Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate AZOBR_RS19025 AZOBR_RS19025 acetylornithine aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__azobra:AZOBR_RS19025 Length = 389 Score = 200 bits (509), Expect = 5e-56 Identities = 139/407 (34%), Positives = 198/407 (48%), Gaps = 40/407 (9%) Query: 25 DFYADRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPY 84 D +R E L+ +GR + DFAAG+AV GH +P +++A+ AQ + HT+ + Sbjct: 13 DIVFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTS-NLFRV 71 Query: 85 QGYVTLAERINALVPIQGLNKTALFT-TGAEAVENAIKIARAH------TGRPGVIAFSG 137 G +LA+R+ T FT +GAEA E K+ R + R +I F Sbjct: 72 AGQESLAKRLTEAT----FADTVFFTNSGAEAWECGAKLIRKYHYEKGDKARTRIITFEQ 127 Query: 138 AFHGRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDID 197 AFHGRTL ++ + K GFGP PF LE + D Sbjct: 128 AFHGRTLAAVSAAQQEKLIK-GFGPLLDGFDLVPFGD-------------LEAVRNAVTD 173 Query: 198 PARVAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSH 257 A I +EP+QGEGG +A +F+RGLR +CD+HG++L DE+Q G GRTGK+FA Sbjct: 174 --ETAGICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAHEW 231 Query: 258 HDVEPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIE 317 + PD++ +AK + GG PL A G G TY GNPLA A +AV+D + Sbjct: 232 AGITPDVMAVAKGIGGGFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLDKVL 291 Query: 318 EEKLCERSASLGQQLREHLLAQRKHCPAMAE-VRGLGSMVAAEFCDPATGQPSAEHAKRV 376 E + +G L++ L PA+ + VRG G M+ C PA G V Sbjct: 292 EPGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLA-CGPAVGD--------V 342 Query: 377 QTRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423 GL+ + G NV+R L PL I +A+ + A+A+L + E Sbjct: 343 VVALRANGLLSVPAG--DNVVRLLPPLNIGEAEVEEAVAILAKTAKE 387 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: 431 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: 389 Length adjustment: 31 Effective length of query: 392 Effective length of database: 358 Effective search space: 140336 Effective search space used: 140336 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