Query psy11611
Match_columns 60
No_of_seqs 39 out of 41
Neff 3.1
Searched_HMMs 46136
Date Fri Aug 16 23:04:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11611.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11611hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4403|consensus 99.8 2.6E-22 5.7E-27 157.1 1.4 54 2-56 92-145 (575)
2 PF12550 GCR1_C: Transcription 58.0 6.8 0.00015 23.3 1.4 14 28-41 8-21 (81)
3 TIGR03076 near_not_gcvH Chlamy 38.8 15 0.00033 30.8 1.0 24 14-37 114-137 (686)
4 KOG3767|consensus 36.9 24 0.00053 27.3 1.8 21 22-42 59-79 (328)
5 PF07535 zf-DBF: DBF zinc fing 35.8 12 0.00026 21.4 -0.0 23 13-36 23-45 (49)
6 PF03820 Mtc: Tricarboxylate c 28.7 34 0.00074 25.6 1.4 15 28-42 47-61 (308)
7 PF14641 HTH_44: Helix-turn-he 28.1 33 0.00072 22.4 1.1 14 27-40 80-93 (121)
8 PF02281 Dimer_Tnp_Tn5: Transp 22.2 79 0.0017 20.9 2.0 17 23-40 72-88 (109)
9 PF14659 Phage_int_SAM_3: Phag 21.9 73 0.0016 16.3 1.5 14 30-43 1-14 (58)
10 cd07826 SRPBCC_CalC_Aha1-like_ 21.4 45 0.00097 20.6 0.7 20 29-48 10-30 (142)
11 cd08897 SRPBCC_CalC_Aha1-like_ 21.0 48 0.001 20.0 0.8 20 28-47 9-29 (133)
12 cd08892 SRPBCC_Aha1 Putative h 20.6 50 0.0011 20.1 0.8 19 29-47 10-29 (126)
13 PTZ00220 Activator of HSP-90 A 20.0 52 0.0011 20.5 0.8 19 29-47 3-22 (132)
No 1
>KOG4403|consensus
Probab=99.84 E-value=2.6e-22 Score=157.10 Aligned_cols=54 Identities=37% Similarity=0.716 Sum_probs=48.8
Q ss_pred chhhhhccCCchHHHHHhhhhcCCCcceeHHHHHHHHhhccceecCccceeeccc
Q psy11611 2 SFLREELKYDDGAEKRQKAFHKNDDMHVSVKELWDVWIKSECCREDAGGQQHGGI 56 (60)
Q Consensus 2 eFLREdl~y~d~~~~r~~~fH~~D~~~ISVedLW~~Wk~Sev~NWT~~~~~~~~~ 56 (60)
|||||||||+++.++|.++||++|+ ||||+|||++|+.|||||||++++++=-|
T Consensus 92 eFlrEdmky~~~~~kr~~~fH~dD~-~ItVedLWeaW~~Sev~nWT~e~tvqWLi 145 (575)
T KOG4403|consen 92 EFLREDMKYRDSTRKRSEKFHGDDK-HITVEDLWEAWKESEVHNWTNERTVQWLI 145 (575)
T ss_pred HHHHHHhhcccchhhhhhhccCCcc-ceeHHHHHHHHHhhhhhcchHHHHHHHHH
Confidence 7999999999999777779999777 99999999999999999999999876444
No 2
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=57.98 E-value=6.8 Score=23.33 Aligned_cols=14 Identities=29% Similarity=0.793 Sum_probs=12.4
Q ss_pred ceeHHHHHHHHhhc
Q psy11611 28 HVSVKELWDVWIKS 41 (60)
Q Consensus 28 ~ISVedLW~~Wk~S 41 (60)
.=||.|||.-|..+
T Consensus 8 ~~TV~dlw~Ew~~g 21 (81)
T PF12550_consen 8 IKTVYDLWREWFTG 21 (81)
T ss_pred CCcHHHHHHHHhcC
Confidence 56999999999986
No 3
>TIGR03076 near_not_gcvH Chlamydial GcvH-like protein upstream region protein. The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia but lack the P and T proteins, and have a single homolog of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The protein family modeled here is observed so far only in the Chlamydiae, always as part of a two-gene operon, upstream of the homolog of GcvH. Its function is unknown.
