Query psy6150
Match_columns 148
No_of_seqs 114 out of 320
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 18:57:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6150.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6150hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3611|consensus 100.0 4.4E-40 9.4E-45 306.4 6.7 124 6-141 209-360 (737)
2 smart00630 Sema semaphorin dom 100.0 4.5E-34 9.7E-39 248.6 5.2 123 6-140 130-281 (390)
3 PF01403 Sema: Sema domain; I 99.9 3.5E-28 7.5E-33 210.8 6.1 131 6-141 158-317 (433)
4 KOG3611|consensus 54.3 6.5 0.00014 38.2 1.3 27 111-138 499-526 (737)
5 PF01437 PSI: Plexin repeat; 45.2 14 0.0003 23.4 1.4 27 112-138 8-34 (51)
6 PHA02872 EFc gene family prote 41.9 40 0.00086 26.2 3.6 41 6-56 42-83 (124)
7 COG2932 Predicted transcriptio 20.0 1.8E+02 0.0039 23.1 4.1 45 14-62 134-179 (214)
8 PF04810 zf-Sec23_Sec24: Sec23 17.2 96 0.0021 18.9 1.5 21 113-133 6-26 (40)
9 PF12093 Corona_NS8: Coronavir 15.6 49 0.0011 25.4 -0.1 44 38-81 45-93 (118)
10 PF10674 Ycf54: Protein of unk 14.5 45 0.00097 24.8 -0.5 34 50-83 56-89 (93)
No 1
>KOG3611|consensus
Probab=100.00 E-value=4.4e-40 Score=306.44 Aligned_cols=124 Identities=37% Similarity=0.621 Sum_probs=112.8
Q ss_pred cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEe--------cCceeeeeeecccccCCCCCcccCcceehhhhhhhc
Q psy6150 6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLT--------KKNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLN 77 (148)
Q Consensus 6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~--------~~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~ 77 (148)
+|+++|||||+||.|.-| .|+|||||+ +++++|||||||||||+||++.|+++|||||||||+
T Consensus 209 ~~dskwLneP~FV~a~~i---------~~~vyFFFrE~a~e~~~~~~~v~sRVARVCknD~GG~~~l~~~WTSFLKARL~ 279 (737)
T KOG3611|consen 209 KYDSKWLNEPNFVGAFDI---------GDHVYFFFREIAVENNNCGKAVYSRVARVCKNDVGGRRVLEKKWTSFLKARLN 279 (737)
T ss_pred cCCchhccCCcEEEeeee---------CCEEEEEecccccccCcccceEEeeeeeEeccCCCCceEcccchhHhhhhhee
Confidence 799999999999999776 389999997 468999999999999999999999999999999999
Q ss_pred CCCCCCCCccCccccceeeecc--C----------------CCceeEEeee-eccccccCCCCeeeeecCCCeeeecCC-
Q psy6150 78 CSVPGDYPFYFDEIRLPEDCVN--L----------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPYQE- 137 (148)
Q Consensus 78 Cs~pg~~~~~Fn~lqdv~~l~~--~----------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~q~- 137 (148)
||+||+.+||||+||+||.+.. . .++.|+|+|. |++ +|+|||++.+++.++|+||++
T Consensus 280 CSvp~~~~fyFn~lq~v~~~~~~~~~~~~YgvFtt~~n~~~~SAVC~f~l~dI~~---vF~G~fk~q~~~~~~W~pv~~~ 356 (737)
T KOG3611|consen 280 CSVPGDSPFYFNELQSVFLLVSLGGRDVFYAVFSTSSNSIPGSAVCAFSLSDIRA---VFDGPFKEQKGPNSAWLPVPGD 356 (737)
T ss_pred cccCCCCCCcccccceeeeccccCCCceEEEEEcccccCcceeEEecCCHHHHHH---HhCCccccccCCcccceeccCC
Confidence 9999999999999999985332 2 2334999999 999 999999999999999999999
Q ss_pred Ccee
Q psy6150 138 RTLE 141 (148)
Q Consensus 138 ~~~~ 141 (148)
+||.
T Consensus 357 ~vP~ 360 (737)
T KOG3611|consen 357 KVPK 360 (737)
T ss_pred cCCC
Confidence 9985
No 2
>smart00630 Sema semaphorin domain.
