Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_043743334.1 AMB_RS03565 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000009985.1:WP_043743334.1 Length = 386 Score = 171 bits (434), Expect = 2e-47 Identities = 112/358 (31%), Positives = 180/358 (50%), Gaps = 15/358 (4%) Query: 34 VALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSVTP-E 92 V L G P+ P V A AL G +Y G P+LR+A+A RR G + P Sbjct: 29 VNLGQGFPEGLEPADVVARAAEALVAGPNQYPSMMGTPDLRQAIARHERRFYGTELDPMA 88 Query: 93 ETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFVP 152 E +VT G +AL + +++PGDEV+++ P + SY ++R AGG+ V P +P Sbjct: 89 EVMVTSGATEALADCLFGLIEPGDEVVLIEPLYDSYLPIIRRAGGIPKLVRVEPPHWDLP 148 Query: 153 DPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYE 212 E + A +PRTK +++N+P NP+G V+ ++ + +A L D Y V DE+YEHL+Y+ Sbjct: 149 R-ETLAAAFSPRTKLMILNTPMNPSGKVWSRDEMAFVAGLLERFDAYCVCDEVYEHLVYD 207 Query: 213 GEHFSPGRVAP---EHTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPDT 269 G P P E L + A K F++TGW++G+ +++ +A V T + Sbjct: 208 GRRHLPLMTLPGMRERCLKIGSAGKIFSLTGWKVGWVVAAPDLLAPLAKVHQYLTFATPP 267 Query: 270 IAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSP 329 Q A L ++ ++ + RRD L EGL +G + + G++++ D P Sbjct: 268 NLQSAVAWGLDKED---SYYDGLAAMLAERRDRLAEGLRGVGFEVMAAGGSYFLTADFRP 324 Query: 330 I--APDEVRAAERLLE-AGVAVVPGTDFAAFGHV----RLSYATSEENLRKALERFAR 380 + A D+ + E AGVA +P + F G V R +A +E + +A+ R R Sbjct: 325 LGFAGDDDDFCRHITEKAGVAAIPISTFYQGGDVDHFARFCFAKTESAIDEAVMRLRR 382 Lambda K H 0.317 0.133 0.379 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: 354 Number of extensions: 22 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: 385 Length of database: 386 Length adjustment: 30 Effective length of query: 355 Effective length of database: 356 Effective search space: 126380 Effective search space used: 126380 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