Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 181 bits (460), Expect = 3e-50 Identities = 125/401 (31%), Positives = 195/401 (48%), Gaps = 40/401 (9%) Query: 30 RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPYQGYVT 89 R + + LWDV+GR Y D +GIAV + GH H + + AAQ + H + + + + Sbjct: 29 RGQGSRLWDVDGREYVDLLSGIAVTSLGHCHEELAEVAAAQARKLVHVS-NLFYQEEQLD 87 Query: 90 LAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHTGRPG------VIAFSGAFHGRT 143 LAER L+ K +GAEA E AIK+AR + R +I +GAFHGRT Sbjct: 88 LAER---LLSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQGREAYEIITLTGAFHGRT 144 Query: 144 LLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPARVAA 203 L +A TG+ A ++ GF P P P AL+A G + A Sbjct: 145 LATVAATGQ-AKFQDGFYPMPEGFRQVPSGDI-------EALRAAIG--------PQTAG 188 Query: 204 IIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVEPD 263 ++VE VQGEGG D+ R ++A+C + G++ + DE+Q G RTG+ ++ ++ +EPD Sbjct: 189 VLVEVVQGEGGVCPLDPDYARAVQALCREKGVLFMTDEIQAGMCRTGRFWSFQNYGLEPD 248 Query: 264 LITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEKLCE 323 +++ AK+LA G+P+ A+ + + G T+ L A A ++++ + L Sbjct: 249 IVSCAKALANGLPMGAMMTTDEVARGFVAGSHATTFGAGALVSAVASRTVEIMLRDDLAG 308 Query: 324 RSASLGQQLREHLLAQRKHCPAMAE-VRGLGSMVAAEFCDPATGQPSAEHAKRVQTRALE 382 R+A+ G ++ + A + P + VRGLG M+ P K V ++ Sbjct: 309 RAATEGARIMDRFRAMGQKLPGTIDHVRGLGLMIGVVLAFP---------GKEVWQALID 359 Query: 383 AGLVLLTCG-TYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422 G + C T V+R L LTIP+A DA L L+ Sbjct: 360 RGFI---CNLTQDCVLRLLPALTIPRADLDAFADALEDILS 397 Lambda K H 0.321 0.136 0.400 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: 412 Number of extensions: 19 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: 423 Length of database: 402 Length adjustment: 31 Effective length of query: 392 Effective length of database: 371 Effective search space: 145432 Effective search space used: 145432 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 (21.9 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