Query psy13251
Match_columns 166
No_of_seqs 106 out of 119
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 23:59:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13251.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13251hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00243 NGF: Nerve growth fac 98.2 1.1E-05 2.4E-10 62.7 8.5 94 69-165 7-107 (116)
2 PF02035 Coagulin: Coagulin; 97.4 0.0011 2.4E-08 53.7 8.9 78 72-159 84-164 (174)
3 smart00140 NGF Nerve growth fa 96.4 0.013 2.8E-07 45.2 6.5 94 69-165 4-104 (106)
4 PF06083 IL17: Interleukin-17; 88.1 3.2 6.9E-05 30.3 7.0 71 92-164 6-80 (84)
5 PF11325 DUF3127: Domain of un 37.1 80 0.0017 23.3 4.5 47 78-129 7-56 (84)
6 KOG3463|consensus 28.7 54 0.0012 25.6 2.5 29 89-117 69-102 (109)
7 KOG4214|consensus 24.4 25 0.00054 27.6 -0.0 12 13-24 33-44 (117)
8 cd04894 ACT_ACR-like_1 ACT dom 23.2 58 0.0013 23.5 1.7 17 84-100 30-46 (69)
9 PF13225 DUF4033: Domain of un 21.3 53 0.0012 24.6 1.2 13 105-117 19-31 (86)
10 PF06433 Me-amine-dh_H: Methyl 17.8 1.5E+02 0.0032 27.2 3.5 60 37-100 43-115 (342)
No 1
>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=98.19 E-value=1.1e-05 Score=62.73 Aligned_cols=94 Identities=22% Similarity=0.409 Sum_probs=73.1
Q ss_pred ccccCCcceeeeee-ceeeeeCCCcEEEEEeccCCCC-ceeeeEEEEeecCC-----ccCCccCCCCCCcCeeEEeeece
Q psy13251 69 STFTLCPTRSQFVM-PQAAVNNKGNWMYVVNINEVDN-RYKQLVKSEVCLST-----ECNGVCGLPPGYTSRCEQKYVQK 141 (166)
Q Consensus 69 ~~~~LC~S~~~~i~-Pk~A~N~~g~Wr~IVNt~e~~n-~y~Q~VRvE~C~~~-----~C~~~~~lp~gY~S~CkQKYv~r 141 (166)
||-..|+|....+. ...|.|..|+-..|+......| .|+|-+..-+|.+. .|.+++. ..+.|.|+++..+-
T Consensus 7 ge~sVCdS~S~WV~nk~tA~Di~G~~VtVL~~v~~n~~~~kQyF~EtkC~~~~~~~~gCrGiD~--~hw~S~C~t~~s~V 84 (116)
T PF00243_consen 7 GEYSVCDSVSVWVTNKTTAVDIKGNEVTVLGEVNINNGVYKQYFFETKCRNPNPVKSGCRGIDS--RHWNSYCTTTQSYV 84 (116)
T ss_dssp SEEESS-EEEEEESHH-EEEBTTS-EEEE-SEEESSSSEEE-EEEEEEESCSSSCTTCSTTB-T--TTEEEEEEEEEEEE
T ss_pred ccEeecccceeEEcccceeecCCCCEEEEEeeEecCCceEEEEEEEEEEcCCCCCCCCCCCccc--ccCCCEeeccEeEE
Confidence 47899999999997 7899999998888875443322 79999999999872 7988875 46899999999999
Q ss_pred EEEEEeCCCCcEEEEEEecCCCcC
Q psy13251 142 RLIALQGEGNQLYTDVFWIPSCCM 165 (166)
Q Consensus 142 rLlAld~~g~~l~~D~Fk~PScC~ 165 (166)
|.|.+|.++ ..--.+..|.++|+
T Consensus 85 rAlt~~~~~-~~~Wr~IrI~tsCv 107 (116)
T PF00243_consen 85 RALTMDDNQ-KVGWRWIRIDTSCV 107 (116)
T ss_dssp EEEEECSSS-CEEEEEEEEEEEEE
T ss_pred EEEEEcCCc-ccceeEEEECCceE
Confidence 999998763 36777899999985
No 2
