Align Putative aspartate aminotransferase YhdR; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_093395391.1 BM091_RS09820 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O07587 (393 letters) >NCBI__GCF_900114975.1:WP_093395391.1 Length = 396 Score = 341 bits (875), Expect = 2e-98 Identities = 174/390 (44%), Positives = 254/390 (65%), Gaps = 5/390 (1%) Query: 5 GLSREVEENLNKGSWIRKLFDEGARLKKEFGEDQVFDFSLGNPIVEPPEAFKRALIEEAE 64 G + ++ + + + SWIRK+F+EGARL+ +G D+V DFSLGNP V PPE + L+ A+ Sbjct: 2 GAAAKMLKFMEQSSWIRKMFEEGARLRAIYGSDRVCDFSLGNPNVYPPEVVHQELVNLAK 61 Query: 65 KG---SHGYIQNQGLLAAREKVAQFLGSRFEADFSAERIVMTVGAGGALNVALKSIVNPG 121 SHGY+ N GL RE +A+++ F+AE IVMT GA GA+NV LK++++PG Sbjct: 62 SSTGASHGYMPNAGLPEVREAIAEYISPVHGVSFTAEDIVMTCGAAGAMNVILKALLDPG 121 Query: 122 EEVIILAPYFAEYKLYIENYGGKAVSCPLTSRFEIDIEAVRQSITPQTKGLILNTPHNPT 181 +EV++ APYF EY Y +N+GG P T F D++A+ +I+P+TK LILN+P+NPT Sbjct: 122 DEVLVPAPYFVEYGFYADNHGGILKPIPTTDDFLPDLDALENAISPKTKVLILNSPNNPT 181 Query: 182 GTVLSQKNIDDLGALLKEIEEKSGQTIYVLFDEPYSQLIYDE-ELANPFQSYHRVILASS 240 G V + + D+ +L + + IY++ DEPY + +D E+ + + Y R I+A+S Sbjct: 182 GQVYGEALLRDISEILSKRSTDLNRPIYIVSDEPYRNIAFDGIEVPSVLKFYSRSIIATS 241 Query: 241 FSKDLGIAGERLGYIGLDSRMPDADLLINAFVYCNRTLGFVNAPVMMQRAVARMDDLRVD 300 +SKDL +AGER+GY+ + M D L+ A V NR LGFVNAP MQR VAR+ + VD Sbjct: 242 YSKDLCLAGERIGYLAVHPEMEKKDSLLGALVLANRILGFVNAPAFMQRLVARLQGITVD 301 Query: 301 ASAYKERRDLMVDILKEAGFEFEMPKGGFFVFPKSPIEDEVAFCVHAAQKYKLLIVPSSG 360 Y+++RD++V +KE G+EF +PKG F++FPKSP+ D+V F V Q+ +L+VP SG Sbjct: 302 PMTYQKKRDMLVAAMKEIGYEFIVPKGAFYLFPKSPVPDDVEF-VRMLQEELILVVPGSG 360 Query: 361 FGMSGHFRLSFSVPIEQIKNSRDIFISLYK 390 FG G+FR++F V E I S + F YK Sbjct: 361 FGKPGYFRIAFCVDDEVISRSFNGFEKAYK 390 Lambda K H 0.320 0.139 0.396 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: 416 Number of extensions: 14 Number of successful extensions: 4 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: 393 Length of database: 396 Length adjustment: 31 Effective length of query: 362 Effective length of database: 365 Effective search space: 132130 Effective search space used: 132130 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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