Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_207545101.1 BM299_RS02525 4-aminobutyrate--2-oxoglutarate transaminase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_900115975.1:WP_207545101.1 Length = 434 Score = 326 bits (835), Expect = 9e-94 Identities = 180/429 (41%), Positives = 258/429 (60%), Gaps = 29/429 (6%) Query: 6 ISQSIAIVHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLT 65 I++ I+ + + + A + D +GK YIDF GGIG LN GHC VVEAI+ QA +L Sbjct: 16 IARGISNSTEVFVEKAQGATIVDVEGKEYIDFYGGIGTLNAGHCPAPVVEAIKNQAEKLL 75 Query: 66 HYAFNAAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAF 125 H F + PYL L E+L + P ++ M NSGAE ENA+K+AR + II+F Sbjct: 76 HTCFMVTMYEPYLDLAEKLIELTPGNFDKRVMFVNSGAECVENAVKIARSYAKRTGIISF 135 Query: 126 DGGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLP------------YPSADTGVTCEQ 173 + FHGRTL T++L KV PYK G VY +P YP + G+ C Sbjct: 136 ECAFHGRTLMTMSLTSKVKPYKFGFGPFAPEVYKIPSAYCYRCTYRSTYP--ECGLHC-- 191 Query: 174 ALKAMDRLFSVELAVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQ 233 L+ DR+F+ E+ E++AA I EPVQGEGGF+ P F LR+ CD+ GI++I DE+Q Sbjct: 192 -LEQFDRMFAAEVPPENIAAMIIEPVQGEGGFIVPPPEFLPGLRKICDKHGIILIADEVQ 250 Query: 234 SGFGRTGQRFAFPRLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNP 293 +GFGRTG+ FA G+EPDL+ +AKSIA GMPL AVVG+ ++M A G +GGTYSGNP Sbjct: 251 TGFGRTGKMFACEHFGLEPDLMTMAKSIAAGMPLSAVVGKADIMNAPNPGEIGGTYSGNP 310 Query: 294 ISCAAALASLAQMTDENLA----TWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRG 349 +SCAA LA++ M +NL G++ +Q +++ E++ P IG + G+GAM Sbjct: 311 VSCAAGLATIDFMQQQNLVERANVIGDKTKQRMLAMQEKY------PIIGDVRGLGAMNA 364 Query: 350 IEFANADGS--PAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDI 407 +E + PA + A V++ G++++ +G +++R L PL I E LE+GLD+ Sbjct: 365 MELVKDRNTKEPAKEETAAVIKHCVDNGVIVIGAGIFSNVVRTLIPLVITDEQLEKGLDV 424 Query: 408 LEQCLAELN 416 LEQ +A ++ Sbjct: 425 LEQAVASVS 433 Lambda K H 0.320 0.137 0.402 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: 461 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: 416 Length of database: 434 Length adjustment: 32 Effective length of query: 384 Effective length of database: 402 Effective search space: 154368 Effective search space used: 154368 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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