Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_028321083.1 H567_RS0108520 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000422285.1:WP_028321083.1 Length = 379 Score = 234 bits (597), Expect = 3e-66 Identities = 131/362 (36%), Positives = 203/362 (56%), Gaps = 6/362 (1%) Query: 7 PSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGR- 65 P Y+R YI KP E+ + +G D + +L +NEN LG P AQR + + Sbjct: 11 PDYIRRFEAYIPSKPDPELKKLYGCDR--LYRLNNNENCLGPPPEAQRIIQRFPPPAAAV 68 Query: 66 YPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYAL 125 YP + + L+ AL+E +G D +GNG+N+++ F ++G +IV A ++AVY Sbjct: 69 YPSGDCYYLRTALAETFGKHPDQFIVGNGANEVITCVIKTFCQQGDNIVTADKTYAVYEW 128 Query: 126 ATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKV 185 + G A +VP + D AML + D T++ FV NPNNPTG++ + ++ AFLD V Sbjct: 129 VAEFSGLEARLVPLKDFEFDDQAMLERMDDRTKIAFVCNPNNPTGSYWDTERMRAFLDAV 188 Query: 186 PRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPEL 245 +VV+DEAY E++ Q D ++ + YPNL+V RTFSK +GLAGLR+G+ PE+ Sbjct: 189 DGRRIVVVDEAYCEFVDQPDYPDGMSLMEDYPNLVVFRTFSKMYGLAGLRIGYLAGSPEV 248 Query: 246 TDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSD 305 + + ++VN LAQ AA AA+ D +E++ ++ QG L ++ L V + Sbjct: 249 VQTIRKTMTVYSVNVLAQEAAQAAIRDAEHVERTRSMVRQGKDFLGRELARMHLPVVVGE 308 Query: 306 GNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALER 365 GNF++VR+ D R L+ +GV+VR + + P +RIT+ E EA + ALE+ Sbjct: 309 GNFMMVRLPISDTLAYR---RLMAEGVMVRTMTGFRFPNCIRITLSRMEALEALVEALEK 365 Query: 366 TL 367 L Sbjct: 366 IL 367 Lambda K H 0.318 0.135 0.385 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: 348 Number of extensions: 13 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: 370 Length of database: 379 Length adjustment: 30 Effective length of query: 340 Effective length of database: 349 Effective search space: 118660 Effective search space used: 118660 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 (21.7 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