Align histidinol-phosphate aminotransferase (EC 2.6.1.9) (characterized)
to candidate WP_015944380.1 DHAF_RS15445 diaminopimelate aminotransferase
Query= reanno::Putida:PP_0967 (348 letters) >NCBI__GCF_000021925.1:WP_015944380.1 Length = 388 Score = 79.7 bits (195), Expect = 1e-19 Identities = 83/252 (32%), Positives = 120/252 (47%), Gaps = 20/252 (7%) Query: 85 GSDEVLAHIFHGLFQHDAPLLFPDISYSFYPVYCGLYGIAFEQVALDEQFQ-------IR 137 GS + LAHIF L L PD Y Y GL E+VAL + + Sbjct: 99 GSQDGLAHIFLALCDPGDVALIPDPGYPIYTA--GLVLAGGEKVALPLREENGFLPDLSA 156 Query: 138 IEDYKKPNAGIIFPN-PNAPTGCLMPLQAVEELLQANRDSVVVV--DEAYID--FGGETA 192 IED A I+F N PN PT + PL EE++ R + +VV D AY + F G Sbjct: 157 IEDEVAQQAKIMFLNYPNNPTAAVAPLSFFEEVVDFARRNRIVVCHDAAYSELAFDGYRP 216 Query: 193 ISLVD---RYDNLLVTQTLSKSRSLAGLRVGLAVGHPDLIEALERIKNSFNSYPLDRAAI 249 +S + + + ++SK+ +LAG+R+G AVG+ ++I AL +K++ + + A Sbjct: 217 VSFLQVPGAKEVGIEFHSVSKTYNLAGVRLGFAVGNGEIIGALAELKSNIDYGVFEPALQ 276 Query: 250 VGAAVAFEDREYFEETCRKVIDSREVLV-GQLQAKGFEVLPSAANFIFARHP-QQDAGEL 307 GA +E E+ R + R++ V G QA P + FI+A P QD+ Sbjct: 277 AGAYALSASQENVEQNRRAYQERRDIWVKGCAQAGWSMPSPRGSMFIWAPVPTAQDSRSF 336 Query: 308 A-ARLREQGVIV 318 A A RE GVIV Sbjct: 337 AFALAREAGVIV 348 Lambda K H 0.321 0.139 0.408 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: 340 Number of extensions: 22 Number of successful extensions: 3 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: 348 Length of database: 388 Length adjustment: 30 Effective length of query: 318 Effective length of database: 358 Effective search space: 113844 Effective search space used: 113844 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: 49 (23.5 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