Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)
Query= curated2:Q9YBY6 (388 letters) >FitnessBrowser__Dino:3608039 Length = 444 Score = 156 bits (395), Expect = 1e-42 Identities = 124/382 (32%), Positives = 183/382 (47%), Gaps = 37/382 (9%) Query: 19 VKGSMQYVWDDSGRKYLDCHAGHGAAFLGHSNPAIVEAVVRQARELVAASSSFSTPSLEE 78 V G+ Y+ D G++YLD G + LGH +PA+ A+ Q ++ A + F T E Sbjct: 17 VAGAGCYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGFFTSEPAE 76 Query: 79 ALTE-FSRIAPPWAEEIVFLNTGTEAVEAALKAA---WLATG---KRGIVALKNSFHGRT 131 L + AP E++ L+ G+E+VEAALK A +L TG + ++A + S+HG T Sbjct: 77 VLCDALIAAAPKGIEKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGNT 136 Query: 132 LASLSVTWNP-RYRRGVPVL-DTRFLSP----------STDPG-----------EVEKLV 168 L +L+ N R + P+L +T + P +D E+E+L Sbjct: 137 LGALAAGGNAWRREKYAPLLVETYHIDPCYAYRHQAVGESDAAYGRRAADALRTEIERLG 196 Query: 169 PEDTAAIIVEPIQGE-GGLTKIYAELAKALREAADRVGALLIFDEIQTGFGRTGRVWAHE 227 PE A I EP+ G G + +RE D G LLI DE+ G GRTG ++A E Sbjct: 197 PETVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFACE 256 Query: 228 SLGVEPDIMTAGKSI-AGGLPASAVLSREGVLATLASG----RHGSTHAANPLSMAAVAA 282 G+ PDI+T K + AG P A+L+ + +A G +HG T+ +PL+ AA A Sbjct: 257 QDGISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAAGA 316 Query: 283 ASRFLREEGVPDKARAAGALLEGLLRDRIEGLRLVRGVRGEGLMLGVELRLDPGPVLRCL 342 LR G + RA GA L+ L + V +RG GL G+EL ++ R L Sbjct: 317 VVETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIEL-VEDRDTKRPL 375 Query: 343 QESERVLALRSGATVVRLLPPY 364 + +V A A + R L Y Sbjct: 376 DPARKVSARIKAAAMARGLICY 397 Lambda K H 0.319 0.136 0.398 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: 390 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: 388 Length of database: 444 Length adjustment: 31 Effective length of query: 357 Effective length of database: 413 Effective search space: 147441 Effective search space used: 147441 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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