Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate Ac3H11_3135 Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3135 Length = 394 Score = 191 bits (484), Expect = 4e-53 Identities = 121/357 (33%), Positives = 191/357 (53%), Gaps = 10/357 (2%) Query: 28 EDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADFNYD 87 E +I L IG+PDF P V+ AA +A+ T YT G LR+ + + + + N Sbjct: 34 EPMIFLNIGEPDFTAPPLVQEAAARAVHSGATQYTNALGLDALRERISSWYQSRFGVNVP 93 Query: 88 AESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDTTS-HG 146 A I++T GAS A+ A ++ GDE++MP P YP ++ K V++ TT+ Sbjct: 94 AR-RIVVTAGASAALQLACLALIESGDEILMPDPSYPCNRHFVSAAEGKAVLLPTTAAER 152 Query: 147 FKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIYSEL 206 ++L+A + A T+ V+L PSNPTG +++ +EL+ I +++ + + DEIY L Sbjct: 153 YQLSADKVRAAWNEKTRGVLLASPSNPTGTSIAPDELRRIHDVVRSHDGITMIDEIYLGL 212 Query: 207 TYDRPHYSIATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQYNVSCASS 266 +Y+ A + D I IN SK +MTGWR+G++ P+ + + ++ Q CAS+ Sbjct: 213 SYEEEFGHTALAIDDNIISINSFSKYFNMTGWRLGWMVVPEAMVPVVERLAQNLFICAST 272 Query: 267 ISQKAALEAV-TNGFDDALIMREQYKKRLDYVYDRLVSMGLDV-VKPSGAFYIF----PS 320 +SQ AAL + R ++K R D+ L +GL V VKP GAFY + + Sbjct: 273 VSQYAALACFEAESIAEYERRRAEFKARRDFFIPALEKLGLAVPVKPDGAFYAWADCTQA 332 Query: 321 IKSFGMT-SFDFSMALLEDAGVALVPGSSFSTYG-EGYVRLSFACSMDTLREGLDRL 375 + G+T S+DF+ L+ A +A+ PG F T+ E ++R S A SM L E + RL Sbjct: 333 AQRLGVTGSWDFAFELMRRAHIAVTPGRDFGTFDPERFIRFSTANSMAQLEESVARL 389 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: 276 Number of extensions: 14 Number of successful extensions: 4 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: 394 Length adjustment: 31 Effective length of query: 362 Effective length of database: 363 Effective search space: 131406 Effective search space used: 131406 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