Query psy5392
Match_columns 100
No_of_seqs 123 out of 368
Neff 5.7
Searched_HMMs 46136
Date Sat Aug 17 01:25:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5392.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5392hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3611|consensus 100.0 1.1E-41 2.3E-46 289.4 6.8 100 1-100 191-295 (737)
2 smart00630 Sema semaphorin dom 100.0 2.4E-37 5.2E-42 246.9 9.0 99 2-100 106-216 (390)
3 PF01403 Sema: Sema domain; I 100.0 2.6E-30 5.7E-35 206.4 8.4 99 2-100 141-252 (433)
4 COG2947 Uncharacterized conser 56.8 8 0.00017 28.1 1.8 62 20-89 33-108 (156)
5 COG3350 Uncharacterized conser 26.6 45 0.00098 20.2 1.4 22 23-46 17-38 (53)
6 cd00559 Cyanase_C Cyanase C-te 23.0 38 0.00082 21.5 0.6 8 1-8 4-11 (69)
7 PF12996 DUF3880: DUF based on 22.4 39 0.00084 21.0 0.6 28 2-29 49-76 (79)
8 PF00045 Hemopexin: Hemopexin; 22.1 93 0.002 16.9 2.1 11 28-38 4-15 (45)
9 PHA02658 hypothetical protein; 21.8 47 0.001 21.5 0.9 9 59-67 43-51 (92)
10 PF13964 Kelch_6: Kelch motif 21.5 88 0.0019 17.1 1.9 17 27-43 6-22 (50)
11 PF04146 YTH: YT521-B-like dom 21.1 33 0.00071 23.8 0.1 56 22-84 31-93 (140)
12 TIGR02616 tnaC_leader tryptoph 20.7 40 0.00086 17.6 0.3 18 14-40 5-22 (26)
No 1
>KOG3611|consensus
Probab=100.00 E-value=1.1e-41 Score=289.42 Aligned_cols=100 Identities=66% Similarity=1.127 Sum_probs=96.0
Q ss_pred CCCeeecC-----CccccccCccCCCCCceEEeeecCCEEEEEEeeeccccccCCceeeEEEeeeecCCCCCCcccccce
Q psy5392 1 MDPIIYRE-----PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSRVARVCKYDRGGPHRFRNRW 75 (100)
Q Consensus 1 ~~~~i~R~-----~lrTe~~~~~wl~~p~FV~~~~~~dkvYffF~E~a~e~~~~~~~~~srVaRVCk~D~GG~~~L~~kW 75 (100)
.||+|||+ +|||++||++|||+|+||+++.++|+|||||||.++|...+++.++||||||||||+||++.|+++|
T Consensus 191 ~d~~I~Rs~g~~~~lrT~~~dskwLneP~FV~a~~i~~~vyFFFrE~a~e~~~~~~~v~sRVARVCknD~GG~~~l~~~W 270 (737)
T KOG3611|consen 191 SDALIYRSLGKNPTLRTVKYDSKWLNEPNFVGAFDIGDHVYFFFREIAVENNNCGKAVYSRVARVCKNDVGGRRVLEKKW 270 (737)
T ss_pred CCceEEEecCCCCCceeccCCchhccCCcEEEeeeeCCEEEEEecccccccCcccceEEeeeeeEeccCCCCceEcccch
Confidence 48999993 7999999999999999999999999999999999999767999999999999999999999999999
Q ss_pred eeeeeeeeccCCCCCCCCcCccccC
Q psy5392 76 TSFLKSRLNCSVPGDFPFYFDEIQV 100 (100)
Q Consensus 76 tTFlKArL~Cs~p~~~~~~fn~lq~ 100 (100)
||||||||+||+||+.+||||+||+
T Consensus 271 TSFLKARL~CSvp~~~~fyFn~lq~ 295 (737)
T KOG3611|consen 271 TSFLKARLNCSVPGDSPFYFNELQS 295 (737)
T ss_pred hHhhhhheecccCCCCCCcccccce
Confidence 9999999999999989999999995
No 2
>smart00630 Sema semaphorin domain.
