Align Putative aspartate aminotransferase YhdR; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate NP_349436.1 CA_C2832 aspartate aminotransferase
Query= curated2:O07587 (393 letters) >NCBI__GCF_000008765.1:NP_349436.1 Length = 393 Score = 274 bits (701), Expect = 3e-78 Identities = 146/392 (37%), Positives = 230/392 (58%), Gaps = 6/392 (1%) Query: 6 LSREVEENLNKGSWIRKLFDEGARLKKEFGEDQVFDFSLGNPIVEPPEAFKRALIEEAEK 65 +S ++ E +K S IR++F+ G + +E G + V+DFS+GNP V PEA K+A++E E+ Sbjct: 2 VSEKMYELGSKRSVIREIFEFGKKRAEEVGVENVYDFSIGNPNVPAPEAVKKAILEILEE 61 Query: 66 GS----HGYIQNQGLLAAREKVAQFLGSRFEADFSAERIVMTVGAGGALNVALKSIVNPG 121 + H Y QG L R+ +A+ + RF FS + MTVGA ++++ ++ NPG Sbjct: 62 ENPVDIHSYTSAQGDLKVRDTLAESINKRFSTSFSGNNLYMTVGAAASIHICFSALANPG 121 Query: 122 EEVIILAPYFAEYKLYIENYGGKAVSCPLTSR-FEIDIEAVRQSITPQTKGLILNTPHNP 180 +E I APYF EY+ ++E GGK V P F+ID E + I +TK +I+NTP+NP Sbjct: 122 DEFITFAPYFPEYRCFVEAAGGKLVVVPAKIEDFQIDFEEFEKRINEKTKAVIVNTPNNP 181 Query: 181 TGTVLSQKNIDDLGALLKEIEEKSGQTIYVLFDEPYSQLIYDEELANPFQSYHRVILASS 240 +G V +++ I L +L+ ++ G IY++ DEPY ++ YD E+ + Y + S Sbjct: 182 SGVVYTEETITKLAKVLENKAKEYGHAIYLISDEPYREIAYDVEVPYLTKYYDNTFVCYS 241 Query: 241 FSKDLGIAGERLGYIGLDSRMPDADLLINAFVYCNRTLGFVNAPVMMQRAVARMDDLRVD 300 +SK L + GER+GYI + S M + + + A R LG+V AP + Q+ VA+ + D Sbjct: 242 YSKSLSLPGERIGYIVVPSEMEEFNKVYAAICGAGRALGYVCAPSLFQKVVAKCAGITAD 301 Query: 301 ASAYKERRDLMVDILKEAGFEFEMPKGGFFVFPKSPIEDEVAFCVHAAQKYKLLIVPSSG 360 S YK+ RDL+ + L + G++ P+G F++FP++ +D AF A+KY LLIVP Sbjct: 302 ISIYKKNRDLLYEGLIKLGYKCVKPEGAFYLFPQALEKDAYAF-TEKAKKYDLLIVPGDD 360 Query: 361 FGMSGHFRLSFSVPIEQIKNSRDIFISLYKDF 392 FG GH R+S+ V +QI + F L K++ Sbjct: 361 FGCPGHVRISYCVTTDQILRALPAFEKLAKEY 392 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: 400 Number of extensions: 23 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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