Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate Echvi_2055 Echvi_2055 dihydroxy-acid dehydratase
Query= BRENDA::A0A481UJA7 (614 letters) >FitnessBrowser__Cola:Echvi_2055 Length = 561 Score = 644 bits (1660), Expect = 0.0 Identities = 311/557 (55%), Positives = 414/557 (74%), Gaps = 2/557 (0%) Query: 59 LNKYSSRITEPKSQGGSQAILHGVGLSDEDLNKPQIGISSVWYEGNTCNMHLLRLSEAVK 118 L KYS I++ + + A+L+ G++D+ + +P +G++S YE N CNMHL +E +K Sbjct: 5 LKKYSWEISDNEENPAAMAMLYATGITDKKMKQPFVGVASCGYESNPCNMHLNSFAEDIK 64 Query: 119 EGVKEAGMVGFRFNTIGVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIPG 178 +A + GF FNTIG+SD SMGT GM YSL SR++IADSIE+ + +DG ++IPG Sbjct: 65 ASTNQADLSGFIFNTIGISDGQSMGTSGMRYSLPSREVIADSIESFILGHSFDGVVTIPG 124 Query: 179 CDKNMPGTIMAMGRLNRPSIMVYGGTIKPGHYNGHSYDIISAFQAYGEYVNGSISDEDRK 238 CDKNMPG +M M R+NRP IMV+GGTI+ G+Y G +I+SAF+AYG+ +NG ISDED Sbjct: 125 CDKNMPGVVMGMLRVNRPGIMVFGGTIRSGNYKGEKLNIVSAFEAYGKKINGQISDEDYM 184 Query: 239 NVVHNSCPGAGACGGMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLEL 298 V+ N+CPGAGACGGMYTANTM+SAIEAMG+ LP+SSS PA + K +EC+ GKY+ +L Sbjct: 185 GVIKNACPGAGACGGMYTANTMSSAIEAMGLSLPFSSSYPATSKEKREECKNIGKYIKQL 244 Query: 299 LKMDLKPQNIITPQSLRNAMVVVMALGGSTNAVLHLIPIARSVGLELTLEDFQKVSDEVP 358 L +D+KP++IIT +SL NA+ V +ALGGSTNA LH++ IAR+ G++ TLEDF++++ E P Sbjct: 245 LALDIKPKDIITKKSLENAVRVTVALGGSTNAALHILAIARTAGIDFTLEDFKRINAETP 304 Query: 359 FLADLKPSGKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSEG 418 L D KPSGK++MED++++GG PA L+Y L G L GDCLTVTGKT+AEN+++ P+ Sbjct: 305 VLGDFKPSGKFMMEDLYEMGGLPAFLKYFLNEGLLHGDCLTVTGKTMAENLEDIDPVKPS 364 Query: 419 QD-IIRPLENPIKKTGHIQILQGNLAPEGSVAKITGKEGLYFSGPALVFEGEEAMLAAIS 477 ++ +I PL+NPIK +GH+ +L GNLAPEG+VAKI+GKEG F+G A VF+ E + AA+ Sbjct: 365 KESVIHPLDNPIKPSGHLCVLHGNLAPEGAVAKISGKEGKSFTGTAKVFDDEPSANAAMK 424 Query: 478 ENPMNFKGKVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKDCALLTDGRFSGGSHGFVV 537 + KG VVVIR GPKGGPGMPEML PTS I+GAGLG D AL+TDGRFSGG+HGFVV Sbjct: 425 NKEIQ-KGDVVVIRYVGPKGGPGMPEMLKPTSIIIGAGLGSDVALITDGRFSGGTHGFVV 483 Query: 538 GHICPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQEMEERRKNWTPPPYKATCGVLY 597 GH+ PEA GGPIGL+++GD+I ID I VDV++ E ER+KNW G L Sbjct: 484 GHVTPEAYLGGPIGLLKDGDVITIDAESLEIRVDVSEAEFAERKKNWKNKDLSHLQGTLK 543 Query: 598 KYIKNVQSASRGCVTDE 614 KY++ V +AS GCVTD+ Sbjct: 544 KYVQLVSTASEGCVTDK 560 Lambda K H 0.316 0.135 0.401 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: 1060 Number of extensions: 42 Number of successful extensions: 3 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: 614 Length of database: 561 Length adjustment: 37 Effective length of query: 577 Effective length of database: 524 Effective search space: 302348 Effective search space used: 302348 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 (21.6 bits) S2: 53 (25.0 bits)
