Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_066329202.1 BLR17_RS10870 pyridoxal phosphate-dependent aminotransferase
Query= curated2:Q60317 (375 letters) >NCBI__GCF_900100165.1:WP_066329202.1 Length = 398 Score = 171 bits (433), Expect = 3e-47 Identities = 125/397 (31%), Positives = 206/397 (51%), Gaps = 36/397 (9%) Query: 2 ISSRCKNIKPSAIR------EIFNLATSDCINLGIGEPDFDTPKHIIEAAKRALDEGKTH 55 IS R + + S IR +I N +L IG+PD +P+ I+A K ++ Sbjct: 4 ISIRGRRMPESPIRKLAPFADIANKKGLKVYHLNIGQPDIKSPEIAIQAIKN-INMDIIE 62 Query: 56 YSPNNGIPELREEISNKLKDDYNLDVDKDNIIVTCGASEALMLSIMTLIDRGDEVLIPNP 115 Y P+ G R +++ + + N+ VD +I++T G SEAL+ ++ +++D GDEV+IP P Sbjct: 63 YGPSAGYESYRRKLA-QFYTNQNVRVDFADIMITTGGSEALLFALGSIMDPGDEVIIPEP 121 Query: 116 SFVSYFSLTEFAEGKI--KNIDLDENFNI-DLEKVKESITKKTKLIIFNSPSNPTGKVYD 172 + +Y + +E + + N D +E F + +E ++ IT KTK II +PSNPTG +Y Sbjct: 122 FYANYHAFSEESSATVIPVNSDFEEGFTLPSIEAFEKLITPKTKAIIICNPSNPTGNLYS 181 Query: 173 KETIKGLAEIAEDYNLIIVSDEVYDKIIYDKK--HYSPMQ---FTDRCILINGFSKTYAM 227 + I+ L E+ + ++L +++DEVY + IYD+K HYS M I+I+ SK Y+M Sbjct: 182 ESEIQQLGELVKKHDLFLIADEVYREFIYDEKDRHYSVMNLIGLEQNVIMIDSVSKRYSM 241 Query: 228 TGWRIGYLAVSDELNKELDLINNMIKIHQYSFACATTFAQYGALAALRGSQKCVEDMVRE 287 G RIG + + K ++I +K Q + C T Q AA+ + +++++E Sbjct: 242 CGARIGCM-----VTKNKEVIATAMKFAQ-ARLCPPTIEQIACEAAIDTPKSYFDEVIKE 295 Query: 288 FKMRRDLIYNGLKDI--FKVNKPDGAFYIFPDVSEYGDGVEV-AKKLIEN------KVLC 338 +K RRD + L I KV P AFY ++ D E A+ L+E+ V+ Sbjct: 296 YKDRRDTLITELLKIEGVKVTPPKAAFYCIAELPV--DNTETFAQWLLESYNLNGETVMV 353 Query: 339 VPGVAFGEN---GANYIRFSYATKYEDIEKALGIIKE 372 P F G +R +Y ED+ KA+ I+K+ Sbjct: 354 APAAGFYSTPGMGLKQVRIAYVLNKEDLTKAVHILKD 390 Lambda K H 0.318 0.138 0.397 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: 350 Number of extensions: 22 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: 375 Length of database: 398 Length adjustment: 30 Effective length of query: 345 Effective length of database: 368 Effective search space: 126960 Effective search space used: 126960 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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