Query psy7536
Match_columns 265
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 46136
Date Fri Aug 16 20:52:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7536.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7536hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11691 DUF3288: Protein of u 92.0 0.37 8E-06 37.9 5.0 55 40-104 30-84 (90)
2 COG2405 Predicted nucleic acid 40.4 34 0.00073 29.6 3.3 50 32-91 107-156 (157)
3 PF07889 DUF1664: Protein of u 36.0 47 0.001 26.9 3.4 28 228-255 51-78 (126)
4 PF08711 Med26: TFIIS helical 34.7 69 0.0015 20.9 3.5 20 28-47 12-31 (53)
5 PF00616 RasGAP: GTPase-activa 29.1 2.2E+02 0.0047 21.7 5.9 52 34-89 23-75 (197)
6 PF00993 MHC_II_alpha: Class I 27.5 52 0.0011 24.4 2.2 20 35-54 62-81 (82)
7 smart00455 RBD Raf-like Ras-bi 24.6 43 0.00092 23.9 1.2 37 22-58 7-43 (70)
8 PF05262 Borrelia_P83: Borreli 23.7 6.2E+02 0.013 24.7 9.1 12 63-74 181-192 (489)
9 PF01580 FtsK_SpoIIIE: FtsK/Sp 21.7 65 0.0014 24.9 1.8 66 21-93 45-115 (205)
10 KOG0396|consensus 20.9 1.3E+02 0.0027 29.1 3.8 33 29-61 110-142 (389)
11 PRK14616 4-diphosphocytidyl-2- 20.9 55 0.0012 27.5 1.4 46 3-48 222-274 (287)
No 1
>PF11691 DUF3288: Protein of unknown function (DUF3288); InterPro: IPR021705 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=91.97 E-value=0.37 Score=37.89 Aligned_cols=55 Identities=35% Similarity=0.397 Sum_probs=44.2
Q ss_pred HHHHHHHhccccchhhhhhhHHHHHHhhhhhhhhccCCChhhhHHHHHhhHHHHhhcccCCcchh
Q psy7536 40 LLAALMKRYNYFPAASVLLKDAAQVLDKLKHEEAKFNVDSDKIDSLIKKSEEILESKKIESPSAA 104 (265)
Q Consensus 40 llaalmkrynyfpaasvllkdaaqvldklkheeakfnvdsdkidslikkseeileskkiespsaa 104 (265)
=||.|+-||.-||.|.-+-+|...||.+..-.+ +.|..|..+|-.+..+-|....
T Consensus 30 eLARL~iRY~gFPGA~diq~DL~kiL~~W~lte----------eeLf~kTR~I~~~g~v~~~~d~ 84 (90)
T PF11691_consen 30 ELARLRIRYQGFPGARDIQKDLDKILQKWGLTE----------EELFEKTREIHASGGVYSGFDT 84 (90)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCH----------HHHHHHHHHHHHcCCcCCCCCc
Confidence 379999999999999999999999997654332 4677888899888877766543
No 2
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=40.44 E-value=34 Score=29.57 Aligned_cols=50 Identities=28% Similarity=0.474 Sum_probs=37.5
Q ss_pred hchhhHHHHHHHHHHhccccchhhhhhhHHHHHHhhhhhhhhccCCChhhhHHHHHhhHH
Q psy7536 32 LKTSGIKKLLAALMKRYNYFPAASVLLKDAAQVLDKLKHEEAKFNVDSDKIDSLIKKSEE 91 (265)
Q Consensus 32 lktsgikkllaalmkrynyfpaasvllkdaaqvldklkheeakfnvdsdkidslikksee 91 (265)
|+-+|+--+| ++.|+-||.|-. -++||+|. ++.|.+...-++..+++..|
T Consensus 107 L~V~GtlGvL-~~ak~kgLisk~-------Kpild~LI--~~GF~iS~~~~eeiL~~~~E 156 (157)