Probab=38.84 E-value=15 Score=30.79 Aligned_cols=24 Identities=25% Similarity=0.533 Sum_probs=18.6
Q ss_pred HHHHHhhhhcCCCcceeHHHHHHH
Q psy11611 14 AEKRQKAFHKNDDMHVSVKELWDV 37 (60)
Q Consensus 14 ~~~r~~~fH~~D~~~ISVedLW~~ 37 (60)
.|+|-..+-|-|.++||+|+.|++
T Consensus 114 KEK~y~~YrrfdapFissEevWks 137 (686)
T TIGR03076 114 KEKSYQGYRRFDAPFISSEEVWKS 137 (686)
T ss_pred hhhccccccCCCCccccHHHHHhc
Confidence 345555667889999999999975
No 4
>KOG3767|consensus
Probab=36.91 E-value=24 Score=27.33 Aligned_cols=21 Identities=14% Similarity=0.128 Sum_probs=15.7
Q ss_pred hcCCCcceeHHHHHHHHhhcc
Q psy11611 22 HKNDDMHVSVKELWDVWIKSE 42 (60)
Q Consensus 22 H~~D~~~ISVedLW~~Wk~Se 42 (60)
|+...+-+|+++||+||+...
T Consensus 59 ~G~~~p~~t~~~lW~Akkl~d 79 (328)
T KOG3767|consen 59 AGKVPPGLTDDELWKAKKLYD 79 (328)
T ss_pred cCCcCCCCcHHHHHHHHHHHh
Confidence 344555689999999998643
No 5
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=35.76 E-value=12 Score=21.37 Aligned_cols=23 Identities=17% Similarity=0.368 Sum_probs=18.5
Q ss_pred hHHHHHhhhhcCCCcceeHHHHHH
Q psy11611 13 GAEKRQKAFHKNDDMHVSVKELWD 36 (60)
Q Consensus 13 ~~~~r~~~fH~~D~~~ISVedLW~ 36 (60)
.+ .+|..|=.+|.-+..|++|=.
T Consensus 23 ~s-~~Hr~FA~~~~Nf~~lD~li~ 45 (49)
T PF07535_consen 23 QS-EKHRKFAENDSNFKELDSLIS 45 (49)
T ss_pred CC-HHHHHHHcCcccHHHHHHHHH
Confidence 44 599999888887999998843
No 6
>PF03820 Mtc: Tricarboxylate carrier; InterPro: IPR004686 The MTC family consists of a limited number of homologues, all from eukaryotes. One member of the family has been functionally characterised as a tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism. The rest of the characterised proteins appear to be sideroflexins involved in iron transport.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016020 membrane
Probab=28.66 E-value=34 Score=25.63 Aligned_cols=15 Identities=20% Similarity=0.335 Sum_probs=12.9
Q ss_pred ceeHHHHHHHHhhcc
Q psy11611 28 HVSVKELWDVWIKSE 42 (60)
Q Consensus 28 ~ISVedLW~~Wk~Se 42 (60)
-+|.++||++|+.++
T Consensus 47 ~~~~~~lw~Ak~l~~ 61 (308)
T PF03820_consen 47 GLTDDELWKAKKLYD 61 (308)
T ss_pred CCCHHHHHHHHHHhh
Confidence 469999999999765
No 7
>PF14641 HTH_44: Helix-turn-helix DNA-binding domain of SPT6; PDB: 3PSI_A 3PSF_A.
Probab=28.10 E-value=33 Score=22.42 Aligned_cols=14 Identities=14% Similarity=0.451 Sum_probs=8.7
Q ss_pred cceeHHHHHHHHhh
Q psy11611 27 MHVSVKELWDVWIK 40 (60)
Q Consensus 27 ~~ISVedLW~~Wk~ 40 (60)
+.+|.+|||+-..-
T Consensus 80 ~lL~~~DLWrI~~l 93 (121)
T PF14641_consen 80 PLLNEDDLWRIYDL 93 (121)
T ss_dssp -B--HHHHHHHHHH
T ss_pred hhccHHHHHHHHHh
Confidence 37999999986653
No 8
>PF02281 Dimer_Tnp_Tn5: Transposase Tn5 dimerisation domain; InterPro: IPR003201 Transposons are mobile DNA sequences capable of replication and insertion into the chromosome. Typically transposons code for the transposase enzyme, which catalyses insertion, found between terminal inverted repeats []. Tn5 has a unique method of self- regulation in which a truncated version of the transposase enzyme acts as an inhibitor []. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=22.21 E-value=79 Score=20.95 Aligned_cols=17 Identities=35% Similarity=0.790 Sum_probs=11.7
Q ss_pred cCCCcceeHHHHHHHHhh
Q psy11611 23 KNDDMHVSVKELWDVWIK 40 (60)
Q Consensus 23 ~~D~~~ISVedLW~~Wk~ 40 (60)
..|- ..++.-||.+|+.
