Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate GFF1396 HP15_1363 histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Marino:GFF1396 Length = 374 Score = 402 bits (1032), Expect = e-116 Identities = 205/361 (56%), Positives = 264/361 (73%), Gaps = 3/361 (0%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 V+A++PY GKPI E+ARE GL+ A I+KLASNENPLG E A A +A SEL YPD Sbjct: 13 VQALSPYQPGKPIEELARELGLNPAEIIKLASNENPLGPSEKALSAARRALSELCLYPDG 72 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 N F LK ALS R V D +TLGNGSND+LE+ F + +V++QY+FAVY L TQ Sbjct: 73 NGFNLKQALSTRLNVGMDQITLGNGSNDVLEVITRCFADADSEVVFSQYAFAVYPLVTQA 132 Query: 130 LGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHV 189 +GAR + VPA ++GHDLDAM AAV+D TRL+FVANPNNPTGT +EAFL K+P +V Sbjct: 133 IGARGVSVPAREWGHDLDAMAAAVTDRTRLVFVANPNNPTGTVHTAEAIEAFLKKIPENV 192 Query: 190 VVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLL 249 +VVLDEAY EYL ++ D + + R+PNL+V RTFSKA+GLA LRVG++I+ P + D+L Sbjct: 193 LVVLDEAYCEYLTGDQYPDGVELLARFPNLIVCRTFSKAWGLAALRVGYSISSPAIADIL 252 Query: 250 NRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFV 309 NRVRQPFNV+T+A +AA A L+D+ +L++S +N G R+L EAFD++GL Y+PS GNFV Sbjct: 253 NRVRQPFNVDTVALSAATAVLDDEDYLQRSRDVNTAGLRQLQEAFDRMGLGYIPSAGNFV 312 Query: 310 LVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTLAA 369 V VG + A G V LL GVIVRP+ YG+P+ LR+++GLPEENE FI AL + L A Sbjct: 313 AVEVG-EQAMG--VYQALLAHGVIVRPIAGYGMPRHLRVSVGLPEENERFIEALAQALTA 369 Query: 370 A 370 + Sbjct: 370 S 370 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: 407 Number of extensions: 9 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: 374 Length adjustment: 30 Effective length of query: 340 Effective length of database: 344 Effective search space: 116960 Effective search space used: 116960 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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