Query 034248
Match_columns 100
No_of_seqs 37 out of 39
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 11:24:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034248.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034248hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09943 DUF2175: Uncharacteri 45.6 12 0.00026 26.8 1.2 18 59-76 26-43 (101)
2 PF12443 AKNA: AT-hook-contain 37.1 23 0.00051 25.6 1.6 14 41-54 60-73 (106)
3 PF03735 ENT: ENT domain; Int 30.3 91 0.002 20.8 3.5 27 43-69 31-57 (73)
4 PF10283 zf-CCHH: Zinc-finger 28.1 23 0.0005 19.9 0.3 17 28-55 7-23 (26)
5 KOG1556 26S proteasome regulat 26.0 35 0.00075 28.8 1.1 21 61-81 69-89 (309)
6 smart00153 VHP Villin headpiec 25.2 39 0.00084 19.8 0.9 11 67-77 6-16 (36)
7 PF02022 Integrase_Zn: Integra 18.2 1.4E+02 0.0031 17.7 2.4 21 61-81 8-28 (40)
8 PF02209 VHP: Villin headpiece 18.1 63 0.0014 19.1 0.8 10 68-77 7-16 (36)
9 PF14659 Phage_int_SAM_3: Phag 18.1 2E+02 0.0044 16.0 3.1 22 56-77 21-42 (58)
10 PF01627 Hpt: Hpt domain; Int 17.5 2.2E+02 0.0047 16.7 3.1 37 40-76 5-44 (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=45.64 E-value=12 Score=26.84 Aligned_cols=18 Identities=22% Similarity=0.296 Sum_probs=15.1
Q ss_pred HHHhHHHHHHHHHhchhh
Q 034248 59 EHKTCFSKTIKKMFGMSK 76 (100)
Q Consensus 59 EHktCfknti~kmFG~sK 76 (100)
=||+||...+.+.+...+
T Consensus 26 VH~~C~~~~~~~k~~~~~ 43 (101)
T PF09943_consen 26 VHYECFREKASKKLYGDV 43 (101)
T ss_pred EeHHHHHHHHhhhcccCh
Confidence 399999999998877665
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=37.12 E-value=23 Score=25.55 Aligned_cols=14 Identities=43% Similarity=0.698 Sum_probs=11.4
Q ss_pred hhHHHHHHHHHHhh
Q 034248 41 FLEDLKDHIDEFVN 54 (100)
Q Consensus 41 F~e~lKDh~~EFi~ 54 (100)
=++.||||++||-.
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=30.32 E-value=91 Score=20.79 Aligned_cols=27 Identities=26% Similarity=0.388 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhhcChHHHHhHHHHHHH
Q 034248 43 EDLKDHIDEFVNASMEEHKTCFSKTIK 69 (100)
Q Consensus 43 e~lKDh~~EFi~As~dEHktCfknti~ 69 (100)
+.|-.+.+...++|-++|..++.+-..
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 445556667789999999999987655
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=28.09 E-value=23 Score=19.92 Aligned_cols=17 Identities=29% Similarity=0.522 Sum_probs=9.5
Q ss_pred cchhhhccCCCchhhHHHHHHHHHHhhc
Q 034248 28 MTSCRKKKKDDATFLEDLKDHIDEFVNA 55 (100)
Q Consensus 28 ~sscRk~~~e~aTF~e~lKDh~~EFi~A 55 (100)
.+|+||+. +||.||-|-
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=26.03 E-value=35 Score=28.80 Aligned_cols=21 Identities=33% Similarity=0.303 Sum_probs=16.3
Q ss_pred HhHHHHHHHHHhchhhHhhhh
Q 034248 61 KTCFSKTIKKMFGMSKVVAER 81 (100)
Q Consensus 61 ktCfknti~kmFG~sK~vae~ 81 (100)
|---.++|.+||||.|.|.-+
T Consensus 69 WFlDh~Y~esM~~mfkKvNak 89 (309)
T KOG1556|consen 69 WFLDHNYIESMFGMFKKVNAK 89 (309)
T ss_pred EEeccHHHHHHHHHHHHhcch
Confidence 333458999999999988765
No 6
>smart00153 VHP Villin headpiece domain.
