Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_083763404.1 AMB_RS01605 aspartate aminotransferase family protein
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_000009985.1:WP_083763404.1 Length = 384 Score = 215 bits (548), Expect = 2e-60 Identities = 149/406 (36%), Positives = 205/406 (50%), Gaps = 38/406 (9%) Query: 25 DFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPY 84 D +R E A L+ +GR Y DFAAG+AV GH HPR+++A+ AQ + HT+ + Sbjct: 8 DLAFERGEGAYLFTADGRRYLDFAAGVAVNALGHCHPRLVKALTAQAAKVWHTS-NLYRV 66 Query: 85 QGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAH---TGRPG---VIAFSGA 138 G ++A + LV + +GAEA+E +IK+AR H G P +I GA Sbjct: 67 AGQESVAAK---LVERSFADTVFFCNSGAEALECSIKMARRHHFAAGNPQRYRIICAEGA 123 Query: 139 FHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDP 198 FHGRTL +A G+ + GF P H P+ + L AL + Sbjct: 124 FHGRTLATVAAGGQKKHLE-GFAPAVDGFDHVPYGN----------LNALRASITEE--- 169 Query: 199 ARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHH 258 AAI+VEPVQGEGG D++R LRA D+ G++LI DEVQTG GRTG +FA Sbjct: 170 --TAAILVEPVQGEGGIVPGDPDYLRRLRATADEFGLLLIFDEVQTGMGRTGTLFAHEQA 227 Query: 259 DVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEE 318 + PD++ +AK L GG P+ A +PG G T+ GNPLA+A A V+D++ E Sbjct: 228 GIAPDIMGVAKGLGGGFPVGACLATTKAASGMVPGTHGSTFGGNPLAMAVAGEVLDIMAE 287 Query: 319 EKLCERSASLGQQLREHLLAQRKHCPAMA-EVRGLGSMVAAEFCDPATGQPSAEHAKRVQ 377 E ++ LR + P + EVRGLG M+ + P T + Sbjct: 288 PGFLEHVQAMAALLRSKVEDTAARFPGVVEEVRGLGLMLGIKPRMPNT---------EMV 338 Query: 378 TRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423 R E G LLT G N++R L PL I AQ D A+ +L +A E Sbjct: 339 ARLAEGG--LLTVGAGDNIVRLLPPLIINDAQVDEAVGILARAFDE 382 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: 447 Number of extensions: 23 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: 384 Length adjustment: 31 Effective length of query: 392 Effective length of database: 353 Effective search space: 138376 Effective search space used: 138376 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