Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate WP_101446604.1 BD749_RS13355 dihydroxy-acid dehydratase
Query= BRENDA::A0A481UJA7 (614 letters) >NCBI__GCF_002846395.1:WP_101446604.1 Length = 573 Score = 664 bits (1714), Expect = 0.0 Identities = 329/555 (59%), Positives = 411/555 (74%), Gaps = 1/555 (0%) Query: 59 LNKYSSRITEPKSQGGSQAILHGVGLSDEDLNKPQIGISSVWYEGNTCNMHLLRLSEAVK 118 LNKYS T+ S SQA+L G GLS EDL KP +GI S ++GNTCNMHL L++ VK Sbjct: 4 LNKYSRIYTQDDSLPASQAMLMGAGLSAEDLRKPFVGICSTGFDGNTCNMHLNDLADEVK 63 Query: 119 EGVKEAGMVGFRFNTIGVSDAISMGTRGMCYSLQSRDLIADSIETVMSAQWYDGNISIPG 178 GV + GMVG RFNTIGVSD I+ GT+GM YSL SR++IADSIET+ A YD + G Sbjct: 64 RGVNKQGMVGLRFNTIGVSDGITNGTQGMNYSLVSREIIADSIETITGAHNYDALACVVG 123 Query: 179 CDKNMPGTIMAMGRLNRPSIMVYGGTIKPGHYNGHSYDIISAFQAYGEYVNGSISDEDRK 238 CDKNMPG++MAM RLNRP++MVYGGTIK G + G +I+S F+AYG+ +NG +S+ED + Sbjct: 124 CDKNMPGSLMAMARLNRPALMVYGGTIKGGEFKGEKLNIVSCFEAYGKKLNGQLSEEDYR 183 Query: 239 NVVHNSCPGAGACGGMYTANTMASAIEAMGMCLPYSSSIPAENPLKLDECRLAGKYLLEL 298 ++ N+CPG GACGGMYTANTMASA EA+GM +P+SSS PA + K +EC G+YLL L Sbjct: 184 GIIRNACPGPGACGGMYTANTMASAAEALGMSVPFSSSSPAVSQSKKEECLGTGEYLLRL 243 Query: 299 LKMDLKPQNIITPQSLRNAMVVVMALGGSTNAVLHLIPIARSVGLELTLEDFQKVSDEVP 358 L+MDLKPQ+I+ ++ NA+V++ LGGSTNAVLHLI IA + G+ L+L DFQ VS+ VP Sbjct: 244 LEMDLKPQDILVREAFENALVLITVLGGSTNAVLHLIAIAHAAGVPLSLRDFQAVSNRVP 303 Query: 359 FLADLKPSGKYVMEDVHKIGGTPAVLRYLLEHGFLDGDCLTVTGKTLAENVQNCPPLSEG 418 LADLKPSGKY+MED+ +GG PAV++ LL G + GD LTVTGKT+AEN+ PL E Sbjct: 304 VLADLKPSGKYLMEDLSTLGGVPAVMKTLLNEGLITGDLLTVTGKTVAENLAGVKPLGEE 363 Query: 419 QDIIRPLENPIKKTGHIQILQGNLAPEGSVAKITGKEGLYFSGPALVFEGEEAMLAAISE 478 QD++RPL NPIK GHIQ L GNLAP+G+VAKI+GKEGL F GPA+VF EE + I+ Sbjct: 364 QDLLRPLSNPIKADGHIQTLYGNLAPKGAVAKISGKEGLTFEGPAIVFNSEEELNQGIAT 423 Query: 479 NPMNFKGKVVVIRGEGPKGGPGMPEMLTPTSAIMGAGLGKDCALLTDGRFSGGSHGFVVG 538 + G+VVVIR GPKGGPGMPEML PTSAIMGAGLG AL+TDGRFSGG+HGFV+G Sbjct: 424 GKI-VAGQVVVIRYVGPKGGPGMPEMLKPTSAIMGAGLGDKVALITDGRFSGGTHGFVIG 482 Query: 539 HICPEAQEGGPIGLVRNGDIIRIDVRERRIDVDVTDQEMEERRKNWTPPPYKATCGVLYK 598 H+CPEA +GG + LV +GD I ++ + I + V + ++ RR W P K GVL K Sbjct: 483 HVCPEAYDGGTLALVEDGDWISLNANKNTIHLHVEEAVLDLRRDKWQQPAPKVEKGVLLK 542 Query: 599 YIKNVQSASRGCVTD 613 YI+ V ASRGC+TD Sbjct: 543 YIRTVSDASRGCITD 557 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: 1102 Number of extensions: 48 Number of successful extensions: 2 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: 573 Length adjustment: 37 Effective length of query: 577 Effective length of database: 536 Effective search space: 309272 Effective search space used: 309272 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 WP_101446604.1 BD749_RS13355 (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.673308.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-219 714.8 2.7 4e-219 714.6 2.7 1.0 1 NCBI__GCF_002846395.1:WP_101446604.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101446604.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 714.6 2.7 4e-219 4e-219 2 542 .. 20 557 .. 19 558 .. 