Query 042855
Match_columns 85
No_of_seqs 14 out of 16
Neff 2.1
Searched_HMMs 46136
Date Fri Mar 29 10:14:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042855.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042855hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05479 PsaN: Photosystem I r 100.0 4.5E-53 9.8E-58 304.3 0.1 75 9-85 64-138 (138)
2 PLN00054 photosystem I reactio 100.0 1.3E-51 2.8E-56 297.3 2.1 75 9-85 64-138 (139)
3 PF01160 Opiods_neuropep: Vert 42.9 10 0.00022 23.0 0.5 9 65-73 25-33 (48)
4 PF03002 Somatostatin: Somatos 36.4 14 0.00031 19.2 0.3 6 79-84 8-13 (18)
5 PF09416 UPF1_Zn_bind: RNA hel 22.4 27 0.00059 25.7 -0.2 25 53-82 43-72 (152)
6 PF05413 Peptidase_C34: Putati 18.6 65 0.0014 22.5 1.1 16 64-79 57-73 (92)
7 PF01634 HisG: ATP phosphoribo 18.3 35 0.00075 24.7 -0.3 42 12-55 62-103 (163)
8 PF07596 SBP_bac_10: Protein o 16.9 25 0.00054 24.6 -1.3 21 48-68 245-265 (265)
9 PRK01686 hisG ATP phosphoribos 16.8 39 0.00085 25.5 -0.4 24 13-38 111-134 (215)
10 TIGR02269 Myxococcus xanthus p 16.6 48 0.0011 26.0 0.1 35 46-80 11-45 (211)
No 1
>PF05479 PsaN: Photosystem I reaction centre subunit N (PSAN or PSI-N); InterPro: IPR008796 This family contains several Photosystem I reaction centre subunit N (PSI-N) proteins. The protein has no known function although it is localised in the thylakoid lumen []. PSI-N is a small extrinsic subunit at the lumen side and is very likely involved in the docking of plastocyanin.; GO: 0005516 calmodulin binding, 0015979 photosynthesis, 0009522 photosystem I, 0042651 thylakoid membrane; PDB: 2WSE_N 2WSC_N 2WSF_N 2O01_N.
Probab=100.00 E-value=4.5e-53 Score=304.28 Aligned_cols=75 Identities=65% Similarity=1.073 Sum_probs=61.1
Q ss_pred CCCcccccccceecccccceeeeeeeeeecceecCccccccHHHHhcCCCcceecCceeeeeccccceecccceeeC
Q 042855 9 PPRNETAGEKGLAACGKSKRIAVKQNVQFGTCKLLENFTDSQDLAKQKKVPFISDDLELECKGKDKYKCGSNVFWKW 85 (85)
Q Consensus 9 p~nkelndkKRlAtsg~~Anfars~tV~~g~C~Fp~Nf~gcq~~a~~k~V~FlSdDl~lECeGkdk~kCgSnvfwkw 85 (85)
-+|||||||||||||| |||||+|||+||+|+||+|||||||||++|+||||||||+|||||||+|||||||||||
T Consensus 64 kaNKelNDKkRlaTs~--aNfaR~~tv~fg~c~fP~n~~gc~~la~~~~v~f~sdd~~lecegkd~~kc~s~~~~k~ 138 (138)
T PF05479_consen 64 KANKELNDKKRLATSY--ANFARAYTVQFGTCKFPENFTGCQDLAKQKKVPFLSDDLKLECEGKDKYKCGSNVFWKW 138 (138)
T ss_dssp HSSSSSTTTSS-TSSS--SSSTSGTT--TSTSSSSS-SSSSSSS-STT-TTSS--SSSSS-TTTSSS-SSSS-SS--
T ss_pred HhhhhhhhHHHhhhhh--hhhhhheeeecccccCCccchhhHHHHHcCCCceecccceeeecCccccccccceeecC
Confidence 4799999999999999 99999999999999999999999999999999999999999999999999999999999
No 2
>PLN00054 photosystem I reaction center subunit N; Provisional
Probab=100.00 E-value=1.3e-51 Score=297.28 Aligned_cols=75 Identities=61% Similarity=1.015 Sum_probs=73.9
Q ss_pred CCCcccccccceecccccceeeeeeeeeecceecCccccccHHHHhcCCCcceecCceeeeeccccceecccceeeC
Q 042855 9 PPRNETAGEKGLAACGKSKRIAVKQNVQFGTCKLLENFTDSQDLAKQKKVPFISDDLELECKGKDKYKCGSNVFWKW 85 (85)
Q Consensus 9 p~nkelndkKRlAtsg~~Anfars~tV~~g~C~Fp~Nf~gcq~~a~~k~V~FlSdDl~lECeGkdk~kCgSnvfwkw 85 (85)
-+|||||||||||||| |||||+||||||+|+||||||||||||+||+||||||||+|||||+|+|+|||||||+|
T Consensus 64 ~aNKeLNDKKRlATS~--ANfaRa~TV~~G~C~FP~Nf~GCqdlA~~k~V~flsdDl~iECEGkd~~~CgS~~~~~~ 138 (139)
T PLN00054 64 KANKELNDKKRLATSG--ANFARSRTVQDGTCKFPENFTGCEDLAKQKKVPFISEDLALECEGKDKKKCGSKVFWKW 138 (139)
T ss_pred hhhhhhhhHHhhhhcc--hhhhhheeeecccccCCcccccHHHHHhcCCCCccccccceeecCCccceecccccccC
Confidence 4799999999999999 99999999999999999999999999999999999999999999999999999999999
No 3
