Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate GFF1996 PGA1_c20300 aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Phaeo:GFF1996 Length = 382 Score = 155 bits (391), Expect = 2e-42 Identities = 111/361 (30%), Positives = 179/361 (49%), Gaps = 17/361 (4%) Query: 30 VISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAV-QLYMKKKADFNYDA 88 +I + +GQP P + A KA+D + YT G LR+ + QLY + +N D Sbjct: 31 IIHMEVGQPSTGAPVAAREALAKALDHDSLGYTVALGLPALRKRIAQLYGEW---YNVDL 87 Query: 89 ESE-IIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTSHGF 147 E ++IT G+S A +F + GD V + P YP Y I++ G PV ++T+ Sbjct: 88 NPERVVITPGSSGAFLLSFTALFDSGDRVGIGAPGYPSYRQILHALGLTPVDIETS---- 143 Query: 148 KLTARLI---EDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYS 204 L RL +D + +++ P+NPTG L + + ++ +G+ +SDEIY Sbjct: 144 -LDHRLQPVPQDLTGLDLAGLMVASPANPTGTMLDKPAMAALIDAAQGQGAAFISDEIYH 202 Query: 205 ELTYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCA 264 + Y+ + A + D+ VIN SK SMTGWR+G++ P+D + + ++ Q CA Sbjct: 203 GIEYEAKAVT-ALEVTDECYVINSFSKYFSMTGWRVGWMVVPEDHVRVVERIAQNMFICA 261 Query: 265 SSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSMGLD-VVKPSGAFYIFPSIKS 323 SQ AAL A+ + D+ Y + + + L G D + P GAFY++ + Sbjct: 262 PHASQVAALAAM-DCRDELEGNLAVYARNRALMLEGLPKAGFDRIAPPDGAFYVYADVSE 320 Query: 324 FGMTSFDFSMALLEDAGVALVPGSSFS-TYGEGYVRLSFACSMDTLREGLDRLELFVLKK 382 S F+ +L++AGVA+ PG F G +R S+A + + EGL RL F+ + Sbjct: 321 LTHDSRAFAQEILDEAGVAVTPGLDFDPKRGATTLRFSYARATADIEEGLTRLAAFMAAR 380 Query: 383 R 383 R Sbjct: 381 R 381 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: 343 Number of extensions: 27 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: 382 Length adjustment: 30 Effective length of query: 363 Effective length of database: 352 Effective search space: 127776 Effective search space used: 127776 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