Query psy1698
Match_columns 258
No_of_seqs 19 out of 21
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 18:37:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1698.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1698hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07629 DUF1590: Protein of u 2.8 7.5E+02 0.016 16.6 0.9 8 1-8 1-8 (32)
2 PF03223 V-ATPase_C: V-ATPase 2.7 5.1E+02 0.011 25.5 0.0 10 240-249 305-314 (371)
3 PF11105 CCAP: Arthropod cardi 2.4 5.7E+02 0.012 22.3 -0.1 6 253-258 50-55 (133)
4 KOG2096|consensus 2.2 5.7E+02 0.012 25.8 -0.3 70 132-201 310-383 (420)
5 KOG2909|consensus 2.1 6.9E+02 0.015 25.2 0.0 6 241-246 309-314 (381)
6 cd02336 ZZ_RSC8 Zinc finger, Z 2.0 1E+03 0.022 16.6 0.7 11 4-14 7-17 (45)
7 PF08515 TGF_beta_GS: Transfor 1.9 8.9E+02 0.019 16.0 0.3 9 2-10 14-22 (29)
8 PRK15421 DNA-binding transcrip 1.8 1.2E+03 0.025 21.1 1.0 23 224-248 294-316 (317)
9 smart00710 PbH1 Parallel beta- 1.8 1E+03 0.023 12.4 0.5 7 251-257 3-9 (26)
10 PF01396 zf-C4_Topoisom: Topoi 1.8 1.1E+03 0.025 15.6 0.7 9 249-258 17-25 (39)
No 1
>PF07629 DUF1590: Protein of unknown function (DUF1590); InterPro: IPR011481 These hypothetical proteins in Rhodopirellula baltica have a conserved C-terminal region.
Probab=2.79 E-value=7.5e+02 Score=16.61 Aligned_cols=8 Identities=50% Similarity=0.899 Sum_probs=4.7
Q ss_pred CCCCCCCC
Q psy1698 1 MGSGQDLP 8 (258)
Q Consensus 1 ~~~~~~~~ 8 (258)
|++|.|.|
T Consensus 1 m~~ga~~p 8 (32)
T PF07629_consen 1 MENGADCP 8 (32)
T ss_pred CCCCCCCC
Confidence 56666655
No 2
>PF03223 V-ATPase_C: V-ATPase subunit C; InterPro: IPR004907 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents the C subunit that is part of the V1 complex, and is localised to the interface between the V1 and V0 complexes []. This subunit does not show any homology with F-ATPase subunits. The C subunit plays an essential role in controlling the assembly of V-ATPase, acting as a flexible stator that holds together the catalytic (V1) and membrane (V0) sectors of the enzyme []. The release of subunit C from the ATPase complex results in the dissociation of the V1 and V0 subcomplexes, which is an important mechanism in controlling V-ATPase activity in cells. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0015991 ATP hydrolysis coupled proton transport, 0033180 proton-transporting V-type ATPase, V1 domain; PDB: 1U7L_A.
Probab=2.71 E-value=5.1e+02 Score=25.51 Aligned_cols=10 Identities=50% Similarity=0.803 Sum_probs=4.2
Q ss_pred ccccCCcccc
Q psy1698 240 TLRMGLPARR 249 (258)
Q Consensus 240 t~r~~~~~~~ 249 (258)
-||||+|..-
T Consensus 305 VLRYGLP~~F 314 (371)
T PF03223_consen 305 VLRYGLPPNF 314 (371)
T ss_dssp HHHH-SS--E
T ss_pred hhhcCCCCCc
Confidence 4677776543
No 3
>PF11105 CCAP: Arthropod cardioacceleratory peptide 2a; InterPro: IPR024276 Crustacean cardioactive peptide (CCAP), also known as cardioacceleratory peptide 2a, exerts a reversible and dose-dependent cardio-stimulatory effect on the semi-isolated heart of experimental beetles. CCAP also increases free hemolymph sugar concentration in young larvae and adults of the meal-worm beetle [].; PDB: 1Y49_A 1V46_A.
Probab=2.36 E-value=5.7e+02 Score=22.26 Aligned_cols=6 Identities=67% Similarity=1.503 Sum_probs=2.0
Q ss_pred eeeccC
Q psy1698 253 TFTGCT 258 (258)
Q Consensus 253 ~~~~~~ 258 (258)
.||||+
T Consensus 50 AFTGCG 55 (133)
T PF11105_consen 50 AFTGCG 55 (133)
T ss_dssp SSS---
T ss_pred hhcccC
Confidence 577774
No 4
>KOG2096|consensus
Probab=2.23 E-value=5.7e+02 Score=25.84 Aligned_cols=70 Identities=21% Similarity=0.245 Sum_probs=48.3
Q ss_pred cCCCCCCCCCcccCC----CCCCCCccCCCCCCCCCccCCCCCCCCCCCCCCCCCCCCCCCCccccCCccccCc
Q psy1698 132 RTGSEQDLPTLRTGS----GQDLPTLRTGSEQDLPTLRTGSEQDLPTLRTGSEQDLPTLRMGSEQDLSTLRMGS 201 (258)
Q Consensus 132 R~~~~~~~~tlR~~~----e~d~~tlR~~~e~d~~tlR~~~ehd~~tlR~~~e~d~~tlR~~~eh~~~tlR~~~ 201 (258)
||+.++|-.+||.++ ..+..++|-+-.-...-|=.++..++.++=.+-+.+.+++..-++.++.-+=|..
