Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_041565154.1 NPUN_RS02975 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O33822 (383 letters) >NCBI__GCF_000020025.1:WP_041565154.1 Length = 388 Score = 180 bits (456), Expect = 7e-50 Identities = 131/393 (33%), Positives = 201/393 (51%), Gaps = 20/393 (5%) Query: 1 MRGLSQRVKSMKPSATVAVNARALELRRKGVDLVALTAGEPDFDTPEHVKEAGRRALAQ- 59 M L+ R++ ++ V EL + ++L G ++ P E + LA Sbjct: 1 MESLTSRMQDVQSPIIPVVG----ELIKNSPGTISLGQGVVHYNPPPEAIEFLSKFLADP 56 Query: 60 GKTKYAPPAGIPELREAVAEKFRRENGLEVTPEETIV-TVGGKQALFNLFQAILDPGDEV 118 Y GIP L A+A K + NG+E+ E IV T G N AI +PGDE+ Sbjct: 57 ANNLYKSVEGIPPLLTAIAGKLQAFNGIEINGENCIVVTAGSNMGFMNAILAITNPGDEI 116 Query: 119 IVLAPYWVSYPEMVRFAGGVPVEVPTLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTG 178 I+ PY+ ++ + AG V V T +E + PE + +AITP+T+A+V SPNNPTG Sbjct: 117 ILNTPYYFNHEMAIAIAGCRAVLVAT--DENYQLRPEAIAQAITPKTRAIVTISPNNPTG 174 Query: 179 VVYPEEVLRALAEMALQHDFYLVSDEIYEHLIYEGA-HFSPGTLA-PEHTITVNGAAKAF 236 VVY E LR + ++ H Y +SDE Y++ Y G H SPG ++TI++ +KA+ Sbjct: 175 VVYSEAALRQVNQICDTHRIYHISDEAYQYFTYNGVKHVSPGAFGKSKYTISLFSLSKAY 234 Query: 237 AMTGWRIGYACGPKAVIKAMADVSSQSTTSPDTIAQWATLEALTNREASMAFIAMAREAY 296 WRIGY PK + A+ V P I+Q+A L AL +A ++ A Sbjct: 235 GFASWRIGYMVIPKHLFVAIKKVQDTILICPPVISQYAALGAL---QAKEEYLQSNIGAI 291 Query: 297 RKRRDLLLEGLSRI-GLEAVRP-SGAFYVLMDTSPFAPNEVEAAERLLMA-GVAVVPGTE 353 + R L+L+ L+R+ GL ++ P +GAFY + + + E +RL+ VAV+PGT Sbjct: 292 FQVRQLVLDSLNRLEGLCSITPANGAFYFFLKVNT-QMDAFELVKRLIQEHKVAVIPGTT 350 Query: 354 FAAFG--HVRLSY-ATGEENLKKALERFAQALQ 383 F ++R++Y A +E K+ +ER Q L+ Sbjct: 351 FGMDDGCYLRVAYGALQKETAKEGIERLVQGLE 383 Lambda K H 0.317 0.133 0.382 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: 380 Number of extensions: 26 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: 383 Length of database: 388 Length adjustment: 30 Effective length of query: 353 Effective length of database: 358 Effective search space: 126374 Effective search space used: 126374 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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