Probab=100.00 E-value=2.4e-37 Score=246.95 Aligned_cols=99 Identities=67% Similarity=1.121 Sum_probs=93.8
Q ss_pred CCeeecC------------CccccccCccCCCCCceEEeeecCCEEEEEEeeeccccccCCceeeEEEeeeecCCCCCCc
Q psy5392 2 DPIIYRE------------PLQTEQYDSMSLNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSRVARVCKYDRGGPH 69 (100)
Q Consensus 2 ~~~i~R~------------~lrTe~~~~~wl~~p~FV~~~~~~dkvYffF~E~a~e~~~~~~~~~srVaRVCk~D~GG~~ 69 (100)
+|+|+|+ .+||+.++++||++|+||++|..|++|||||+|++.|.+.+++.++||||||||||.||++
T Consensus 106 ~~~i~r~~~~r~l~~~~~~~l~t~~~~~~~l~~~~FV~sf~~~~~vYFff~e~~~e~~~~~~~~~SRVaRVCk~D~Gg~~ 185 (390)
T smart00630 106 DPAIPRSLSVRRLKGTSGVSLRTVLYDSKWLNEPNFVYAFESGDFVYFFFRETAVEDDNCGKAVHSRVARVCKNDVGGPR 185 (390)
T ss_pred CcceeccccccccccccCceeeccccCcccccCCcEEEEEEcCCEEEEEEEEEccccCcCCceeeeeeeeecccCcCccc
Confidence 5788884 5799999999999999999999999999999999999888899999999999999999999
Q ss_pred ccccceeeeeeeeeccCCCCCCCCcCccccC
Q psy5392 70 RFRNRWTSFLKSRLNCSVPGDFPFYFDEIQV 100 (100)
Q Consensus 70 ~L~~kWtTFlKArL~Cs~p~~~~~~fn~lq~ 100 (100)
+|+++||||+||||+|+.||+.++|||+||+
T Consensus 186 ~l~~~wtSflka~L~Cs~~g~~~~~fn~lQ~ 216 (390)
T smart00630 186 SLDKKWTSFLKARLECSVPGESPFYFNELQA 216 (390)
T ss_pred cccccccEEEEEEEEecCCCcCCccchhhhh
Confidence 9999999999999999999988999999996
No 3
>PF01403 Sema: Sema domain; InterPro: IPR001627 The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in a hepatocyte growth factor receptor, in SEX protein [] and in viral proteins. CD100 (also called SEMA4D) is associated with PTPase and serine kinase activity. CD100 increases PMA, CD3 and CD2 induced T cell proliferation, increases CD45 induced T cell adhesion, induces B cell homotypic adhesion and down-regulates B cell expression of CD23. The Sema domain is characterised by a conserved set of cysteine residues, which form four disulphide bonds to stabilise the structure. The Sema domain fold is a variation of the beta propeller topology, with seven blades radially arranged around a central axis. Each blade contains a four- stranded (strands A to D) antiparallel beta sheet. The inner strand of each blade (A) lines the channel at the centre of the propeller, with strands B and C of the same repeat radiating outward, and strand D of the next repeat forming the outer edge of the blade. The large size of the Sema domain is not due to a single inserted domain but results from the presence of additional secondary structure elements inserted in most of the blades. The Sema domain uses a 'loop and hook' system to close the circle between the first and the last blades. The blades are constructed sequentially with an N-terminal beta- strand closing the circle by providing the outermost strand (D) of the seventh (C-terminal) blade. The beta-propeller is further stabilised by an extension of the N terminus, providing an additional, fifth beta-strand on the outer edge of blade 6 [, , ]. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0005515 protein binding; PDB: 3NVX_A 3NVQ_A 3OL2_A 1OLZ_B 3OKT_A 3AL9_B 3OKY_A 3AL8_B 3NVN_A 3OKW_A ....
