Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_086508681.1 BZY95_RS03940 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_002151265.1:WP_086508681.1 Length = 351 Score = 159 bits (402), Expect = 1e-43 Identities = 121/368 (32%), Positives = 186/368 (50%), Gaps = 28/368 (7%) Query: 3 ASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQ-AAS 61 + F VR + PY+ G+ E ++KL +NENP + A+ + Sbjct: 2 SQFWSPAVRELTPYVPGEQPRE----------KLIKLNTNENPYPPAPGVEAALREYPVD 51 Query: 62 ELGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFV--EKGQSIVYAQYS 119 L YPD + L+ AL+ +GV + V +GNGS+++L +A AF E+ + YS Sbjct: 52 HLRLYPDPQSLALRQALAREHGVAVEQVFVGNGSDEVLALAFQAFFCHERPLEMPDITYS 111 Query: 120 FAVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLE 179 F G+ R++ + ++ DLDA A D IF ANPN PT + Sbjct: 112 FYPVYCKLYGIERRSLPLDD-RWRVDLDAFTA---DSGGAIF-ANPNAPTAHGHPRDAIA 166 Query: 180 AFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFA 239 L+++ VV+V DEAY ++ + + + R+PNLLV+ TFSK+ LAGLR+G+A Sbjct: 167 GLLERLTDQVVLV-DEAYVDFGGESV----VPLIERFPNLLVTGTFSKSRSLAGLRLGYA 221 Query: 240 IAQPELTDLLNRVRQPFN---VNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDK 296 I EL + L RV+ FN +++LA A AIA+L D+ + R + Sbjct: 222 IGSSELIEGLVRVKDSFNSYPIDSLASALAIASLEDREHFDACRERVVTTRERTVRRLGE 281 Query: 297 LGLEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEEN 356 LG E +PS NFVL R DAA ++ + L ++G++VR L +LRI+IG +E Sbjct: 282 LGFEVLPSQANFVLARHPEHDAA--QLFVGLRERGILVRHFNTEALRDFLRISIGTDDEM 339 Query: 357 EAFIAALE 364 ++ I A E Sbjct: 340 DSLIEAFE 347 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: 325 Number of extensions: 20 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: 370 Length of database: 351 Length adjustment: 29 Effective length of query: 341 Effective length of database: 322 Effective search space: 109802 Effective search space used: 109802 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: 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