T COG2405 107 LKVTGTLGVL-ALAKSKGLISKD-------KPILDELI--EKGFRISRSILEEILRKLQE 156 (157)
T ss_pred CeeeehhHHH-HHHHHcCcccch-------HHHHHHHH--HhcCcccHHHHHHHHHHhcc
Confidence 5556666665 467888888754 29999999 89999998888777766543
No 3
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=36.01 E-value=47 Score=26.92 Aligned_cols=28 Identities=39% Similarity=0.555 Sum_probs=21.1
Q ss_pred HHHHhhchHHHHHHHHHHhHHHHHhhhc
Q psy7536 228 EMEKQFDSQAEAKKHLAQRYDDFMKELD 255 (265)
Q Consensus 228 emekqfdsqaeakkhlaqryddfmkeld 255 (265)
.|+.-.++-+.+|+||.||-|..=..||
T Consensus 51 ql~~vs~~l~~tKkhLsqRId~vd~klD 78 (126)
T PF07889_consen 51 QLEQVSESLSSTKKHLSQRIDRVDDKLD 78 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHH
Confidence 4666667888999999999887655444
No 4
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=34.68 E-value=69 Score=20.88 Aligned_cols=20 Identities=35% Similarity=0.509 Sum_probs=18.0
Q ss_pred ccchhchhhHHHHHHHHHHh
Q psy7536 28 SLSHLKTSGIKKLLAALMKR 47 (265)
Q Consensus 28 slshlktsgikkllaalmkr 47 (265)
+..+|+.+||-+.+..|.+.
T Consensus 12 t~~~L~~T~IGk~V~~l~k~ 31 (53)
T PF08711_consen 12 TVELLKSTGIGKAVNKLRKH 31 (53)
T ss_dssp SHHHHHHHSHHHHHHHHHHC
T ss_pred CHHHHHhCChhHHHHHHHcC
Confidence 47899999999999999887
No 5
>PF00616 RasGAP: GTPase-activator protein for Ras-like GTPase; InterPro: IPR001936 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. This intrinsic GTPase activity of ras is stimulated by a family of proteins collectively known as 'GAP' or GTPase-activating proteins [, ]. As it is the GTP bound form of ras which is active, these proteins are said to be down-regulators of ras. The Ras GTPase-activating proteins are quite large (from 765 residues for sar1 to 3079 residues for IRA2) but share only a limited (about 250 residues) region of sequence similarity, referred to as the 'catalytic domain' or rasGAP domain. Note: There are distinctly different GAPs for the rap and rho/rac subfamilies of ras-like proteins (reviewed in reference []) that do not share sequence similarity with ras GAPs.; GO: 0005096 GTPase activator activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3BXJ_B 1WQ1_G 1WER_A 1NF1_A 3FAY_A.
Probab=29.15 E-value=2.2e+02 Score=21.71 Aligned_cols=52 Identities=23% Similarity=0.402 Sum_probs=32.3
Q ss_pred hhhHHHHHHHHHHhccccchhhhhhhHHH-HHHhhhhhhhhccCCChhhhHHHHHhh
Q psy7536 34 TSGIKKLLAALMKRYNYFPAASVLLKDAA-QVLDKLKHEEAKFNVDSDKIDSLIKKS 89 (265)
Q Consensus 34 tsgikkllaalmkrynyfpaasvllkdaa-qvldklkheeakfnvdsdkidslikks 89 (265)
.+..-+++...+++ |.....|+++- .+++++-++...|.+|+.+|..-+...
