Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79; Transaminase A (uncharacterized)
to candidate WP_026329593.1 F612_RS0102765 alanine transaminase
Query= curated2:Q4UND3 (409 letters) >NCBI__GCF_000381085.1:WP_026329593.1 Length = 398 Score = 158 bits (400), Expect = 2e-43 Identities = 114/372 (30%), Positives = 197/372 (52%), Gaps = 27/372 (7%) Query: 7 RLNSIKPSPTLAVVKKTLELKKAGVDIIALGAGEPDFDTPDNIKEAAIKAI-KDGFTKYT 65 R+N + P V + E ++ G DII G G PD DTP +I + I+ + ++G +Y+ Sbjct: 7 RINRLPPYVFNIVGELKAEARRRGEDIIDFGMGNPDQDTPKHIVDKLIEVVQREGTHRYS 66 Query: 66 NVEGMPLLKQAIKDKFKRENNIDYELD---EIIVSTGGKQVIYNLFMASLDKGDKVIIPA 122 +G+P L++AI + +K + D ELD E +V+ G K+ + +L MA++DKGD V++P Sbjct: 67 VSQGIPRLRKAICNWYKTK--FDVELDYATEAVVTIGSKEGLAHLAMATVDKGDTVLVPN 124 Query: 123 PYWVSYPDMVALSTGTPVFVNCGIENNFKLSAEALERSITD---KTKWLIINSPSNPTGA 179 P + +P ++ V + +F E LE++I + K K LI+N P NPT Sbjct: 125 PAYPIHPFGFVIAGADVRHVKMTPDVDF---FEELEKAIKESWPKPKMLILNFPGNPTTQ 181 Query: 180 SYNFEELENIAKVLRKYPHVNVMSDDIYEHITFDDFKFYTLAQI--APDLKERIFTVNGV 237 + E E + + +++ ++ V+ D Y I FD + ++ Q+ A D+ +T+ Sbjct: 182 TVELEFFERVIAIAKEH-NIWVIHDLAYADIVFDGYIAPSILQVEGAKDIAVEFYTL--- 237 Query: 238 SKAYSMTGWRIGYGVGSKALIKAMTIIQSQSTSNPCSISQMAAIESLNGPQDYIKPNALN 297 SK+Y+M GWR+G+ VG+ L+ A+ I+S + Q+AAI +L GPQ+ ++ Sbjct: 238 SKSYNMPGWRVGFMVGNPTLVNALKRIKSYLDYGTFTPIQVAAIAALEGPQECVQEICDM 297 Query: 298 FQKKRDLALSILKRVKYFECYKPEGAFYLFVKCDKIFGHKTKSGKIIANSNDFAEYLLEE 357 ++ +RD+ L + + P+ +++ K + S +F++ LL E Sbjct: 298 YKLRRDVLCEGLNTIGW-PVVPPKATMFIWAPIPKEYK--------AMGSIEFSKKLLTE 348 Query: 358 AKVAVVPGIAFG 369 AKVAV PGI FG Sbjct: 349 AKVAVSPGIGFG 360 Lambda K H 0.317 0.135 0.387 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: 404 Number of extensions: 26 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: 409 Length of database: 398 Length adjustment: 31 Effective length of query: 378 Effective length of database: 367 Effective search space: 138726 Effective search space used: 138726 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 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