Query psy3838
Match_columns 74
No_of_seqs 33 out of 35
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 18:42:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3838.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3838hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12129 Phtf-FEM1B_bdg: Male 100.0 5.7E-43 1.2E-47 250.2 4.5 67 8-74 1-67 (159)
2 PF06799 DUF1230: Protein of u 76.3 0.52 1.1E-05 33.7 -1.1 16 21-36 104-119 (144)
3 PF14703 DUF4463: Domain of un 57.6 7.6 0.00017 23.1 1.5 15 9-23 69-83 (85)
4 PF01756 ACOX: Acyl-CoA oxidas 34.7 28 0.00062 23.8 1.7 24 20-43 146-169 (187)
5 smart00052 EAL Putative diguan 31.9 23 0.00049 23.4 0.8 19 55-73 222-240 (241)
6 PHA02503 putative transcriptio 28.3 53 0.0012 20.6 2.0 23 11-33 16-38 (57)
7 COG3083 Predicted hydrolase of 27.3 72 0.0016 27.8 3.2 54 17-71 217-281 (600)
8 cd01948 EAL EAL domain. This d 25.6 35 0.00076 22.5 0.9 19 55-73 221-239 (240)
9 cd01239 PH_PKD Protein kinase 25.5 41 0.00088 23.5 1.2 17 20-36 101-117 (117)
10 PF12292 DUF3624: Protein of u 24.7 36 0.00077 22.3 0.7 20 13-32 7-26 (77)
11 cd08355 Glo_EDI_BRP_like_14 Th 23.0 38 0.00083 20.2 0.6 15 9-23 9-23 (122)
12 PF02052 Gallidermin: Gallider 22.7 28 0.00061 21.3 0.0 19 47-65 2-20 (52)
No 1
>PF12129 Phtf-FEM1B_bdg: Male germ-cell putative homeodomain transcription factor; InterPro: IPR021980 This domain is found in bacteria and eukaryotes, and is typically between 101 and 140 amino acids in length. Phtf proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84 kDa Phtf1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies []. Phtf1 enhances the binding of FEM1B -feminisation homologue 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHTF1 is directly implicated in apoptosis in spermatogenesis. It is the ANK domain of FEM1B that is necessary for the interaction with the N-terminal region of Phtf1 [].
Probab=100.00 E-value=5.7e-43 Score=250.17 Aligned_cols=67 Identities=51% Similarity=0.671 Sum_probs=64.6
Q ss_pred cccchhhhhhHHhhhchhHHHHHHHhhhhhccCCccccceecccCCceEEEeeeeeceecccCccCC
Q psy3838 8 MCSVTSVIGYQKKIGAYDKQQWETTVEQRILNGFTHVPKKTAKLKTELIDVDLVRVVFINDFKSIEH 74 (74)
Q Consensus 8 ~~~~~~i~wyqkKig~YD~q~WEKsvEq~~l~gl~~kpkk~~~iKpdLIDvDLVrGstF~KaKp~~~ 74 (74)
|+.+|+|+|||+|||+||+|+|||||||++++||+|+|||++++|||||||||||||||+||||+.+
T Consensus 1 ~~~~d~i~wyQkKig~YD~q~WEksveq~~l~gl~~~~kk~~~lk~dLIDvDLVRGStF~KAKP~~~ 67 (159)
T PF12129_consen 1 SKVDDAIAWYQKKIGAYDQQIWEKSVEQRELKGLTNKPKKTGHLKPDLIDVDLVRGSTFPKAKPESP 67 (159)
T ss_pred CcHHHHHHHHHHHHhhhHHHHHHHHHHHHHhcccccCCcccCCCChhheeeeeeeeecccccCCcch
Confidence 4678999999999999999999999999999999999999999999999999999999999999864
No 2
>PF06799 DUF1230: Protein of unknown function (DUF1230); InterPro: IPR009631 This family represents Ycf36, which is found in plants, encoded in the genomes of algal chloroplasts and in cyanobacteria. As the family is exclusively found in phototrophic organisms it may play a role in photosynthesis.
Probab=76.30 E-value=0.52 Score=33.72 Aligned_cols=16 Identities=38% Similarity=0.509 Sum_probs=13.6
Q ss_pred hhchhHHHHHHHhhhh
Q psy3838 21 IGAYDKQQWETTVEQR 36 (74)
Q Consensus 21 ig~YD~q~WEKsvEq~ 36 (74)
=|=||+|+|+|+.|-.
T Consensus 104 SGWYDGQ~W~Kp~e~l 119 (144)
T PF06799_consen 104 SGWYDGQVWVKPPEVL 119 (144)
T ss_pred cCccCCccccCCHHHH
Confidence 4889999999998853
No 3
>PF14703 DUF4463: Domain of unknown function (DUF4463)
Probab=57.62 E-value=7.6 Score=23.14 Aligned_cols=15 Identities=13% Similarity=0.235 Sum_probs=12.8
Q ss_pred ccchhhhhhHHhhhc
Q psy3838 9 CSVTSVIGYQKKIGA 23 (74)
Q Consensus 9 ~~~~~i~wyqkKig~ 23 (74)
...|||.||+++|..
T Consensus 69 ~kVDaIdyy~~el~~ 83 (85)
T PF14703_consen 69 KKVDAIDYYREELKE 83 (85)
T ss_pred CcchHHHHHHHHHHH
Confidence 568999999999864
No 4
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=34.73 E-value=28 Score=23.80 Aligned_cols=24 Identities=25% Similarity=0.368 Sum_probs=16.3
Q ss_pred hhhchhHHHHHHHhhhhhccCCcc
Q psy3838 20 KIGAYDKQQWETTVEQRILNGFTH 43 (74)
Q Consensus 20 Kig~YD~q~WEKsvEq~~l~gl~~ 43 (74)
-||.||+.+-|.-.+......+.+
T Consensus 146 ~iG~~DG~vYe~l~~~a~~~~~n~ 169 (187)
T PF01756_consen 146 PIGRYDGDVYEALFEWAKKSPLNQ 169 (187)
T ss_dssp STT-TT--HHHHHHHHHHHSGGGC
T ss_pred hhccccchHHHHHHHHHHHCCCCC
Confidence 499999999999988866655554
No 5
>smart00052 EAL Putative diguanylate phosphodiesterase. Putative diguanylate phosphodiesterase, present in a variety of bacteria.
Probab=31.86 E-value=23 Score=23.44 Aligned_cols=19 Identities=5% Similarity=0.053 Sum_probs=16.3
Q ss_pred eEEEeeeeeceecccCccC
Q psy3838 55 LIDVDLVRVVFINDFKSIE 73 (74)
Q Consensus 55 LIDvDLVrGstF~KaKp~~ 73 (74)
-+.+|+++|.-|++..|.+
T Consensus 222 ~~Gi~~~QG~~~~~p~~~~ 240 (241)
T smart00052 222 SLGCDYGQGYLFSRPLPLD 240 (241)
T ss_pred HcCCCEEeeceeccCCCCC
Confidence 4678999999999998875
No 6
>PHA02503 putative transcription regulator; Provisional
Probab=28.33 E-value=53 Score=20.57 Aligned_cols=23 Identities=26% Similarity=0.403 Sum_probs=18.1
Q ss_pred chhhhhhHHhhhchhHHHHHHHh
Q psy3838 11 VTSVIGYQKKIGAYDKQQWETTV 33 (74)
Q Consensus 11 ~~~i~wyqkKig~YD~q~WEKsv 33 (74)
..++.||.+|+-.|+.|--..|+
T Consensus 16 q~sve~yke~l~~~s~~fl~~sl 38 (57)
T PHA02503 16 QESVEFYKEKLSVYSKDFLQNSL 38 (57)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Confidence 35789999999999988655543
No 7
>COG3083 Predicted hydrolase of alkaline phosphatase superfamily [General function prediction only]
Probab=27.34 E-value=72 Score=27.78 Aligned_cols=54 Identities=19% Similarity=0.290 Sum_probs=40.7
Q ss_pred hHHhhhchhHHHHHHHhhhhh---ccCCccccceecccCCc-------eEEEeeeeecee-cccCc
Q psy3838 17 YQKKIGAYDKQQWETTVEQRI---LNGFTHVPKKTAKLKTE-------LIDVDLVRVVFI-NDFKS 71 (74)
Q Consensus 17 yqkKig~YD~q~WEKsvEq~~---l~gl~~kpkk~~~iKpd-------LIDvDLVrGstF-~KaKp 71 (74)
|-+|.|.-|+|.-.+-++|.. ..++ +=|++.-++.|- ||-||-+|++++ .+--|
T Consensus 217 FlekhGllD~qey~r~l~eqg~pda~~l-~YPl~pL~~~~~a~~~NillI~vdglR~d~l~~~~MP 281 (600)
T COG3083 217 FLEKHGLLDAQEYRRRLVEQGNPDASSL-NYPLRPLTISDPAHGPNILLITVDGLRYDALDEKQMP 281 (600)
T ss_pred HHHHcCCCchHHHHHHHHHcCCCCcccc-cCCCCCceecCCCCCCCEEEEEeccccccccChhhCh
Confidence 568999999999998888763 2344 577777776644 999999999998 44333
No 8
>cd01948 EAL EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria.
Probab=25.57 E-value=35 Score=22.50 Aligned_cols=19 Identities=16% Similarity=0.111 Sum_probs=16.1
Q ss_pred eEEEeeeeeceecccCccC
Q psy3838 55 LIDVDLVRVVFINDFKSIE 73 (74)
Q Consensus 55 LIDvDLVrGstF~KaKp~~ 73 (74)
-+.+|+++|..|++..|.+
T Consensus 221 ~~gi~~~QG~~~~~p~~~~ 239 (240)
T cd01948 221 ELGCDYVQGYLFSRPLPAE 239 (240)
T ss_pred HcCCCeeeeceeccCCCCC
Confidence 5788999999999887765
No 9
>cd01239 PH_PKD Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain. Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain. PKD consists of 2 C1 domains, followed by a PH domain and a kinase domain. While the PKD PH domain has not been shown to bind phosphorylated inositol lipids and is not required for membrane translocation, it is required for nuclear export. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=25.53 E-value=41 Score=23.54 Aligned_cols=17 Identities=35% Similarity=0.640 Sum_probs=14.8
Q ss_pred hhhchhHHHHHHHhhhh
Q psy3838 20 KIGAYDKQQWETTVEQR 36 (74)
Q Consensus 20 Kig~YD~q~WEKsvEq~ 36 (74)
-+|+...+.||++|.|.
T Consensus 101 g~g~~~a~~We~aI~qA 117 (117)
T cd01239 101 GRGSDNAQSWETAIRQA 117 (117)
T ss_pred cchhHHHHHHHHHHhcC
Confidence 48999999999999873
No 10
>PF12292 DUF3624: Protein of unknown function (DUF3624); InterPro: IPR022072 This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif.
Probab=24.70 E-value=36 Score=22.34 Aligned_cols=20 Identities=25% Similarity=0.441 Sum_probs=14.7
Q ss_pred hhhhhHHhhhchhHHHHHHH
Q psy3838 13 SVIGYQKKIGAYDKQQWETT 32 (74)
Q Consensus 13 ~i~wyqkKig~YD~q~WEKs 32 (74)
.-+||.+|||+=-.=.|.=+
T Consensus 7 ~~~~F~~KiGRC~rCM~QLt 26 (77)
T PF12292_consen 7 QESWFWQKIGRCQRCMWQLT 26 (77)
T ss_pred HHHHHHHHhccHHHHHHHHH
Confidence 45799999999766655543
No 11
>cd08355 Glo_EDI_BRP_like_14 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The structures of this family demonstrate domain swapping, which is shared by glyoxalase I and antibiotic resistance proteins.
Probab=22.97 E-value=38 Score=20.19 Aligned_cols=15 Identities=7% Similarity=0.011 Sum_probs=12.6
Q ss_pred ccchhhhhhHHhhhc
Q psy3838 9 CSVTSVIGYQKKIGA 23 (74)
Q Consensus 9 ~~~~~i~wyqkKig~ 23 (74)
....++.||++.+|.
T Consensus 9 d~~~a~~FY~~~lG~ 23 (122)
T cd08355 9 DAAAAIDWLTDAFGF 23 (122)
T ss_pred CHHHHHHHHHHhcCC
Confidence 457899999999984
No 12
>PF02052 Gallidermin: Gallidermin; InterPro: IPR006079 Lantibiotics are heavily-modified bacteriocin-like peptides from Gram- positive bacteria. They contain alpha,beta-unsaturated amino acids (dehydroalanine and dehydrobutyrine) and lanthionine or 3-methyllanthionine rings (collectively known as thioether rings). There are 2 types of lantibiotic: Type A (which include nisin, subtilin, epidermin, gallidermin and Pep5) are strongly cationic and bactericidal - nisin, subtilin and Pep5 inhibit the growth of Gram-positive bacteria, probably by voltage-dependent pore formation in the cytoplasmic membrane, resulting in cellular efflux of electrolytes, amino acids and ATP; Type B lantibiotics possess at most one positive charge and are not bactericidal. This family contains both type A and type B molecules. ; GO: 0050830 defense response to Gram-positive bacterium; PDB: 1WCO_N.
Probab=22.70 E-value=28 Score=21.27 Aligned_cols=19 Identities=21% Similarity=0.422 Sum_probs=0.0
Q ss_pred eecccCCceEEEeeeeece
Q psy3838 47 KTAKLKTELIDVDLVRVVF 65 (74)
Q Consensus 47 k~~~iKpdLIDvDLVrGst 65 (74)
++..++.||.|+||+-.+.
T Consensus 2 ~~~~~~edlFdlDv~~~~~ 20 (52)
T PF02052_consen 2 ETFDVQEDLFDLDVTVTAV 20 (52)
T ss_dssp -------------------
T ss_pred ccccccccceeeeeEEeEE
Confidence 4567888999999986653
Done!