T Consensus 23 ns~~~k~l~~y~~~----~~~~~yL~~~l~~~v~~i~~~~~~~eidp~~i~~~~~~~ 75 (197)
T PF00616_consen 23 NSVATKLLSAYARR----PVGKEYLKEILKPIVQEIINSDLDLEIDPSKIYQSLSSQ 75 (197)
T ss_dssp SSHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHTTS-----CCCCHHHHHHH
T ss_pred CcHHHHHHHHHHhh----hhhHHHHHHHHHHHHHHHhCCCCCeeecHHHHHHHHhhh
Confidence 34566788888887 44555555554 778888788889999999998544443
No 6
>PF00993 MHC_II_alpha: Class II histocompatibility antigen, alpha domain; InterPro: IPR001003 Major Histocompatibility Complex (MHC) glycoproteins are heterodimeric cell surface receptors that function to present antigen peptide fragments to T cells responsible for cell-mediated immune responses. MHC molecules can be subdivided into two groups on the basis of structure and function: class I molecules present intracellular antigen peptide fragments (~10 amino acids) on the surface of the host cells to cytotoxic T cells; class II molecules present exogenously derived antigenic peptides (~15 amino acids) to helper T cells. MHC class I and II molecules are assembled and loaded with their peptide ligands via different mechanisms. However, both present peptide fragments rather than entire proteins to T cells, and are required to mount an immune response. Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection) []. MHC class II molecules are comprised of two membrane-spanning chains, alpha and beta, of similar size. Both chains consist of two globular domains (N- and C-terminal), and a transmembrane segment to anchor them to the membrane []. A groove in the structure acts as the peptide-binding site. This entry represents the N-terminal domain (also called alpha-1 domain) of the alpha chain. More information about these proteins can be found at Protein of the Month: MHC [].; GO: 0006955 immune response, 0019882 antigen processing and presentation, 0016020 membrane, 0042613 MHC class II protein complex; PDB: 3LQZ_A 2ICW_D 1SJH_A 1KG0_A 1D6E_A 1D5M_A 1ZGL_G 1SJE_A 1J8H_A 2IAM_A ....
Probab=27.46 E-value=52 Score=24.40 Aligned_cols=20 Identities=40% Similarity=0.358 Sum_probs=14.8
Q ss_pred hhHHHHHHHHHHhccccchh
Q psy7536 35 SGIKKLLAALMKRYNYFPAA 54 (265)
Q Consensus 35 sgikkllaalmkrynyfpaa 54 (265)
...|.-|..+||+||..|+.
T Consensus 62 ~~ck~NL~~~~k~~~~~p~~ 81 (82)
T PF00993_consen 62 AICKHNLDVLIKRSNDTPAE 81 (82)
T ss_dssp HHHHHHHHHHHHHTTTC---
T ss_pred HHHHHHHHHHHhhcCCCCCC
Confidence 35688899999999999973
No 7
>smart00455 RBD Raf-like Ras-binding domain.
Probab=24.57 E-value=43 Score=23.91 Aligned_cols=37 Identities=16% Similarity=0.258 Sum_probs=25.1
Q ss_pred CCCCCCccchhchhhHHHHHHHHHHhccccchhhhhh
Q psy7536 22 PSGSGSSLSHLKTSGIKKLLAALMKRYNYFPAASVLL 58 (265)
Q Consensus 22 psgsgsslshlktsgikkllaalmkrynyfpaasvll 58 (265)
|-|..++..-=-..-|...|..++++|||-|.+-.+.
T Consensus 7 P~~~~~~V~vrpg~tl~e~L~~~~~kr~l~~~~~~v~ 43 (70)
T smart00455 7 PDNQRTVVKVRPGKTVRDALAKALKKRGLNPECCVVR 43 (70)
T ss_pred CCCCEEEEEECCCCCHHHHHHHHHHHcCCCHHHEEEE
Confidence 3344444333334457899999999999999876654
No 8
>PF05262 Borrelia_P83: Borrelia P83/100 protein; InterPro: IPR007926 This family consists of several Borrelia P83/P100 antigen proteins.
Probab=23.73 E-value=6.2e+02 Score=24.67 Aligned_cols=12 Identities=25% Similarity=0.631 Sum_probs=5.9
Q ss_pred HHHhhhhhhhhc
Q psy7536 63 QVLDKLKHEEAK 74 (265)
Q Consensus 63 qvldklkheeak 74 (265)
.|++.|+.+.-+
T Consensus 181 ~vv~~l~~~~dk 192 (489)
T PF05262_consen 181 KVVQELREDKDK 192 (489)
T ss_pred HHHHHHhhcccc
Confidence 455555554443
No 9
>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies.The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.