Probab=25.15 E-value=39 Score=19.84 Aligned_cols=11 Identities=27% Similarity=0.764 Sum_probs=8.6
Q ss_pred HHHHHhchhhH
Q 034248 67 TIKKMFGMSKV 77 (100)
Q Consensus 67 ti~kmFG~sK~ 77 (100)
-++++|||++.
T Consensus 6 eF~~vfgmsr~ 16 (36)
T smart00153 6 DFEEVFGMTRE 16 (36)
T ss_pred HHHHHHCCCHH
Confidence 36789999875
No 7
>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=18.19 E-value=1.4e+02 Score=17.73 Aligned_cols=21 Identities=24% Similarity=0.536 Sum_probs=14.3
Q ss_pred HhHHHHHHHHHhchhhHhhhh
Q 034248 61 KTCFSKTIKKMFGMSKVVAER 81 (100)
Q Consensus 61 ktCfknti~kmFG~sK~vae~ 81 (100)
+.+--+.+...||.++.||+.
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 445567888999999999975
No 8
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=18.10 E-value=63 Score=19.08 Aligned_cols=10 Identities=50% Similarity=0.929 Sum_probs=7.1
Q ss_pred HHHHhchhhH
Q 034248 68 IKKMFGMSKV 77 (100)
Q Consensus 68 i~kmFG~sK~ 77 (100)
+.++|||++.
T Consensus 7 F~~vFgm~~~ 16 (36)
T PF02209_consen 7 FEKVFGMSRE 16 (36)
T ss_dssp HHHHHSS-HH
T ss_pred HHHHHCCCHH
Confidence 5688999875
No 9
>PF14659 Phage_int_SAM_3: Phage integrase, N-terminal SAM-like domain; PDB: 2KD1_A 2KOB_A 2KHQ_A 3LYS_E 2KIW_A 2KKP_A.
Probab=18.07 E-value=2e+02 Score=16.01 Aligned_cols=22 Identities=23% Similarity=0.385 Sum_probs=16.6
Q ss_pred ChHHHHhHHHHHHHHHhchhhH
Q 034248 56 SMEEHKTCFSKTIKKMFGMSKV 77 (100)
Q Consensus 56 s~dEHktCfknti~kmFG~sK~ 77 (100)
+....+..+++.|...||--++
T Consensus 21 T~~~y~~~~~~~i~p~~g~~~i 42 (58)
T PF14659_consen 21 TYKNYKSIIKNHILPYFGNKKI 42 (58)
T ss_dssp HHHHHHHHHHHHHHHHTTSSBG
T ss_pred HHHHHHHHHHHHHHHHHCcCcH
Confidence 4466778999999999996443
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=17.54 E-value=2.2e+02 Score=16.75 Aligned_cols=37 Identities=16% Similarity=0.306 Sum_probs=24.1
Q ss_pred hhhHHHHHHHHHHhhcC---hHHHHhHHHHHHHHHhchhh
Q 034248 40 TFLEDLKDHIDEFVNAS---MEEHKTCFSKTIKKMFGMSK 76 (100)
Q Consensus 40 TF~e~lKDh~~EFi~As---~dEHktCfknti~kmFG~sK 76 (100)
.|++++.+++++...+- ..+=+.=+...+.++=|.+.
T Consensus 5 ~f~~~~~~~~~~l~~~~~~~~~~d~~~l~~~~H~lkG~a~ 44 (90)
T PF01627_consen 5 IFLEEAPEDLEQLEQALQALEQEDWEELRRLAHRLKGSAG 44 (90)
T ss_dssp HHHHHHHHHHHHHHHHHCSSHHCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhHhhHHHHHHHHHHHhhhHH
Confidence 68888888888887776 44444445555555444433
Done!