Query 045042
Match_columns 111
No_of_seqs 90 out of 92
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 09:18:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045042.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045042hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12023 DUF3511: Domain of un 100.0 3.7E-33 8E-38 178.3 2.3 47 64-110 1-47 (47)
2 COG4334 Uncharacterized protei 42.3 20 0.00043 27.4 2.0 56 6-86 26-82 (131)
3 PF12355 Dscam_C: Down syndrom 34.4 39 0.00084 25.7 2.5 17 41-57 58-74 (124)
4 PF03520 KCNQ_channel: KCNQ vo 30.8 16 0.00036 29.5 0.0 26 45-70 3-28 (202)
5 PF06270 DUF1030: Protein of u 24.4 26 0.00056 23.1 0.1 17 95-111 7-26 (53)
6 PF07849 DUF1641: Protein of u 19.6 53 0.0011 19.8 0.7 9 66-74 20-28 (42)
7 PF07347 CI-B14_5a: NADH:ubiqu 15.6 1.1E+02 0.0024 22.1 1.7 20 33-52 42-61 (97)
8 PF02009 Rifin_STEVOR: Rifin/s 15.5 74 0.0016 26.5 0.9 8 66-73 32-39 (299)
9 PF15625 CC2D2AN-C2: CC2D2A N- 15.4 90 0.0019 23.1 1.2 17 67-83 24-40 (168)
10 cd07402 MPP_GpdQ Enterobacter 15.2 70 0.0015 23.1 0.6 28 61-88 211-239 (240)
No 1
>PF12023 DUF3511: Domain of unknown function (DUF3511); InterPro: IPR021899 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important.
Probab=99.97 E-value=3.7e-33 Score=178.33 Aligned_cols=47 Identities=79% Similarity=1.387 Sum_probs=46.5
Q ss_pred CCCCCHHHHhhhhhheeeeeeeechhhhhhhccchhhcccccccccc
Q 045042 64 WGFTDPEMKRRKRIAKYKVYTVEGKVKASLRKGLRWIKNKCSQIVHG 110 (111)
Q Consensus 64 W~~~DpE~kRkkRVA~YK~YavEGKvK~S~R~sfrWiK~k~s~iv~g 110 (111)
|+|+|||||||||||+||+|+||||||+|||+||||||+||++||||
T Consensus 1 w~~~dpE~kRkkRVA~Yk~y~vEGKvK~S~R~sfrWiK~k~s~iv~G 47 (47)
T PF12023_consen 1 WGFNDPEMKRKKRVASYKVYAVEGKVKGSLRKSFRWIKNKCSRIVYG 47 (47)
T ss_pred CCCCCHHHHHHHHHHhhheeeeehHHHHHHHhhhHHHHHHhhHhhcC
Confidence 89999999999999999999999999999999999999999999998
No 2
>COG4334 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.32 E-value=20 Score=27.43 Aligned_cols=56 Identities=25% Similarity=0.446 Sum_probs=36.7
Q ss_pred CCCCCCCCCCCceeEEeecCCCcccccccccceeeeeccCCCCCCCCCCCCCCCCCCCCCCCCHHHHhhhhhh-eeeeee
Q 045042 6 YGSGQRPYGGDRRLEIVSVSGKSFTSAAVGGNQIYATHDLPQIPPRMPRQSHDASLKPWGFTDPEMKRRKRIA-KYKVYT 84 (111)
Q Consensus 6 ygs~~r~y~~drr~eiVs~~gk~~~~~~g~~n~iy~tr~~p~~~p~p~~~s~~~ss~~W~~~DpE~kRkkRVA-~YK~Ya 84 (111)
+--.+|+||.+-+|=.|-++|.-...+|- ..+++| ++-+-.||+-|+. .=++|.
