Query psy17660
Match_columns 126
No_of_seqs 110 out of 434
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 19:44:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17660.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17660hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3641|consensus 99.9 4.7E-28 1E-32 206.3 8.5 106 16-125 242-347 (650)
2 smart00140 NGF Nerve growth fa 45.5 33 0.00072 24.1 3.4 35 34-69 18-52 (106)
3 PF00243 NGF: Nerve growth fac 42.9 22 0.00047 25.3 2.2 37 34-71 21-57 (116)
4 PF06030 DUF916: Bacterial pro 25.7 1.2E+02 0.0025 21.3 3.7 38 52-90 8-45 (121)
5 KOG3641|consensus 23.9 26 0.00056 31.5 -0.0 21 81-101 1-21 (650)
6 PF04151 PPC: Bacterial pre-pe 23.5 1.2E+02 0.0026 18.5 3.0 21 61-84 3-23 (70)
7 COG0139 HisI Phosphoribosyl-AM 18.3 1.6E+02 0.0034 20.9 3.0 33 31-64 67-107 (111)
8 COG4813 ThuA Trehalose utiliza 17.2 89 0.0019 24.6 1.7 16 108-123 181-196 (261)
9 KOG4705|consensus 16.9 1.3E+02 0.0028 24.7 2.6 38 29-66 28-76 (303)
10 PF11948 DUF3465: Protein of u 15.9 4.5E+02 0.0098 19.1 5.1 62 48-113 46-111 (131)
No 1
>KOG3641|consensus
Probab=99.95 E-value=4.7e-28 Score=206.26 Aligned_cols=106 Identities=42% Similarity=0.728 Sum_probs=99.8
Q ss_pred cCCCCCCceEEEeecCCcchheeeeeCCeeEEEEeecCCCCCCeeeEEEEEEeeeccCeeEEEEEeccccccccccCCCe
Q psy17660 16 FQSEKSNDLRFESRFESGNLAKAVKISDNYYELYLRTDLYTNRHMQWFYFRINNTRANVYYRFSIVNLSKSESLYSVGMK 95 (126)
Q Consensus 16 ~~~~~~~~l~F~S~FeSGNL~~v~~~~~~ey~L~l~~D~~t~~~~qWFyF~V~~~~~~~~~~f~I~N~~k~~sly~~Gm~ 95 (126)
.+.+..+.|.|.|.||||||.+|.++...||+|.++||++.+.|.|||||.|+| .+++.+.|+|+|+.|+.++|+.||+
T Consensus 242 ~~~p~~~~l~f~s~fesgnLr~Viqv~~~eydL~~~pDtn~~~~~~wfYfevsg-~~s~ry~FnivN~sk~~tqfe~gmq 320 (650)
T KOG3641|consen 242 STIPHNAELWFQSEFESGNLRSVIQVPQQEYDLFLAPDTNPNEYGVWFYFEVSG-RASVRYCFNIVNFSKSSTQFENGMQ 320 (650)
T ss_pred cCCCCCcceeeecccccCCcceeEEecccccceeecCCCCCcccceEEEEEecC-CcCcceEEEEEeeccchhHHhcccC
Confidence 445688999999999999999999999999999999999999999999999999 8999999999999999999999999
Q ss_pred EEEEechhhhcCCCCeEEeCCCeEEeecCC
Q psy17660 96 PLMYSTKEAELNKIGWRRCGENITYFRNDL 125 (126)
Q Consensus 96 P~v~s~~~~~~~~~~W~R~g~~i~Yyrn~~ 125 (126)
|.|+|.+++ .-+|.|.|++||||||..
T Consensus 321 p~mys~nea---~~~~~r~~~~icYyrn~~ 347 (650)
T KOG3641|consen 321 PKMYSLNEA---HNDFRRFSEKICYYRNRR 347 (650)
T ss_pred cceeehhhh---hccccccCcceeeeeccc
Confidence 999999877 567899999999999974
No 2
>smart00140 NGF Nerve growth factor (NGF or beta-NGF). NGF is important for the development and maintenance of the sympathetic and sensory nervous systems.
