Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 207835 DVU2347 acetylornithine aminotransferase
Query= uniprot:A1S8Y2 (425 letters) >MicrobesOnline__882:207835 Length = 399 Score = 191 bits (486), Expect = 3e-53 Identities = 140/432 (32%), Positives = 213/432 (49%), Gaps = 41/432 (9%) Query: 1 MSLTNDSLMVRRRAAVAGGVGQIHPVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLH 60 M+ + ++L R + + G+ +P+ +RAE + +WD EGREYID GIAV + GH H Sbjct: 1 MTTSFEALKNREESLLCRTYGR-YPISVQRAEGSRMWDHEGREYIDLLSGIAVTSLGHCH 59 Query: 61 PKVKAAVAEQLEKFSHTCFMVLGYESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAI 120 P++ +A Q K H + E + + EKL + K+ SG+EA E AI Sbjct: 60 PELAEVMARQARKLVHVSNLFY-QEEQLDLAEKLLSTL---HCTKAFFCNSGAEANEAAI 115 Query: 121 KVARAYTKRAG------VIAFTSGYHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPC 174 K+AR Y +R V+ T +HGRT+A +A TG+ + G M A +AE+ Sbjct: 116 KLARRYMQRVRGVDAHEVVTLTGAFHGRTLATVAATGQER-FQDGFAPMPAGFRQAEW-- 172 Query: 175 ALHGVSEDDAMASIERIFKNDAEPSDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREG 234 + DA+ + A A +++E VQGEGG T + + + +LC +G Sbjct: 173 -----GDIDALRA--------AITPATAGVLVEMVQGEGGVRPMTQDYARAVADLCREKG 219 Query: 235 IMLIADEVQTGAGRTGTFFAMEQMGVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGG 294 ++L+ DE+QTG RTG F+A + GV DI T AK++A G P+ + EV G Sbjct: 220 VLLMVDEIQTGLCRTGRFWAHQHYGVEPDIVTSAKALANGLPMGAMMTTDEVAQGFVAGS 279 Query: 295 LGGTYGGSPLACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYP-QIAEVRGLG 353 T+G L + A A +++ + ++L ER+ A+G + ++ P I EVRG G Sbjct: 280 HATTFGAGALVSSVAAATLDIMKRDRLDERATAVGGRAMERFRAIGAKLPGTIEEVRGYG 339 Query: 354 SMIAIELMENGKPAPEYCPQVLTEARNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLE 413 MI I L +GK +V E RG + + T VLR LVP DE L Sbjct: 340 LMIGIVLTFSGK-------EVWKELVARGFVCNN--TQEKVLR-LVPALTIDE---ADLT 386 Query: 414 IMAECFEAVLGK 425 A+ E +L + Sbjct: 387 AFADTLEDILAR 398 Lambda K H 0.319 0.136 0.391 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: 363 Number of extensions: 22 Number of successful extensions: 5 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: 399 Length adjustment: 31 Effective length of query: 394 Effective length of database: 368 Effective search space: 144992 Effective search space used: 144992 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 17 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