Query 014678
Match_columns 420
No_of_seqs 44 out of 46
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 07:28:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014678.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014678hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00054 EFh EF-hand, calciu 46.4 16 0.00035 21.0 1.7 27 353-384 2-28 (29)
2 PF06161 DUF975: Protein of un 45.9 73 0.0016 29.7 6.8 41 83-123 143-189 (243)
3 PF04911 ATP-synt_J: ATP synth 44.8 28 0.0006 27.8 3.2 18 244-261 9-26 (54)
4 PF00725 3HCDH: 3-hydroxyacyl- 29.2 67 0.0015 25.8 3.3 33 353-385 4-36 (97)
5 PRK00523 hypothetical protein; 27.3 51 0.0011 27.6 2.3 21 88-109 4-24 (72)
6 PRK11234 nfrB bacteriophage N4 26.0 44 0.00095 37.5 2.2 35 351-385 641-675 (727)
7 COG4859 Uncharacterized protei 25.6 23 0.00049 31.3 -0.0 9 290-298 50-58 (105)
8 cd08785 CARD_CARD9-like Caspas 24.5 36 0.00078 28.7 1.0 30 346-386 15-44 (86)
9 cd08810 CARD_BCL10 Caspase act 23.6 38 0.00082 28.6 0.9 31 346-387 15-45 (84)
10 cd04371 DEP DEP domain, named 22.3 45 0.00097 25.8 1.0 30 348-377 30-67 (81)
No 1
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=46.41 E-value=16 Score=20.96 Aligned_cols=27 Identities=22% Similarity=0.462 Sum_probs=20.6
Q ss_pred HHHHHHHHHhchhhhHhcCCCChhchHHHHhC
Q 014678 353 LERLFKECQRHGEIWVSEGLITAKDIEDAKSN 384 (420)
Q Consensus 353 wd~lFk~ce~~G~~Ll~~G~It~~Diee~~~~ 384 (420)
|+.+|+.+..++ .|.|+.+|+.+++++
T Consensus 2 ~~~~f~~~d~~~-----~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDG-----DGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCC-----CCcEeHHHHHHHHHh
Confidence 567888887765 678888888877653
No 2
>PF06161 DUF975: Protein of unknown function (DUF975); InterPro: IPR010380 This is a family of uncharacterised bacterial proteins.
Probab=45.92 E-value=73 Score=29.70 Aligned_cols=41 Identities=24% Similarity=0.401 Sum_probs=26.8
Q ss_pred HhhHHHHHHHHHHHhhHHHhhhhhhhhhhHhh------hhhhhccCc
Q 014678 83 CIPVFLILWPVVSIGASIIGGALYGFLSPIFA------TFDAVGEGK 123 (420)
Q Consensus 83 ~lP~~l~LW~vvgI~GSvl~G~gYGff~P~~a------TFeAvgeg~ 123 (420)
.....+.+|.+++++..++.+..|.+-..+++ .+||+++.+
T Consensus 143 ~~~~~~~~~~l~~~i~~i~~~~~y~~~~yil~d~~~~~~~~al~~S~ 189 (243)
T PF06161_consen 143 SLLLLLVLLLLLLIIPGIIVSYSYSMVPYILADNPELGAFEALKRSR 189 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCHHHHHHHHH
Confidence 33344556667777778888888888766653 566665543
No 3
>PF04911 ATP-synt_J: ATP synthase j chain; InterPro: IPR006995 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. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit J found in the F0 complex of F-ATPases from fungal mitochondria. This subunit does not appear to display sequence similarity with subunits of F-ATPases found in other organisms []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0045263 proton-transporting ATP synthase complex, coupling factor F(o)
Probab=44.85 E-value=28 Score=27.79 Aligned_cols=18 Identities=28% Similarity=0.564 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 014678 244 ILWPLAVVGAVLGSMVTS 261 (420)
Q Consensus 244 lLWPl~Vvgavl~si~sS 261 (420)
-+||+.+-|+|..--++|
T Consensus 9 P~wPFf~ag~iv~ygv~k 26 (54)
T PF04911_consen 9 PMWPFFAAGAIVYYGVNK 26 (54)
T ss_pred hhhHHHHHHHHHHHHHHH
Confidence 379999999887654444
No 4
>PF00725 3HCDH: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR006108 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major region of similarities in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3MOG_A 2WTB_A 3ADP_A 3ADO_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B 3K6J_A 1ZCJ_A ....