Align candidate Echvi_2055 Echvi_2055 (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.4353.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9e-224 729.9 3.6 1e-223 729.7 3.6 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2055 Echvi_2055 dihydroxy-acid dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_2055 Echvi_2055 dihydroxy-acid dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 729.7 3.6 1e-223 1e-223 2 542 .. 21 559 .. 20 560 .. 0.99 Alignments for each domain: == domain 1 score: 729.7 bits; conditional E-value: 1e-223 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGmk 75 a a+l+atG++d+ +++P+++v+++ e +P+++hl+ +a+ +k++ ++a + fnti++sDG +mg++Gm+ lcl|FitnessBrowser__Cola:Echvi_2055 21 AMAMLYATGITDKKMKQPFVGVASCGYESNPCNMHLNSFAEDIKASTNQADLSGFIFNTIGISDGQSMGTSGMR 94 579*********************************************************************** PP TIGR00110 76 ysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvdvf 149 ysLpsre+iaDs+e+ + +h +D++v+i+ CDk++PG++m++lr+n+P i+v GG++ +g++k +ek+++v++f lcl|FitnessBrowser__Cola:Echvi_2055 95 YSLPSREVIADSIESFILGHSFDGVVTIPGCDKNMPGVVMGMLRVNRPGIMVFGGTIRSGNYK-GEKLNIVSAF 167 ***************************************************************.9********* PP TIGR00110 150 eavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksgkri 223 ea+g+ +g++s+e+ + ++acP+ag+C+G++tan+m+++ ea+GlslP ss+ +ats+ek+e +k++gk+i lcl|FitnessBrowser__Cola:Echvi_2055 168 EAYGKKINGQISDEDYMGVIKNACPGAGACGGMYTANTMSSAIEAMGLSLPFSSSYPATSKEKREECKNIGKYI 241 ************************************************************************** PP TIGR00110 224 velvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkPsgkk 297 ++l+ +ikP+di+tk+++ena+ + +alGGstn+ Lh+laia++ag++++l+df+r++ ++P+l+++kPsgk lcl|FitnessBrowser__Cola:Echvi_2055 242 KQLLALDIKPKDIITKKSLENAVRVTVALGGSTNAALHILAIARTAGIDFTLEDFKRINAETPVLGDFKPSGKF 315 ************************************************************************** PP TIGR00110 298 viedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvk.vlrvdqdvirsldnpvkkegglavLkGnl 370 ++edl + GG++a lk+ +egllh d+ltvtGkt+ae+le+++ v++ +++vi++ldnp+k g+l vL+Gnl lcl|FitnessBrowser__Cola:Echvi_2055 316 MMEDLYEMGGLPAFLKYFLNEGLLHGDCLTVTGKTMAENLEDIDpVKPSKESVIHPLDNPIKPSGHLCVLHGNL 389 ******************************************9735667888********************** PP TIGR00110 371 aeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsalvglG 444 a+eGav+ki+g+e f+G+akvf++e a +a+ ++++++Gdvvviry GPkGgPGm+emL+Pts ++g+G lcl|FitnessBrowser__Cola:Echvi_2055 390 APEGAVAKISGKEG--KSFTGTAKVFDDEPSANAAMKNKEIQKGDVVVIRYVGPKGGPGMPEMLKPTSIIIGAG 461 **************..99******************************************************** PP TIGR00110 445 LgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrakakkkea 518 Lg++vaLitDGrfsGgt+G+++Ghv+Pea+ gG+i+l++dGD i+iD+e+ ++ ++vse+e+aer++++k+k+ lcl|FitnessBrowser__Cola:Echvi_2055 462 LGSDVALITDGRFSGGTHGFVVGHVTPEAYLGGPIGLLKDGDVITIDAESLEIRVDVSEAEFAERKKNWKNKDL 535 ************************************************************************** PP TIGR00110 519 revkgaLakyaklvssadkGavld 542 + +g+L+ky +lvs+a++G+v+d lcl|FitnessBrowser__Cola:Echvi_2055 536 SHLQGTLKKYVQLVSTASEGCVTD 559 **********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (561 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.83 // [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