Probab=45.52 E-value=33 Score=24.07 Aligned_cols=35 Identities=20% Similarity=0.230 Sum_probs=26.6
Q ss_pred chheeeeeCCeeEEEEeecCCCCCCeeeEEEEEEee
Q psy17660 34 NLAKAVKISDNYYELYLRTDLYTNRHMQWFYFRINN 69 (126)
Q Consensus 34 NL~~v~~~~~~ey~L~l~~D~~t~~~~qWFyF~V~~ 69 (126)
|...+..+.+.+-.+.-..+.+.....|||| ..+.
T Consensus 18 nKt~a~Di~G~~VtVL~~v~~nn~~~kQyF~-ET~C 52 (106)
T smart00140 18 DKTTATDISGNEVTVLGEVPVNNGPLKQYFY-ETRC 52 (106)
T ss_pred ccCEEEecCCCEEEEEEEEEeCCceEEEEEE-Eeec
Confidence 5666777778888887777888878999998 4443
No 3
>PF00243 NGF: Nerve growth factor family; InterPro: IPR002072 During the development of the vertebrate nervous system, many neurons become redundant (because they have died, failed to connect to target cells, etc.) and are eliminated. At the same time, developing neurons send out axon outgrowths that contact their target cells []. Such cells control their degree of innervation (the number of axon connections) by the secretion of various specific neurotrophic factors that are essential for neuron survival. One of these is nerve growth factor (NGF or beta-NGF), a vertebrate protein that stimulates division and differentiation of sympathetic and embryonic sensory neurons [, ]. NGF is mostly found outside the central nervous system (CNS), but slight traces have been detected in adult CNS tissues, although a physiological role for this is unknown []; it has also been found in several snake venoms [, ]. NGF is a protein of about 120 residues that is cleaved from a larger precursor molecule. It contains six cysteines all involved in intrachain disulphide bonds. A schematic representation of the structure of NGF is shown below: +------------------------+ | | | | xxxxxxCxxxxxxxxxxxxxxxxxxxxxCxxxxCxxxxxCxxxxxxxxxxxxxCxCxxxx | | | | +--------------------------|-----+ | +---------------------+ 'C': conserved cysteine involved in a disulphide bond. This entry also contains NGF-related proteins such as neutrophin 3, which promotes the survival of visceral and proprioceptive sensory neurons, and brain-derived neurotrophin, which promotes the survival of neuronal populations that are located either in the central nervous system or directly connected to it [, ].; GO: 0005102 receptor binding; PDB: 1NT3_A 1BND_B 3BUK_A 1B8K_A 1B98_A 1HCF_A 1WWW_V 1SG1_A 2IFG_E 1BTG_A ....
Probab=42.88 E-value=22 Score=25.32 Aligned_cols=37 Identities=22% Similarity=0.265 Sum_probs=24.6
Q ss_pred chheeeeeCCeeEEEEeecCCCCCCeeeEEEEEEeeec
Q psy17660 34 NLAKAVKISDNYYELYLRTDLYTNRHMQWFYFRINNTR 71 (126)
Q Consensus 34 NL~~v~~~~~~ey~L~l~~D~~t~~~~qWFyF~V~~~~ 71 (126)
|...+..+.+.+..++-..+.+...+.||| |.++...