Probab=99.96 E-value=2.6e-30 Score=206.40 Aligned_cols=99 Identities=66% Similarity=1.131 Sum_probs=92.0
Q ss_pred CCeeec-----CCccccccCccCCCCCceEEeeecC-------CEEEEEEeeeccccccCCceeeEEEeeeecCCCCCCc
Q psy5392 2 DPIIYR-----EPLQTEQYDSMSLNAPNFVSSLTQG-------DFVYFFFRETAVEFINCGKAVYSRVARVCKYDRGGPH 69 (100)
Q Consensus 2 ~~~i~R-----~~lrTe~~~~~wl~~p~FV~~~~~~-------dkvYffF~E~a~e~~~~~~~~~srVaRVCk~D~GG~~ 69 (100)
+|+|+| ..++|+.++++|+++|+||+++.++ ++|||||+|.+.+....++.++||||||||+|.||.+
T Consensus 141 ~~~i~R~~~~~~~l~~~~~~~~~~~~p~fv~~~~~~~v~~f~~~~vYF~f~e~~~~~~~~~~~~~srvaRvCk~D~g~~~ 220 (433)
T PF01403_consen 141 SPIISRSLGSQPPLRTEQYDSKWLNEPSFVSSFEIGYVYGFSDDFVYFFFRERASEYDSCGKPYYSRVARVCKNDPGGYS 220 (433)
T ss_dssp SEEEEEEETSSSTEESCCCCTTSSSSTEEEEEEEEEECEEEETTEEEEEEEEEESSSSTSSCCEEEEEEEEETTSSTBSS
T ss_pred CcceeecccccccccccccccccccccccccccccccccccCCcEEEEEEEeeccccccccccceeeeeeccccCCcccc
Confidence 689999 3689999999999999999998877 9999999999999987889999999999999999998
Q ss_pred ccccceeeeeeeeeccCCCC-CCCCcCccccC
Q psy5392 70 RFRNRWTSFLKSRLNCSVPG-DFPFYFDEIQV 100 (100)
Q Consensus 70 ~L~~kWtTFlKArL~Cs~p~-~~~~~fn~lq~ 100 (100)
.++++||||+||||+|+.|+ ..|++||+||+
T Consensus 221 ~~e~~wttf~karL~C~~~~~~~~~~fn~lq~ 252 (433)
T PF01403_consen 221 YLEPLWTTFLKARLNCSVPGDGSPFYFNELQA 252 (433)
T ss_dssp SCCTBESSEEEEEEECEETTCSCTEECHEEEE
T ss_pred chhhccccccccceeccccCcCCCchhhhhhh
Confidence 87799999999999999999 67899999985
No 4
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=56.82 E-value=8 Score=28.13 Aligned_cols=62 Identities=27% Similarity=0.607 Sum_probs=39.6
Q ss_pred CCCCceEEeeecCCEEEEEEeeeccccccCCceeeEEEeeeecCCCCCCccc--------------ccceeeeeeeeecc
Q psy5392 20 LNAPNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSRVARVCKYDRGGPHRF--------------RNRWTSFLKSRLNC 85 (100)
Q Consensus 20 l~~p~FV~~~~~~dkvYffF~E~a~e~~~~~~~~~srVaRVCk~D~GG~~~L--------------~~kWtTFlKArL~C 85 (100)
...-+|+-...+||+++|.- - .|...-+.-+++||..+.--.-.. ..+|.+ +.++.++
T Consensus 33 YqARNfmR~M~iGD~~fFYH-S------Nc~~pgIvGl~~V~~~a~pD~tq~d~~spYyDPka~~e~pRW~~-Vdv~~v~ 104 (156)
T COG2947 33 YQARNFMRDMKIGDLGFFYH-S------NCKPPGIVGLAEVCALAHPDPTQFDPASPYYDPKATPEDPRWYC-VDVRFVR 104 (156)
T ss_pred HHHHHHHHhcccCceEEEEe-c------CCCCCCceehhhhhhccCCCccccCCCCcccCcccccCCCCeeE-EeeHHHh
Confidence 34567888888999884433 2 233344577999997655432222 568988 7777777
Q ss_pred CCCC
Q psy5392 86 SVPG 89 (100)
Q Consensus 86 s~p~ 89 (100)
..+.
T Consensus 105 ~~~~ 108 (156)
T COG2947 105 KLPR 108 (156)
T ss_pred hcCC
Confidence 7664
No 5
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=26.64 E-value=45 Score=20.16 Aligned_cols=22 Identities=32% Similarity=0.489 Sum_probs=16.8
Q ss_pred CceEEeeecCCEEEEEEeeecccc
Q psy5392 23 PNFVSSLTQGDFVYFFFRETAVEF 46 (100)
Q Consensus 23 p~FV~~~~~~dkvYffF~E~a~e~ 46 (100)
..|.++ .++|.|+|-+|...+.
T Consensus 17 a~~k~~--Y~GktYYFcse~~~~~ 38 (53)
T COG3350 17 AEYKSS--YGGKTYYFCSEECKEK 38 (53)
T ss_pred cceeEE--eCCEEEEEeCHHHHHH
Confidence 455555 6899999999998664
No 6
>cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Probab=22.98 E-value=38 Score=21.55 Aligned_cols=8 Identities=63% Similarity=1.128 Sum_probs=6.2
Q ss_pred CCCeeecC
Q psy5392 1 MDPIIYRE 8 (100)
Q Consensus 1 ~~~~i~R~ 8 (100)
+||+|||.