T Consensus 310 rY~~~qDpk~Lk~g~~pl~aag~~p~RL~lsP~g~~lA~s~gs~l~~~~se~g~~~~~~e~~h~~~Is~is~~~ 383 (420)
T KOG2096|consen 310 RYEAGQDPKILKEGSAPLHAAGSEPVRLELSPSGDSLAVSFGSDLKVFASEDGKDYPELEDIHSTTISSISYSS 383 (420)
T ss_pred eEecCCCchHhhcCCcchhhcCCCceEEEeCCCCcEEEeecCCceEEEEcccCccchhHHHhhcCceeeEEecC
Confidence 777777777777663 4445556666666666666677777777777778888888877777777665544
No 5
>KOG2909|consensus
Probab=2.09 E-value=6.9e+02 Score=25.16 Aligned_cols=6 Identities=83% Similarity=1.481 Sum_probs=2.6
Q ss_pred cccCCc
Q psy1698 241 LRMGLP 246 (258)
Q Consensus 241 ~r~~~~ 246 (258)
||||+|
T Consensus 309 lRYGLP 314 (381)
T KOG2909|consen 309 LRYGLP 314 (381)
T ss_pred HHhcCC
Confidence 344444
No 6
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=1.97 E-value=1e+03 Score=16.64 Aligned_cols=11 Identities=27% Similarity=0.440 Sum_probs=6.8
Q ss_pred CCCCCceeccC
Q psy1698 4 GQDLPTLRTGS 14 (258)
Q Consensus 4 ~~~~~~~~~~~ 14 (258)
|+|+.++||-.
T Consensus 7 g~D~t~vryh~ 17 (45)
T cd02336 7 GNDCTRVRYHN 17 (45)
T ss_pred CCccCceEEEe
Confidence 56666666643
No 7
>PF08515 TGF_beta_GS: Transforming growth factor beta type I GS-motif; InterPro: IPR003605 Transforming growth factor beta (TGF-beta) is a member of a large family of secreted growth factors of central importance in eukaryotic development and homeostasis. Members of this family, which includes the activins, inhibins and bone morphogenic proteins (BMPs), bind to receptors that consist of two transmembrane serine/threonine (Ser/Thr) kinases called the type I and type II receptors. Type II activates Type I upon formation of the ligand receptor complex by multiply phosphorylating the GS domain, a short (~30 residues), highly conserved regulatory sequence just N-terminal to the kinase domain on the cytoplasmic side of the receptor. The GS domain is found only in the type I receptor family and is named for the TTSGSGSG sequence at its core. At least three, and perhaps four to five of the serines and threonines in the GS domain, must be phosphorylated to fully activate TbetaR-1 []. The GS domain forms a helix-loop-helix structure in which the sites of activating phosphorylation are situated in a loop known as the GS loop. One key role for phosphorylation is to block the adoption of an inactivating configuration by the GS domain [].; GO: 0004675 transmembrane receptor protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation, 0016020 membrane; PDB: 3MY0_H 3Q4U_B 3H9R_A 3MTF_B 3OOM_A 3KCF_C 3FAA_A 1IAS_A 1PY5_A 2X7O_C ....
Probab=1.89 E-value=8.9e+02 Score=16.04 Aligned_cols=9 Identities=67% Similarity=1.110 Sum_probs=5.2
Q ss_pred CCCCCCCce
Q psy1698 2 GSGQDLPTL 10 (258)
Q Consensus 2 ~~~~~~~~~ 10 (258)
|||.-||.|
T Consensus 14 GSGSGlplL 22 (29)
T PF08515_consen 14 GSGSGLPLL 22 (29)
T ss_dssp TSSSSS-HH
T ss_pred CCCCCchhh
Confidence 666667655
No 8
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=1.81 E-value=1.2e+03 Score=21.12 Aligned_cols=23 Identities=43% Similarity=0.447 Sum_probs=16.4
Q ss_pred ccccCCccCCCccCCCccccCCccc
Q psy1698 224 EQDLSTLRTGSEQDLPTLRMGLPAR 248 (258)
Q Consensus 224 e~~~~tLr~~~eh~~~t~r~~~~~~ 248 (258)
....|-.|+. -|++|.|-|-|||
T Consensus 294 ~~~~~~~~~~--~~~~~~~~~~~~~ 316 (317)
T PRK15421 294 PFVKSAERPT--YDAPTVRPGSPAR 316 (317)
T ss_pred cccccccccC--CCCCccCCCCCCC
Confidence 3445555654 4789999999987
No 9
>smart00710 PbH1 Parallel beta-helix repeats. The tertiary structures of pectate lyases and rhamnogalacturonase A show a stack of parallel beta strands that are coiled into a large helix. Each coil of the helix represents a structural repeat that, in some homologues, can be recognised from sequence information alone. Conservation of asparagines might be connected with asparagine-ladders that contribute to the stability of the fold. Proteins containing these repeats most often are enzymes with polysaccharide substrates.
Probab=1.78 E-value=1e+03 Score=12.40 Aligned_cols=7 Identities=14% Similarity=0.264 Sum_probs=3.3
Q ss_pred ceeeecc
Q psy1698 251 GITFTGC 257 (258)
Q Consensus 251 ~~~~~~~ 257 (258)
+++|.+|
T Consensus 3 ~~~i~~n 9 (26)
T smart00710 3 NVTIENN 9 (26)
T ss_pred CEEEECC
Confidence 3445444
No 10
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=1.77 E-value=1.1e+03 Score=15.59 Aligned_cols=9 Identities=44% Similarity=1.383 Sum_probs=0.0
Q ss_pred ccceeeeccC
Q psy1698 249 RRGITFTGCT 258 (258)
Q Consensus 249 ~~~~~~~~~~ 258 (258)
+.| .|.||+
T Consensus 17 k~g-~F~~Cs 25 (39)
T PF01396_consen 17 KKG-KFLGCS 25 (39)
T ss_pred CCC-CEEECC
Done!