Query psy375
Match_columns 93
No_of_seqs 71 out of 73
Neff 4.0
Searched_HMMs 46136
Date Sat Aug 17 00:31:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy375.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/375hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14228 MOR2-PAG1_mid: Cell m 99.8 6.4E-20 1.4E-24 163.7 6.3 80 8-91 584-667 (1120)
2 KOG1825|consensus 83.4 1.4 2.9E-05 43.8 3.8 68 7-74 1283-1354(2206)
3 PF10410 DnaB_bind: DnaB-helic 47.8 34 0.00073 19.7 3.3 32 42-73 5-36 (59)
4 smart00229 RasGEFN Guanine nuc 46.1 41 0.00089 22.1 3.8 33 41-73 44-87 (127)
5 cd06224 REM Guanine nucleotide 39.2 48 0.001 21.3 3.3 32 41-72 36-81 (122)
6 PF12717 Cnd1: non-SMC mitotic 35.5 1.2E+02 0.0027 21.4 5.2 55 16-70 76-139 (178)
7 PRK11127 autonomous glycyl rad 33.1 12 0.00025 27.3 -0.5 33 31-63 85-120 (127)
8 PF04003 Utp12: Dip2/Utp12 Fam 28.4 1.2E+02 0.0026 19.4 3.8 57 14-74 5-61 (110)
9 COG3445 Acid-induced glycyl ra 26.2 14 0.00031 26.5 -1.0 44 19-63 77-120 (127)
10 PF12717 Cnd1: non-SMC mitotic 25.7 1.2E+02 0.0027 21.4 3.8 42 27-68 11-52 (178)
11 PF00273 Serum_albumin: Serum 20.9 68 0.0015 23.2 1.7 23 30-52 141-163 (178)
No 1
>PF14228 MOR2-PAG1_mid: Cell morphogenesis central region
Probab=99.80 E-value=6.4e-20 Score=163.74 Aligned_cols=80 Identities=41% Similarity=0.754 Sum_probs=67.6
Q ss_pred ccccccch--hhHhHhhhHHHHHHHHHhhCCCchhHhHHHHhhh-hcccCcHHHHHHHHHHHHHHHHHHhcC-CCCCCCC
Q psy375 8 ERNVDAAL--LSNTYCRSQMHLSEQLAQLHPELTMPMFSEITHR-FQTARPEVRQILLQYLLPWLHNMELLD-PNVPPAN 83 (93)
Q Consensus 8 ~~~~~~~l--~~~vYk~aq~~LS~~LA~~hPElt~~iFSEiT~r-f~~~~p~~Rr~~L~~LLPWiqniELvD-p~~~p~~ 83 (93)
..+..++. +|++||++|++||++||++|||++|.+||||+.| |+..+++.||+||++|+||||||||++ +++
T Consensus 584 ~~f~~si~s~l~~vYk~aQ~eLS~~LA~~hPELs~~ifSEi~~R~~~~~~~~~rr~mL~~LlPWvqnleL~~~~~~---- 659 (1120)
T PF14228_consen 584 GDFRESISSKLPAVYKKAQFELSKRLAKQHPELSFPIFSEISQRFFNAVPPDARRDMLAYLLPWVQNLELVSLPES---- 659 (1120)
T ss_pred cceehhccCCcHHHHHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHhcCChhHHHHHHHHHHHHHhhceecccCCC----
Confidence 34555555 9999999999999999999999999999999987 567788999999999999999999954 333
Q ss_pred CCcchhhc
Q psy375 84 PLSYYQLN 91 (93)
Q Consensus 84 ~~sy~~~~ 91 (93)
+.+||++.
T Consensus 660 g~s~~vL~ 667 (1120)
T PF14228_consen 660 GWSEMVLN 667 (1120)
T ss_pred CcHHHHHH
Confidence 35777653
No 2
>KOG1825|consensus
Probab=83.35 E-value=1.4 Score=43.77 Aligned_cols=68 Identities=18% Similarity=0.087 Sum_probs=51.9
Q ss_pred cccccccchhhHhHhhhHHHHHHHHHhhCCCchhHhHHHHhhhhcccC----cHHHHHHHHHHHHHHHHHHh
Q psy375 7 TERNVDAALLSNTYCRSQMHLSEQLAQLHPELTMPMFSEITHRFQTAR----PEVRQILLQYLLPWLHNMEL 74 (93)
Q Consensus 7 ~~~~~~~~l~~~vYk~aq~~LS~~LA~~hPElt~~iFSEiT~rf~~~~----p~~Rr~~L~~LLPWiqniEL 74 (93)
....+..++++++|.+.|.+.++.+|+.--+.++.--.++..+++..+ ......++.++.+|..|+..