Probab=29.25 E-value=67 Score=25.75 Aligned_cols=33 Identities=24% Similarity=0.372 Sum_probs=25.5
Q ss_pred HHHHHHHHHhchhhhHhcCCCChhchHHHHhCC
Q 014678 353 LERLFKECQRHGEIWVSEGLITAKDIEDAKSNS 385 (420)
Q Consensus 353 wd~lFk~ce~~G~~Ll~~G~It~~Diee~~~~k 385 (420)
.+.++-.--...-.|++||+.|++|||...+.+
T Consensus 4 ~nRl~~~~~~ea~~l~~egvas~~~ID~~~~~~ 36 (97)
T PF00725_consen 4 VNRLLAALLNEAARLVEEGVASPEDIDRAMRYG 36 (97)
T ss_dssp HHHHHHHHHHHHHHHHHTTSSSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 445555555666789999999999999988763
No 5
>PRK00523 hypothetical protein; Provisional
Probab=27.27 E-value=51 Score=27.63 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=0.0
Q ss_pred HHHHHHHHHhhHHHhhhhhhhh
Q 014678 88 LILWPVVSIGASIIGGALYGFL 109 (420)
Q Consensus 88 l~LW~vvgI~GSvl~G~gYGff 109 (420)
+.+|..++|++ +++|+.-|||
T Consensus 4 ~~l~I~l~i~~-li~G~~~Gff 24 (72)
T PRK00523 4 IGLALGLGIPL-LIVGGIIGYF 24 (72)
T ss_pred HHHHHHHHHHH-HHHHHHHHHH
No 6
>PRK11234 nfrB bacteriophage N4 adsorption protein B; Provisional
Probab=26.02 E-value=44 Score=37.51 Aligned_cols=35 Identities=17% Similarity=0.107 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHhchhhhHhcCCCChhchHHHHhCC
Q 014678 351 ELLERLFKECQRHGEIWVSEGLITAKDIEDAKSNS 385 (420)
Q Consensus 351 qiwd~lFk~ce~~G~~Ll~~G~It~~Diee~~~~k 385 (420)
|+|+..+..=-.-|+.|+++|.|+.+.+++++...
T Consensus 641 ~~~~~~~~~~~~lGe~L~~~g~i~~~~l~~aL~~~ 675 (727)
T PRK11234 641 EIWRQYVPHQFLFAEILTTLGHIPRSAINVLLLRH 675 (727)
T ss_pred hhhhhhhhhhhhHHHHHHHcCCCCHHHHHHHHHHh
Confidence 35555555555556666666666666666655544
No 7
>COG4859 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.61 E-value=23 Score=31.32 Aligned_cols=9 Identities=56% Similarity=0.815 Sum_probs=7.0
Q ss_pred hhhhhcccc
Q 014678 290 SIYDEYSND 298 (420)
Q Consensus 290 a~fDEYtND 298 (420)
-+=|||+||
T Consensus 50 de~DeY~N~ 58 (105)
T COG4859 50 DETDEYTND 58 (105)
T ss_pred CcchhhccC
Confidence 456999997
No 8
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=24.54 E-value=36 Score=28.69 Aligned_cols=30 Identities=17% Similarity=0.210 Sum_probs=23.8
Q ss_pred eccchHHHHHHHHHHHhchhhhHhcCCCChhchHHHHhCCC
Q 014678 346 DLKPLELLERLFKECQRHGEIWVSEGLITAKDIEDAKSNSG 386 (420)
Q Consensus 346 e~k~~qiwd~lFk~ce~~G~~Ll~~G~It~~Diee~~~~k~ 386 (420)
++++=++||+ |.++|++|.+|.||-.+...
T Consensus 15 ~l~~~~l~d~-----------L~q~~VLt~~d~EeI~~~~t 44 (86)
T cd08785 15 KINPSRLTPY-----------LRQCKVLDEQDEEEVLSSPR 44 (86)
T ss_pred HhhHHHHHHH-----------HHhcCCCCHHHHHHHhCCCc
Confidence 5666666665 57899999999999998764
No 9
>cd08810 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by asso
Probab=23.57 E-value=38 Score=28.64 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=24.6
Q ss_pred eccchHHHHHHHHHHHhchhhhHhcCCCChhchHHHHhCCCC
Q 014678 346 DLKPLELLERLFKECQRHGEIWVSEGLITAKDIEDAKSNSGS 387 (420)
Q Consensus 346 e~k~~qiwd~lFk~ce~~G~~Ll~~G~It~~Diee~~~~k~~ 387 (420)
++++=++||+ |.++|++|.+|.||-.+...+
T Consensus 15 ~L~~~~l~d~-----------L~s~~ILt~~d~EeI~~~~t~ 45 (84)
T cd08810 15 KIIADRHFDY-----------LRSKRILTRDDCEEISCRTTS 45 (84)
T ss_pred HhcHHHHHHH-----------HHHcCCCCHHHHHHHhccCCc
Confidence 5666667765 578999999999999987755
No 10
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=22.28 E-value=45 Score=25.81 Aligned_cols=30 Identities=23% Similarity=0.384 Sum_probs=23.9
Q ss_pred cchHHHHHHHHHHH--------hchhhhHhcCCCChhc
Q 014678 348 KPLELLERLFKECQ--------RHGEIWVSEGLITAKD 377 (420)
Q Consensus 348 k~~qiwd~lFk~ce--------~~G~~Ll~~G~It~~D 377 (420)
.--|++|||.+.++ .-|+.|++.|+|..-+
T Consensus 30 ~G~e~v~WL~~~~~~~~r~ea~~~~~~ll~~g~i~~v~ 67 (81)
T cd04371 30 TGSELVDWLLDNLEAITREEAVELGQALLKHGLIHHVS 67 (81)
T ss_pred EcHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 36689999997665 5688899999998765
Done!