>PF01160 Opiods_neuropep: Vertebrate endogenous opioids neuropeptide; InterPro: IPR006024 Vertebrate endogenous opioid neuropeptides are released by post-translational proteolytic cleavage of precursor proteins. The precursors consist of the following components: a signal sequence that precedes a conserved region of about 50 residues; a variable-length region; and the sequence of the neuropeptide itself. Three types of precursor are known: preproenkephalin A (gene PENK), which is processed to produce 6 copies of Met-enkephalin, plus Leu-enkephalin; preproenkephalin B (gene PDYN), which is processed to produce neoendorphin, dynorphin, leumorphin, rimorphin and Leu-enkephalin; and prepronocipeptin (gene PNOC), whose processing produces nociceptin (orphanin FQ) and two other potential neuropeptides. Sequence analysis reveals that the conserved N-terminal region of the precursors contains 6 cysteines, which are probably involved in disulphide bond formation. It is speculated that this region might be important for neuropeptide processing [].; GO: 0007218 neuropeptide signaling pathway
Probab=42.86 E-value=10 Score=23.04 Aligned_cols=9 Identities=56% Similarity=0.907 Sum_probs=7.2
Q ss_pred ceeeeeccc
Q 042855 65 LELECKGKD 73 (85)
Q Consensus 65 l~lECeGkd 73 (85)
=-|||||+-
T Consensus 25 C~LECEg~l 33 (48)
T PF01160_consen 25 CTLECEGKL 33 (48)
T ss_pred heeeeCCCC
Confidence 368999985
No 4
>PF03002 Somatostatin: Somatostatin/Cortistatin family; InterPro: IPR018142 Somatostatin inhibits the release of the pituitary growth hormone, somatotropin and inhibits the release of glucagon and insulin from the pancreas of fasted animals. Cortistatin is a cortical neuropeptide with neuronal depressant and sleep-modulating properties [].; GO: 0005179 hormone activity, 0005576 extracellular region
Probab=36.35 E-value=14 Score=19.22 Aligned_cols=6 Identities=67% Similarity=1.575 Sum_probs=4.7
Q ss_pred ccceee
Q 042855 79 SNVFWK 84 (85)
Q Consensus 79 Snvfwk 84 (85)
-|+|||
T Consensus 8 knffWK 13 (18)
T PF03002_consen 8 KNFFWK 13 (18)
T ss_pred cceeec
Confidence 488997
No 5
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=22.41 E-value=27 Score=25.73 Aligned_cols=25 Identities=56% Similarity=1.089 Sum_probs=8.3
Q ss_pred HhcCCCcceec----Cceeeeeccccceecc-cce
Q 042855 53 AKQKKVPFISD----DLELECKGKDKYKCGS-NVF 82 (85)
Q Consensus 53 a~~k~V~FlSd----Dl~lECeGkdk~kCgS-nvf 82 (85)
++.+.|..-.| |..||| |.||+ |||
T Consensus 43 srh~ev~LH~~s~lgdt~leC-----y~Cg~~NvF 72 (152)
T PF09416_consen 43 SRHKEVSLHPDSPLGDTVLEC-----YNCGSRNVF 72 (152)
T ss_dssp HT---EEE-TTSTT-S-B--------TTT----TT
T ss_pred ccCCceeeCCCCCCCCcEEEE-----EecCCCcee
Confidence 44555555544 778999 78876 444
No 6
>PF05413 Peptidase_C34: Putative closterovirus papain-like endopeptidase; InterPro: IPR008744 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This signature is found in the RNA-direct RNA polymerase of apple chlorotic leaf spot virus and cherry mottle virus.; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0019079 viral genome replication
Probab=18.60 E-value=65 Score=22.53 Aligned_cols=16 Identities=38% Similarity=1.022 Sum_probs=11.2
Q ss_pred Cceeeeeccccc-eecc
Q 042855 64 DLELECKGKDKY-KCGS 79 (85)
Q Consensus 64 Dl~lECeGkdk~-kCgS 79 (85)
.+++||||.=.- -|||
T Consensus 57 EiKveceGDCGlvE~Gs 73 (92)
T PF05413_consen 57 EIKVECEGDCGLVECGS 73 (92)
T ss_pred EEeeEecCccceEEecC
Confidence 468999997654 3665
No 7
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=18.29 E-value=35 Score=24.71 Aligned_cols=42 Identities=12% Similarity=0.067 Sum_probs=23.8
Q ss_pred cccccccceecccccceeeeeeeeeecceecCccccccHHHHhc
Q 042855 12 NETAGEKGLAACGKSKRIAVKQNVQFGTCKLLENFTDSQDLAKQ 55 (85)
Q Consensus 12 kelndkKRlAtsg~~Anfars~tV~~g~C~Fp~Nf~gcq~~a~~ 55 (85)
..+...+|.||++ -|++|.+--+-|.=.---.+.|+-.+|-.
