Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate 8499751 DvMF_0516 aminotransferase class-III (RefSeq)
Query= BRENDA::B1XNF8 (418 letters) >FitnessBrowser__Miya:8499751 Length = 459 Score = 191 bits (485), Expect = 4e-53 Identities = 130/370 (35%), Positives = 194/370 (52%), Gaps = 47/370 (12%) Query: 29 GRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCT-LGHAHPALIQAVSAQIQKLHHIS-- 85 G+ P+ + +GEG L D GK YLD +G C +G+ + +AV Q++ + + + Sbjct: 32 GKGPMIVVEGEGLTLRDINGKEYLDATSGGVWCVNVGYGRERIARAVYEQMKAMPYYAAT 91 Query: 86 --NLYYIPEQGALAQWIVEHSCA-DKVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142 N+ YI AQ ++ H + + NSG+EANE A K+VR AH + ++ ++ Sbjct: 92 AGNIPYIE----FAQKLLAHMPGLTRAYLSNSGSEANEKAYKMVRSLAHLSGNPAKKKIL 147 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPLPDGFAYVPYN--------------DI---R 185 A+ +HG TL +++TGQ + ++ F PL GF P+ DI R Sbjct: 148 FRARD-YHGTTLGALSSTGQAERKEWFGPLVPGFVEFPHACCYRCAFNKTYPGCDIDCAR 206 Query: 186 ALEEAITDIDEGNRRVAAIMLEALQGEGGVRPGDVEYFKAVRRICDENGILLVLDEVQVG 245 A+E I EG V +++E + GGV P EY+ + IC +G+LL++DEV G Sbjct: 207 AVERIIEQ--EGPETVGGLIVEPITAGGGVIPPVAEYYTVLADICRRHGVLLIMDEVVCG 264 Query: 246 VGRTGKYWGYENLGIEPDIFTSAKGLAGG-IPIGAMMC------------KDSCAVFNPG 292 +GRTG +GY++ G+ PDI T AKG+A +PI D A F Sbjct: 265 MGRTGTMFGYQHYGVTPDIVTMAKGVASAYMPISVTATTEEVFKAFLNDPADKMAYF--- 321 Query: 293 EHASTFGGNPFSCAAALAVVETLEQENLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWG 352 ST+GG C+AAL + +E+E LL+NVNA G+ L AGLK L + PY DVRG G Sbjct: 322 RDISTYGGCAAGCSAALENMAIIEEEKLLDNVNAMGDYLLAGLKELGD-LPYVGDVRGKG 380 Query: 353 LINGMEIKAD 362 L+ G+E+ D Sbjct: 381 LLCGIELVQD 390 Lambda K H 0.319 0.136 0.406 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: 457 Number of extensions: 23 Number of successful extensions: 7 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: 418 Length of database: 459 Length adjustment: 32 Effective length of query: 386 Effective length of database: 427 Effective search space: 164822 Effective search space used: 164822 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 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