Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate CCNA_03139 CCNA_03139 dihydroxy-acid dehydratase
Query= SwissProt::P55186 (617 letters) >FitnessBrowser__Caulo:CCNA_03139 Length = 617 Score = 1224 bits (3168), Expect = 0.0 Identities = 617/617 (100%), Positives = 617/617 (100%) Query: 1 MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60 MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV Sbjct: 1 MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60 Query: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120 AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS Sbjct: 61 AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120 Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180 Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV Sbjct: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240 Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD Sbjct: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300 Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA Sbjct: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360 Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG Sbjct: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420 Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY Sbjct: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480 Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL Sbjct: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540 Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT Sbjct: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPLNRKRDLTPALRAYAAMT 600 Query: 601 TNAARGAVRDVSQIERG 617 TNAARGAVRDVSQIERG Sbjct: 601 TNAARGAVRDVSQIERG 617 Lambda K H 0.318 0.134 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1577 Number of extensions: 38 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 617 Length of database: 617 Length adjustment: 37 Effective length of query: 580 Effective length of database: 580 Effective search space: 336400 Effective search space used: 336400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
Align candidate CCNA_03139 CCNA_03139 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00110.hmm # target sequence database: /tmp/gapView.13071.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00110 [M=543] Accession: TIGR00110 Description: ilvD: dihydroxy-acid dehydratase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-248 811.0 3.5 2.8e-248 810.8 3.5 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_03139 CCNA_03139 dihydroxy-acid dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_03139 CCNA_03139 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 810.8 3.5 2.8e-248 2.8e-248 2 542 .. 18 610 .. 17 611 .. 0.99 Alignments for each domain: == domain 1 score: 810.8 bits; conditional E-value: 2.8e-248 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 ar l++atG+kded++kPiiav+ns+t++vPghvhlkdl++lv++eieaaGgvakefntiav+DGiamgh+Gm lcl|FitnessBrowser__Caulo:CCNA_03139 18 ARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHGGM 90 689********************************************************************** PP TIGR00110 75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147 +ysLpsr++iaDsve++v+ah++Da+v+is+CDki+PGmlmaa+rlniP+++vsGGpmeagk+++ ki +d lcl|FitnessBrowser__Caulo:CCNA_03139 91 LYSLPSRDLIADSVEYMVNAHCADAIVCISNCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALD 163 ************************************************************************* PP TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220 +++a++ +a++ s+ee+e+ie+ acPt+gsCsG+ftansm+cltealGlslPg++++lat+a++++l+k++g lcl|FitnessBrowser__Caulo:CCNA_03139 164 LVDAMVVAADDSYSDEEVEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAG 236 ************************************************************************* PP TIGR00110 221 krivelvkknik.......PrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvP 286 + +v+l+++ ++ Pr i+t++afena++ld+a+GGstntvLhlla+a+e g+++s+ d+drlsr+vP lcl|FitnessBrowser__Caulo:CCNA_03139 237 RVVVDLCQRWYEqedatalPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMADIDRLSRHVP 309 ***********99************************************************************ PP TIGR00110 287 llaklkPsgkkv.iedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlr.............. 344 +l+k++P+ + v +ed+hraGGv+a+l+el++ gl++ tv t++e l++ ++ r lcl|FitnessBrowser__Caulo:CCNA_03139 310 CLSKVAPAKSDVhMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEALARWDIGRtnsqiaheffkaap 382 ********88888********************************************999************* PP TIGR00110 345 .....................vdqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvf 396 ++ virs+++p++k+gglavL+Gnla+eG++vk+agv+e+il+f+G+a+vf lcl|FitnessBrowser__Caulo:CCNA_03139 383 ggkptqvafsqaarweeldldRENGVIRSVEHPFSKDGGLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVF 455 *****************99665666************************************************ PP TIGR00110 397 eseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhv 469 es+++a+ +ilgg+vk+G+vvviryeGPkGgPGm+emL+Pt++l++ GLg ++aL+tDGrfsGgt+GlsiGhv lcl|FitnessBrowser__Caulo:CCNA_03139 456 ESQDAAVSGILGGQVKAGEVVVIRYEGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHV 528 ************************************************************************* PP TIGR00110 470 sPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea.........revkgaLakyaklvs 533 sPea egG ialve GD i iDi+ r + levs++ la+rr+++ ++++ r aL++ya + + lcl|FitnessBrowser__Caulo:CCNA_03139 529 SPEAGEGGLIALVETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKdawtplnrkRDLTPALRAYAAMTT 601 ********************************************99999999****9999999********** PP TIGR00110 534 sadkGavld 542 +a +Gav+d lcl|FitnessBrowser__Caulo:CCNA_03139 602 NAARGAVRD 610 *******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (617 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 12.80 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory