Query psy15890
Match_columns 126
No_of_seqs 43 out of 45
Neff 1.8
Searched_HMMs 46136
Date Sat Aug 17 00:15:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15890.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15890hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0486|consensus 99.8 4.7E-19 1E-23 150.0 3.7 73 26-115 277-350 (351)
2 PF03826 OAR: OAR domain; Int 98.6 3.3E-09 7.2E-14 59.8 -0.7 18 68-88 2-19 (21)
3 cd04010 C2B_RasA3 C2 domain se 16.3 1E+02 0.0022 22.6 1.7 25 56-84 123-147 (148)
4 PF10937 DUF2638: Protein of u 15.9 1.8E+02 0.004 21.3 3.0 17 75-91 35-51 (112)
5 PF06174 DUF987: Protein of un 15.7 68 0.0015 22.6 0.6 39 84-126 13-54 (66)
6 cd06355 PBP1_FmdD_like Peripla 15.0 98 0.0021 24.0 1.4 31 5-35 3-33 (348)
7 cd06370 PBP1_Speract_GC_like L 13.2 1.3E+02 0.0028 24.0 1.7 32 4-35 3-35 (404)
8 PF13696 zf-CCHC_2: Zinc knuck 10.3 1.5E+02 0.0033 17.9 0.9 19 106-124 12-30 (32)
9 cd06346 PBP1_ABC_ligand_bindin 9.1 1.8E+02 0.0039 21.9 1.2 32 4-35 2-33 (312)
10 cd06349 PBP1_ABC_ligand_bindin 9.0 1.7E+02 0.0037 22.1 1.0 30 5-34 3-32 (340)
No 1
>KOG0486|consensus
Probab=99.75 E-value=4.7e-19 Score=150.03 Aligned_cols=73 Identities=48% Similarity=0.853 Sum_probs=64.1
Q ss_pred hhhhhhccC-cCCCCCCCCCCCCCCccccccCCCCCCCCCccccccccccccchhceecccccCCCccCCCCCCCCCCCC
Q psy15890 26 CLWVAELDG-SVAAATCPYVPPTTPYSMYTHRPASSDPSLSRVAECNVMSSSIASLRLKAKQHSNFNYTSITPPVSSANN 104 (126)
Q Consensus 26 ~l~~a~l~~-avs~a~CPY~~pa~PYsmYrhr~a~~~~~~~~~d~C~~msSSIASLRLKAKQHs~f~Y~sv~~p~s~s~~ 104 (126)
-|....+++ +++.+.|||++|++||.||| |+|+ ||||+||||||||.+|+|+.|+.|. ++.+
T Consensus 277 nL~~s~~~~~a~~~s~~~~~t~aspy~~yr-------------dtcn---SslaslrlkakQH~S~~~~~v~~p~-pa~~ 339 (351)
T KOG0486|consen 277 NLSPSSLNSHAVSTSACPYATPASPYDVYR-------------DTCN---SSLASLRLKAKQHSSFGYPSVQNPN-PASN 339 (351)
T ss_pred cCCccccccccccCCCCcCCCCCChhhhhh-------------hhhh---chhHhhhcccccccccCCccccCCC-Cccc
Confidence 455555555 88889999999999999999 9999 9999999999999999999999975 4679
Q ss_pred CCcccccCCcc
Q psy15890 105 RAACQYSDESV 115 (126)
Q Consensus 105 LsACQYa~~~~ 115 (126)
|+||||++++.
