHHHCCC---ceEEEEECCCCC
Confidence 456678888744 4443 49999999953 677999876543
Done!