Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_092991509.1 BLP65_RS00425 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_900102855.1:WP_092991509.1 Length = 368 Score = 361 bits (926), Expect = e-104 Identities = 187/360 (51%), Positives = 252/360 (70%), Gaps = 7/360 (1%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 VR + PY GKPI E+ RE G+ A VKLASNENPLG A A +A +++G YPD Sbjct: 12 VRGLQPYQPGKPIEELERELGITNA--VKLASNENPLGPSPLAVEAGRKAMTDVGLYPDG 69 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 N F LK L+ER GV + +TLGNGS+DILE AFV+ G ++++++++FA+Y + Sbjct: 70 NGFRLKQKLAERIGVAMERITLGNGSSDILEFVVRAFVQPGDTVLFSEHAFAIYPILAMT 129 Query: 130 LGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHV 189 + A+ + VPA ++GHDL AM AA++ +T+++FVANPNNPTGT++ G +LEAF+ K+P Sbjct: 130 VSAKPVSVPAREWGHDLAAMAAAITPETKVVFVANPNNPTGTWLRGDELEAFIAKMPAET 189 Query: 190 VVVLDEAYTEYLPQ-EKRY-DSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTD 247 VVV+DEAY EY + E Y D++AWV +YPNL+VSRTFSK GLAGLRVG+ I+ P + D Sbjct: 190 VVVVDEAYFEYGRRLESDYPDAVAWVEKYPNLVVSRTFSKCHGLAGLRVGYGISHPGVAD 249 Query: 248 LLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGN 307 LLNRVR PFNVN++A AAA AAL+D A L ++ +NA+G ++L FD LGL Y+ S GN Sbjct: 250 LLNRVRPPFNVNSVALAAAEAALDDDAHLSRTLEVNAEGMKQLAAGFDTLGLSYIGSVGN 309 Query: 308 FVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTL 367 F+ V VG + V LL++GVIVRP+ YG+P LRITIG E+NE + AL L Sbjct: 310 FISVNVGRE---AGPVYEALLREGVIVRPIAGYGMPDHLRITIGAAEQNERVLTALNTVL 366 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: 435 Number of extensions: 18 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: 368 Length adjustment: 30 Effective length of query: 340 Effective length of database: 338 Effective search space: 114920 Effective search space used: 114920 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