1.00 Alignments for each domain: == domain 1 score: 714.6 bits; conditional E-value: 4e-219 TIGR00110 2 arallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiamgheGm 74 ++a+l +Gl+ edl kP+++++++ + + +++hl+dla+ vk+++++ G v +fnti+vsDGi+ g++Gm NCBI__GCF_002846395.1:WP_101446604.1 20 SQAMLMGAGLSAEDLRKPFVGICSTGFDGNTCNMHLNDLADEVKRGVNKQGMVGLRFNTIGVSDGITNGTQGM 92 79*********************************************************************** PP TIGR00110 75 kysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktklsekidlvd 147 +ysL+sreiiaDs+et+ ah +Dal ++ CDk++PG lma++rln+Pa++v+GG+++ g++k +ek+++v+ NCBI__GCF_002846395.1:WP_101446604.1 93 NYSLVSREIIADSIETITGAHNYDALACVVGCDKNMPGSLMAMARLNRPALMVYGGTIKGGEFK-GEKLNIVS 164 ****************************************************************.9******* PP TIGR00110 148 vfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstllatsaekkelakksg 220 fea+g+ +g+lsee+ + i r+acP++g+C+G++tan+ma+++ealG+s+P ss+++a+s+ kke + +g NCBI__GCF_002846395.1:WP_101446604.1 165 CFEAYGKKLNGQLSEEDYRGIIRNACPGPGACGGMYTANTMASAAEALGMSVPFSSSSPAVSQSKKEECLGTG 237 ************************************************************************* PP TIGR00110 221 krivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklslddfdrlsrkvPllaklkP 293 +++ l++ ++kP+dil +eafena++l+ +lGGstn+vLhl+aia+ agv lsl df+ +s++vP+la+lkP NCBI__GCF_002846395.1:WP_101446604.1 238 EYLLRLLEMDLKPQDILVREAFENALVLITVLGGSTNAVLHLIAIAHAAGVPLSLRDFQAVSNRVPVLADLKP 310 ************************************************************************* PP TIGR00110 294 sgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrvdqdvirsldnpvkkegglavL 366 sgk+++edl GGv+av+k+l +egl+ d ltvtGkt+ae+l+ vk l ++qd++r+l+np+k++g+++ L NCBI__GCF_002846395.1:WP_101446604.1 311 SGKYLMEDLSTLGGVPAVMKTLLNEGLITGDLLTVTGKTVAENLAGVKPLGEEQDLLRPLSNPIKADGHIQTL 383 ************************************************************************* PP TIGR00110 367 kGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeGdvvviryeGPkGgPGmremLaPtsa 439 +Gnla++Gav+ki+g+e l+feGpa vf+seee ++i +gk+ +G+vvviry GPkGgPGm+emL+Ptsa NCBI__GCF_002846395.1:WP_101446604.1 384 YGNLAPKGAVAKISGKEG--LTFEGPAIVFNSEEELNQGIATGKIVAGQVVVIRYVGPKGGPGMPEMLKPTSA 454 ******************..9**************************************************** PP TIGR00110 440 lvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialvedGDkikiDienrkldlevseeelaerrak 512 ++g+GLg+kvaLitDGrfsGgt+G++iGhv Pea+ gG++alvedGD i++++++++++l+v+e+ l+ rr+k NCBI__GCF_002846395.1:WP_101446604.1 455 IMGAGLGDKVALITDGRFSGGTHGFVIGHVCPEAYDGGTLALVEDGDWISLNANKNTIHLHVEEAVLDLRRDK 527 ************************************************************************* PP TIGR00110 513 akkkearevkgaLakyaklvssadkGavld 542 ++++ ++ kg+L ky + vs a++G+++d NCBI__GCF_002846395.1:WP_101446604.1 528 WQQPAPKVEKGVLLKYIRTVSDASRGCITD 557 ***************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (543 nodes) Target sequences: 1 (573 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 21.51 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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