Query 005230
Match_columns 707
No_of_seqs 18 out of 20
Neff 2.2
Searched_HMMs 46136
Date Thu Mar 28 20:09:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005230hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12735 Trs65: TRAPP traffick 67.8 22 0.00048 37.1 7.9 40 641-680 249-288 (306)
2 PF09478 CBM49: Carbohydrate b 49.2 12 0.00027 31.6 2.0 53 366-430 21-75 (80)
3 PF15451 DUF4632: Domain of un 41.8 4.6 0.0001 35.2 -1.6 26 334-374 42-67 (71)
4 PF05606 DUF777: Borrelia burg 26.7 39 0.00084 34.2 1.7 17 154-170 72-88 (181)
5 PF04313 HSDR_N: Type I restri 25.0 38 0.00082 32.2 1.3 23 376-414 121-143 (194)
6 PRK07636 ligB ATP-dependent DN 24.9 41 0.0009 34.5 1.6 16 332-348 169-187 (275)
7 PHA00454 ATP-dependent DNA lig 24.7 38 0.00083 35.2 1.4 15 332-347 204-220 (315)
8 PF04502 DUF572: Family of unk 24.5 35 0.00077 35.9 1.1 62 292-361 14-81 (324)
9 KOG4350 Uncharacterized conser 23.8 70 0.0015 36.5 3.2 22 248-270 585-606 (620)
10 KOG1924 RhoA GTPase effector D 22.2 2.2E+02 0.0048 35.0 6.8 12 215-226 520-531 (1102)
No 1
>PF12735 Trs65: TRAPP trafficking subunit Trs65; InterPro: IPR024662 This family is one of the subunits of the TRAPP Golgi trafficking complex []. TRAPP subunits are found in two different sized complexes, TRAPP I and TRAPP II. While both complexes contain the same seven subunits, Bet3p, Bet5p, Trs20p, Trs23p, Trs31p, Trs33p and Trs85p, with TRAPPC human equivalents, TRAPP II has the additional three subunits ,Trs65p, Trs120p and Trs130p []. While it has been implicated in cell wall biogenesis and stress response, the role of Trs65 in TRAPP II is supported by the findings that the protein co-localises with Trs130p, and deletion of TRS65 in yeast leads to a conditional lethal phenotype if either one of the other TRAPP II-specific subunits is modified []. Furthermore, the trs65 mutant has reduced Ypt31/32p guanine nucleotide exchange, GEF, activity []. Trs65 is also known as killer toxin-resistance protein 11.
Probab=67.81 E-value=22 Score=37.07 Aligned_cols=40 Identities=18% Similarity=0.446 Sum_probs=37.4
Q ss_pred eeecccccCCcccCccceEEEEeeecCCcceeeeeceeee
Q 005230 641 LWLQSRVPLGCVPAQSTATIKLELLPLTDGIITLDTLHID 680 (707)
Q Consensus 641 LWLQSrVPLGcvPaqStaTiKLELLPLTDGIITLDTLqId 680 (707)
++|-..+=+|=+..+.+..+.|++|||.-|+..||.|.|-
T Consensus 249 i~LsnDiriGpL~P~~c~~~eL~fi~l~~G~~~L~~lkvv 288 (306)
T PF12735_consen 249 ICLSNDIRIGPLAPGACYSVELRFIALSPGVHNLEGLKVV 288 (306)
T ss_pred EEecccccccccCCCceEEEEEEEEEeccceEeecceEEE
Confidence 5788999999999999999999999999999999999874
No 2
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=49.16 E-value=12 Score=31.62 Aligned_cols=53 Identities=25% Similarity=0.358 Sum_probs=39.0
Q ss_pred EEEEeeecCCCCCCCeEEEEeeeEEEEecccCCCCCCCccceeeeecCCCCCCc--hhhccCcccee