T Consensus 26 fre~grtygtptWIW~v~vDgdLyVrgy~------------------------G~aSrW-yqaA~~qraGrItaaG~t~~ 80 (131)
T COG4334 26 FREEGRTYGTPTWIWFVYVDGDLYVRGYR------------------------GRASRW-YQAAMIQRAGRITAAGKTYQ 80 (131)
T ss_pred ccccCcccCCccEEEEEEECCceEEeecC------------------------cchhHH-HHHHHHhhCCeEEecceEEE
Confidence 34578999999999887777844111111 113456 6778889999985 456776
Q ss_pred ee
Q 045042 85 VE 86 (111)
Q Consensus 85 vE 86 (111)
||
T Consensus 81 V~ 82 (131)
T COG4334 81 VE 82 (131)
T ss_pred EE
Confidence 54
No 3
>PF12355 Dscam_C: Down syndrome cell adhesion molecule C terminal ; InterPro: IPR021012 This entry is specific to the insecta, predominantly Drosophila spp. This entry is found in association with PF00047 from PFAM, PF07679 from PFAM and PF00041 from PFAM. The Down syndrome cell adhesion molecule (Dscam) belongs to a family of cell membrane molecules involved in the differentiation of the nervous system. This is the C-terminal cytoplasmic tail region of Dscam. In Drosophila melanogaster (Fruit fly) the gene has at least 59 different transcripts. Dscam may play a role in the nervous and immune systems [].
Probab=34.39 E-value=39 Score=25.71 Aligned_cols=17 Identities=29% Similarity=0.593 Sum_probs=11.0
Q ss_pred eeccCCCCCCCCCCCCC
Q 045042 41 ATHDLPQIPPRMPRQSH 57 (111)
Q Consensus 41 ~tr~~p~~~p~p~~~s~ 57 (111)
.+..+|..||+|+|...
T Consensus 58 ~~~gSPePPpPPPRn~D 74 (124)
T PF12355_consen 58 PGNGSPEPPPPPPRNHD 74 (124)
T ss_pred CCCCCCCCCCcCCCCCC
Confidence 33447777777777654
No 4
>PF03520 KCNQ_channel: KCNQ voltage-gated potassium channel; InterPro: IPR013821 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. KCNQ channels (also known as KQT-like channels) differ from other voltage-gated 6 TM helix channels, chiefly in that they possess no tetramerisation domain. Consequently, they rely on interaction with accessory subunits, or form heterotetramers with other members of the family []. Currently, 5 members of the KCNQ family are known. These have been found to be widely distributed within the body, having been shown to be expressed in the heart, brain, pancreas, lung, placenta and ear. They were initially cloned as a result of a search for proteins involved in cardiac arhythmia. Subsequently, mutations in other KCNQ family members have been shown to be responsible for some forms of hereditary deafness [] and benign familial neonatal epilepsy []. This entry represents a region found at the C terminus of these proteins.; PDB: 3HFE_B 3HFC_C 3BJ4_B 2OVC_A.
Probab=30.76 E-value=16 Score=29.51 Aligned_cols=26 Identities=23% Similarity=0.365 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCHH
Q 045042 45 LPQIPPRMPRQSHDASLKPWGFTDPE 70 (111)
Q Consensus 45 ~p~~~p~p~~~s~~~ss~~W~~~DpE 70 (111)
+|+........|.+...++|+|||-+
T Consensus 3 sps~~~~~~e~SPsKv~kSwsfndRt 28 (202)
T PF03520_consen 3 SPSAEVDGEEESPSKVQKSWSFNDRT 28 (202)
T ss_dssp --------------------------
T ss_pred CCCCCCCCCCCCCCCCCCCcchhhhh
Confidence 34444333445555667799999866
No 5
>PF06270 DUF1030: Protein of unknown function (DUF1030); InterPro: IPR009373 This family consists of several short Circovirus proteins of unknown function.
Probab=24.37 E-value=26 Score=23.08 Aligned_cols=17 Identities=41% Similarity=0.962 Sum_probs=11.8
Q ss_pred ccchh--hccccccc-cccC
Q 045042 95 KGLRW--IKNKCSQI-VHGC 111 (111)
Q Consensus 95 ~sfrW--iK~k~s~i-v~g~ 111 (111)
-+|+| +|-|++++ +|||
T Consensus 7 lgfkwgvfkikfselyihgy 26 (53)
T PF06270_consen 7 LGFKWGVFKIKFSELYIHGY 26 (53)
T ss_pred ecceeEEEEEEEEEEEEecc
Confidence 37888 67888876 5554
No 6
>PF07849 DUF1641: Protein of unknown function (DUF1641); InterPro: IPR012440 Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long.
