Align Aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate NP_348995.1 CA_C2380 PLP-dependent aminotransferase
Query= curated2:O58489 (391 letters) >NCBI__GCF_000008765.1:NP_348995.1 Length = 395 Score = 281 bits (719), Expect = 2e-80 Identities = 158/376 (42%), Positives = 238/376 (63%), Gaps = 9/376 (2%) Query: 16 IKRSKIRELFERASKMEDVISLGIGEPDFDTPKNIKEAAKRALDEGWTHYTPNAGIPELR 75 I+ S IR+ + + K++ ISL +G+PDF P +K A RA+++ T YT NAGI ELR Sbjct: 21 IQISGIRKFYNKVIKVQGAISLTLGQPDFPVPDKVKRAMVRAIEDNKTVYTSNAGIDELR 80 Query: 76 EAVVEYYKKFYGIDIEVENVIITAGAYEGTYLAFESLLERGDEVIIPDPAFVSYAEDAKV 135 + +Y K+F I+ + + ITAG EG F++LL +GD+V++PDP+F +YA K+ Sbjct: 81 NEISKYLKRF-NINYSKDEICITAGGTEGILDIFQALLNKGDKVLVPDPSFPAYASCTKL 139 Query: 136 AEAKPVRIPLREENNFLPDPNELLEKI-SKNTRMIVINYPNNPTGATLDKELAKTIADIA 194 E + + L + F D NEL KI ++ + +V++YP+NPTG + KE + + I Sbjct: 140 LEGEVITYGLYG-SEFSIDFNELENKIKNEKPKFMVLSYPSNPTGTVISKEDNEKLHKII 198 Query: 195 EDYNIYILSDEPYEHFIYEDAKHYPMIKFAP--ENTILANSFSKTFAMTGWRLGFVVAPS 252 +D +I ++DE Y YED +Y + ++ E I+ + FSKTF+MTG R+G+V A S Sbjct: 199 KDNDIIAVTDEMYSALCYED-DYYSVSQYEDIREKVIVVSGFSKTFSMTGLRIGYVCAES 257 Query: 253 QVIKEMTKLHAYVIGNVASFVQIAGIEALRSEESWKAVEEMKKEYNERRKIVVKRLKNMP 312 + + K+H Y S Q +E L++ + + V+ MK E+ +RR V KRLK+M Sbjct: 258 SFMSSILKVHQYTTTCAPSISQYGALEGLKNCD--EDVQYMKNEFKKRRDYVYKRLKDM- 314 Query: 313 GIKVKEPKGAFYVFPNISGTGMSSEKFSEWLLEKARVVVIPGTAFGRMGEGYVRISYATS 372 G +V+ PKGAFY+FP+IS GM+SE+F E LL +A+V ++PG+AFG GEG+ RISYA S Sbjct: 315 GFEVRLPKGAFYIFPDISRFGMTSEQFCEKLLNEAKVAIVPGSAFGEKGEGFARISYAYS 374 Query: 373 KEKLIEAMNRIEKALE 388 K++L E MNRIEK +E Sbjct: 375 KKELEECMNRIEKWVE 390 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: 429 Number of extensions: 27 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: 391 Length of database: 395 Length adjustment: 31 Effective length of query: 360 Effective length of database: 364 Effective search space: 131040 Effective search space used: 131040 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