>PF02035 Coagulin: Coagulin; InterPro: IPR000275 Coagulogen is a gel-forming protein of hemolymph that hinders the spread of invaders by immobilising them [, ]. The protein contains a single 175- residue polypeptide chain; this is cleaved after Arg-18 and Arg-46 by a clotting enzyme contained in the hemocyte and activated by a bacterial endotoxin (lipopolysaccharide). Cleavage releases two chains of coagulin, A and B, linked by two disulphide bonds, together with the peptide C [, ]. Gel formation results from interlinking of coagulin molecules. Secondary structure prediction suggests the C peptide forms an alpha- helix, which is released during the proteolytic conversion of coagulogen to coagulin gel []. The beta-sheet structure and 16 half-cystines found in the molecule appear to yield a compact protein stable to acid and heat. Mammalian blood coagulation is based on the proteolytically induced polymerisation of fibrinogens. Initially, fibrin monomers noncovalently interact with each other. The resulting homopolymers are further stabilised when the plasma transglutaminase (TGase) intermolecularly cross-links epsilon-(gamma-glutamyl)lysine bonds. In crustaceans, hemolymph coagulation depends on the TGase-mediated cross-linking of specific plasma-clotting proteins, but without the proteolytic cascade. In horseshoe crabs, the proteolytic coagulation cascade triggered by lipopolysaccharides and beta-1,3-glucans leads to the conversion of coagulogen into coagulin, resulting in noncovalent coagulin homopolymers through head-to-tail interaction. Horseshoe crab TGase, however, does not cross-link coagulins intermolecularly. Recently, we found that coagulins are cross-linked on hemocyte cell surface proteins called proxins. This indicates that a cross-linking reaction at the final stage of hemolymph coagulation is an important innate immune system of horseshoe crabs [].; GO: 0042381 hemolymph coagulation, 0005576 extracellular region; PDB: 1AOC_A.
Probab=97.43 E-value=0.0011 Score=53.69 Aligned_cols=78 Identities=22% Similarity=0.460 Sum_probs=52.4
Q ss_pred cCCcceeeeeeceeeeeCCCcEEEEEeccCCCCceeeeEEEEeecC---CccCCccCCCCCCcCeeEEeeeceEEEEEeC
Q psy13251 72 TLCPTRSQFVMPQAAVNNKGNWMYVVNINEVDNRYKQLVKSEVCLS---TECNGVCGLPPGYTSRCEQKYVQKRLIALQG 148 (166)
Q Consensus 72 ~LC~S~~~~i~Pk~A~N~~g~Wr~IVNt~e~~n~y~Q~VRvE~C~~---~~C~~~~~lp~gY~S~CkQKYv~rrLlAld~ 148 (166)
.-||..++---|..+.++.|+.++|||.+.- .|.|-|-.-+|.. ..| ||+.+|.|+=+.-||+++|-
T Consensus 84 secpvstrdcepvfgyt~a~efrvivqapra--gfrqcvwqhkcraygsn~c--------~~~grctqqrsvvrlvtynl 153 (174)
T PF02035_consen 84 SECPVSTRDCEPVFGYTVAGEFRVIVQAPRA--GFRQCVWQHKCRAYGSNNC--------GFNGRCTQQRSVVRLVTYNL 153 (174)
