Query 034476
Match_columns 93
No_of_seqs 37 out of 39
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 03:16:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034476.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034476hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09943 DUF2175: Uncharacteri 48.3 10 0.00022 26.9 1.2 18 52-69 26-43 (101)
2 PF12443 AKNA: AT-hook-contain 41.7 18 0.00039 25.8 1.6 14 34-47 60-73 (106)
3 PF03735 ENT: ENT domain; Int 33.8 74 0.0016 20.9 3.5 27 36-62 31-57 (73)
4 PF10283 zf-CCHH: Zinc-finger 29.8 20 0.00044 19.9 0.3 17 21-48 7-23 (26)
5 KOG1556 26S proteasome regulat 27.6 32 0.00069 28.7 1.1 22 54-75 69-90 (309)
6 smart00153 VHP Villin headpiec 26.1 36 0.00079 19.7 0.9 11 60-70 6-16 (36)
7 PF10940 DUF2618: Protein of u 20.1 60 0.0013 19.9 1.1 25 36-60 3-27 (40)
8 COG1473 AbgB Metal-dependent a 20.0 71 0.0015 26.5 1.8 26 31-56 10-35 (392)
9 PF02022 Integrase_Zn: Integra 19.6 1.3E+02 0.0028 17.7 2.4 21 54-74 8-28 (40)
10 PF01627 Hpt: Hpt domain; Int 19.6 1.9E+02 0.0042 16.8 3.2 38 32-69 4-44 (90)
No 1
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=48.29 E-value=10 Score=26.86 Aligned_cols=18 Identities=22% Similarity=0.296 Sum_probs=15.1
Q ss_pred HHHhHHHHHHHHHhchhh
Q 034476 52 EHKTCFSKTIKKMFGMSK 69 (93)
Q Consensus 52 EHktCfk~ti~kmFG~sK 69 (93)
=||+||...+.+.+...+
T Consensus 26 VH~~C~~~~~~~k~~~~~ 43 (101)
T PF09943_consen 26 VHYECFREKASKKLYGDV 43 (101)
T ss_pred EeHHHHHHHHhhhcccCh
Confidence 399999999998887665
No 2
>PF12443 AKNA: AT-hook-containing transcription factor; InterPro: IPR022150 This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes.
Probab=41.74 E-value=18 Score=25.82 Aligned_cols=14 Identities=43% Similarity=0.698 Sum_probs=11.4
Q ss_pred hhHHHHHHHHHHhh
Q 034476 34 FLEDLKDHIDEFVN 47 (93)
Q Consensus 34 F~e~lKDh~~eFi~ 47 (93)
=++.||||++||-.
T Consensus 60 qteeLK~kvqe~sk 73 (106)
T PF12443_consen 60 QTEELKDKVQEFSK 73 (106)
T ss_pred HHHHHHHHHHHHhc
Confidence 36899999999953
No 3
>PF03735 ENT: ENT domain; InterPro: IPR005491 This entry represents a protein regulator which is able to repress transcription, possibly via its interaction with a multi protein chromatin re-modeling complex that modifies the chromatin. Its interaction with BRCA2 suggests that it may play a central role in the DNA repair function of BRCA2 []. ; PDB: 1UZ3_B 1UTU_B 2FMM_E.
Probab=33.84 E-value=74 Score=20.94 Aligned_cols=27 Identities=26% Similarity=0.388 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhhcChHHHHhHHHHHHH
Q 034476 36 EDLKDHIDEFVNASMEEHKTCFSKTIK 62 (93)
Q Consensus 36 e~lKDh~~eFi~As~dEHktCfk~ti~ 62 (93)
+.|-.+.+...++|-++|..++.+-..
T Consensus 31 e~lLt~Lr~~L~IS~e~H~~~l~~~~~ 57 (73)
T PF03735_consen 31 EKLLTELRKELNISDEEHREELRRAVS 57 (73)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHHHhc
Confidence 445556667789999999999987654
No 4
>PF10283 zf-CCHH: Zinc-finger (CX5CX6HX5H) motif; InterPro: IPR019406 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type Znf motif that in humans is part of the APLF (aprataxin- and PNK-like) forkead association domain-containing protein []. The Znf is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues, and is configured CX5CX6HX5H. Many of the proteins containing this Znf are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism. This Znf motif appears to be specialised for the non-covalent binding of poly ADP-ribose; Aprataxin also appears to covalently bind poly ADP-ribose, but not through its Znf motif [].; PDB: 2KQC_A 2KUO_A 2KQE_A 2KQD_A 2KQB_A.
