Query 023478
Match_columns 281
No_of_seqs 96 out of 113
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:20:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023478.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023478hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05542 DUF760: Protein of un 99.9 3.2E-27 7E-32 185.3 8.8 84 11-140 2-86 (86)
2 PF05542 DUF760: Protein of un 97.8 0.0001 2.3E-09 58.1 7.4 76 194-270 2-77 (86)
3 PF08763 Ca_chan_IQ: Voltage g 74.7 3 6.6E-05 28.6 2.4 25 109-133 3-27 (35)
4 PF12037 DUF3523: Domain of un 47.8 27 0.00058 33.6 4.3 27 199-225 26-60 (276)
5 KOG0742 AAA+-type ATPase [Post 33.5 89 0.0019 32.7 5.6 28 200-227 71-106 (630)
6 PF09454 Vps23_core: Vps23 cor 29.4 91 0.002 23.6 3.8 26 8-35 6-31 (65)
7 PF14164 YqzH: YqzH-like prote 22.6 81 0.0018 24.3 2.4 27 10-36 32-62 (64)
8 KOG4826 C-8,7 sterol isomerase 16.7 29 0.00062 32.6 -1.3 59 223-281 40-112 (229)
9 PF11226 DUF3022: Protein of u 14.5 84 0.0018 26.5 1.0 35 199-233 53-90 (111)
10 PF06745 KaiC: KaiC; InterPro 13.3 84 0.0018 27.5 0.7 46 227-274 22-80 (226)
No 1
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=99.94 E-value=3.2e-27 Score=185.30 Aligned_cols=84 Identities=30% Similarity=0.413 Sum_probs=79.6
Q ss_pred hHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHhhCCCcccCCcccccCCccccCCCcchhhcccCchHHHHHHHHHHHHhh
Q 023478 11 PLHRRIAQLKEHECQTAVEDVMYMLILYKFSEIRVQLVPKLSRCIYNGRLEIWPSKDWELESIHEFEVLEMIREHISTVI 90 (281)
Q Consensus 11 ~LyrRIAevKe~Err~alEdImY~lIv~KF~e~~V~mvP~ls~~~~~Grl~~wp~~~~~Le~ihS~Ev~emI~~hl~~vL 90 (281)
+||++|++++. |+..+++| +|||||+|+|++||.++|
T Consensus 2 ~L~~yi~~l~p-e~~~~l~~------------------------------------------~~s~ev~e~m~~~v~~ll 38 (86)
T PF05542_consen 2 DLLQYIQSLKP-ERIQQLSE------------------------------------------PASPEVLEAMKQHVSGLL 38 (86)
T ss_pred hHHHHHHHCCH-HHHHHhhc------------------------------------------cCCHHHHHHHHHHHHHHH
Confidence 69999999999 99999998 899999999999999999
Q ss_pred ccc-cCCCCCCCcceEeechhhhhhHHHHHhhhhHhhhhhhhHhHHHHHHh
Q 023478 91 GLR-ANCSVTDSWATTEIQRLRLGRVYVASILYGYFLKSASLRYYLEECLA 140 (281)
Q Consensus 91 G~~-~~~~~~~~~~~~~isr~~Lg~vyAAsmM~GYFLr~~eqR~~LE~sl~ 140 (281)
|++ |++.|+ ++++++|++||+||+++||+|||||++|+|++||++|+
T Consensus 39 G~l~p~~~~~---~~i~~s~~~La~L~~~~mm~GYfLr~~E~R~~Le~sL~ 86 (86)
T PF05542_consen 39 GNLSPSDQFN---VTIQTSRENLAQLLAWSMMTGYFLRNAEQRLELERSLK 86 (86)
T ss_pred cCCCCcccCc---ceeEECHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhcC
Confidence 999 877665 89999999999999999999999999999999999985
No 2
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=97.77 E-value=0.0001 Score=58.07 Aligned_cols=76 Identities=26% Similarity=0.369 Sum_probs=69.0
Q ss_pred hhhhhhhcCCHHHHHHHhhhhhHHHHHHHHHhhhhhccCCCCCCCCCCceEEechhhhHHHHHHHHhhhhhhhhhhh
Q 023478 194 NLKCYVMGFDPETLQRCAKLRSREAVNLVEKHSCALFGDGQTGLLDTDEVILTSFSSLKRLVLEAIAFGSFLWDAEE 270 (281)
Q Consensus 194 ~Lr~YVm~fD~eTLqr~A~irSkEav~liEkht~ALFG~~~~g~~~~dE~i~isf~~LkrLVLEAvAFGSFLwDvEs 270 (281)
