Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate Echvi_2919 Echvi_2919 Ornithine/acetylornithine aminotransferase
Query= BRENDA::Q0K2K2 (423 letters) >FitnessBrowser__Cola:Echvi_2919 Length = 393 Score = 201 bits (512), Expect = 2e-56 Identities = 131/406 (32%), Positives = 213/406 (52%), Gaps = 48/406 (11%) Query: 29 DRAENATLWDVEGRAYTDFAAGIAVLNTGHRHPRVMQAIAAQLERFTHTAYQIVPYQGYV 88 ++AE ++ +G Y D +GI V N GHRHP+V++AI QL+++ H ++ Y YV Sbjct: 24 EKAEGIYMYGPKGEKYIDLISGIGVSNVGHRHPKVLKAIQDQLDKYMH----LMVYGEYV 79 Query: 89 T-----LAERINALVPIQGLNKTALFTTGAEAVENAIKIARAHTGRPGVIAFSGAFHGRT 143 LA+ + +P + L+ L +G+EAVE A+K+A+ +TGR +++ A+HG + Sbjct: 80 QSPQTQLAKALTDTLP-KKLDNVYLVNSGSEAVEGALKLAKRYTGRREILSCVNAYHGSS 138 Query: 144 LLGMALTGKVAPYKIGFGPFPSDIYHAPF--PSALHGVSTERALQALEGLFKTDIDPARV 201 +++ G +K + P I H F P L ++ E Sbjct: 139 HGALSVGGNEI-FKRAYRPLLPGIRHLDFNEPDQLDQITEE------------------T 179 Query: 202 AAIIVEPVQGEGGFQAAPADFMRGLRAVCDQHGIVLIADEVQTGFGRTGKMFAMSHHDVE 261 AAI+VE VQGE G + ++ + LR CD+ G +LI DE+Q GFGRTGK +A H+D+ Sbjct: 180 AAIMVETVQGEAGIRVGTKEYFKALRHRCDETGTLLILDEIQAGFGRTGKFWAFQHYDIV 239 Query: 262 PDLITMAKSLAGGMPLSAVSGRAAIMDA----PLPGGLGGTYAGNPLAVAAAHAVIDVIE 317 PD++ AK + GGMP+ A +IM PL G + T+ G+P++ AAA A ID++ Sbjct: 240 PDIVVCAKGMGGGMPIGAFIAPQSIMSVFKNNPLLGHI-TTFGGHPVSCAAALATIDILR 298 Query: 318 EEKLCERSASLGQQLREHLLAQRKHCPAMAEVRGLGSMVAAEFCDPATGQPSAEHAKRVQ 377 +EKL + ++HL + P + E+R G M+A +F + E K + Sbjct: 299 DEKLIQHVERKANLFKKHL-----NHPKIQEIRNKGLMMAVKF-------EAFEVLKPII 346 Query: 378 TRALEAGLVLLTCGTYGNVIRFLYPLTIPQAQFDAALAVLTQALAE 423 RA+E G++ + +R PLTI + + A A++ Q++ E Sbjct: 347 DRAIELGIITDWFLFCEDSMRIAPPLTITDEEIEKACAIILQSIDE 392 Lambda K H 0.321 0.136 0.400 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: 358 Number of extensions: 25 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: 423 Length of database: 393 Length adjustment: 31 Effective length of query: 392 Effective length of database: 362 Effective search space: 141904 Effective search space used: 141904 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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