Probab=29.84 E-value=20 Score=19.89 Aligned_cols=17 Identities=29% Similarity=0.522 Sum_probs=9.4
Q ss_pred cchhhhccCCCchhhHHHHHHHHHHhhc
Q 034476 21 MTSCRKKKKDDATFLEDLKDHIDEFVNA 48 (93)
Q Consensus 21 ~sscRk~~~e~atF~e~lKDh~~eFi~A 48 (93)
.+|+||+. +||.||-|-
T Consensus 7 ~~CYRkNp-----------~H~~~f~Hp 23 (26)
T PF10283_consen 7 AKCYRKNP-----------QHFKEFSHP 23 (26)
T ss_dssp GG-S--SC-----------CHHHHCEST
T ss_pred hhhhcCCH-----------HHHhhcCCC
Confidence 46777754 488888774
No 5
>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]
Probab=27.55 E-value=32 Score=28.68 Aligned_cols=22 Identities=32% Similarity=0.303 Sum_probs=16.6
Q ss_pred HhHHHHHHHHHhchhhHhhhhh
Q 034476 54 KTCFSKTIKKMFGMSKVVAERN 75 (93)
Q Consensus 54 ktCfk~ti~kmFG~sK~vae~~ 75 (93)
|---.++|.+||||.|.|..+.
T Consensus 69 WFlDh~Y~esM~~mfkKvNake 90 (309)
T KOG1556|consen 69 WFLDHNYIESMFGMFKKVNAKE 90 (309)
T ss_pred EEeccHHHHHHHHHHHHhcchh
Confidence 3334589999999999887653
No 6
>smart00153 VHP Villin headpiece domain.
Probab=26.14 E-value=36 Score=19.71 Aligned_cols=11 Identities=27% Similarity=0.764 Sum_probs=8.6
Q ss_pred HHHHHhchhhH
Q 034476 60 TIKKMFGMSKV 70 (93)
Q Consensus 60 ti~kmFG~sK~ 70 (93)
-++++|||++.
T Consensus 6 eF~~vfgmsr~ 16 (36)
T smart00153 6 DFEEVFGMTRE 16 (36)
T ss_pred HHHHHHCCCHH
Confidence 36789999875
No 7
>PF10940 DUF2618: Protein of unknown function (DUF2618); InterPro: IPR021237 This bacterial family of proteins has no known function. The sequences within the family are highly conserved.
Probab=20.11 E-value=60 Score=19.91 Aligned_cols=25 Identities=28% Similarity=0.527 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhcChHHHHhHHHHH
Q 034476 36 EDLKDHIDEFVNASMEEHKTCFSKT 60 (93)
Q Consensus 36 e~lKDh~~eFi~As~dEHktCfk~t 60 (93)
..|.-||+.=-|+=|--|+.||.-.
T Consensus 3 ~~lMaHIRRtrHiMmpshR~~Fd~~ 27 (40)
T PF10940_consen 3 RSLMAHIRRTRHIMMPSHRSCFDFS 27 (40)
T ss_pred chHHHHHHhhhhhhchhhhcccchh
Confidence 3578899999999999999999754
No 8
>COG1473 AbgB Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]
Probab=19.99 E-value=71 Score=26.48 Aligned_cols=26 Identities=19% Similarity=0.195 Sum_probs=23.1
Q ss_pred CchhhHHHHHHHHHHhhcChHHHHhH
Q 034476 31 DATFLEDLKDHIDEFVNASMEEHKTC 56 (93)
Q Consensus 31 ~atF~e~lKDh~~eFi~As~dEHktC 56 (93)
....+.+++.|||+|=+.+-+|.||+
T Consensus 10 ~~~~l~~~rr~lH~~PEL~f~E~~Ta 35 (392)
T COG1473 10 LKDELIEWRRDLHEHPELGFEEYRTA 35 (392)
T ss_pred hhHHHHHHHHHHhhCCccchhHHHHH
Confidence 34567899999999999999999997
No 9
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=19.63 E-value=1.3e+02 Score=17.68 Aligned_cols=21 Identities=24% Similarity=0.536 Sum_probs=14.3
Q ss_pred HhHHHHHHHHHhchhhHhhhh
Q 034476 54 KTCFSKTIKKMFGMSKVVAER 74 (93)
Q Consensus 54 ktCfk~ti~kmFG~sK~vae~ 74 (93)
+.+--+.+...||.++.||+.
T Consensus 8 ~H~n~~~L~~~f~ip~~vAk~ 28 (40)
T PF02022_consen 8 YHSNAKALRHKFGIPRLVAKQ 28 (40)
T ss_dssp HHH-HHHHHHHHT--HHHHHH
T ss_pred HccCHHHHHHHHccCHHHHHH
Confidence 345567888999999999975
No 10
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=19.56 E-value=1.9e+02 Score=16.78 Aligned_cols=38 Identities=16% Similarity=0.296 Sum_probs=24.6
Q ss_pred chhhHHHHHHHHHHhhcC---hHHHHhHHHHHHHHHhchhh
Q 034476 32 ATFLEDLKDHIDEFVNAS---MEEHKTCFSKTIKKMFGMSK 69 (93)
Q Consensus 32 atF~e~lKDh~~eFi~As---~dEHktCfk~ti~kmFG~sK 69 (93)
..|++++.+++++...+- ..+=+.=+...+.++=|.+.
T Consensus 4 ~~f~~~~~~~~~~l~~~~~~~~~~d~~~l~~~~H~lkG~a~ 44 (90)
T PF01627_consen 4 DIFLEEAPEDLEQLEQALQALEQEDWEELRRLAHRLKGSAG 44 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHCSSHHCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHhhHHHHHHHHHHHhhhHH
Confidence 368888888888887776 44444455555555544433
Done!