Probab=100.00 E-value=4.5e-34 Score=248.58 Aligned_cols=123 Identities=35% Similarity=0.644 Sum_probs=108.8
Q ss_pred cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEec--------CceeeeeeecccccCCCCCcccCcceehhhhhhhc
Q psy6150 6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLN 77 (148)
Q Consensus 6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~ 77 (148)
+++++||++|+||++.. .+|+|||||.+ ++.++||||||||||.||+++|+++||||+||||+
T Consensus 130 ~~~~~~l~~~~FV~sf~---------~~~~vYFff~e~~~e~~~~~~~~~SRVaRVCk~D~Gg~~~l~~~wtSflka~L~ 200 (390)
T smart00630 130 LYDSKWLNEPNFVYAFE---------SGDFVYFFFRETAVEDDNCGKAVHSRVARVCKNDVGGPRSLDKKWTSFLKARLE 200 (390)
T ss_pred ccCcccccCCcEEEEEE---------cCCEEEEEEEEEccccCcCCceeeeeeeeecccCcCccccccccccEEEEEEEE
Confidence 35789999999999843 57899999974 67899999999999999999999999999999999
Q ss_pred CCCCCCCCccCccccceeeeccC-------------------CCceeEEeee-eccccccCCCCeeeeecCCCeeeec-C
Q psy6150 78 CSVPGDYPFYFDEIRLPEDCVNL-------------------QDPYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPY-Q 136 (148)
Q Consensus 78 Cs~pg~~~~~Fn~lqdv~~l~~~-------------------~~~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~-q 136 (148)
|+.||+.+++||+||||+.+..+ +++.|||+|. |++ +|+|+|++-+..+.+|.++ .
T Consensus 201 Cs~~g~~~~~fn~lQ~v~~~~~g~~~~~vlygvFst~~~~~~~SAvC~f~l~~I~~---~F~~~~~~~~~~~~~~~~~~~ 277 (390)
T smart00630 201 CSVPGESPFYFNELQAAFLLPPGSESDDVLYGVFSTSSNPIPGSAVCAFSLKDINA---VFNGPFKECETSTSQWLPYSR 277 (390)
T ss_pred ecCCCcCCccchhhhheeecccCCCCCCEEEEEEeCCCCCCCccEEEEeEHHHHHH---HHhhhhhhccCcCcceecccC
Confidence 99999889999999999965531 3445999999 999 9999999999999999988 6
Q ss_pred CCce
Q psy6150 137 ERTL 140 (148)
Q Consensus 137 ~~~~ 140 (148)
+.+|
T Consensus 278 ~~vp 281 (390)
T smart00630 278 GKVP 281 (390)
T ss_pred CcCC
Confidence 6665
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=99.95 E-value=3.5e-28 Score=210.75 Aligned_cols=131 Identities=33% Similarity=0.569 Sum_probs=113.4
Q ss_pred cccCCCCCCCceeeeeeeEeecCCCCCCceEEEEEec--------CceeeeeeecccccCCCCCcccCcceehhhhhhhc
Q psy6150 6 TWSTPSLDEVNLCCRGSVRFQSTSIDGVDHVWTQLTK--------KNAVYSRVARVCKSDKGGPHHFGDRWTTFLKSRLN 77 (148)
Q Consensus 6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~ddkvY~ff~~--------~k~~~sRVaRVCknD~GG~~~L~~kWTTFlKArL~ 77 (148)
.++..||++|.|+.+..+.+...- .+++|||||.+ ++..+||||||||+|.||.+.+.++||||+||||+
T Consensus 158 ~~~~~~~~~p~fv~~~~~~~v~~f--~~~~vYF~f~e~~~~~~~~~~~~~srvaRvCk~D~g~~~~~e~~wttf~karL~ 235 (433)
T PF01403_consen 158 QYDSKWLNEPSFVSSFEIGYVYGF--SDDFVYFFFRERASEYDSCGKPYYSRVARVCKNDPGGYSYLEPLWTTFLKARLN 235 (433)
T ss_dssp CCCTTSSSSTEEEEEEEEEECEEE--ETTEEEEEEEEEESSSSTSSCCEEEEEEEEETTSSTBSSSCCTBESSEEEEEEE
T ss_pred cccccccccccccccccccccccc--CCcEEEEEEEeeccccccccccceeeeeeccccCCccccchhhcccccccccee
Confidence 346789999999999888655543 67899999973 47889999999999999998777999999999999
Q ss_pred CCCCC-CCCccCccccceeeeccCCC-------------------ceeEEeee-eccccccCCCCeeeeecCCCeeeecC
Q psy6150 78 CSVPG-DYPFYFDEIRLPEDCVNLQD-------------------PYCAWDLK-LRKDCVNLQDPYCAWDLKLRKCVPYQ 136 (148)
Q Consensus 78 Cs~pg-~~~~~Fn~lqdv~~l~~~~~-------------------~~c~ysl~-i~~~~~~f~Gp~~~~~~~~~~wv~~q 136 (148)
|+.|+ ..+++||+||+++.+.++.+ +.|+|+|. |.+ +|+|++...++++.+|.++.