T ss_dssp SB--EEEE----SEEE-TTS-EEEE--BCCC--TB-B---EEEET-TSSSB---------SSS-EE--EEEEEEEEEEET
T ss_pred ccCCcccccccccccceecceEEEEEeCchh--hHHHHHHHhhhcccccccc--------CcCceeccceeEEEEEEEec
Confidence 4699999999999999999999999999965 7999999999983 245 57789999999999999999
Q ss_pred CCCcEEEEEEe
Q psy13251 149 EGNQLYTDVFW 159 (166)
Q Consensus 149 ~g~~l~~D~Fk 159 (166)
..+++.-+.|+
T Consensus 154 ek~~flce~~r 164 (174)
T PF02035_consen 154 EKDGFLCESFR 164 (174)
T ss_dssp TTTEEEEEEEE
T ss_pred ccCcEeehhhh
Confidence 98888888887
No 3
>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=96.39 E-value=0.013 Score=45.18 Aligned_cols=94 Identities=21% Similarity=0.380 Sum_probs=77.9
Q ss_pred ccccCCcceeeeee-ceeeeeCCCcEEEEEeccCCCC-ceeeeEEEEeecCC-----ccCCccCCCCCCcCeeEEeeece
Q psy13251 69 STFTLCPTRSQFVM-PQAAVNNKGNWMYVVNINEVDN-RYKQLVKSEVCLST-----ECNGVCGLPPGYTSRCEQKYVQK 141 (166)
Q Consensus 69 ~~~~LC~S~~~~i~-Pk~A~N~~g~Wr~IVNt~e~~n-~y~Q~VRvE~C~~~-----~C~~~~~lp~gY~S~CkQKYv~r 141 (166)
||-..|.|....+. =..|.+..|+=..|+.....+| .|+|-.-..+|.++ .|.+++. ..++|.|+-+=.+=
T Consensus 4 GE~sVCDS~S~WV~nKt~a~Di~G~~VtVL~~v~~nn~~~kQyF~ET~C~~~~~~~sgCrGID~--rhWnS~C~ttqtfV 81 (106)
T smart00140 4 GEYSVCDSISVWVTDKTTATDISGNEVTVLGEVPVNNGPLKQYFYETRCKSPNPVKSGCRGIDS--RHWNSQCKTTQTYV 81 (106)
T ss_pred cceeeccceeeEEeccCEEEecCCCEEEEEEEEEeCCceEEEEEEEeecCCCCCcCCCccCccc--ccccccccccchhh
Confidence 47889999999998 7778999999998877665534 89999998889973 6998875 57899999998999
Q ss_pred EEEEEeCCCCcEEEEEEecCCCcC
Q psy13251 142 RLIALQGEGNQLYTDVFWIPSCCM 165 (166)
Q Consensus 142 rLlAld~~g~~l~~D~Fk~PScC~ 165 (166)
|.|..+.++ .+.-.+.+|=++|+
T Consensus 82 rALT~~~~~-~~~Wr~IrI~taCv 104 (106)
T smart00140 82 RALTSDANK-RVGWRFIRIDTACV 104 (106)
T ss_pred hhhhhccCc-eeeEEEEEEcceee
Confidence 999988653 47777888888885
No 4
>PF06083 IL17: Interleukin-17; InterPro: IPR010345 Interleukins (IL) are a group of cytokines that play an important role in the immune system. They modulate inflammation and immunity by regulating growth, mobility and differentiation of lymphoid and other cells. Interleukin-17 (IL-17) is a potent proinflammatory cytokine produced by activated memory T cells []. The IL-17 family (of which there are 6 known members, termed IL-17A to IL-17F) is thought to represent a distinct signalling system that appears to have been highly conserved across vertebrate evolution []. Family members play an active role in inflammatory diseases, autoimmune diseases and cancer []. ; GO: 0005125 cytokine activity, 0006954 inflammatory response, 0005576 extracellular region; PDB: 2VXS_C 1JPY_Y 3JVF_B.
