Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_092481937.1 BM299_RS02765 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= metacyc::MONOMER-21143 (387 letters) >NCBI__GCF_900115975.1:WP_092481937.1 Length = 414 Score = 234 bits (596), Expect = 4e-66 Identities = 126/363 (34%), Positives = 212/363 (58%), Gaps = 4/363 (1%) Query: 25 LEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQAVTRKIKKLY 84 L A+ + +I LG+G+PDF TP H+ +A +L++G+ Y + G+LE R+AV +++ Y Sbjct: 28 LVAETRGVISLGVGEPDFVTPWHIREACIYSLEKGYTMYTSNWGLLELREAVAADLERTY 87 Query: 85 NKDIDPER-VLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYTGSTPVPYDL 143 N +P+ +LI G + A++ PG E++ P P++ Y G PV Sbjct: 88 NVKYNPKNEILITVGVSEALDLAMRALLVPGDEVLIPEPSYVSYAPCTTLAGGVPVFMPT 147 Query: 144 TEDKDLKFDPEKILSLITDKTRLLILINPNNPTGSFVEKSAIDVLAEGLKKHPHVAILSD 203 + + + + +++ S IT +T++L+L PNNPTG+ +E+ + +AE +H + ++SD Sbjct: 148 SMENNFRISADQVRSAITPRTKVLLLCYPNNPTGAVMEREELAKIAEVAVEHDLI-VISD 206 Query: 204 EIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRMGWSVWPEELIPHVNKLI 263 EIY R Y G E + P +Q+R ++L+G+SKAYAMTGWR+G++ + I + K+ Sbjct: 207 EIYDRLTYVG-EHTCLASLPGMQERTVLLNGFSKAYAMTGWRVGYAAGNPDFIGAMTKIH 265 Query: 264 INSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLNSLPGVECSLPGGAFY 323 S+ C Q A + AL + M+ +++RR L+ + + GV C PGGAFY Sbjct: 266 QYSMLCTPITGQMAALEALKNGQPGMRRMVGHYNRRRHLVVQAFRDM-GVPCFEPGGAFY 324 Query: 324 AFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKTCQDYVRFSYAASQDNISNALENIK 383 AFP+V TG+ EFA++ + + VA+VPG AFG++ + + R SYAAS D++S A + Sbjct: 325 AFPQVSVTGLGSEEFAEELLKQEQVALVPGNAFGRSGEGFARVSYAASLDDLSEAFRRMA 384 Query: 384 KML 386 + + Sbjct: 385 RFV 387 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: 425 Number of extensions: 30 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: 387 Length of database: 414 Length adjustment: 31 Effective length of query: 356 Effective length of database: 383 Effective search space: 136348 Effective search space used: 136348 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