T Consensus 21 nk~tA~Di~G~~VtVL~~v~~n~~~~kQyF-~EtkC~~ 57 (116)
T PF00243_consen 21 NKTTAVDIKGNEVTVLGEVNINNGVYKQYF-FETKCRN 57 (116)
T ss_dssp HH-EEEBTTS-EEEE-SEEESSSSEEE-EE-EEEEESC
T ss_pred ccceeecCCCCEEEEEeeEecCCceEEEEE-EEEEEcC
Confidence 666777778888998888888876788854 6776543
No 4
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=25.74 E-value=1.2e+02 Score=21.29 Aligned_cols=38 Identities=13% Similarity=0.219 Sum_probs=22.4
Q ss_pred cCCCCCCeeeEEEEEEeeeccCeeEEEEEeccccccccc
Q psy17660 52 TDLYTNRHMQWFYFRINNTRANVYYRFSIVNLSKSESLY 90 (126)
Q Consensus 52 ~D~~t~~~~qWFyF~V~~~~~~~~~~f~I~N~~k~~sly 90 (126)
||.+......+|.+.|+-. ..+++.+.|.|...+.--|
T Consensus 8 p~~Q~~~~~~YFdL~~~P~-q~~~l~v~i~N~s~~~~tv 45 (121)
T PF06030_consen 8 PENQIDKNVSYFDLKVKPG-QKQTLEVRITNNSDKEITV 45 (121)
T ss_pred CccccCCCCCeEEEEeCCC-CEEEEEEEEEeCCCCCEEE
Confidence 4555555566777777633 3456777777776543333
No 5
>KOG3641|consensus
Probab=23.87 E-value=26 Score=31.53 Aligned_cols=21 Identities=33% Similarity=0.801 Sum_probs=18.5
Q ss_pred eccccccccccCCCeEEEEec
Q psy17660 81 VNLSKSESLYSVGMKPLMYST 101 (126)
Q Consensus 81 ~N~~k~~sly~~Gm~P~v~s~ 101 (126)
+++.+|..||++||+|+++..
T Consensus 1 ~d~~~q~~L~sk~~~~f~~t~ 21 (650)
T KOG3641|consen 1 MDMNKQSKLYSKGMAPFVFTL 21 (650)
T ss_pred CcchhhHHHHhccCccceeec
Confidence 467889999999999999984
No 6
>PF04151 PPC: Bacterial pre-peptidase C-terminal domain; InterPro: IPR007280 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. This domain is normally found at the C terminus of secreted archaeal and bacterial peptidases, the majority of which belong to MEROPS peptidase families M4 (vibriolysin, IPR001570 from INTERPRO), M9A amd M9B (microbial collangenase, IPR002169 from INTERPRO), M28 (aminopeptidase Ap1, IPR007484 from INTERPRO) and S8 (subtilisin family peptidases, IPR000209 from INTERPRO).; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 4DY5_B 4DXZ_A 4DY3_B 3JQW_A 3JQX_C 1NQJ_B 1NQD_A 2O8O_A 1WMF_A 1WME_A ....
Probab=23.53 E-value=1.2e+02 Score=18.50 Aligned_cols=21 Identities=14% Similarity=0.257 Sum_probs=15.4
Q ss_pred eEEEEEEeeeccCeeEEEEEeccc
Q psy17660 61 QWFYFRINNTRANVYYRFSIVNLS 84 (126)
Q Consensus 61 qWFyF~V~~~~~~~~~~f~I~N~~ 84 (126)
.||.|.|. .+..+++.+.+..
