Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_077243517.1 B1A74_RS01050 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_001995255.1:WP_077243517.1 Length = 383 Score = 351 bits (900), Expect = e-101 Identities = 185/368 (50%), Positives = 245/368 (66%), Gaps = 12/368 (3%) Query: 8 SYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYP 67 S V+ + PY GKP+SE+ RE G+ EA VKLASNENPLG A +A E YP Sbjct: 21 SGVQGLQPYQPGKPVSELERELGISEA--VKLASNENPLGPSPRAVKAARGVLGEAHVYP 78 Query: 68 DANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALAT 127 D N FELKAAL+ R+GV +TLGNGSN++LE+ A ++ G++ V++ ++FAVY L T Sbjct: 79 DGNGFELKAALAARHGVDPAQITLGNGSNEVLELIARTWLAPGRASVFSAHAFAVYPLVT 138 Query: 128 QGLGARAIVVPAVK-------YGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEA 180 Q GA A VVPAV +GHDLDAM A V DDT ++FVANPNNPTGT+++ LEA Sbjct: 139 QATGAEARVVPAVSADDARQPFGHDLDAMRARVDDDTAVVFVANPNNPTGTWLDAQALEA 198 Query: 181 FLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAI 240 F+ +P +VV+DEAY EY+ ++ D+ W+ RYPN++V+RTFSK GLAGLR+G+A+ Sbjct: 199 FVAAMPPQTIVVIDEAYAEYVEEDGYPDATRWLDRYPNVVVTRTFSKIQGLAGLRLGYAV 258 Query: 241 AQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLE 300 + + D+LNRVRQPFNVN +AQAA +AAL D + S A+N +G +L +GL Sbjct: 259 SSAPVADMLNRVRQPFNVNAVAQAAGLAALEDSDHIRHSVAVNREGLVQLGRELRAMGLR 318 Query: 301 YVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFI 360 +PS GNF+ G D N V+ L ++GVI RPV NYGLP LR+T+ E+NE F+ Sbjct: 319 VIPSVGNFITFDTGTD---VNAVHDRLQRRGVIARPVENYGLPGHLRVTVSTAEDNERFL 375 Query: 361 AALERTLA 368 AAL LA Sbjct: 376 AALREALA 383 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: 472 Number of extensions: 17 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: 383 Length adjustment: 30 Effective length of query: 340 Effective length of database: 353 Effective search space: 120020 Effective search space used: 120020 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