Align L-lysine 6-transaminase (EC 2.6.1.36) (characterized)
to candidate 3607384 Dshi_0798 acetylornithine and succinylornithine aminotransferase (RefSeq)
Query= BRENDA::A4F7V1 (447 letters) >FitnessBrowser__Dino:3607384 Length = 393 Score = 112 bits (280), Expect = 2e-29 Identities = 109/407 (26%), Positives = 174/407 (42%), Gaps = 47/407 (11%) Query: 40 GDGCRLRDLRDGTEYLDMTMFFSSATLGHGHPGLRTPEFEAALVRAGRVKPSNPDFATVE 99 G+G L + DG +LD+ + LGH HP L A +A + + + Sbjct: 19 GEGAWLIEA-DGRRFLDLGAGIAVNALGHAHPRL----VAALTDQAQALWHVSNLYQIPA 73 Query: 100 QARFAETFRRVAGDPQLPLLFFIDGGTLAVENALKVAFDWKTKVNARKGVAIRGSRVLHL 159 Q + AE + + +FF + GT + E A+K+ + V +L Sbjct: 74 QQKLAE---MLVAETFADTVFFTNSGTESCELAVKMVRKHFHDAGQPERV-----EILTF 125 Query: 160 EKAFHGRSGYTLSLTNTDPSKIRDYPMFDWPRIPSPAVVPGDDWDDPELLPHERVAVEAA 219 E +FHGRS ++ ++ P+ +PG + Sbjct: 126 EGSFHGRSSAGIAAAGSEKMTKGFGPL-----------LPG----------FRHLPFGNH 164 Query: 220 EAALRRYGREIACFVYEPIQGEGGDRHLRPRFLRAVQELCREHDVLTVADEVQTG-ALTG 278 EA A + EP+QGEGG R L L+ +++LC +H +L + DEVQ G TG Sbjct: 165 EALQSAVNDRTAAIMVEPVQGEGGIRALPDACLKGLRDLCDQHGILMILDEVQCGVGRTG 224 Query: 279 RAWAYQALGLEPDLVAFGKRMQVCGVMGG---RRVLEVEENAF-REASRISSTWGGSLTD 334 R +A++ G+ PD++ K G+ GG VL + A A ST+GG+ Sbjct: 225 RLFAHEWAGVSPDIMMVAK-----GIGGGFPLGAVLATADAASGMTAGTHGSTYGGNPLG 279 Query: 335 MVRATRILEVIESEDLFEHSRQMGELLLGELRALVAEFPSVVRDARGRGLMCAISFADPD 394 +LE + ++ E R+ L+ L LVAEFP V + RG GLM + P Sbjct: 280 CAVGCAVLETVCADGFLEEVRRKAGLMRQALEGLVAEFPGVFAEVRGAGLMLGLVCRAP- 338 Query: 395 KRNRALAVARDHHRTLFLPSGTDSLRCRPPLSVRPEEVVDAVSALRK 441 N + A L +P+ + +R PPL++ E+ +A++ LRK Sbjct: 339 --NTDVVQAGYGAEVLVVPAAENVVRLLPPLTITDAEIREALARLRK 383 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: 450 Number of extensions: 26 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 447 Length of database: 393 Length adjustment: 32 Effective length of query: 415 Effective length of database: 361 Effective search space: 149815 Effective search space used: 149815 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