Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_013420621.1 RVAN_RS15315 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000166055.1:WP_013420621.1 Length = 366 Score = 243 bits (621), Expect = 5e-69 Identities = 142/357 (39%), Positives = 203/357 (56%), Gaps = 8/357 (2%) Query: 8 SYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYP 67 S V AI PY+ G+ S++A E ++KL+SNE PLG A A AAS L RYP Sbjct: 11 SGVLAIDPYVPGR--SKLA-----GEGPVIKLSSNETPLGPSPHAVEAYRAAASHLDRYP 63 Query: 68 DANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALAT 127 D L+ A+ YG+ + GNGS+++ I A A++ G +Y ++ F VY +A Sbjct: 64 DGACTALREAIGAAYGLNPAHIICGNGSDELFHILAQAYLGPGDEAIYTEHGFLVYRIAI 123 Query: 128 QGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPR 187 GA +V P +D++L V+ T+ +F+ANPNNPTGT++ ++ +P Sbjct: 124 LAAGAEPVVAPEKNLTASVDSILECVTPRTKAVFIANPNNPTGTYLPHQEVRRLRAALPD 183 Query: 188 HVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTD 247 +V++VLD AY EY+ + I V PN +++RTFSK FGLA RVG+A A + D Sbjct: 184 NVLLVLDGAYAEYVNRNDYEAGIEMVATTPNTIMTRTFSKIFGLAAARVGWAYAPAAIAD 243 Query: 248 LLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGN 307 LNR+R PFN+ + AAIAAL DKA +E + A N +T F K+G + S GN Sbjct: 244 ALNRIRSPFNLAQPSMDAAIAALADKAHIEAAKAHNNTWRDIVTLEFRKMGFDVRSSAGN 303 Query: 308 FVLVRVGNDDA-AGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAAL 363 FVL+ G++ + L ++ +I+R V YGLP LR+TIGL EEN A +AAL Sbjct: 304 FVLIPFGSEQGRTAQDADAFLNERRIILRQVSAYGLPHALRMTIGLEEENRAVLAAL 360 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: 384 Number of extensions: 21 Number of successful extensions: 2 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: 366 Length adjustment: 30 Effective length of query: 340 Effective length of database: 336 Effective search space: 114240 Effective search space used: 114240 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