T Consensus 236 C~~~~~~~~~~fn~lq~~~~~~~~~~~~~vlyavFt~~~~~~~~SAvC~ysl~~I~~---~F~g~~~~~~~~~~~~~~~~ 312 (433)
T PF01403_consen 236 CSVPGDGSPFYFNELQAVFVSKPGSGDDDVLYAVFTTSWNSSPGSAVCAYSLSDINQ---AFNGPFKCCDGSTSKWLPYP 312 (433)
T ss_dssp CEETTCSCTEECHEEEEEEEEECTTTTSEEEEEEEEESSSSSSCEEEEEEEHHHHHH---HHCSHBEECCSCHTTBCCTT
T ss_pred ccccCcCCCchhhhhhhhccccccccCCceEEEEEEecccccCCceEEEEEHHHHHH---HhhcchhhcccccCcccccc
Confidence 99998 67899999999997776433 34999999 999 99999999999999999977
Q ss_pred CCcee
Q psy6150 137 ERTLE 141 (148)
Q Consensus 137 ~~~~~ 141 (148)
+.+|+
T Consensus 313 ~~~~~ 317 (433)
T PF01403_consen 313 NSVPS 317 (433)
T ss_dssp SCCCS
T ss_pred CcccC
Confidence 66654
No 4
>KOG3611|consensus
Probab=54.30 E-value=6.5 Score=38.22 Aligned_cols=27 Identities=41% Similarity=0.851 Sum_probs=22.4
Q ss_pred eccc-cccCCCCeeeeecCCCeeeecCCC
Q psy6150 111 LRKD-CVNLQDPYCAWDLKLRKCVPYQER 138 (148)
Q Consensus 111 i~~~-~~~f~Gp~~~~~~~~~~wv~~q~~ 138 (148)
-+.| |++ ++|||+|++++++|+.+.+-
T Consensus 499 ~C~dccla-rDPYCAWd~~~~~C~~~~~~ 526 (737)
T KOG3611|consen 499 SCADCCLA-RDPYCAWDGVNSKCSLLSPT 526 (737)
T ss_pred chhhhhhc-cCCCccccCCCCcceECCCC
Confidence 4666 555 99999999999999988654
No 5
>PF01437 PSI: Plexin repeat; InterPro: IPR002165 This is a cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found in plexin (P70206 from SWISSPROT) []. Two copies of the repeat are found in mahogany protein. A related Caenorhabditis elegans protein (Q19981 from SWISSPROT) contains four copies of the repeat, while the Met receptor contains a single copy of the repeat.; GO: 0016020 membrane; PDB: 3NVQ_B 3NVN_B 3OL2_B 3OKT_A 3AL8_A 3OKW_A 3OKY_B 3AFC_B 1OLZ_B 1SHY_B ....
Probab=45.17 E-value=14 Score=23.35 Aligned_cols=27 Identities=30% Similarity=0.808 Sum_probs=23.2
Q ss_pred ccccccCCCCeeeeecCCCeeeecCCC
Q psy6150 112 RKDCVNLQDPYCAWDLKLRKCVPYQER 138 (148)
Q Consensus 112 ~~~~~~f~Gp~~~~~~~~~~wv~~q~~ 138 (148)
..+|++-.+||+.+....++++..++.
T Consensus 8 C~~Cl~~~dp~CgWc~~~~~C~~~~~~ 34 (51)
T PF01437_consen 8 CSSCLSSRDPYCGWCSSENRCVSGSGQ 34 (51)
T ss_dssp HHHHHHSTCTTEEEETTTTEEEECCGG
T ss_pred HHHHHcCCCcCccccCCCCcccCCccc
Confidence 457999999999999999999988743
No 6
>PHA02872 EFc gene family protein; Provisional
Probab=41.89 E-value=40 Score=26.18 Aligned_cols=41 Identities=17% Similarity=0.201 Sum_probs=27.4
Q ss_pred cccCCCCCCCceeeeeeeEeecCCCCCC-ceEEEEEecCceeeeeeeccccc
Q psy6150 6 TWSTPSLDEVNLCCRGSVRFQSTSIDGV-DHVWTQLTKKNAVYSRVARVCKS 56 (148)
Q Consensus 6 ~~~~~wL~~P~Fv~~~~i~f~~~s~d~d-dkvY~ff~~~k~~~sRVaRVCkn 56 (148)
++.+--.++|..++++ .+| -||||+-..+..++| |.||=..
