Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_011383255.1 AMB_RS04150 acetylornithine transaminase
Query= BRENDA::Q0K2K2 (423 letters) >NCBI__GCF_000009985.1:WP_011383255.1 Length = 388 Score = 212 bits (539), Expect = 2e-59 Identities = 146/401 (36%), Positives = 208/401 (51%), Gaps = 40/401 (9%) Query: 25 DFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPY 84 D ++ E A L +GR + DF AG+AV GH HPR++ A+ AQ + H + + Sbjct: 14 DVIFEQGEGAWLTASDGRRFLDFGAGVAVNALGHAHPRLVAALEAQAGKLWHCS-NLYRV 72 Query: 85 QGYVTLAERINALVPIQGLNKTALFTTGAEAVENAIKIARAH---TGRPG---VIAFSGA 138 G +AER L+ + TGAEA+E IKIAR + GRP ++A +G+ Sbjct: 73 PGQERVAER---LIKASFADTAFFCNTGAEAMELVIKIARRYHHCAGRPERNRIVACTGS 129 Query: 139 FHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDP 198 FHGRT+ +A G Y GFGP H P+ L+A G ++ Sbjct: 130 FHGRTIATLAAAG-TPKYLEGFGPVAQGFDHVPYGD----------LEAARGAIGSN--- 175 Query: 199 ARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHH 258 AA++VEPVQGEGG + A ++RGLRA+ DQ G++L+ DEVQTG GRTGK+FA Sbjct: 176 --TAALLVEPVQGEGGIRPADPAYLRGLRALADQFGLLLLMDEVQTGIGRTGKLFAHEWS 233 Query: 259 DVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEE 318 + PD++ +AK L GG P+ AV PG G T+ GNPLA+A A AV+D + Sbjct: 234 GIAPDVMGLAKGLGGGFPVGAVLATEKAASCMTPGTHGCTFGGNPLAMAVAEAVLDEVMA 293 Query: 319 EKLCERSASLGQQLREHL--LAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRV 376 ER ++ LR L LA R++ A+A+VRG G M+ G + Sbjct: 294 PGFLERVQAVAALLRGRLDDLA-RRYPGAIAQVRGQGLML---------GLKTVPVNTEF 343 Query: 377 QTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVL 417 + AG LL G NV+R + PL I +A+ + A+ ++ Sbjct: 344 NAKLFAAG--LLAVGAGDNVVRLVPPLIIGEAEVERAVEII 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: 463 Number of extensions: 22 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: 423 Length of database: 388 Length adjustment: 31 Effective length of query: 392 Effective length of database: 357 Effective search space: 139944 Effective search space used: 139944 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