Q 005230 366 LCVQIRNVSPAHAPDIVLYIDAITIVFEEASKGGPSSPLPIACIEAGNDHNLPN--LALRRGEEHSF 430 (707)
Q Consensus 366 LCVqIkNV~P~h~pDIvvyIDaITIVfEEask~g~p~slPiacIEaGndhsLPN--LaLRrGEeHSF 430 (707)
-=|.|+|....-..++.+.+|... +.-=.| -. +.|+...||+ ..|..|+.|+|
T Consensus 21 y~v~I~N~~~~~I~~~~i~~~~l~---------~~iW~l--~~-~~~~~y~lPs~~~~i~pg~s~~F 75 (80)
T PF09478_consen 21 YDVTITNNGSKPIKSLKISIDNLY---------GSIWGL--DK-VSGNTYTLPSYQPTIKPGQSFTF 75 (80)
T ss_pred EEEEEEECCCCeEEEEEEEECccc---------hhheeE--Ee-ccCCEEECCccccccCCCCEEEE
Confidence 458899999999999998888332 111111 12 5688999999 47999999998
No 3
>PF15451 DUF4632: Domain of unknown function (DUF4632)
Probab=41.79 E-value=4.6 Score=35.16 Aligned_cols=26 Identities=38% Similarity=0.975 Sum_probs=20.1
Q ss_pred eeeCCcccceeeeeeeeeeeecccccCCCCceEEEEeeecC
Q 005230 334 IYVPGRRWRRKLEIIQPVEIHSFAADCNTDDLLCVQIRNVS 374 (707)
Q Consensus 334 iyiPGrRWrRKleIIQPveIhSfaAdCntdDLLCVqIkNV~ 374 (707)
+..|.|||||-| .+.=|.|-+||+++
T Consensus 42 vl~parrwrrpl---------------psnvlycpeikdia 67 (71)
T PF15451_consen 42 VLAPARRWRRPL---------------PSNVLYCPEIKDIA 67 (71)
T ss_pred HHhHHHHhccCC---------------CccceechhHhHHH
Confidence 567999999866 23458999999874
No 4
>PF05606 DUF777: Borrelia burgdorferi protein of unknown function (DUF777); InterPro: IPR008495 This family consists of several hypothetical proteins of unknown function, found in Borrelia burgdorferi and Borrelia garinii.
Probab=26.70 E-value=39 Score=34.22 Aligned_cols=17 Identities=47% Similarity=0.659 Sum_probs=14.7
Q ss_pred eeccCCCEEEEEEEEee
Q 005230 154 CSLSNGDIVVLLQVNVG 170 (707)
Q Consensus 154 caL~NGDIVVlLQVnVg 170 (707)
.-|+-||-|||||-||-
T Consensus 72 leLs~~D~VlLLQSsiN 88 (181)
T PF05606_consen 72 LELSKGDEVLLLQSSIN 88 (181)
T ss_pred eEecCCCEEEEEecccc
Confidence 46899999999999874
No 5
>PF04313 HSDR_N: Type I restriction enzyme R protein N terminus (HSDR_N); InterPro: IPR007409 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the N-terminal domain found in both the R subunit (HsdR) of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoRI, which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity [, , ]. This domain is often found adjacent to a methylase domain (IPR002052 from INTERPRO) in restriction endonucleases or methylases. In one of the proteins, Q97RD0 from SWISSPROT, it is adjacent to a helicase domain (IPR011545 from INTERPRO) in a putative restriction endonuclease.; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0006304 DNA modification; PDB: 2Y3T_B 2W74_B 2W00_B.
Probab=25.00 E-value=38 Score=32.16 Aligned_cols=23 Identities=43% Similarity=0.772 Sum_probs=16.1
Q ss_pred CCCCCeEEEEeeeEEEEecccCCCCCCCccceeeeecCC
Q 005230 376 AHAPDIVLYIDAITIVFEEASKGGPSSPLPIACIEAGND 414 (707)
Q Consensus 376 ~h~pDIvvyIDaITIVfEEask~g~p~slPiacIEaGnd 414 (707)
...||+|+||. .||++.||+-+.