.|=.||.+.+|+++++-++..|.|++..|++|+..+-|.-. -....+-.|.++-..|-+|..=++.+|=|||.+|-
T Consensus 2 ~L~~yi~~l~pe~~~~l~~~~s~ev~e~m~~~v~~llG~l~-p~~~~~~~i~~s~~~La~L~~~~mm~GYfLr~~E~ 77 (86)
T PF05542_consen 2 DLLQYIQSLKPERIQQLSEPASPEVLEAMKQHVSGLLGNLS-PSDQFNVTIQTSRENLAQLLAWSMMTGYFLRNAEQ 77 (86)
T ss_pred hHHHHHHHCCHHHHHHhhccCCHHHHHHHHHHHHHHHcCCC-CcccCcceeEECHHHHHHHHHHHHHHhHHHHHHHH
Confidence 57789999999999999999999999999999999999875 23456678999999999999999999999999884
No 3
>PF08763 Ca_chan_IQ: Voltage gated calcium channel IQ domain; InterPro: IPR014873 Ca2+ ions are unique in that they not only carry charge but they are also the most widely used of diffusible second messengers. Voltage-dependent Ca2+ channels (VDCC) are a family of molecules that allow cells to couple electrical activity to intracellular Ca2+ signalling. The opening and closing of these channels by depolarizing stimuli, such as action potentials, allows Ca2+ ions to enter neurons down a steep electrochemical gradient, producing transient intracellular Ca2+ signals. Many of the processes that occur in neurons, including transmitter release, gene transcription and metabolism are controlled by Ca2+ influx occurring simultaneously at different cellular locales. The pore is formed by the alpha-1 subunit which incorporates the conduction pore, the voltage sensor and gating apparatus, and the known sites of channel regulation by second messengers, drugs, and toxins []. The activity of this pore is modulated by 4 tightly-coupled subunits: an intracellular beta subunit; a transmembrane gamma subunit; and a disulphide-linked complex of alpha-2 and delta subunits, which are proteolytically cleaved from the same gene product. Properties of the protein including gating voltage-dependence, G protein modulation and kinase susceptibility can be influenced by these subunits. Voltage-gated calcium channels are classified as T, L, N, P, Q and R, and are distinguished by their sensitivity to pharmacological blocks, single-channel conductance kinetics, and voltage-dependence. On the basis of their voltage activation properties, the voltage-gated calcium classes can be further divided into two broad groups: the low (T-type) and high (L, N, P, Q and R-type) threshold-activated channels. The voltage-gated calcium channel alpha 1 subunit contains an IQ domain, named for its isoleucine-glutamine (IQ) motif, which interacts with hydrophobic pockets of Ca2+/calmodulin []. The interaction regulates two self-regulatory calcium dependent feedback mechanisms, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF). ; PDB: 3OXQ_F 2F3Z_B 3G43_E 2F3Y_B 2BE6_D 3DVM_B 3BXK_D 2VAY_B 3DVK_B 3BXL_B ....
Probab=74.71 E-value=3 Score=28.58 Aligned_cols=25 Identities=16% Similarity=0.433 Sum_probs=20.3
Q ss_pred hhhhhhHHHHHhhhhHhhhhhhhHh
Q 023478 109 RLRLGRVYVASILYGYFLKSASLRY 133 (281)
Q Consensus 109 r~~Lg~vyAAsmM~GYFLr~~eqR~ 133 (281)
..++|++|||=|++-||-+.-..|.
