Align Homocitrate synthase; EC 2.3.3.14 (uncharacterized)
to candidate 8501897 DvMF_2612 pyruvate carboxyltransferase (RefSeq)
Query= curated2:Q01181 (391 letters) >FitnessBrowser__Miya:8501897 Length = 455 Score = 213 bits (542), Expect = 9e-60 Identities = 146/375 (38%), Positives = 199/375 (53%), Gaps = 20/375 (5%) Query: 21 LCDTTLRDGEQTAGVAFTRAEKRAIAEALQAAGVAEVEVGVPAMGEEERADIRAVAA-VL 79 L DTTLR+GEQ+ G + A++ + L A GV E EVG G E+ D+ A++A V Sbjct: 2 LLDTTLREGEQSFGTYLSMADRERVLRGLAAVGVPEAEVGWA--GREDLTDMLALSARVA 59 Query: 80 KTAAPVVWCRLRAEDLAAAQRTGVVRLHIGVPVSERQISAKLGKDAAWVRDKVEKLVRAA 139 A WCR R DL AA G R+ +GVPVS+ ++ +LG A + D + + A Sbjct: 60 PGLAAAAWCRCRPGDLRAAVACGASRVCVGVPVSDAHLARRLGLGRAALLDLLAATLAEA 119 Query: 140 SWAG-HKVSVGAEDASRADPFFLAEIAHVAAEAGAIRFRISDTLGVLDPFAAHELV---- 194 G V+VG EDASRAD F+ +A AA GA R R+SDT+G+ P ++V Sbjct: 120 RMLGIEHVTVGMEDASRADRAFVFAVACHAAAHGAHRVRLSDTVGLYTPLEVADVVRALR 179 Query: 195 -----GRVVTRCP----LPVEFHGHNDLGMATANSLAAARAGASHLSVTVNGLGERAGNA 245 R P + + H HND GMATAN+L A GA V+V GLGERAG A Sbjct: 180 AELEGARQDDTAPRARRVSIGTHFHNDCGMATANALTALECGADCADVSVLGLGERAGVA 239 Query: 246 ALEEVAAALEAAGRATGVALGQLCALSELVARASGRPLSPQKPIVGEGVFTHECGIHVDG 305 LEE+AAAL GRA L L AL VA+A+ + P+ G +F E G+H G Sbjct: 240 RLEELAAALVVRGRAR-FELAPLRALCGQVAQAASLSVPRHWPVAGRDIFAVESGLHAHG 298 Query: 306 LMKDRATYESADLRPERFGRSHRIAIGKHSSAAGLARALAEAGLPADAATLAALMPALRD 365 + +D + +E PE G S R+ +G+ S A +A ALAE + L A++ A+RD Sbjct: 299 VRRDPSLFE--PFPPELVGDSRRMGVGRKSGVAAVAAALAELSILPPPDELPAIVEAVRD 356 Query: 366 WAAITKRAAAPEDLA 380 +A +R P +LA Sbjct: 357 LSATLRRPLTPAELA 371 Lambda K H 0.318 0.130 0.371 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: 375 Number of extensions: 15 Number of successful extensions: 4 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: 391 Length of database: 455 Length adjustment: 32 Effective length of query: 359 Effective length of database: 423 Effective search space: 151857 Effective search space used: 151857 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: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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