T Consensus 4 tDP~iYRl 11 (69)
T cd00559 4 TDPLIYRF 11 (69)
T ss_pred CCceeeeh
Confidence 58888884
No 7
>PF12996 DUF3880: DUF based on E. rectale Gene description (DUF3880); InterPro: IPR024542 This entry represents proteins of unknown function. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=22.35 E-value=39 Score=21.03 Aligned_cols=28 Identities=21% Similarity=0.157 Sum_probs=17.1
Q ss_pred CCeeecCCccccccCccCCCCCceEEee
Q psy5392 2 DPIIYREPLQTEQYDSMSLNAPNFVSSL 29 (100)
Q Consensus 2 ~~~i~R~~lrTe~~~~~wl~~p~FV~~~ 29 (100)
+|.++|...........+..|-.|||+.
T Consensus 49 ~~~~~~p~~~~~~~~~~~~~dIsFVG~~ 76 (79)
T PF12996_consen 49 NPERFRPIPVDPEERKKYECDISFVGSL 76 (79)
T ss_pred CHHHhCcccCCcccccccCCCEEEeCcC
Confidence 3445554444322345788999999974
No 8
>PF00045 Hemopexin: Hemopexin; InterPro: IPR018487 Hemopexin (3.2.1.35 from EC) is a serum glycoprotein that binds haem and transports it to the liver for breakdown and iron recovery, after which the free hemopexin returns to the circulation []. Hemopexin prevents haem-mediated oxidative stress. Structurally hemopexin consists of two similar halves of approximately two hundred amino acid residues connected by a histidine-rich hinge region. Each half is itself formed by the repetition of a basic unit of some 35 to 45 residues. Hemopexin-like domains have been found in two other types of proteins, vitronectin [], a cell adhesion and spreading factor found in plasma and tissues, and matrixins MMP-1, MMP-2, MMP-3, MMP-9, MMP-10, MMP-11, MMP-12, MMP-14, MMP-15 and MMP-16, members of the matrix metalloproteinase family that cleave extracellular matrix constituents []. These zinc endopeptidases, which belong to MEROPS peptidase subfamily M10A, have a single hemopexin-like domain in their C-terminal section. It is suggested that the hemopexin domain facilitates binding to a variety of molecules and proteins, for example the HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs). This entry represents the repeat found in hempoxein and related domains.; PDB: 1SU3_B 2CLT_B 3V6N_B 3C7X_A 1GXD_A 1RTG_A 1CK7_A 1GEN_A 1ITV_A 2JXY_A ....
Probab=22.12 E-value=93 Score=16.90 Aligned_cols=11 Identities=36% Similarity=0.775 Sum_probs=6.1
Q ss_pred eeecC-CEEEEE
Q psy5392 28 SLTQG-DFVYFF 38 (100)
Q Consensus 28 ~~~~~-dkvYff 38 (100)
++..+ +++|||
T Consensus 4 a~~~~~g~~yfF 15 (45)
T PF00045_consen 4 AFQWGNGKTYFF 15 (45)
T ss_dssp EEEETTTEEEEE
T ss_pred EEEeCCCcEEEE
Confidence 34444 677665
No 9
>PHA02658 hypothetical protein; Provisional
Probab=21.76 E-value=47 Score=21.54 Aligned_cols=9 Identities=56% Similarity=0.922 Sum_probs=6.8
Q ss_pred eeecCCCCC
Q psy5392 59 RVCKYDRGG 67 (100)
Q Consensus 59 RVCk~D~GG 67 (100)
-|||||.-|
T Consensus 43 yvckndttg 51 (92)
T PHA02658 43 YVCKNDTTG 51 (92)
T ss_pred eeccCCCCC
Confidence 479999655
No 10
>PF13964 Kelch_6: Kelch motif
Probab=21.53 E-value=88 Score=17.07 Aligned_cols=17 Identities=24% Similarity=0.311 Sum_probs=11.4
Q ss_pred EeeecCCEEEEEEeeec
Q psy5392 27 SSLTQGDFVYFFFRETA 43 (100)
Q Consensus 27 ~~~~~~dkvYffF~E~a 43 (100)
++...+++||+|=-..+
T Consensus 6 s~v~~~~~iyv~GG~~~ 22 (50)
T PF13964_consen 6 SAVVVGGKIYVFGGYDN 22 (50)
T ss_pred EEEEECCEEEEECCCCC
Confidence 45557889998754443
No 11
