Align acetylornithine/N-succinyldiaminopimelate aminotransferase [EC:2.6.1.11 2.6.1.17] (characterized)
to candidate WP_025273703.1 HALAL_RS0109075 diaminobutyrate--2-oxoglutarate transaminase
Query= reanno::azobra:AZOBR_RS19025 (389 letters) >NCBI__GCF_000527155.1:WP_025273703.1 Length = 425 Score = 145 bits (365), Expect = 3e-39 Identities = 119/395 (30%), Positives = 170/395 (43%), Gaps = 42/395 (10%) Query: 15 VFERGEGPYLYATDGRRFLDFAAGVAVNVLGHANPYLVEALTAQAHKLWHTSNLFRVAGQ 74 VF G + G+ ++DF AG GH NP + + L + N+ Sbjct: 21 VFTTARGSKMSDEAGKEYIDFFAGAGSLNYGHNNPEIKKKLLEYLAE----DNVIHTLDT 76 Query: 75 ESLAKRLTEATFADTV-----------FFTNSGAEAWECGAKLIRKYHYEKGDKARTRII 123 S AKR TF + + F +G A E KL RKY R +I Sbjct: 77 YSTAKREFLKTFDELILQPRGMDYKMMFPGPAGNNAVEGALKLARKY------TGRETVI 130 Query: 124 TFEQAFHGRTLAAVSAAQQEKLIKGFGPLLDGFDLVPFG--------DLEAVRNAVTDET 175 +F FHG TL A++ G G L+ +PF D +R + D Sbjct: 131 SFTNGFHGMTLGALAVTGNSMKRGGAGVPLNNTATMPFDGYMDGQTPDFLWLRTLLEDPG 190 Query: 176 AG------ICLEPIQGEGGIRAGSVEFLRGLREICDEHGLLLFLDEIQCGMGRTGKLFAH 229 +G + +E +QGEGGI S E+L+GL+E+C +H +LL +D+IQ G GRTG F+ Sbjct: 191 SGLDKPAAVIVETVQGEGGINVASPEWLKGLQEVCHDHDVLLIVDDIQMGCGRTGSYFSF 250 Query: 230 EWAGITPDVMAVAKGIGG-GFPLGACLATEKAASGMTAGTHGSTYGGNPLATAVGNAVLD 288 E AGI PD++ ++K + G G PL L + G H T+ G A A L+ Sbjct: 251 EEAGIKPDIITLSKSLSGIGLPLAVTL-MRRELDVWDPGEHNGTFRGFAPAFVTATAALE 309 Query: 289 KVLE-PGFLDHVQRIGGLLQDRLAGLVAENPAVFKGVRGKGLMLGLACGPA--VGDVVVA 345 + F V G L ++L +V E P + RG+GL L A + Sbjct: 310 TYWKNDAFAKSVVAQGEWLHEQLEAIVREFPGLGLSTRGRGLARALEFSVAEHADETAAE 369 Query: 346 LRANGLLSVPAG--DNVVRLLPPLNIGEAEVEEAV 378 GLL G D V++ LPPLN + E E + Sbjct: 370 SFKQGLLMETCGAEDEVIKFLPPLNTTQEEFIEGL 404 Lambda K H 0.321 0.139 0.414 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: 441 Number of extensions: 27 Number of successful extensions: 5 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: 389 Length of database: 425 Length adjustment: 31 Effective length of query: 358 Effective length of database: 394 Effective search space: 141052 Effective search space used: 141052 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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