T Consensus 1283 ~~~~~~a~~t~~l~~~~q~~~~s~~~~~~~~~~~~~~~~c~~~~~~~~~a~~r~~~~~~l~~l~~~~~~~~~ 1354 (2206)
T KOG1825|consen 1283 GFKEFLAAVTGTLYLSPQQFQSSLSAKLAKIDPELSQLLCLVIINRYLDAVDRFAQHQVLLCLAAWIHNLNF 1354 (2206)
T ss_pred ccccHHHhccCccCCccHHHHHHHHHHHhhhchhhhhhhHHHHhcCcccccccchhHHHHHHHHHHHhhhhh
Confidence 445566778999999999999999999888888888889998888744 44555556666666666554
No 3
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=47.81 E-value=34 Score=19.73 Aligned_cols=32 Identities=9% Similarity=0.302 Sum_probs=24.2
Q ss_pred hHHHHhhhhcccCcHHHHHHHHHHHHHHHHHH
Q psy375 42 MFSEITHRFQTARPEVRQILLQYLLPWLHNME 73 (93)
Q Consensus 42 iFSEiT~rf~~~~p~~Rr~~L~~LLPWiqniE 73 (93)
.|..+........|+.|...+.-+.|+|..|.
T Consensus 5 ~~~~l~~~~dl~~~egk~~~~~~~~~~i~~i~ 36 (59)
T PF10410_consen 5 LIERLSKGYDLDTPEGKAEAVREAAPLIAQIP 36 (59)
T ss_dssp HHHHHGGGS-TTSHHHHHHHHHHHHHHHTT--
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCC
Confidence 35566677777889999999999999998874
No 4
>smart00229 RasGEFN Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a "purely structural role" (Nature 394, 337-343).
Probab=46.06 E-value=41 Score=22.15 Aligned_cols=33 Identities=24% Similarity=0.488 Sum_probs=26.0
Q ss_pred HhHHHHhhhhcccCcH-----------HHHHHHHHHHHHHHHHH
Q psy375 41 PMFSEITHRFQTARPE-----------VRQILLQYLLPWLHNME 73 (93)
Q Consensus 41 ~iFSEiT~rf~~~~p~-----------~Rr~~L~~LLPWiqniE 73 (93)
.+++.+..||+...+. .|..++.++.=|+++-=
T Consensus 44 ~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~rv~~~l~~Wv~~~~ 87 (127)
T smart00229 44 ELLQLLLYRYNAIPPESWVERKVNPLRVKNRVLNILRHWVENYW 87 (127)
T ss_pred HHHHHHHHHhCCCCcHHHHHHHhhHHHHHHHHHHHHHHHHHHCC
Confidence 5677888888876665 67789999999998753
No 5
>cd06224 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few.
Probab=39.22 E-value=48 Score=21.33 Aligned_cols=32 Identities=28% Similarity=0.657 Sum_probs=23.9
Q ss_pred HhHHHHhhhhcccCcH--------------HHHHHHHHHHHHHHHH
Q psy375 41 PMFSEITHRFQTARPE--------------VRQILLQYLLPWLHNM 72 (93)
Q Consensus 41 ~iFSEiT~rf~~~~p~--------------~Rr~~L~~LLPWiqni 72 (93)
.++..+..||+...+. .|+.++.++.=|+++-
T Consensus 36 ~ll~~L~~rf~~~~~~~~~~~~~~~~~~~~~~~~v~~~l~~Wv~~~ 81 (122)
T cd06224 36 ELLEKLIERYEIAPPENLEYNDWDKKKSKPIRLRVLNVLRTWVENY 81 (122)
T ss_pred HHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4667777788766542 5778999999999863
No 6
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=35.49 E-value=1.2e+02 Score=21.42 Aligned_cols=55 Identities=18% Similarity=0.339 Sum_probs=46.2
Q ss_pred hhHhHhhhHHHHHHHHHhhCCCchhHhHHHHhhhhcc---------cCcHHHHHHHHHHHHHHH
Q psy375 16 LSNTYCRSQMHLSEQLAQLHPELTMPMFSEITHRFQT---------ARPEVRQILLQYLLPWLH 70 (93)
Q Consensus 16 ~~~vYk~aq~~LS~~LA~~hPElt~~iFSEiT~rf~~---------~~p~~Rr~~L~~LLPWiq 70 (93)
.+.|=..|..-+..-+.+.+|+.-+..|.|+--+|+. ...+.|+.+...|+..+.