T Consensus 72 KrdG-~pG~~tLW~GW~r 88 (109)
T PF02281_consen 72 KRDG-EPGWKTLWRGWFR 88 (109)
T ss_dssp TSSS----HHHHHHHHHH
T ss_pred CCCC-CCchhhHHHHHHH
Confidence 4566 8999999999986
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=21.92 E-value=73 Score=16.35 Aligned_cols=14 Identities=14% Similarity=0.586 Sum_probs=10.8
Q ss_pred eHHHHHHHHhhccc
Q psy11611 30 SVKELWDVWIKSEC 43 (60)
Q Consensus 30 SVedLW~~Wk~Sev 43 (60)
|++++++.|...-.
T Consensus 1 Tf~~~~~~wl~~~~ 14 (58)
T PF14659_consen 1 TFSEFFEEWLEEYK 14 (58)
T ss_dssp BHHHHHHHHHHHHT
T ss_pred CHHHHHHHHHHHhc
Confidence 68899999987633
No 10
>cd07826 SRPBCC_CalC_Aha1-like_9 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands.
Probab=21.35 E-value=45 Score=20.61 Aligned_cols=20 Identities=10% Similarity=-0.054 Sum_probs=14.6
Q ss_pred eeHHHHHHHHhhccc-eecCc
Q psy11611 29 VSVKELWDVWIKSEC-CREDA 48 (60)
Q Consensus 29 ISVedLW~~Wk~Sev-~NWT~ 48 (60)
-+++.||++|...+. -.|..
T Consensus 10 ap~e~Vw~a~Tdpe~l~~W~~ 30 (142)
T cd07826 10 APRELVFRAHTDPELVKRWWG 30 (142)
T ss_pred CCHHHHHHHhCCHHHHhhccC
Confidence 478999999998873 34543
No 11
>cd08897 SRPBCC_CalC_Aha1-like_4 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands.
Probab=21.03 E-value=48 Score=20.03 Aligned_cols=20 Identities=15% Similarity=0.696 Sum_probs=15.3
Q ss_pred ceeHHHHHHHHhhccc-eecC
Q psy11611 28 HVSVKELWDVWIKSEC-CRED 47 (60)
Q Consensus 28 ~ISVedLW~~Wk~Sev-~NWT 47 (60)
..+++.+|++|...+. ..|.
T Consensus 9 ~ap~e~Vw~a~td~e~~~~W~ 29 (133)
T cd08897 9 DAPIEKVWEAWTTPEHITKWN 29 (133)
T ss_pred CCCHHHHHHHhCCHHHHhhCC
Confidence 3589999999998874 4563
No 12
>cd08892 SRPBCC_Aha1 Putative hydrophobic ligand-binding SRPBCC domain of the Hsp90 co-chaperone Aha1 and related proteins. This subfamily includes the C-terminal SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Aha1, and related domains. Proteins in this group belong to the SRPBCC domain superfamily of proteins which bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Aha1 is one of several co-chaperones, which regulate the dimeric chaperone Hsp90. Hsp90, Aha1, and other accessory proteins interact in a chaperone cycle driven by ATP binding and hydrolysis. Aha1 promotes dimerization of the N-terminal domains of Hsp90, and stimulates its low intrinsic ATPase activity. One Aha1 molecule binds per Hsp90 dimer. The N- and C- terminal domains of Aha1 cooperatively bind across the dimer interface of Hsp90. The C-terminal domain of Aha1 binds the N-terminal Hsp90 ATPase domain. Aha1 may regulate the dwell time of Hsp90 with client proteins. Aha1 m
Probab=20.57 E-value=50 Score=20.06 Aligned_cols=19 Identities=21% Similarity=0.277 Sum_probs=13.8
Q ss_pred eeHHHHHHHHhhcc-ceecC
Q psy11611 29 VSVKELWDVWIKSE-CCRED 47 (60)
Q Consensus 29 ISVedLW~~Wk~Se-v~NWT 47 (60)
.+++.+|++|...+ ...|.
T Consensus 10 ap~e~Vw~A~T~~e~l~~W~ 29 (126)
T cd08892 10 VPAEELYEALTDEERVQAFT 29 (126)
T ss_pred CCHHHHHHHHCCHHHHHhhc
Confidence 57899999998875 34454
No 13
>PTZ00220 Activator of HSP-90 ATPase; Provisional
Probab=20.03 E-value=52 Score=20.53 Aligned_cols=19 Identities=11% Similarity=0.221 Sum_probs=15.0
Q ss_pred eeHHHHHHHHhhcccee-cC
Q psy11611 29 VSVKELWDVWIKSECCR-ED 47 (60)
Q Consensus 29 ISVedLW~~Wk~Sev~N-WT 47 (60)
.|++.||++|...+-.. |.
T Consensus 3 ap~e~Vw~A~Tdp~~l~~w~ 22 (132)
T PTZ00220 3 VPPEVLYNAFLDAYTLTRLS 22 (132)
T ss_pred CCHHHHHHHHcCHHHHHHHh
Confidence 47899999999988644 64
Done!