>PF04146 YTH: YT521-B-like domain; InterPro: IPR007275 A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells []. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanaisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B, Q9QY02 from SWISSPROT, is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner []. The domain is predicted to have four alpha helices and six beta strands []. In plant cells environmental stimuli, which light, pathogens, hormones, and abiotic stresses, elicit changes in the cytosolic Ca levels but little is known of the cytosolic-nuclear Ca-signaling pathway; where gene regulation occurs to respond appropriately to the stress. It has been demonstrated that two novel Arabidopsis thaliana (Mouse-ear cress) proteins, (ECT1 and ECT2), specifically associated with Calcineurin B-Like-Interacting Protein Kinase1 (CIPK1), a member of Ser/Thr protein kinases that interact with the calcineurin B-like Ca-binding proteins. These two proteins contain a very similar C-terminal region (180 amino acids in length, 81% similarity), which is required and sufficient for both interaction with CIPK1 and translocation to the nucleus. This domain, the YTH-domain, is conserved across all eukaryotes and suggests that the conserved C-terminal region plays a critical role in relaying the cytosolic Ca-signals to the nucleus, thereby regulating gene expression [].; PDB: 2YUD_A 2YU6_A.
Probab=21.13 E-value=33 Score=23.85 Aligned_cols=56 Identities=16% Similarity=0.341 Sum_probs=29.8
Q ss_pred CCceEEeeecCCEEEEEEeeeccccccCCceeeEEEeeeecC-CCCCCcc------cccceeeeeeeeec
Q psy5392 22 APNFVSSLTQGDFVYFFFRETAVEFINCGKAVYSRVARVCKY-DRGGPHR------FRNRWTSFLKSRLN 84 (100)
Q Consensus 22 ~p~FV~~~~~~dkvYffF~E~a~e~~~~~~~~~srVaRVCk~-D~GG~~~------L~~kWtTFlKArL~ 84 (100)
++..-.||...+.||+||+.+.... +--+|||+.. |.+.... ...+|....+.+=+
T Consensus 31 ~~~L~~Af~~~~~V~L~FSvn~S~~-------F~G~A~M~s~~~~~~~~~~w~~~~~~~~~~g~F~v~Wl 93 (140)
T PF04146_consen 31 EKKLNEAFKESRNVYLFFSVNGSGH-------FQGYARMTSPIDPDSPKPFWQQDSSSSKWGGPFRVEWL 93 (140)
T ss_dssp HHHHHHHHHHSS-EEEEEEETTTSE-------EEEEEEEECECCSSS------SS-SGCGG-SEEEEEEE
T ss_pred hHHHHHHHHhCCCEEEEEeecCcce-------EEEEEEEccCCCCcccCccccccccccccCCceEEEEE
Confidence 3444456666779999999876443 2447777642 2221111 23577776666533
No 12
>TIGR02616 tnaC_leader tryptophanase leader peptide. Members of this family are the apparent leader peptides of tryptophanase operons in Esherichia coli, Vibrio cholerae, Photobacterium profundum, Haemophilus influenzae type b, and related species. All members of the seed alignment are examples ORFs upstream of tryptophanase, with a start codon, a conserved single Trp residue, and several other conserved residues. It is suggested (Konan KV and Yanofsky C) that the nascent peptide interacts with the ribosome once (if) the ribosome reaches the stop codon. Note that this model describes a much broader set (and shorter protein region) than Pfam model pfam08053.
Probab=20.69 E-value=40 Score=17.57 Aligned_cols=18 Identities=28% Similarity=0.266 Sum_probs=11.4
Q ss_pred ccCccCCCCCceEEeeecCCEEEEEEe
Q psy5392 14 QYDSMSLNAPNFVSSLTQGDFVYFFFR 40 (100)
Q Consensus 14 ~~~~~wl~~p~FV~~~~~~dkvYffF~ 40 (100)
.-.++|.| +|.++-|||-
T Consensus 5 ~~~s~Wfn---------iD~rIsf~FP 22 (26)
T TIGR02616 5 CVLSKWFN---------IDNRISFFFP 22 (26)
T ss_pred ccCCceEE---------cchhheeccc
Confidence 34567877 6667766663
Done!