Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate Echvi_3848 Echvi_3848 Ornithine/acetylornithine aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__Cola:Echvi_3848 Length = 381 Score = 243 bits (621), Expect = 5e-69 Identities = 146/375 (38%), Positives = 213/375 (56%), Gaps = 8/375 (2%) Query: 23 VYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQ 82 VY D+ V+ G+ +WD +GNEY+D GG+ V ++GH +P + +K Q + + Sbjct: 6 VYPLIDVTPVKASGSTIWDDQGNEYLDLYGGHAVISIGHSHPHYTKRIKEQLDNIAFYSN 65 Query: 83 TLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRKKFVAAMRGFSG 142 ++ P++ E L + +F NSG EANE ALK A TG+K F+A +GF G Sbjct: 66 SVQIPIQKELATKLGQLSGYPDYDLFLCNSGAEANENALKLASFETGKKGFIAFTKGFHG 125 Query: 143 RTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVDEET-AAVILEPVQGEGGVR 201 RT G++++T PK PF E V +P+ND+EA+++ + T A VI+E +QG GG++ Sbjct: 126 RTSGAVALTDNPKIIAPF-NAHEGVHILPFNDLEAVEKQLATGTIAGVIVEGIQGVGGIQ 184 Query: 202 PATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHF-GIVPDILTLAKALGGGV 260 P FL +T++ GA LILDE+Q+G R+GK FA + G+ PD++T+AK +G G Sbjct: 185 VPDPAFLLGLSALTKQYGAKLILDEVQSGYARSGKFFAHQWVEGLKPDLITVAKGMGNGF 244 Query: 261 PLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEK 320 P+G ++ E S G GTTFGGN LA AA +A + ++ L AAE G M Sbjct: 245 PIGGVLISPEFKAS--HGLLGTTFGGNHLACAAALAVLEVIDEENLITAAAENGKAIMAA 302 Query: 321 LRAIPSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQA-GPTVIRFLPPLVIE 379 L + + EVRG GLM+G +L +A P A L EH++ A G IR LPPL IE Sbjct: 303 LEKVAG--VTEVRGKGLMIGFDLATEAGPVRAALIHEHKIFTGSAGGKHTIRLLPPLNIE 360 Query: 380 KEDLERVVEAVRAVL 394 + L +E + VL Sbjct: 361 PKALTLFLEKLETVL 375 Lambda K H 0.319 0.137 0.403 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: 348 Number of extensions: 13 Number of successful extensions: 6 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: 395 Length of database: 381 Length adjustment: 30 Effective length of query: 365 Effective length of database: 351 Effective search space: 128115 Effective search space used: 128115 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 09 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