Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate BPHYT_RS27000 BPHYT_RS27000 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__BFirm:BPHYT_RS27000 Length = 392 Score = 200 bits (509), Expect = 5e-56 Identities = 121/359 (33%), Positives = 191/359 (53%), Gaps = 5/359 (1%) Query: 25 AQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADF 84 A+ EDVI L++G PDF TP + A +A+ T Y+ +G +R A+ + Sbjct: 29 ARGEDVIVLSVGDPDFATPAPIVERAIEALRGGDTHYSAVSGREPVRAAIAAEHTRMTGC 88 Query: 85 NYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT-T 143 A + +I+T GA + AA +L GDEVI+P P+Y YE + GA V V Sbjct: 89 AASA-ANVILTAGAQNGVFAASLCLLEAGDEVIVPEPMYLTYEACVRAAGATLVTVPVDA 147 Query: 144 SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIY 203 + F + +E A+T TK + P NPTGV + +L+ IA L +++VLSDE+Y Sbjct: 148 ARAFHVDCDALEAAVTSRTKAIFFATPCNPTGVVMQRADLERIARLACRHDLWVLSDEVY 207 Query: 204 SELTYDRPHYSIATY--LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNV 261 +ELT++R H SIA + ++T+ + LSKSH+M GWR+G+ P ++ +H+ ++ + Sbjct: 208 AELTFEREHVSIAALPGMAERTVTLGSLSKSHAMAGWRVGWAIGPTELIEHMGRLALAML 267 Query: 262 SCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIFPS 320 Q+AAL AV + A MRE Y++R D V++RL + GL + P ++ Sbjct: 268 YGLPGFIQQAALTAVQHKARIAAEMREIYRRRRDVVFERLHRVPGLRCLLPEAGMFMMVD 327 Query: 321 IKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELFV 379 + G+ + DF+ L GV+L+ S+F G+VRL F L + +R+ FV Sbjct: 328 VSGTGLDTVDFTWQLFRARGVSLLDASAFGETANGFVRLGFVVDEARLIDACERIAAFV 386 Lambda K H 0.319 0.135 0.388 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: 314 Number of extensions: 18 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: 393 Length of database: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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 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