Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_015799315.1 AFER_RS10005 aminotransferase class V-fold PLP-dependent enzyme
Query= curated2:O33822 (383 letters) >NCBI__GCF_000023265.1:WP_015799315.1 Length = 383 Score = 204 bits (518), Expect = 4e-57 Identities = 125/358 (34%), Positives = 192/358 (53%), Gaps = 15/358 (4%) Query: 34 VALTAGEPDFDTPEHVKEAGRRALAQGKTKYAPPAGIPELREAVAEKFRRENGLEVTP-E 92 + L G PD P EAG R+L G +YAP G+PELR VA + + G + P Sbjct: 20 INLGQGFPDTPGPALAIEAGVRSLRAGHNQYAPAGGVPELRTRVASIWSQRLGRPIDPLR 79 Query: 93 ETIVTVGGKQALFNLFQAILDPGDEVIVLAPYWVSYPEMVRFAGGVPVEVPTLPEEGFVP 152 + +TVG +A+ A L+PGDE IVL P + +Y VR AG PV V Sbjct: 80 DVTITVGATEAIAAACLAWLEPGDEAIVLEPAYDAYLWAVRMAGATPVGVDLGSTMRL-- 137 Query: 153 DPERVRRAITPRTKALVVNSPNNPTGVVYPEEVLRALAEMALQHDFYLVSDEIYEHLIYE 212 D ER+ +AITPRT+ L+VNSP+NP+G+V +E L A++ +A +HD ++SDE+YE L+YE Sbjct: 138 DAERLEQAITPRTRMLIVNSPHNPSGMVVSDEELAAISAVATRHDLRVLSDEVYEFLVYE 197 Query: 213 GAHFSPGTL--APEHTITVNGAAKAFAMTGWRIGYACGPKAVIKAMADVSSQSTTSPDTI 270 G+H S T + T+ V+ AAK F +TGW++G+A GP ++ + + T + T Sbjct: 198 GSHRSIATFDAMADRTVVVSSAAKTFGLTGWKVGWAIGPADLVSEVRSQAQYLTYAGATP 257 Query: 271 AQWATLEALTNREASMAFIAMAREAYRKRRDLLLEGLSRIGLEAVRPSGAFYVLMDTSPF 330 Q A +AL N + + + R+ ++RD+L++GL+++G + ++VL D P Sbjct: 258 LQHAVADALGNLD---LIVPLVRDPLARQRDVLVDGLAKLGFTPLATQAGYFVLTDLGPV 314 Query: 331 APNEVEAAERLL--MAGVAVVPGTEFAAFGH-----VRLSYATGEENLKKALERFAQA 381 A +L AG+ +P F +R S+A L+ AL + +A Sbjct: 315 EAETATEAALILAERAGIVTIPIEPFYVEPERAPLVLRWSFARQATTLRDALAQLRRA 372 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: 382 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: 383 Length adjustment: 30 Effective length of query: 353 Effective length of database: 353 Effective search space: 124609 Effective search space used: 124609 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 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