T Consensus 340 l~~cqy~~t~~ 350 (351)
T KOG0486|consen 340 LSACQYAVTRP 350 (351)
T ss_pred cCcCcccccCC
Confidence 99999997654
No 2
>PF03826 OAR: OAR domain; InterPro: IPR003654 This 14 amino acid motif has been identified within the C-terminal region of several Paired-like homeodomain (HD) containing proteins [, ]. It was named OAR domain after the initials of otp, aristaless, and rax []. Although it has been proposed that this domain could be important for transactivation and be involved in protein-protein interactions or DNA binding [, ], is function is not yet known. Some proteins known to contain a OAR domain include human RIEG, defects in which are the cause of Rieger syndrome []; human OG12X and Mus musculus (Mouse) Og12x, whose function is not yet known []; vertebrate Rax, which plays a role in the proliferation and/or differentiation of retinal cells []; Drosophila DRX, which appears to be important in brain development []; and human SHOX, encoded by the short stature homeobox-containing gene. Defects or lack of this protein are the cause of short stature associated with the Turner syndrome [].; GO: 0003677 DNA binding, 0007275 multicellular organismal development, 0005634 nucleus
Probab=98.64 E-value=3.3e-09 Score=59.78 Aligned_cols=18 Identities=67% Similarity=0.780 Sum_probs=16.3
Q ss_pred cccccccccchhceecccccC
Q psy15890 68 AECNVMSSSIASLRLKAKQHS 88 (126)
Q Consensus 68 d~C~~msSSIASLRLKAKQHs 88 (126)
|.|+ ||||+||||||||+
T Consensus 2 d~r~---sSIa~LRlKAkeH~ 19 (21)
T PF03826_consen 2 DRRS---SSIAALRLKAKEHS 19 (21)
T ss_pred Ccch---hhHHHHHHHHHHhc
Confidence 5677 99999999999996
No 3
>cd04010 C2B_RasA3 C2 domain second repeat present in RAS p21 protein activator 3 (RasA3). RasA3 are members of GTPase activating protein 1 (GAP1), a Ras-specific GAP, which suppresses Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras. In this way it can control cellular proliferation and differentiation. RasA3 contains an N-terminal C2 domain, a Ras-GAP domain, a plextrin homology (PH)-like domain, and a Bruton's Tyrosine Kinase (BTK) zinc binding domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain
Probab=16.28 E-value=1e+02 Score=22.58 Aligned_cols=25 Identities=40% Similarity=0.509 Sum_probs=14.9
Q ss_pred CCCCCCCCCccccccccccccchhceecc
Q psy15890 56 RPASSDPSLSRVAECNVMSSSIASLRLKA 84 (126)
Q Consensus 56 r~a~~~~~~~~~d~C~~msSSIASLRLKA 84 (126)
|...+||.+.+..-= .|+.|||||-
T Consensus 123 ~~~~~~~~~~~~~~~----~~~~~~~~~~ 147 (148)
T cd04010 123 REEKSTPPGTRSSKD----NSLGSLRLKI 147 (148)
T ss_pred cccccCCCCCccccc----CCcccEEEec
Confidence 344455555443332 5899999984
No 4
>PF10937 DUF2638: Protein of unknown function (DUF2638); InterPro: IPR020373 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a component of the mitochondrial small ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S). This entry is represented by a mitochondrial ribosomal protein of the small subunit, which has similarity to human mitochondrial ribosomal protein MRP-S36 [, , ].
Probab=15.89 E-value=1.8e+02 Score=21.29 Aligned_cols=17 Identities=35% Similarity=0.477 Sum_probs=13.8
Q ss_pred ccchhceecccccCCCc
Q psy15890 75 SSIASLRLKAKQHSNFN 91 (126)
Q Consensus 75 SSIASLRLKAKQHs~f~ 91 (126)
.|..+.|-+|+||-.|.
T Consensus 35 ~~f~~~~~~a~q~~Pl~ 51 (112)
T PF10937_consen 35 DSFSSYREHAQQHGPLQ 51 (112)
T ss_pred ccchhhhhcccccCCcc
Confidence 45558999999998875
No 5
>PF06174 DUF987: Protein of unknown function (DUF987); InterPro: IPR009329 This is a family of bacterial proteins that are related to the hypothetical protein YeeT.
Probab=15.69 E-value=68 Score=22.59 Aligned_cols=39 Identities=26% Similarity=0.463 Sum_probs=26.6
Q ss_pred ccccCC---CccCCCCCCCCCCCCCCcccccCCcccccCCCCccCC
Q psy15890 84 AKQHSN---FNYTSITPPVSSANNRAACQYSDESVTRCPQASPVYA 126 (126)
Q Consensus 84 AKQHs~---f~Y~sv~~p~s~s~~LsACQYa~~~~t~~~~~~~~~~ 126 (126)
.+||.. |-|-.-...= .-+.|+|.+..|.++|..--||+
T Consensus 13 ~rqhp~sRl~ryctGkY~W----~Gs~~hYtg~~V~di~gvLAVya 54 (66)
T PF06174_consen 13 YRQHPESRLFRYCTGKYQW----HGSVCHYTGRDVPDISGVLAVYA 54 (66)
T ss_pred HHhCchhhcccccccccee----ecccccccCcccCCCcceeeeee
Confidence 356742 5555444432 35789999999999988777764
No 6
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=14.96 E-value=98 Score=24.00 Aligned_cols=31 Identities=16% Similarity=0.230 Sum_probs=23.9
Q ss_pred CCccccccCCCcchhhHHHHHhhhhhhccCc
Q psy15890 5 GMTAPLTGSASPAGRRSALLMCLWVAELDGS 35 (126)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~l~~l~~a~l~~a 35 (126)
|+..||||..+..|+...-=.-|+..++|..
