Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate Ac3H11_1332 Acetylornithine aminotransferase (EC 2.6.1.11)
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1332 Length = 398 Score = 267 bits (683), Expect = 3e-76 Identities = 158/398 (39%), Positives = 226/398 (56%), Gaps = 16/398 (4%) Query: 11 ALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAV 70 A +EA Y + + + RGQG RVWD G EYID +GG V LGH + ++V A+ Sbjct: 3 AFIEAASPHVMNTYGRVPIALERGQGCRVWDVNGKEYIDGLGGIAVNTLGHNHGKLVPAL 62 Query: 71 KRQAETLMAMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAH--- 127 + Q L+ P++ + L + + VF NSG EANEAALK AR Sbjct: 63 QDQIAKLIHTSNYYHVPLQEKLATKLVEL--SGMQNVFFCNSGLEANEAALKIARKFGVD 120 Query: 128 --TGRKKFVAAMRGFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKRAVD-- 183 + + V + F GR++ ++S T PK F PLVE +P ND+EA+K+A + Sbjct: 121 KGIAKPEIVVYEKAFHGRSIATMSATGNPKIHNGFGPLVEGFVRVPMNDIEAIKQATEGN 180 Query: 184 EETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHF 243 AV E +QGEGG+ E+L+ R++ E+G L+++DE+Q GMGRTGK FA + Sbjct: 181 PNVVAVFFETIQGEGGINGMRIEYLQQLRKLCDERGWLMMIDEVQCGMGRTGKWFAHQWA 240 Query: 244 GIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLER 303 GIVPD++ LAK LG GVP+GA V + A + G HGTTFGGNPLAM AGV IR +E Sbjct: 241 GIVPDVMPLAKGLGSGVPIGAVVAGPKAANVLQPGNHGTTFGGNPLAMRAGVETIRIMEE 300 Query: 304 TRLWERAAELGPWFMEKL-RAIPS-PKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVL 361 L AA++G L R + S P ++E+RG GLM+G+EL + I R + +L Sbjct: 301 DGLLHNAAQVGDHLRAALQRELGSLPGVKEIRGQGLMLGIELNKPCGALIGRAAEAGLLL 360 Query: 362 ALQAGPTVIRFLPPLVIEKEDLERVV----EAVRAVLA 395 ++ A +VIR +PPL++ + + +V V+A+LA Sbjct: 361 SVTA-DSVIRLVPPLILTTAEADAIVAILTPLVKAILA 397 Lambda K H 0.319 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: 418 Number of extensions: 22 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: 398 Length adjustment: 31 Effective length of query: 364 Effective length of database: 367 Effective search space: 133588 Effective search space used: 133588 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 Aug 03 2021. The underlying query database was built on Aug 03 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