Align Aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_055435681.1 ASC41_RS05720 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O58489 (391 letters) >NCBI__GCF_001418085.1:WP_055435681.1 Length = 396 Score = 191 bits (484), Expect = 4e-53 Identities = 132/396 (33%), Positives = 222/396 (56%), Gaps = 23/396 (5%) Query: 9 IAERVLLIKRSKIRELF---ERASKM-EDVISLGIGEPDFDTPKNIKEAAKRALDEGWTH 64 I+++ L + S IR+L E A+K + + L IG+PD TP+ +A K E Sbjct: 4 ISKKGLSMPESPIRKLVPFAEIATKQGKSIYHLNIGQPDIKTPQIALDAVKNNSLEILA- 62 Query: 65 YTPNAGIPELREAVVEYYKKFYGIDIEVENVIITAGAYEGTYLAFESLLERGDEVIIPDP 124 YT + G R+ + +YY K I+++ +++I+T G E AF S+++ DEVIIP+P Sbjct: 63 YTRSEGSETYRQKIADYYAK-NDINVKHDDIIVTTGGSEALLFAFGSIMDVDDEVIIPEP 121 Query: 125 AFVSYAEDAKVAEAKPVRIPLREENNFLPDPNELLEK-ISKNTRMIVINYPNNPTGATLD 183 + +Y + + K V + + E+NF P E EK I+ T+ I+I P NPTG Sbjct: 122 FYANYNGFSTASGVKVVPVISKIEDNFALPPIEEFEKLITPKTKAILICNPGNPTGYLYS 181 Query: 184 KELAKTIADIAEDYNIYILSDEPYEHFIYEDAKHYPMI--KFAPENTILANSFSKTFAMT 241 KE K +ADI + +++++++DE Y F Y+ AKHY ++ + + I+ +S SK ++M Sbjct: 182 KEEIKKLADIVKKHDLFLIADEVYREFAYDGAKHYSILQEEGLDDYAIVIDSVSKRYSMC 241 Query: 242 GWRLGFVVAPS-QVIKEMTKLHAYVIGNVASFVQIAGIEALRSEESWKAVEEMKKEYNER 300 G R+G +V+ + QVIK K A + + QIA AL + +S+ +++ +EY ER Sbjct: 242 GARIGCLVSKNKQVIKTALKF-AQARLSPPTLAQIASEAALETPQSY--FDDVIEEYVER 298 Query: 301 RKIVVKRLKNMPGIKVKEPKGAFYVFPNISGTGMSSEKFSEWLLEK-----ARVVVIPGT 355 R ++ L + G+KV PKGAFY + +S+KF++WLLE+ ++V P Sbjct: 299 RNTLITELNKIEGVKVGNPKGAFYCIAEL--PIKNSDKFAQWLLEEFDVDGETIMVAPAA 356 Query: 356 AF---GRMGEGYVRISYATSKEKLIEAMNRIEKALE 388 F +G +RI+Y +KE LI+++N +++AL+ Sbjct: 357 GFYSTPGVGLNQIRIAYVLNKESLIKSVNILKEALK 392 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: 389 Number of extensions: 24 Number of successful extensions: 7 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: 396 Length adjustment: 31 Effective length of query: 360 Effective length of database: 365 Effective search space: 131400 Effective search space used: 131400 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 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