T Consensus 3 G~~~plsG~~a~~G~~~~~g~~la~~~iN~~ 33 (348)
T cd06355 3 GILHSLSGTMAISETTLKDAELLAIEEINAA 33 (348)
T ss_pred EEEEcCCCcccccchhHHHHHHHHHHHHHhc
Confidence 7889999999999986655556677777743
No 7
>cd06370 PBP1_Speract_GC_like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model.
Probab=13.20 E-value=1.3e+02 Score=24.01 Aligned_cols=32 Identities=19% Similarity=0.184 Sum_probs=24.8
Q ss_pred CCCcccccc-CCCcchhhHHHHHhhhhhhccCc
Q psy15890 4 TGMTAPLTG-SASPAGRRSALLMCLWVAELDGS 35 (126)
Q Consensus 4 ~~~~~~~~~-~~~~~~~~~~~l~~l~~a~l~~a 35 (126)
-|+..|||| ..+..|+....-+-|...++|..
T Consensus 3 iG~~~pltG~~~a~~G~~~~~a~~lAv~~IN~~ 35 (404)
T cd06370 3 VGYLAEWTTDRTDRLGLPISGALTLAVEDVNAD 35 (404)
T ss_pred eEecccccCCccccccccHHHHHHHHHHHHhCC
Confidence 488999999 59999987766666677777754
No 8
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=10.35 E-value=1.5e+02 Score=17.95 Aligned_cols=19 Identities=21% Similarity=0.567 Sum_probs=14.7
Q ss_pred CcccccCCcccccCCCCcc
Q psy15890 106 AACQYSDESVTRCPQASPV 124 (126)
Q Consensus 106 sACQYa~~~~t~~~~~~~~ 124 (126)
.-|+-.+.-..+||++.|-
T Consensus 12 ~~C~~~GH~i~dCP~~~Pk 30 (32)
T PF13696_consen 12 HRCGQKGHWIQDCPTNKPK 30 (32)
T ss_pred ecCCCCCccHhHCCCCCCC
Confidence 3577778888999998773
No 9
>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=9.08 E-value=1.8e+02 Score=21.93 Aligned_cols=32 Identities=31% Similarity=0.364 Sum_probs=23.8
Q ss_pred CCCccccccCCCcchhhHHHHHhhhhhhccCc
Q psy15890 4 TGMTAPLTGSASPAGRRSALLMCLWVAELDGS 35 (126)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~l~~l~~a~l~~a 35 (126)
-|+..||+|..+..|+...--+-|+..++|..
T Consensus 2 IG~~~plsG~~a~~g~~~~~g~~lA~~~iN~~ 33 (312)
T cd06346 2 IGILLPLTGDLASYGPPMADAAELAVKEVNAA 33 (312)
T ss_pred ceeeccCCCchhhcChhHHHHHHHHHHHHHHh
Confidence 37889999999888876555556677777743
No 10
>cd06349 PBP1_ABC_ligand_binding_like_14 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=9.04 E-value=1.7e+02 Score=22.13 Aligned_cols=30 Identities=27% Similarity=0.435 Sum_probs=22.9
Q ss_pred CCccccccCCCcchhhHHHHHhhhhhhccC
Q psy15890 5 GMTAPLTGSASPAGRRSALLMCLWVAELDG 34 (126)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~l~~l~~a~l~~ 34 (126)
|+..||+|..++-|+...--+-++..++|.
T Consensus 3 G~~~plsG~~a~~G~~~~~g~~~a~~~iN~ 32 (340)
T cd06349 3 GVAGPLTGDNAQYGTQWKRAFDLALDEINA 32 (340)
T ss_pred eEEecCCCcchhcCccHHHHHHHHHHHHHh
Confidence 788999999998887666555566666764
Done!