Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate WP_010439728.1 G7G_RS0106455 aspartate aminotransferase family protein
Query= BRENDA::B1XNF8 (418 letters) >NCBI__GCF_000192475.1:WP_010439728.1 Length = 438 Score = 208 bits (529), Expect = 3e-58 Identities = 147/432 (34%), Positives = 224/432 (51%), Gaps = 47/432 (10%) Query: 26 HTYGRFPVAIAKGEGCRLWDTEGKSYLDFVAGIATCTLGHAHPALIQAVSAQIQKLHHIS 85 HT PVA A GEGC L D+ G+ YLD +C LGH++ +++AV Q++++ Sbjct: 8 HTKSELPVA-AGGEGCYLIDSTGRRYLDCGDAAVSC-LGHSNETVVKAVQQQVEQIAFAH 65 Query: 86 NLYYIPEQG-ALAQWIVEHSCAD--KVFFCNSGAEANEAAIKLVRKYAHTVSDFLEQPVI 142 + E ALA+ ++EH+ D +V+F + G+EA EAAIKL R+Y + + E+ + Sbjct: 66 TGFMTSEPAEALAELLIEHAPGDLDRVYFVSGGSEATEAAIKLARQY-YLETGQPERRHV 124 Query: 143 LSAKSSFHGRTLATITATGQPKYQKHFDPL----------------PDGFAYVPYNDIRA 186 ++ + S+HG TL ++A G + F P+ P+G + Y A Sbjct: 125 IARRQSYHGNTLGALSAGGNEWRRAQFAPMLIEMTHIAPCYEYAEKPEGESSYDYGQRVA 184 Query: 187 LEEAITDIDEGNRRVAAIMLEALQGEG-GVRPGDVEYFKAVRRICDENGILLVLDEVQVG 245 E + G V A M E + G G P YFK +R ICD+ G+LL+LDEV G Sbjct: 185 NELEAEILRLGPNTVMAFMAEPVVGATLGAVPAVEGYFKRIREICDQYGVLLILDEVMCG 244 Query: 246 VGRTGKYWGYENLGIEPDIFTSAKGLAGGI-PIGAMMCKDSC--AVFNPG---EHASTFG 299 +GRTG + ++ G+ PDI AKGL G PIGAM+C A+ N +H T+ Sbjct: 245 MGRTGHLFACDHDGVAPDILCIAKGLGAGYQPIGAMLCSARIYDAIQNGSGFFQHGHTYI 304 Query: 300 GNPFSCAAALAVVETLEQENLLENVNARGEQLRAGLKTLAEKYPYFSDVRGWGLINGMEI 359 G+P + AAALAVV L Q +L GE+L++ L T ++P+ D+RG GL G+E+ Sbjct: 305 GHPVATAAALAVVTELTQNDLPLRAALMGEKLQSALTTAFGQHPHVGDIRGRGLFRGIEL 364 Query: 360 KADLEL---------TSIEVVKAAMEKGLLLAPA--------GPKVLRFVPPLIVSAAEI 402 A+ E + ++ KAA +GL+ P G +L PP I+ +I Sbjct: 365 VANRETKTPFDPALGVAGKIKKAAFAEGLICYPMSGTRDGQHGDHIL-LAPPFIIEGKQI 423 Query: 403 NEAIALLDQTLA 414 +E +A LD+ ++ Sbjct: 424 DELVAKLDRAIS 435 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: 436 Number of extensions: 26 Number of successful extensions: 8 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: 438 Length adjustment: 32 Effective length of query: 386 Effective length of database: 406 Effective search space: 156716 Effective search space used: 156716 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 Jul 26 2024. The underlying query database was built on Jul 25 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