Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_015948152.1 G491_RS0110270 pyridoxal phosphate-dependent aminotransferase
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_000429905.1:WP_015948152.1 Length = 380 Score = 223 bits (568), Expect = 7e-63 Identities = 124/386 (32%), Positives = 204/386 (52%), Gaps = 9/386 (2%) Query: 1 MKLAKNLQRLGTESAFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGH 60 M ++K + ++ VL AK +E G ++HL +G+PDF TP+ + +A KAL +G+ Sbjct: 1 MTVSKRVDQITPFIVMEVLERAKAMERDGVNIVHLEVGEPDFDTPECITEAGIKALRDGY 60 Query: 61 HGYVLSNGILECRQAVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHP 120 Y S GILE R+A+ Y +++P+ +++ G P ++ E G E+I Sbjct: 61 SHYTHSLGILELREAIAEHYYNEYGVEVNPDHIVVTNGTSPGIFMTFAALLEAGDEVIVS 120 Query: 121 TPAFPIYESMINYTGSTPVPYDLTEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFV 180 P + Y + I + G+ PV +TE++ ++ E+I +TD+T+ +++ +P+NPTG+ + Sbjct: 121 DPHYACYPNFIEFAGAKPVKVAVTEEEGFQYRAEQIQKHMTDRTKAVMINSPSNPTGNLL 180 Query: 181 EKSAIDVLAEGLKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYA 240 + +A+ K ++SDEIY +Y+GKE + D VL+G+SKAYA Sbjct: 181 SPERMQQVADLGK-----VVVSDEIYHGLVYEGKERSIL----EFTDEAFVLNGFSKAYA 231 Query: 241 MTGWRMGWSVWPEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRR 300 MTGWR+G+ + P+ I + KL N NA +Q AGIAAL + M +DQRR Sbjct: 232 MTGWRLGYLIAPKRFIRPLQKLQQNFFISANAMTQMAGIAALKEAGPDVARMREIYDQRR 291 Query: 301 KLIHEGLNSLPGVECSLPGGAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTC 360 + + L + P GAFY G + + A + A V + PG FG+ Sbjct: 292 RFMIRRLREIGLGITVEPTGAFYVLANARHLGSDSYKMAFDILENAHVGVTPGIDFGQQA 351 Query: 361 QDYVRFSYAASQDNISNALENIKKML 386 + Y+RFSYA S +NI + ++K + Sbjct: 352 EGYIRFSYANSLENIEEGMNRLEKYI 377 Lambda K H 0.319 0.137 0.414 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: 18 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: 387 Length of database: 380 Length adjustment: 30 Effective length of query: 357 Effective length of database: 350 Effective search space: 124950 Effective search space used: 124950 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 (21.7 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