T Consensus 42 ~irNi~f~~~~ylca~---------~gdtvkIYflEGkG~LIfS-v~dv~sp 83 (124)
T PHA02872 42 TIRNIDFCRPRYLCAD---------AGDTVKIYFLEGKGGLIFS-VSDVGSP 83 (124)
T ss_pred EEeccccccceEeeec---------CCCeEEEEEEecCCcEEEE-EEecCCC
Confidence 3444456777777751 233 478888888889988 7777543
No 7
>COG2932 Predicted transcriptional regulator [Transcription]
Probab=20.01 E-value=1.8e+02 Score=23.09 Aligned_cols=45 Identities=13% Similarity=0.096 Sum_probs=27.9
Q ss_pred CCceeeeeeeEeecCCCCC-CceEEEEEecCceeeeeeecccccCCCCCc
Q psy6150 14 EVNLCCRGSVRFQSTSIDG-VDHVWTQLTKKNAVYSRVARVCKSDKGGPH 62 (148)
Q Consensus 14 ~P~Fv~~~~i~f~~~s~d~-ddkvY~ff~~~k~~~sRVaRVCknD~GG~~ 62 (148)
+|.+-....|+..++.... +|+||.....+...+.|+.|. .||..
T Consensus 134 eP~~~~Gd~ilVd~~~~~~~gd~v~v~~~g~~~~VK~l~~~----~~~~~ 179 (214)
T COG2932 134 EPTYEDGDTLLVDPGVNTRRGDRVYVETDGGELYVKKLQRE----PGGLL 179 (214)
T ss_pred cccccCCCEEEECCCCceeeCCEEEEEEeCCeEEEEEEEEe----cCCeE
Confidence 3555555555444443443 677888777778887888776 66643
No 8
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=17.20 E-value=96 Score=18.87 Aligned_cols=21 Identities=19% Similarity=0.634 Sum_probs=15.7
Q ss_pred cccccCCCCeeeeecCCCeee
Q psy6150 113 KDCVNLQDPYCAWDLKLRKCV 133 (148)
Q Consensus 113 ~~~~~f~Gp~~~~~~~~~~wv 133 (148)
+.|-++.-||...+..+.+|+
T Consensus 6 ~~C~aylNp~~~~~~~~~~w~ 26 (40)
T PF04810_consen 6 RRCRAYLNPFCQFDDGGKTWI 26 (40)
T ss_dssp TTT--BS-TTSEEETTTTEEE
T ss_pred CCCCCEECCcceEcCCCCEEE
Confidence 457799999999999999995
No 9
>PF12093 Corona_NS8: Coronavirus NS8 protein; InterPro: IPR022722 This family of proteins is functionally uncharacterised. This protein is found in coronaviruses. Proteins in this family are typically between 39 to 121 amino acids in length. This protein has two conserved sequence motifs: EDPCP and INCQ.
Probab=15.62 E-value=49 Score=25.35 Aligned_cols=44 Identities=16% Similarity=0.330 Sum_probs=31.7
Q ss_pred EEEecCceeeeeeecccccCCCCCccc-Ccceehhhh----hhhcCCCC
Q psy6150 38 TQLTKKNAVYSRVARVCKSDKGGPHHF-GDRWTTFLK----SRLNCSVP 81 (148)
Q Consensus 38 ~ff~~~k~~~sRVaRVCknD~GG~~~L-~~kWTTFlK----ArL~Cs~p 81 (148)
+|.+.+.+..||..+.|.+|-|..-+. -.+|.++.- ..+||..|
T Consensus 45 W~ik~~~R~sArL~~Lc~g~yG~~~p~Hye~~~~~~~sC~P~~INCQ~P 93 (118)
T PF12093_consen 45 WFIKIGTRKSARLVQLCEGDYGKRLPIHYEMFGNYTISCEPVEINCQDP 93 (118)
T ss_pred ceEEEcCccchhHhhhccccCCcEeeeehhhhcceEEEeeeeEEeccCC
Confidence 455667777899999999999964333 457877654 35788876
No 10
>PF10674 Ycf54: Protein of unknown function (DUF2488); InterPro: IPR019616 This entry represents proteins annotated as Ycf54. It is found encoded in the chloroplast genomes of algae, it is also found in plants and in the cyanobacteria. The function is unknown. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.; PDB: 3JSR_A 3HZE_D.
Probab=14.54 E-value=45 Score=24.81 Aligned_cols=34 Identities=18% Similarity=0.292 Sum_probs=19.9
Q ss_pred eecccccCCCCCcccCcceehhhhhhhcCCCCCC
Q psy6150 50 VARVCKSDKGGPHHFGDRWTTFLKSRLNCSVPGD 83 (148)
Q Consensus 50 VaRVCknD~GG~~~L~~kWTTFlKArL~Cs~pg~ 83 (148)
++.-|......--+...+|.||||.||.=-..|.
T Consensus 56 ~~~k~~~p~~AiVSTd~~fItwlKLRL~~V~~G~ 89 (93)
T PF10674_consen 56 IKKKLPQPAAAIVSTDKQFITWLKLRLEYVLKGE 89 (93)
T ss_dssp HHHHS-SSEEEEEES-HHHHHHHHHHH-SSEEEE
T ss_pred HHHhCCCCcEEEEecChHHHHHHHHhhheEEEEE
Confidence 4444444444334567899999999997555443
Done!