Probab=88.13 E-value=3.2 Score=30.34 Aligned_cols=71 Identities=14% Similarity=0.241 Sum_probs=48.2
Q ss_pred cEEEEEeccCCCCceeeeEEEEeecCCccCCccCCCCCCcCeeEEeeeceEEEEEe--CCC--CcEEEEEEecCCCc
Q psy13251 92 NWMYVVNINEVDNRYKQLVKSEVCLSTECNGVCGLPPGYTSRCEQKYVQKRLIALQ--GEG--NQLYTDVFWIPSCC 164 (166)
Q Consensus 92 ~Wr~IVNt~e~~n~y~Q~VRvE~C~~~~C~~~~~lp~gY~S~CkQKYv~rrLlAld--~~g--~~l~~D~Fk~PScC 164 (166)
-|.|++|.+.+ .|.|.|-.-.|+...|-...+.-..+.-.|+.-|.....|--. ..+ ..+..+..++|=.|
T Consensus 6 PW~y~~~~d~~--R~P~~i~eA~Clc~gCi~~~~g~e~~~~~svPI~~~i~VLrR~~~~~~~~~~y~~~~~~V~VGC 80 (84)
T PF06083_consen 6 PWTYRINHDPN--RIPSVIAEARCLCSGCINPQTGQEDHSLNSVPIYQEILVLRRECPCAGGRYSYRLEYEKVTVGC 80 (84)
T ss_dssp -EEEEEEE-TT--CCSSEEEEEEES-SSEE-TT-SSEETTSEEEEEEEEEEEEEEE--SSCCG-EEEEEEEEEEEEE
T ss_pred CeeeEECCCCc--CCCCcccEEEEecCCCCCccCCCcCCCeEEEEEEEEEEEEEEEecCCCCccEEEEEEEEeCEEe
Confidence 59999999975 9999999999998888544333455666788877766666666 222 33567777777666
No 5
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=37.10 E-value=80 Score=23.31 Aligned_cols=47 Identities=21% Similarity=0.361 Sum_probs=34.7
Q ss_pred eeeeeceeeeeCCCcEE---EEEeccCCCCceeeeEEEEeecCCccCCccCCCCC
Q psy13251 78 SQFVMPQAAVNNKGNWM---YVVNINEVDNRYKQLVKSEVCLSTECNGVCGLPPG 129 (166)
Q Consensus 78 ~~~i~Pk~A~N~~g~Wr---~IVNt~e~~n~y~Q~VRvE~C~~~~C~~~~~lp~g 129 (166)
...+.+..+.+.+| |+ +||-+.+ .|.|.|.+|..- ..|+-+..+..|
T Consensus 7 i~~l~~~~g~s~~G-w~Kre~Vlet~~---qYP~~i~f~~~~-dk~~~l~~~~~G 56 (84)
T PF11325_consen 7 IKVLPEQQGVSKNG-WKKREFVLETEE---QYPQKICFEFWG-DKIDLLDNFQVG 56 (84)
T ss_pred EEEecCcccCcCCC-cEEEEEEEeCCC---cCCceEEEEEEc-chhhhhccCCCC
Confidence 45667777888888 97 7888775 799999999987 566654454443
No 6
>KOG3463|consensus
Probab=28.74 E-value=54 Score=25.63 Aligned_cols=29 Identities=24% Similarity=0.381 Sum_probs=20.7
Q ss_pred CCCcEEEEEeccCC--CCceee---eEEEEeecC
Q psy13251 89 NKGNWMYVVNINEV--DNRYKQ---LVKSEVCLS 117 (166)
Q Consensus 89 ~~g~Wr~IVNt~e~--~n~y~Q---~VRvE~C~~ 117 (166)
-||.|.+|+|..+. ++++.+ .|+|--|..
T Consensus 69 CDnVWTFil~~~~~r~~~e~~~~vdkvkIVACdg 102 (109)
T KOG3463|consen 69 CDNVWTFILKDVEFREDNESFKTVDKVKIVACDG 102 (109)
T ss_pred ccceeeEEEcCeEEecccccccccceEEEEEecC
Confidence 48899999999855 345544 567777765
No 7
>KOG4214|consensus
Probab=24.41 E-value=25 Score=27.56 Aligned_cols=12 Identities=50% Similarity=0.861 Sum_probs=9.9
Q ss_pred Cccccccccccc
Q psy13251 13 ARRFPLHYGTDA 24 (166)
Q Consensus 13 ~~~~~~~~~~~~ 24 (166)
.-||||||..|-
T Consensus 33 ggR~plhyAAD~ 44 (117)
T KOG4214|consen 33 GGRTPLHYAADY 44 (117)
T ss_pred CCcccchHhhhc
Confidence 569999998774
No 8
>cd04894 ACT_ACR-like_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.18 E-value=58 Score=23.52 Aligned_cols=17 Identities=24% Similarity=0.552 Sum_probs=13.5
Q ss_pred eeeeeCCCcEEEEEecc
Q psy13251 84 QAAVNNKGNWMYVVNIN 100 (166)
Q Consensus 84 k~A~N~~g~Wr~IVNt~ 100 (166)
+....+||+|-|||=..