T Consensus 76 ~~~Ir~~A~~~~~e~~~~~~~~~i~~~~~e~i~~l~~~~~~~~~~~~~~~~~~~I~~fll~~i~ 139 (178)
T PF12717_consen 76 NPEIRSLARSFFSELLKKRNPNIIYNNFPELISSLNNCYEHPVYGPLSREKRKKIYKFLLDFID 139 (178)
T ss_pred CHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHhCccccccccccCHHHHHHHHHHHHHHcC
Confidence 5667777888888888888999999999999888875 456779999999999876
No 7
>PRK11127 autonomous glycyl radical cofactor GrcA; Provisional
Probab=33.14 E-value=12 Score=27.30 Aligned_cols=33 Identities=27% Similarity=0.293 Sum_probs=26.8
Q ss_pred HHhhCCCc---hhHhHHHHhhhhcccCcHHHHHHHH
Q psy375 31 LAQLHPEL---TMPMFSEITHRFQTARPEVRQILLQ 63 (93)
Q Consensus 31 LA~~hPEl---t~~iFSEiT~rf~~~~p~~Rr~~L~ 63 (93)
=|+.|||. -..+.|-.|.||.++.++.|+++++
T Consensus 85 dAqk~PEkYpdLiVRVsGYSa~F~~Lt~e~Q~eVI~ 120 (127)
T PRK11127 85 DAVKHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIA 120 (127)
T ss_pred HHHhChhcCCCeEEEEeeEEeehhhCCHHHHHHHHH
Confidence 36677775 4567789999999999999999874
No 8
>PF04003 Utp12: Dip2/Utp12 Family; InterPro: IPR007148 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. This domain is found at the C terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein. In yeast, these proteins are called Utp5, Utp1 or Pwp2, Utp12 or DIP2 Q12220 from SWISSPROT. They interact with snoRNA U3 and with MPP10 []. Pwp2 is an essential Saccharomyces cerevisiae (Baker's yeast) protein involved in cell separation.
Probab=28.38 E-value=1.2e+02 Score=19.45 Aligned_cols=57 Identities=18% Similarity=0.280 Sum_probs=40.4
Q ss_pred chhhHhHhhhHHHHHHHHHhhCCCchhHhHHHHhhhhcccCcHHHHHHHHHHHHHHHHHHh
Q psy375 14 ALLSNTYCRSQMHLSEQLAQLHPELTMPMFSEITHRFQTARPEVRQILLQYLLPWLHNMEL 74 (93)
Q Consensus 14 ~l~~~vYk~aq~~LS~~LA~~hPElt~~iFSEiT~rf~~~~p~~Rr~~L~~LLPWiqniEL 74 (93)
.+..++-+...-+|..-+...-+.....++..++.+.+.-.+. =+..++.|++.|-.