T Consensus 3 ~~TVGK~YAt~lI~dyfr~~K~rk~ 27 (35)
T PF08763_consen 3 EVTVGKFYATLLIQDYFRQFKKRKE 27 (35)
T ss_dssp -CCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999987766554
No 4
>PF12037 DUF3523: Domain of unknown function (DUF3523); InterPro: IPR021911 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 257 to 277 amino acids in length. This domain is found associated with PF00004 from PFAM. This domain has a conserved LER sequence motif.
Probab=47.82 E-value=27 Score=33.65 Aligned_cols=27 Identities=44% Similarity=0.759 Sum_probs=20.3
Q ss_pred hhcCCHHHHHHHhhhh--------hHHHHHHHHHh
Q 023478 199 VMGFDPETLQRCAKLR--------SREAVNLVEKH 225 (281)
Q Consensus 199 Vm~fD~eTLqr~A~ir--------SkEav~liEkh 225 (281)
--+|||+.|.|.|+-- .|+|.+|+-+|
T Consensus 26 ~~~FDP~aLERaAkAlrel~~S~~Ak~afel~k~Q 60 (276)
T PF12037_consen 26 ASGFDPEALERAAKALRELNSSPHAKKAFELMKKQ 60 (276)
T ss_pred cCCCCcHHHHHHHHHHHHHhcChhHHHHHHHHHHH
Confidence 3489999999999853 46677776555
No 5
>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=33.53 E-value=89 Score=32.70 Aligned_cols=28 Identities=36% Similarity=0.618 Sum_probs=22.7
Q ss_pred hcCCHHHHHHHhhh--------hhHHHHHHHHHhhh
Q 023478 200 MGFDPETLQRCAKL--------RSREAVNLVEKHSC 227 (281)
Q Consensus 200 m~fD~eTLqr~A~i--------rSkEav~liEkht~ 227 (281)
-+|||+.|.|.|+- -+|++.+++.+|-+
T Consensus 71 ~gFDpeaLERaAKAlrein~s~~aK~vfel~r~qE~ 106 (630)
T KOG0742|consen 71 SGFDPEALERAAKALREINHSPYAKDVFELARMQEQ 106 (630)
T ss_pred cCCChHHHHHHHHHHHhhccCccHHHHHHHHHHHHH
Confidence 48999999999984 37888888877644
No 6
>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.
Probab=29.38 E-value=91 Score=23.59 Aligned_cols=26 Identities=35% Similarity=0.653 Sum_probs=21.6
Q ss_pred CchhHHHHHHHHhHHHHHHHHHHHHHHH
Q 023478 8 DEGPLHRRIAQLKEHECQTAVEDVMYML 35 (281)
Q Consensus 8 ~e~~LyrRIAevKe~Err~alEdImY~l 35 (281)
++.+|++.|=|+-++++ |+||.||.|
T Consensus 6 ~~~~l~~Ql~el~Aed~--AieDtiy~L 31 (65)
T PF09454_consen 6 AEDPLSNQLYELVAEDH--AIEDTIYYL 31 (65)
T ss_dssp -SSHHHHHHHHHHHHHH--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHHH--HHHHHHHHH
Confidence 45689999999988874 999999985
No 7
>PF14164 YqzH: YqzH-like protein
Probab=22.58 E-value=81 Score=24.32 Aligned_cols=27 Identities=37% Similarity=0.476 Sum_probs=21.0
Q ss_pred hhHHHHHHHHhHHHHH----HHHHHHHHHHH
Q 023478 10 GPLHRRIAQLKEHECQ----TAVEDVMYMLI 36 (281)
Q Consensus 10 ~~LyrRIAevKe~Err----~alEdImY~lI 36 (281)
-.|.++|++.|.+|-- ..||||.|--|
T Consensus 32 ~~L~~~i~~~~~~~~~~Dl~eiVeDvVY~yi 62 (64)
T PF14164_consen 32 EELCKHIQERKNEEPDEDLHEIVEDVVYDYI 62 (64)
T ss_pred HHHHHHHHHHHhcCCCchHHHHHHHHHHHHh