Probab=19.60 E-value=53 Score=19.79 Aligned_cols=9 Identities=33% Similarity=0.874 Sum_probs=7.7
Q ss_pred CCCHHHHhh
Q 045042 66 FTDPEMKRR 74 (111)
Q Consensus 66 ~~DpE~kRk 74 (111)
+.|||++|=
T Consensus 20 l~Dpdvqrg 28 (42)
T PF07849_consen 20 LRDPDVQRG 28 (42)
T ss_pred HcCHHHHHH
Confidence 699999984
No 7
>PF07347 CI-B14_5a: NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a); InterPro: IPR009947 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family contains the eukaryotic NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane [].; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0042773 ATP synthesis coupled electron transport, 0005743 mitochondrial inner membrane
Probab=15.61 E-value=1.1e+02 Score=22.09 Aligned_cols=20 Identities=15% Similarity=-0.031 Sum_probs=16.0
Q ss_pred ccccceeeeeccCCCCCCCC
Q 045042 33 AVGGNQIYATHDLPQIPPRM 52 (111)
Q Consensus 33 ~g~~n~iy~tr~~p~~~p~p 52 (111)
...++.+|-|||....+-+|
T Consensus 42 hkls~NyYy~RD~RRev~PP 61 (97)
T PF07347_consen 42 HKLSANYYYTRDARREVQPP 61 (97)
T ss_pred cccccccccccccccccCCC
Confidence 66788899999987776666
No 8
>PF02009 Rifin_STEVOR: Rifin/stevor family; InterPro: IPR002858 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see []. Several multicopy gene families have been described in Plasmodium falciparum, including the stevor family of subtelomeric open reading frames and the rif interspersed repetitive elements. Both families contain three predicted transmembrane segments. It has been proposed that stevor and rif are members of a larger superfamily that code for variant surface antigens [].
Probab=15.52 E-value=74 Score=26.54 Aligned_cols=8 Identities=63% Similarity=0.800 Sum_probs=6.9
Q ss_pred CCCHHHHh
Q 045042 66 FTDPEMKR 73 (111)
Q Consensus 66 ~~DpE~kR 73 (111)
-||||||+
T Consensus 32 DNDPeMK~ 39 (299)
T PF02009_consen 32 DNDPEMKS 39 (299)
T ss_pred CCcHHHHH
Confidence 58999986
No 9
>PF15625 CC2D2AN-C2: CC2D2A N-terminal C2 domain
Probab=15.37 E-value=90 Score=23.06 Aligned_cols=17 Identities=35% Similarity=0.641 Sum_probs=15.1
Q ss_pred CCHHHHhhhhhheeeee
Q 045042 67 TDPEMKRRKRIAKYKVY 83 (111)
Q Consensus 67 ~DpE~kRkkRVA~YK~Y 83 (111)
.-.|.+||+++.+++.|
T Consensus 24 p~~E~~RR~~~~~~~~~ 40 (168)
T PF15625_consen 24 PRAEQNRRQRVQKTRYY 40 (168)
T ss_pred ChhHhhhHHHhhheeEE
Confidence 44899999999999988
No 10
>cd07402 MPP_GpdQ Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain. GpdQ (glycerophosphodiesterase Q, also known as Rv0805 in Mycobacterium tuberculosis) is a binuclear metallophosphoesterase from Enterobacter aerogenes that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. The GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide phosphodiesterase activity. GpdQ and Rv0805 belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosa
Probab=15.18 E-value=70 Score=23.12 Aligned_cols=28 Identities=7% Similarity=0.100 Sum_probs=22.8
Q ss_pred CCCCCCCCHHHHhhhhhheeeeeee-ech
Q 045042 61 LKPWGFTDPEMKRRKRIAKYKVYTV-EGK 88 (111)
Q Consensus 61 s~~W~~~DpE~kRkkRVA~YK~Yav-EGK 88 (111)
+-.|...+|+.+|--+.+.|+.|.+ |++
T Consensus 211 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 239 (240)
T cd07402 211 CHQFAPDLDDFALDALAPGYRALSLHEDG 239 (240)
T ss_pred eeeecCCCCcccccccCCCCcEEEEecCC
Confidence 4456678899999999999999998 654
Done!