Probab=21.74 E-value=65 Score=24.85 Aligned_cols=66 Identities=26% Similarity=0.381 Sum_probs=32.1
Q ss_pred CCCCCCCccchhchhhHHHHHHHHHHhccccchhhhhhhHHH----HHHhhhhhhhh-ccCCChhhhHHHHHhhHHHH
Q psy7536 21 SPSGSGSSLSHLKTSGIKKLLAALMKRYNYFPAASVLLKDAA----QVLDKLKHEEA-KFNVDSDKIDSLIKKSEEIL 93 (265)
Q Consensus 21 spsgsgsslshlktsgikkllaalmkrynyfpaasvllkdaa----qvldklkheea-kfnvdsdkidslikkseeil 93 (265)
.++||| ||..+.-++..|+.+|.. +-..+.+-|.. ..+..+.|... .+..+.+.|..++....+.+
T Consensus 45 G~tgsG------KS~~l~~ll~~l~~~~~p-~~~~l~iiD~k~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~em 115 (205)
T PF01580_consen 45 GATGSG------KSTLLRTLLLSLALTYSP-DDVQLYIIDPKGSDLAPLADLPHVAAVAVATDPEEILRLLEELVEEM 115 (205)
T ss_dssp --TTSS------HHHHHHHHHHHHHTT--T-TTEEEEEE-TTSSCCGGGTT-TTBSS-S-B-SHHHHHHHHHHHHHHH
T ss_pred cCCCCC------ccHHHHHHHHHHHHHhcC-CccEEEEEcCCccccchhhhhhhhccccccccHHHHHHHHHHHHHHH
Confidence 346666 788889999999987754 22333343433 22333444433 23345555555555444333
No 10
>KOG0396|consensus
Probab=20.93 E-value=1.3e+02 Score=29.13 Aligned_cols=33 Identities=24% Similarity=0.339 Sum_probs=26.6
Q ss_pred cchhchhhHHHHHHHHHHhccccchhhhhhhHH
Q psy7536 29 LSHLKTSGIKKLLAALMKRYNYFPAASVLLKDA 61 (265)
Q Consensus 29 lshlktsgikkllaalmkrynyfpaasvllkda 61 (265)
+.-....-...++..-|-|-+||-+|-+|.|+.
T Consensus 110 ~~~w~r~~l~r~vvdhmlr~gy~~~A~~L~K~s 142 (389)
T KOG0396|consen 110 SRKWPRNKLDRFVVDHMLRNGYFGAAVLLGKKS 142 (389)
T ss_pred HHHhHHHHHHHHHHHHHHHcCchhHHHHHHHhh
Confidence 344555667789999999999999999999764
No 11
>PRK14616 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional
Probab=20.89 E-value=55 Score=27.48 Aligned_cols=46 Identities=33% Similarity=0.464 Sum_probs=27.7
Q ss_pred ccCCcchhhhh---hhhcCC--CCCCCCCCccchhch--hhHHHHHHHHHHhc
Q psy7536 3 RYNYFPAASVL---LKDAGS--KSPSGSGSSLSHLKT--SGIKKLLAALMKRY 48 (265)
Q Consensus 3 rynyfpaasvl---lkdags--kspsgsgsslshlkt--sgikkllaalmkry 48 (265)
|++.+|....+ +..+|. -.-||||+++--|-. .....+..+|.++|
T Consensus 222 ~~~l~p~l~~v~~~~~~~Galg~~lSGSGptv~al~~~~~~a~~i~~~l~~~~ 274 (287)
T PRK14616 222 VFDHYPAVRKVKDDLLEAGSFFASLSGSGSAVFGLFENEADAEAAAEMMRARY 274 (287)
T ss_pred HHHhChHHHHHHHHHHhCCCCeEEEecccccceEEeCCHHHHHHHHHHhHHhC
Confidence 34567777766 445565 236899999888843 23344555554443
Done!