Confidence 4699999999988765 56788877654
No 8
>KOG4826 consensus C-8,7 sterol isomerase [Lipid transport and metabolism]
Probab=16.72 E-value=29 Score=32.61 Aligned_cols=59 Identities=27% Similarity=0.307 Sum_probs=48.9
Q ss_pred HHhhhhhccCCCCCCCCCCceEEechhhhHHHHHHH--------------HhhhhhhhhhhhhcccccccccC
Q 023478 223 EKHSCALFGDGQTGLLDTDEVILTSFSSLKRLVLEA--------------IAFGSFLWDAEEYADAVYKLKEN 281 (281)
Q Consensus 223 Ekht~ALFG~~~~g~~~~dE~i~isf~~LkrLVLEA--------------vAFGSFLwDvEsyVDs~Y~~~~~ 281 (281)
---+.-|+|+++.+.+.+.-.+=..++|+-++|+|+ -+|=+-+|.-=+-+|+||-.-||
T Consensus 40 v~~~~lls~~~~~~~L~~w~l~Wl~vsGlih~v~egyfv~~p~~~~~~~~s~~L~~~WKeYsk~D~RYv~~d~ 112 (229)
T KOG4826|consen 40 VVTTWLLSGRAAVVVLDKWVLCWLAVSGLIHLVLEGYFVFRPETNLPANSSALLAQLWKEYSKGDSRYVLTDD 112 (229)
T ss_pred HHHHHHHhCCCCCCCCcchhhHHHHhhCeeeeEEEeeEEeeecccCCccHHHHHHHHHHHhcccceeEeccCC
Confidence 344678999999887777777778899999999985 56777899999999999987664
No 9
>PF11226 DUF3022: Protein of unknown function (DUF3022); InterPro: IPR021389 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=14.52 E-value=84 Score=26.55 Aligned_cols=35 Identities=23% Similarity=0.250 Sum_probs=23.8
Q ss_pred hhcCCHHHHHHHhhhhhHHH---HHHHHHhhhhhccCC
Q 023478 199 VMGFDPETLQRCAKLRSREA---VNLVEKHSCALFGDG 233 (281)
Q Consensus 199 Vm~fD~eTLqr~A~irSkEa---v~liEkht~ALFG~~ 233 (281)
+-.|||.+|+|||-+-...= -..+--++++-||.-
T Consensus 53 ~lrf~~~~l~RYaald~~~R~Rv~a~L~a~v~~~l~~l 90 (111)
T PF11226_consen 53 DLRFDPDVLARYAALDTAARARVHARLRAYVRATLDSL 90 (111)
T ss_pred EEEECHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 35799999999986544332 234556777888773
No 10
>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....
Probab=13.32 E-value=84 Score=27.46 Aligned_cols=46 Identities=35% Similarity=0.585 Sum_probs=29.1
Q ss_pred hhhccCCCCCC-----------CCC-Cc-eEEechhhhHHHHHHHHhhhhhhhhhhhhccc
Q 023478 227 CALFGDGQTGL-----------LDT-DE-VILTSFSSLKRLVLEAIAFGSFLWDAEEYADA 274 (281)
Q Consensus 227 ~ALFG~~~~g~-----------~~~-dE-~i~isf~~LkrLVLEAvAFGSFLwDvEsyVDs 274 (281)
-.+.|.|++|. ..+ || ++-+||..=..-+++-.. +|-||.+.|++.
T Consensus 22 ~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~ee~~~~l~~~~~--s~g~d~~~~~~~ 80 (226)
T PF06745_consen 22 VLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSFEEPPEELIENMK--SFGWDLEEYEDS 80 (226)
T ss_dssp EEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEESSS-HHHHHHHHH--TTTS-HHHHHHT
T ss_pred EEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEecCCHHHHHHHHH--HcCCcHHHHhhc
Confidence 35677787752 234 66 566888776666666544 667999999887
Done!