T Consensus 62 ~~l~~~~rIATky--p~l~~~yf~~~g~~~~ii~l~GsvE~ap~ 103 (163)
T PF01634_consen 62 EDLKAGLRIATKY--PNLTRRYFAEKGINVEIIKLSGSVELAPP 103 (163)
T ss_dssp GGGSSTEEEEES---HHHHHHHHHHCT-EEEEEE-SS-TTHHHH
T ss_pred HHhccCCEEEECC--HHHHHHHHHHcCCcEEEEEccCCccccCC
Confidence 3455589999999 99999876655522222334455444433
No 8
>PF07596 SBP_bac_10: Protein of unknown function (DUF1559); InterPro: IPR011453 This is a large family of paralogous proteins apparently unique to planctomycetes.
Probab=16.91 E-value=25 Score=24.61 Aligned_cols=21 Identities=33% Similarity=0.471 Sum_probs=15.8
Q ss_pred ccHHHHhcCCCcceecCceee
Q 042855 48 DSQDLAKQKKVPFISDDLELE 68 (85)
Q Consensus 48 gcq~~a~~k~V~FlSdDl~lE 68 (85)
|++-|-.-+.|.||||-+.+|
T Consensus 245 G~n~~~~DGSVrfis~tId~~ 265 (265)
T PF07596_consen 245 GVNFLMADGSVRFISETIDLE 265 (265)
T ss_pred CceEEEecceEEecccccCCC
Confidence 555556678899999988776
No 9
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=16.84 E-value=39 Score=25.50 Aligned_cols=24 Identities=17% Similarity=0.037 Sum_probs=17.7
Q ss_pred ccccccceecccccceeeeeeeeeec
Q 042855 13 ETAGEKGLAACGKSKRIAVKQNVQFG 38 (85)
Q Consensus 13 elndkKRlAtsg~~Anfars~tV~~g 38 (85)
+...++|.||++ -|++|.+--+-|
T Consensus 111 ~~~~~~rIATkY--p~it~~yf~~~g 134 (215)
T PRK01686 111 KQGPRLRVATKY--PNIARRYFAEKG 134 (215)
T ss_pred hccCCCEEEeCC--HHHHHHHHHHcC
Confidence 445679999999 898887654444
No 10
>TIGR02269 Myxococcus xanthus paralogous lipoprotein family TIGR02269. This family consists of at least 9 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. One appears truncated toward the N-terminus; the others are predicted lipoproteins. The function is unknown.
Probab=16.59 E-value=48 Score=26.04 Aligned_cols=35 Identities=20% Similarity=0.242 Sum_probs=25.1
Q ss_pred ccccHHHHhcCCCcceecCceeeeeccccceeccc
Q 042855 46 FTDSQDLAKQKKVPFISDDLELECKGKDKYKCGSN 80 (85)
Q Consensus 46 f~gcq~~a~~k~V~FlSdDl~lECeGkdk~kCgSn 80 (85)
|.||-..|.+--..---+|-+.||+..|..-|.|-
T Consensus 11 ~~GCast~~~~p~~~~~~~~~e~C~~~ded~CVsl 45 (211)
T TIGR02269 11 FTGCASTAPKSPHAWAEVPHGEECSCTREDRCVSL 45 (211)
T ss_pred HhhcccCCCCCchhhccCcccccccCCCCCceeEE
Confidence 67896655443444556788999999998877663
Done!