Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 8502443 DvMF_3149 acetylornithine aminotransferase (RefSeq)
Query= BRENDA::A4F7V1 (447 letters) >FitnessBrowser__Miya:8502443 Length = 402 Score = 135 bits (340), Expect = 2e-36 Identities = 114/362 (31%), Positives = 167/362 (46%), Gaps = 36/362 (9%) Query: 35 VDLDAGDGCRLRDLRDGTEYLDMTMFFSSATLGHGHPGLRTPEFEAALVRAGRVKPSNPD 94 + + G G RL D+ DG EY+D+ + +LGH H L E A +A ++ + Sbjct: 25 ISVARGQGSRLWDV-DGREYVDLLSGIAVTSLGHCHEELA----EVAAAQARKLVHVSNL 79 Query: 95 FATVEQARFAETFRRVAGDPQLPLLFFIDGGTLAVENALKVAFDWKTKVNARKGVAIRGS 154 F EQ AE R+ FF + G A E A+K+A + +V R+ I Sbjct: 80 FYQEEQLDLAE---RLLSTSHCTKAFFCNSGAEANEAAIKLARRYMQRVQGREAYEI--- 133 Query: 155 RVLHLEKAFHGRSGYTLSLTNTDPSKIRDYPMFDWPRIPSPAVVPGDDWDDPELLPHERV 214 + L AFHGR+ T++ T + YPM + R VP D Sbjct: 134 --ITLTGAFHGRTLATVAATGQAKFQDGFYPMPEGFR-----QVPSGD------------ 174 Query: 215 AVEAAEAALRRYGREIACFVYEPIQGEGGDRHLRPRFLRAVQELCREHDVLTVADEVQTG 274 +EA AA+ G + A + E +QGEGG L P + RAVQ LCRE VL + DE+Q G Sbjct: 175 -IEALRAAI---GPQTAGVLVEVVQGEGGVCPLDPDYARAVQALCREKGVLFMTDEIQAG 230 Query: 275 -ALTGRAWAYQALGLEPDLVAFGKRMQVCGVMGGRRVLEVEENAFREASRISSTWGGSLT 333 TGR W++Q GLEPD+V+ K + MG + F S ++ G+L Sbjct: 231 MCRTGRFWSFQNYGLEPDIVSCAKALANGLPMGAMMTTDEVARGFVAGSHATTFGAGALV 290 Query: 334 DMVRATRILEVIESEDLFEHSRQMGELLLGELRALVAEFPSVVRDARGRGLMCAISFADP 393 V A+R +E++ +DL + G ++ RA+ + P + RG GLM + A P Sbjct: 291 SAV-ASRTVEIMLRDDLAGRAATEGARIMDRFRAMGQKLPGTIDHVRGLGLMIGVVLAFP 349 Query: 394 DK 395 K Sbjct: 350 GK 351 Lambda K H 0.321 0.137 0.410 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: 413 Number of extensions: 28 Number of successful extensions: 6 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: 447 Length of database: 402 Length adjustment: 32 Effective length of query: 415 Effective length of database: 370 Effective search space: 153550 Effective search space used: 153550 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