T Consensus 5 ll~~vl~~~~~~~I~~tv~~Lp~~~~~~LL~~l~~~l~~~~~~----~~e~~l~Wl~~ll~ 61 (110)
T PF04003_consen 5 LLLEVLERIPPSDIENTVRSLPFSYAERLLQFLSERLQTRKSP----HVEFLLRWLKALLK 61 (110)
T ss_pred HHHHHHhhCCHHHHHHHHHhCCHHHHHHHHHHHHHHhcccCCC----chhHHHHHHHHHHH
Confidence 3455566667777888888888888888888888887733322 34577899988754
No 9
>COG3445 Acid-induced glycyl radical enzyme [General function prediction only]
Probab=26.23 E-value=14 Score=26.49 Aligned_cols=44 Identities=20% Similarity=0.312 Sum_probs=31.9
Q ss_pred hHhhhHHHHHHHHHhhCCCchhHhHHHHhhhhcccCcHHHHHHHH
Q psy375 19 TYCRSQMHLSEQLAQLHPELTMPMFSEITHRFQTARPEVRQILLQ 63 (93)
Q Consensus 19 vYk~aq~~LS~~LA~~hPElt~~iFSEiT~rf~~~~p~~Rr~~L~ 63 (93)
|.++.-.+=+..=-..||.||.. .|....||+.+-|+.||++++
T Consensus 77 vl~retledav~~pekypqltir-vsgyavrfnsltpeqqrdvi~ 120 (127)
T COG3445 77 VLRRETLEDAVKHPEKYPQLTIR-VSGYAVRFNSLTPEQQRDVIA 120 (127)
T ss_pred eeehhhHHHHhhCcccCCceEEE-EeeEEEEeccCCHHHhhhHHH
Confidence 44444444444445567888865 478889999999999999886
No 10
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=25.69 E-value=1.2e+02 Score=21.41 Aligned_cols=42 Identities=21% Similarity=0.261 Sum_probs=35.6
Q ss_pred HHHHHHhhCCCchhHhHHHHhhhhcccCcHHHHHHHHHHHHH
Q psy375 27 LSEQLAQLHPELTMPMFSEITHRFQTARPEVRQILLQYLLPW 68 (93)
Q Consensus 27 LS~~LA~~hPElt~~iFSEiT~rf~~~~p~~Rr~~L~~LLPW 68 (93)
.-..|+..||.+.=+....+...+++-.+..|++.+.+|.=-
T Consensus 11 ~l~DL~~r~~~~ve~~~~~l~~~L~D~~~~VR~~al~~Ls~L 52 (178)
T PF12717_consen 11 ALGDLCIRYPNLVEPYLPNLYKCLRDEDPLVRKTALLVLSHL 52 (178)
T ss_pred HHHHHHHhCcHHHHhHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 345788899999999999999999999999999988777543
No 11
>PF00273 Serum_albumin: Serum albumin family; InterPro: IPR014760 A number of serum transport proteins are known to be evolutionarily related, including albumin, alpha-fetoprotein, vitamin D-binding protein and afamin [, , ]. Albumin is the main protein of plasma; it binds water, cations (such as Ca2+, Na+ and K+), fatty acids, hormones, bilirubin and drugs - its main function is to regulate the colloidal osmotic pressure of blood. Alphafeto- protein (alpha-fetoglobulin) is a foetal plasma protein that binds various cations, fatty acids and bilirubin. Vitamin D-binding protein binds to vitamin D and its metabolites, as well as to fatty acids. The biological role of afamin (alpha-albumin) has not yet been characterised. The 3D structure of human serum albumin has been determined by X-ray crystallography to a resolution of 2.8A []. It comprises three homologous domains that assemble to form a heart-shaped molecule []. Each domain is a product of two subdomains that possess common structural motifs []. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and IIIA, which exhibit similar chemistry. Structurally, the serum albumins are similar, each domain containing five or six internal disulphide bonds, as shown schematically below: +---+ +----+ +-----+ | | | | | | xxCxxxxxxxxxxxxxxxxCCxxCxxxxCxxxxxCCxxxCxxxxxxxxxCxxxxxxxxxxxxxxCCxxxxCxxxx | | | | | | +-----------------+ +-----+ +---------------+ ; GO: 0005615 extracellular space; PDB: 3V09_A 3V03_B 3MRK_P 1MA9_A 1KW2_A 1KXP_D 1J7E_A 1J78_A 1LOT_A 2BXL_A ....
Probab=20.95 E-value=68 Score=23.21 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=18.0
Q ss_pred HHHhhCCCchhHhHHHHhhhhcc
Q psy375 30 QLAQLHPELTMPMFSEITHRFQT 52 (93)
Q Consensus 30 ~LA~~hPElt~~iFSEiT~rf~~ 52 (93)
.+++.||+++-+..-.++..|..
T Consensus 141 e~~RrhP~~~~~~l~~~~~~y~~ 163 (178)
T PF00273_consen 141 ELSRRHPELSDPQLLRIAKGYEK 163 (178)
T ss_dssp HHHHHSTTS-HHHHHHHHHHHHH
T ss_pred HHHHhCCCCCHHHHHHHHHHHHH
Confidence 45668999999999999888864
Done!