T Consensus 121 ~~r~D~vLfvN----------------GlPl~~iE~K~~ 143 (194)
T PF04313_consen 121 KRRPDIVLFVN----------------GLPLAIIELKSP 143 (194)
T ss_dssp ---EEEEEEET----------------TEEEEEEEE--T
T ss_pred CCcceEEEEEC----------------CeEEEEEEecCC
Confidence 35799999998 689999998775
No 6
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=24.90 E-value=41 Score=34.48 Aligned_cols=16 Identities=25% Similarity=0.430 Sum_probs=11.3
Q ss_pred ceeeeCCcc---cceeeeee
Q 005230 332 EGIYVPGRR---WRRKLEII 348 (707)
Q Consensus 332 EGiyiPGrR---WrRKleII 348 (707)
.+.|.|||| | -|+...
T Consensus 169 ds~Y~~g~Rs~~W-lKiK~~ 187 (275)
T PRK07636 169 NSPYEINKRSDNW-LKVINY 187 (275)
T ss_pred CCCCCCCCCCCCe-EEEecC
Confidence 457999988 8 566533
No 7
>PHA00454 ATP-dependent DNA ligase
Probab=24.66 E-value=38 Score=35.24 Aligned_cols=15 Identities=33% Similarity=0.754 Sum_probs=10.6
Q ss_pred ceeeeCCcc--cceeeee
Q 005230 332 EGIYVPGRR--WRRKLEI 347 (707)
Q Consensus 332 EGiyiPGrR--WrRKleI 347 (707)
.+.|.|||| |. |+..
T Consensus 204 ds~Y~~Grr~~~~-K~K~ 220 (315)
T PHA00454 204 SLIYRRGKKSGWW-KMKP 220 (315)
T ss_pred CCCCCCCCccCcE-EEcc
Confidence 446999986 55 7763
No 8
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=24.54 E-value=35 Score=35.93 Aligned_cols=62 Identities=27% Similarity=0.501 Sum_probs=44.7
Q ss_pred hhhchhhhhhhcccccCCccceeeeeeeccccceeEEeccceeeeC-Ccccceeeeeeee-----eeeecccccCC
Q 005230 292 DWDQYTSQKLFKGQRTGNEGLLSFRGVSLERERFSVRCGLEGIYVP-GRRWRRKLEIIQP-----VEIHSFAADCN 361 (707)
Q Consensus 292 dWd~~s~qk~~ks~k~g~e~lLSFRGVsLE~eRFSV~CGLEGiyiP-GrRWrRKleIIQP-----veIhSfaAdCn 361 (707)
||| +.|.-+.++.. .|.|.-| +| ==|+|||.-.|-||. |+|.--+-+-|.- +.|.+|-..|.
T Consensus 14 D~d---~~k~~~~kr~k-~~~~~VR---f~-~Pf~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~ 81 (324)
T PF04502_consen 14 DFD---PSKHPLRKRAK-QGILTVR---FM-MPFNIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCP 81 (324)
T ss_pred CCC---cccccccccCc-CcceEEE---Ec-CCccCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcC
Confidence 666 44444433333 6777655 22 138999999999996 8998776776666 99999999987
No 9
>KOG4350 consensus Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only]
Probab=23.80 E-value=70 Score=36.54 Aligned_cols=22 Identities=55% Similarity=0.606 Sum_probs=19.7
Q ss_pred CCCCCceeeccccccccCCCCCC
Q 005230 248 ASSGSQLFSFGHFRSYSMSSLPQ 270 (707)
Q Consensus 248 ~ssgSQLFSfghFRSYSMsslP~ 270 (707)
+.+||||=| ||-||=|-||+|.
T Consensus 585 s~sgssl~s-~~~~sps~ss~ps 606 (620)
T KOG4350|consen 585 STSGSSLAS-GHAESPSTSSTPS 606 (620)
T ss_pred cccccchhc-ccccCCCCCCCCC
Confidence 669999999 9999999999874
No 10
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=22.19 E-value=2.2e+02 Score=35.00 Aligned_cols=12 Identities=58% Similarity=1.348 Sum_probs=9.8
Q ss_pred cccCCCCCCCCC
Q 005230 215 LLPLDNTVPPPA 226 (707)
Q Consensus 215 LLPLDntlp~~~ 226 (707)
+||.|-++|+|+
T Consensus 520 ~~~~~~~iP~PP 531 (1102)
T KOG1924|consen 520 LLPIDGGIPPPP 531 (1102)
T ss_pred CCCCCCCCCCCC
Confidence 889999988764
Done!