Align Aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_092346870.1 BLU87_RS08685 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O58489 (391 letters) >NCBI__GCF_900107645.1:WP_092346870.1 Length = 390 Score = 275 bits (703), Expect = 2e-78 Identities = 144/367 (39%), Positives = 220/367 (59%), Gaps = 4/367 (1%) Query: 19 SKIRELFERASKMEDVISLGIGEPDFDTPKNIKEAAKRALDEGWTHYTPNAGIPELREAV 78 S IR +F+ + DV++L GEPDF TP +I EAA ++ G T Y+P +GI ELR+AV Sbjct: 18 SGIRAMFDLLPEYPDVVNLCNGEPDFSTPSHICEAAIASIQGGDTRYSPTSGILELRQAV 77 Query: 79 VEYYKKFYGIDIEVENVIITAGAYEGTYLAFESLLERGDEVIIPDPAFVSYAEDAKVAEA 138 + Y + I +NV+I G E ++ + + GDEVI+ DP + +Y ++ +A Sbjct: 78 ADKYTQQLKRRITPDNVMIVCGGTEALMMSLLATVNPGDEVIVTDPCYPNYFAQIELVKA 137 Query: 139 KPVRIPLREENNFLPDPNELLEKISKNTRMIVINYPNNPTGATLDKELAKTIADIAEDYN 198 K V IP+ E+NNF DP +L + IS T+ I++NYPNNP G T +E +++ + +D N Sbjct: 138 KCVSIPVYEKNNFQIDPEDLKKAISSRTKGIILNYPNNPLGVTASEEYIQSLEQLIDDNN 197 Query: 199 IYILSDEPYEHFIYEDAKHYPMIK--FAPENTILANSFSKTFAMTGWRLGFVVAPSQVIK 256 + + SDE YE Y + HY + + +N ++ NS SKT+AMTGWR+G++V +++K Sbjct: 198 LIVFSDEVYESLTYGKSGHYSLAQNDRIKDNVLVMNSLSKTYAMTGWRIGYIVGHPKIMK 257 Query: 257 EMTKLHAYVIGNVASFVQIAGIEALRSEESWKAVEEMKKEYNERRKIVVKRLKNMPGIKV 316 M +L V+ + F+Q A + ALR + V+EM Y +R ++V +++MPG K Sbjct: 258 SMFRLQESVLSCLPVFIQKAALAALRGSQD--KVQEMASAYEKRMNLLVDGIQSMPGFKC 315 Query: 317 KEPKGAFYVFPNISGTGMSSEKFSEWLLEKARVVVIPGTAFGRMGEGYVRISYATSKEKL 376 P G V NIS SSE+FS LLE A V+ +PG+AFG MGEGY+R +A S E + Sbjct: 316 IRPMGGLCVMANISAYNKSSEEFSRELLENAGVMTVPGSAFGPMGEGYIRFCFANSFENI 375 Query: 377 IEAMNRI 383 + + R+ Sbjct: 376 QKGVERL 382 Lambda K H 0.316 0.135 0.382 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: 388 Number of extensions: 11 Number of successful extensions: 3 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: 391 Length of database: 390 Length adjustment: 31 Effective length of query: 360 Effective length of database: 359 Effective search space: 129240 Effective search space used: 129240 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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