T Consensus 3 D~y~f~v~---ag~~l~i~l~~~~ 23 (70)
T PF04151_consen 3 DYYSFTVP---AGGTLTIDLSGGS 23 (70)
T ss_dssp EEEEEEES---TTEEEEEEECETT
T ss_pred EEEEEEEc---CCCEEEEEEcCCC
Confidence 58999888 4556888876655
No 7
>COG0139 HisI Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]
Probab=18.26 E-value=1.6e+02 Score=20.88 Aligned_cols=33 Identities=30% Similarity=0.364 Sum_probs=18.8
Q ss_pred CCcchheeeeeC---Ce-eEEEEeec----CCCCCCeeeEEE
Q psy17660 31 ESGNLAKAVKIS---DN-YYELYLRT----DLYTNRHMQWFY 64 (126)
Q Consensus 31 eSGNL~~v~~~~---~~-ey~L~l~~----D~~t~~~~qWFy 64 (126)
+|||..+|..++ |. ..-+...+ =|.+ |.+..||
T Consensus 67 tSG~~q~v~~i~~DCD~Dall~~V~q~gg~aCHt-G~~SCF~ 107 (111)
T COG0139 67 TSGHTQKVVEIRLDCDGDALLLLVEQIGGPACHT-GTRSCFY 107 (111)
T ss_pred ccCceEEEEEEEcCCCCCEEEEEEEeCCCCcccC-CCccccc
Confidence 689999888764 22 33333333 2444 5555665
No 8
>COG4813 ThuA Trehalose utilization protein [Carbohydrate transport and metabolism]
Probab=17.16 E-value=89 Score=24.63 Aligned_cols=16 Identities=44% Similarity=0.750 Sum_probs=14.2
Q ss_pred CCCeEEeCCCeEEeec
Q psy17660 108 KIGWRRCGENITYFRN 123 (126)
Q Consensus 108 ~~~W~R~g~~i~Yyrn 123 (126)
+..|+|+..+|.|||-
T Consensus 181 g~T~rRGaG~ifYFrP 196 (261)
T COG4813 181 GLTYRRGAGNIFYFRP 196 (261)
T ss_pred cceeeecCccEEEeCC
Confidence 6789999999999973
No 9
>KOG4705|consensus
Probab=16.92 E-value=1.3e+02 Score=24.74 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=23.0
Q ss_pred ecCCcchheeeeeCC---eeEEEEe-ecCC-------CCCCeeeEEEEE
Q psy17660 29 RFESGNLAKAVKISD---NYYELYL-RTDL-------YTNRHMQWFYFR 66 (126)
Q Consensus 29 ~FeSGNL~~v~~~~~---~ey~L~l-~~D~-------~t~~~~qWFyF~ 66 (126)
.-+|+||.-|..+.+ .+-.-.. .+|. .+.+|+.||+=.
T Consensus 28 ~~dsknl~fv~l~hp~hgkealyLf~~~~~~~~e~vaf~ekhrSwFvg~ 76 (303)
T KOG4705|consen 28 VVDSKNLQFVELSHPLHGKEALYLFTNDHLLQIEQVAFSEKHRSWFVGD 76 (303)
T ss_pred hhcccCccceeeccCCCCCceeEEEecchhhhhhhhhccccccceeecC
Confidence 447889998877642 2322222 3332 356899999854
No 10
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=15.92 E-value=4.5e+02 Score=19.07 Aligned_cols=62 Identities=16% Similarity=0.188 Sum_probs=33.5
Q ss_pred EEeecCCCCCCeeeEEEEEEeeeccCeeEEEEEeccc--cccccccCCCeEEEEechh--hhcCCCCeEE
Q psy17660 48 LYLRTDLYTNRHMQWFYFRINNTRANVYYRFSIVNLS--KSESLYSVGMKPLMYSTKE--AELNKIGWRR 113 (126)
Q Consensus 48 L~l~~D~~t~~~~qWFyF~V~~~~~~~~~~f~I~N~~--k~~sly~~Gm~P~v~s~~~--~~~~~~~W~R 113 (126)
+.+.||-++..-.|+|+-++.+ ++++.+ .-|+. ..-.-...|.+.-++-+-+ ++-..+.|..
T Consensus 46 ~~vLpdd~~GsrHQ~Fiv~l~~---g~tllI-ahNIDlaprip~l~~GD~V~f~GeYe~n~kggvIHWTH 111 (131)
T PF11948_consen 46 VKVLPDDNKGSRHQRFIVRLSS---GQTLLI-AHNIDLAPRIPWLQKGDQVEFYGEYEWNPKGGVIHWTH 111 (131)
T ss_pred EEECcccCCCCcceEEEEEeCC---CCEEEE-EeccCccccCcCcCCCCEEEEEEEEEECCCCCEEEeec
Confidence 3567777766679999999974 444433 24433 2223345566655543221 2233455554
Done!