Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate WP_092344193.1 BLU87_RS01675 acetylornithine transaminase
Query= metacyc::MONOMER-11537 (425 letters) >NCBI__GCF_900107645.1:WP_092344193.1 Length = 397 Score = 227 bits (579), Expect = 4e-64 Identities = 144/435 (33%), Positives = 223/435 (51%), Gaps = 56/435 (12%) Query: 9 MKRREAAVPRGVGQI------HPIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPK 62 M + + + RG+ + P+ A S K +TD++G+ ++DF G+AV + GH HPK Sbjct: 1 MNKSQNWIDRGLAHVANTYGRFPLVAASGKGCWLTDIDGKRYLDFLAGVAVNSLGHCHPK 60 Query: 63 IIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKI 122 ++AA+ EQ KL H C +EL E + GD + +G+EA E A+K+ Sbjct: 61 VVAALQEQAAKLLH-CSNYYHIPQQIELAEILCEHSFGD---RVFFCNSGAEANEAALKL 116 Query: 123 ARA------ATGRAGVIAFTGAYHGRTMMTLGLTGK------VVPYSAGMGLMPGGIFRA 170 R T R +I ++HGRT+ T+ TG+ P +G +P G A Sbjct: 117 VRKYSADTYGTDRFEIITAIDSFHGRTLATISATGQDRIQSGFAPLISGFKYVPFGDIAA 176 Query: 171 LYPNELHGVSIDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALC 230 L K P+ AI++EP+QGEGG V P+ +++ R LC Sbjct: 177 L---------------------KTAIGPKT-CAIMMEPIQGEGGINVPPQGYLQAARELC 214 Query: 231 DQHGILLIADEVQTGAGRTGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAI 290 D+H +LLI DE+Q G GRTG FA E V D+ T AK++A G P+ + + +Y A+ Sbjct: 215 DKHNLLLIFDEIQVGLGRTGKLFAYEHDNVEPDVMTLAKALAAGPPIGAMIAREKYATAL 274 Query: 291 APGGLGGTYAGSPIACAAALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVR 350 +PG G T+ G+P+ AA +A M+V E+H++D C A+G L L+ +Q KY I +R Sbjct: 275 SPGTHGSTFGGNPLLTAAGVAAMKVLLEDHIIDNCVAMGNYLKAQLEQLQNKYTFIKNIR 334 Query: 351 ALGAMIAVELFENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQ 410 G ++ +EL G A++V A +GL L++C T G VLR + PL + Sbjct: 335 GRGLILGMELTFEG----------AEIVKTALQRGL-LINC-TAGKVLRFVPPLIVTQDE 382 Query: 411 LDKGLAIIEECFAEL 425 +D+ + I++ EL Sbjct: 383 IDQMIEILDGILKEL 397 Lambda K H 0.320 0.137 0.394 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: 394 Number of extensions: 18 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: 425 Length of database: 397 Length adjustment: 31 Effective length of query: 394 Effective length of database: 366 Effective search space: 144204 Effective search space used: 144204 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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