Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate BWI76_RS14020 BWI76_RS14020 aspartate aminotransferase family protein
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Koxy:BWI76_RS14020 Length = 461 Score = 232 bits (592), Expect = 2e-65 Identities = 150/415 (36%), Positives = 224/415 (53%), Gaps = 31/415 (7%) Query: 30 RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFT--HTAYQIVPYQGY 87 +AE L D + + Y D AG L GH HP V+Q+I + + HT P + Sbjct: 47 KAEGVWLTDADNKQYLDCLAGAGTLALGHNHPDVLQSIQSVITSGLPLHTLDLTTPLKD- 105 Query: 88 VTLAERINALVPIQGLNKTALFT--TGAEAVENAIKIARAHTGRPGVIAFSGAFHGRTLL 145 +E + +L+P +G FT +GA+AVE A+K+A+ +TGR VI+FSG +HG T Sbjct: 106 -RFSEYLLSLLPGEGKEYCLQFTGPSGADAVEAALKLAKKYTGRSSVISFSGGYHGMTHG 164 Query: 146 GMALTGKVAPYKIGFGPFPSDIYHAPFPSALH---GVSTERALQALEGLFKTDIDPA--- 199 +++TG ++P G P ++ P+P G+ E ++AL F+ I+ Sbjct: 165 ALSVTGNLSPKAAVNGMMP-EVQFMPYPHQYRCPLGIGGEAGVKALTYYFENLINDVESG 223 Query: 200 --RVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSH 257 + AA+I+E VQGEGG AP ++++ +R V +HGI+LI DEVQ GF RTGK FA H Sbjct: 224 VRKPAAVILEAVQGEGGVNPAPVEWLQRIRKVTQEHGILLIIDEVQAGFARTGKFFAFEH 283 Query: 258 HDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIE 317 +EPD+I M+K++ GG+PL AV G DA PG GT+ GN LA+A + ++ Sbjct: 284 AGIEPDIIVMSKAVGGGLPL-AVLGIKKQFDAWEPGHHTGTFRGNQLAMATGLTTLRHLK 342 Query: 318 EEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEF-----------CDPATG 366 + K+ +++A+ G+ L+ L +K P + VRGLG M+ E C PA G Sbjct: 343 DNKIADKTAAQGEWLKGKLAEMQKRYPVIGHVRGLGLMIGIEIVKPNEAPDHMGCYPADG 402 Query: 367 QPSAEHAKRVQTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQAL 421 + SA +Q + EAGL+L G +G V+R L L I A+ + QAL Sbjct: 403 ELSA----LLQKKCFEAGLILERGGRHGCVLRLLPSLLISNAELEIFFDKFEQAL 453 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: 473 Number of extensions: 21 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: 461 Length adjustment: 32 Effective length of query: 391 Effective length of database: 429 Effective search space: 167739 Effective search space used: 167739 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: 51 (24.3 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