Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Dino:3607384 Length = 393 Score = 207 bits (527), Expect = 5e-58 Identities = 153/405 (37%), Positives = 201/405 (49%), Gaps = 48/405 (11%) Query: 30 RAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTA--YQIVPYQGY 87 + E A L + +GR + D AGIAV GH HPR++ A+ Q + H + YQI Q Sbjct: 18 KGEGAWLIEADGRRFLDLGAGIAVNALGHAHPRLVAALTDQAQALWHVSNLYQIPAQQ-- 75 Query: 88 VTLAERINALVPIQGLNKTALFT-TGAEAVENAIKIARAH---TGRPG---VIAFSGAFH 140 LAE + A + T FT +G E+ E A+K+ R H G+P ++ F G+FH Sbjct: 76 -KLAEMLVA----ETFADTVFFTNSGTESCELAVKMVRKHFHDAGQPERVEILTFEGSFH 130 Query: 141 GRTLLGMALTGKVAPYKIGFGPFPSDIYHAPFPSALHGVSTERALQALEGLFKTDIDPAR 200 GR+ G+A G K GFGP H PF ALQ+ R Sbjct: 131 GRSSAGIAAAGSEKMTK-GFGPLLPGFRHLPF-------GNHEALQSAVN--------DR 174 Query: 201 VAAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDV 260 AAI+VEPVQGEGG +A P ++GLR +CDQHGI++I DEVQ G GRTG++FA V Sbjct: 175 TAAIMVEPVQGEGGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTGRLFAHEWAGV 234 Query: 261 EPDLITMAKSLAGGMPLSAVSGRAAIMDAPLPGGLGGTYAGNPLAVAAAHAVIDVIEEEK 320 PD++ +AK + GG PL AV A G G TY GNPL A AV++ + + Sbjct: 235 SPDIMMVAKGIGGGFPLGAVLATADAASGMTAGTHGSTYGGNPLGCAVGCAVLETVCADG 294 Query: 321 LCE---RSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQ 377 E R A L +Q E L+A+ AEVRG G M+ P T A + Sbjct: 295 FLEEVRRKAGLMRQALEGLVAE--FPGVFAEVRGAGLMLGLVCRAPNTDVVQAGY----- 347 Query: 378 TRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALA 422 G +L NV+R L PLTI A+ ALA L +A A Sbjct: 348 ------GAEVLVVPAAENVVRLLPPLTITDAEIREALARLRKAAA 386 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: 459 Number of extensions: 29 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: 393 Length adjustment: 31 Effective length of query: 392 Effective length of database: 362 Effective search space: 141904 Effective search space used: 141904 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