T Consensus 30 rgd~sTDGkWCyiv~wV 46 (69)
T cd04894 30 RGDDSTDGRWCYIVFWV 46 (69)
T ss_pred ecccccCCcEEEEEEEE
Confidence 44578999999999655
No 9
>PF13225 DUF4033: Domain of unknown function (DUF4033)
Probab=21.34 E-value=53 Score=24.61 Aligned_cols=13 Identities=31% Similarity=0.202 Sum_probs=11.6
Q ss_pred ceeeeEEEEeecC
Q psy13251 105 RYKQLVKSEVCLS 117 (166)
Q Consensus 105 ~y~Q~VRvE~C~~ 117 (166)
...|+|.||+|+.
T Consensus 19 ~~~sgV~i~kCRy 31 (86)
T PF13225_consen 19 GQKSGVHIEKCRY 31 (86)
T ss_pred cccceEEEEEeEE
Confidence 6799999999985
No 10
>PF06433 Me-amine-dh_H: Methylamine dehydrogenase heavy chain (MADH); InterPro: IPR009451 Methylamine dehydrogenase (1.4.99.3 from EC) is a periplasmic quinoprotein found in several methyltrophic bacteria []. It is induced when grown on methylamine as a carbon source MADH and catalyses the oxidative deamination of amines to their corresponding aldehydes. The redox cofactor of this enzyme is tryptophan tryptophylquinone (TTQ). Electrons derived from the oxidation of methylamine are passed to an electron acceptor, which is usually the blue-copper protein amicyanin (IPR002386 from INTERPRO). RCH2NH2 + H2O + acceptor = RCHO + NH3 + reduced acceptor MADH is a hetero-tetramer, comprised of two heavy subunits and two light subunits. The heavy subunit forms a seven-bladed beta-propeller like structure [].; GO: 0030058 amine dehydrogenase activity, 0030416 methylamine metabolic process, 0055114 oxidation-reduction process, 0042597 periplasmic space; PDB: 3RN1_F 3SVW_F 3PXT_F 3L4O_F 3L4M_D 3SJL_F 3PXS_D 3ORV_F 3RMZ_F 3RLM_F ....
Probab=17.75 E-value=1.5e+02 Score=27.17 Aligned_cols=60 Identities=25% Similarity=0.383 Sum_probs=36.5
Q ss_pred cCCCCceeeCcchhhhhhcc--ccccccccCCCCccccCCcceeeeeece-e----------eeeCCCcEEEEEecc
Q psy13251 37 LTAPPVSYYDPGYWWKRYRR--NADREKRQSSSTSTFTLCPTRSQFVMPQ-A----------AVNNKGNWMYVVNIN 100 (166)
Q Consensus 37 ~~~~~~~~~~~~~~~~r~~~--~~~~~kR~~~~d~~~~LC~S~~~~i~Pk-~----------A~N~~g~Wr~IVNt~ 100 (166)
+...--..|.++-||.|..| +.+-.+=.+. ..|=+..+-.|.|+ + +++.+|+|.+|-|.-
T Consensus 43 ~spdgk~~y~a~T~~sR~~rG~RtDvv~~~D~----~TL~~~~EI~iP~k~R~~~~~~~~~~~ls~dgk~~~V~N~T 115 (342)
T PF06433_consen 43 LSPDGKTIYVAETFYSRGTRGERTDVVEIWDT----QTLSPTGEIEIPPKPRAQVVPYKNMFALSADGKFLYVQNFT 115 (342)
T ss_dssp E-TTSSEEEEEEEEEEETTEEEEEEEEEEEET----TTTEEEEEEEETTS-B--BS--GGGEEE-TTSSEEEEEEES
T ss_pred ECCCCCEEEEEEEEEeccccccceeEEEEEec----CcCcccceEecCCcchheecccccceEEccCCcEEEEEccC
Confidence 33445567888888887665 2222222233 34666666666665 3 356899999999876
Done!