Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate 8501897 DvMF_2612 pyruvate carboxyltransferase (RefSeq)
Query= BRENDA::A0A1Y6KBA1 (416 letters) >FitnessBrowser__Miya:8501897 Length = 455 Score = 221 bits (562), Expect = 5e-62 Identities = 140/377 (37%), Positives = 209/377 (55%), Gaps = 19/377 (5%) Query: 42 ILNDTTLRDGEQAPGVAFALSEKVAIARALARAGVPEIEAGTPAM-GADEISAIRAIVEA 100 +L DTTLR+GEQ+ G +++++ + R LA GVPE E G ++ A+ A V Sbjct: 1 MLLDTTLREGEQSFGTYLSMADRERVLRGLAAVGVPEAEVGWAGREDLTDMLALSARVAP 60 Query: 101 GLPATIIGWCRMREADVDAAIAAGVSMVNVSIPTSDVQIAAKLGGGRSVALELLKRVVSY 160 GL A WCR R D+ AA+A G S V V +P SD +A +LG GR+ L+LL ++ Sbjct: 61 GLAAA--AWCRCRPGDLRAAVACGASRVCVGVPVSDAHLARRLGLGRAALLDLLAATLAE 118 Query: 161 ARSRGLG-VAVGGEDSSRADVGFLAEVIATAKALGARRFRVADTLSVLDPDATSALVGAL 219 AR G+ V VG ED+SRAD F+ V A A GA R R++DT+ + P + +V AL Sbjct: 119 ARMLGIEHVTVGMEDASRADRAFVFAVACHAAAHGAHRVRLSDTVGLYTPLEVADVVRAL 178 Query: 220 RATTD-------------LEIEFHGHDDLGLATANTLAAIKAGATHASVTVIGLGERAGN 266 RA + + I H H+D G+ATAN L A++ GA A V+V+GLGERAG Sbjct: 179 RAELEGARQDDTAPRARRVSIGTHFHNDCGMATANALTALECGADCADVSVLGLGERAGV 238 Query: 267 APLEEVAVALRQLYRRETGIVLAELDHVANVVAAAAARAIPLNKAIVGEHVFTHESGIHV 326 A LEE+A AL + R LA L + VA AA+ ++P + + G +F ESG+H Sbjct: 239 ARLEELAAAL--VVRGRARFELAPLRALCGQVAQAASLSVPRHWPVAGRDIFAVESGLHA 296 Query: 327 DGLLKDQRTYQALDPMLFGRSNRIVIGKHSGLSAITSLLSDLRLPASADQAQRILARVRK 386 G+ +D ++ P L G S R+ +G+ SG++A+ + L++L + D+ I+ VR Sbjct: 297 HGVRRDPSLFEPFPPELVGDSRRMGVGRKSGVAAVAAALAELSILPPPDELPAIVEAVRD 356 Query: 387 HAVAHKGPVPKEAVAAI 403 + + P+ +A + Sbjct: 357 LSATLRRPLTPAELAEV 373 Lambda K H 0.317 0.132 0.369 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: 523 Number of extensions: 30 Number of successful extensions: 6 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: 416 Length of database: 455 Length adjustment: 32 Effective length of query: 384 Effective length of database: 423 Effective search space: 162432 Effective search space used: 162432 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: 51 (24.3 bits)
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