Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_028321243.1 H567_RS0109640 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000422285.1:WP_028321243.1 Length = 366 Score = 287 bits (734), Expect = 4e-82 Identities = 158/360 (43%), Positives = 221/360 (61%), Gaps = 9/360 (2%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 V + PY GKPI E+ RE G+ + +KLASNENPLG A +A+ + L RYPD Sbjct: 9 VETLVPYPPGKPIEELERELGIFGS--IKLASNENPLGPSPMAVKAIVEKIPNLHRYPDG 66 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 + + LK L + +P + + LGNGSN+I+E+ F+ G V A +F VY G Sbjct: 67 SGYYLKRRLGQLLSLPMEQIILGNGSNEIIELIIRTFLAPGDEAVQAFPTFLVYEKMVLG 126 Query: 130 LGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHV 189 G I VP + LD + AAV+ T++IF+ NPNNPTGT + ++ FL+ +PR + Sbjct: 127 AGGLMISVPLKDFRIGLDDVHAAVTPRTKIIFINNPNNPTGTILLKDEMLRFLEDIPRDI 186 Query: 190 VVVLDEAYTEYL--PQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTD 247 VVVLDEAY E+ P R + + V P L+V RTFSK +GLAGLR+G+ AQPEL D Sbjct: 187 VVVLDEAYIEFTTDPNVARGEDLLAV--CPRLIVLRTFSKLYGLAGLRIGYGFAQPELID 244 Query: 248 LLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGN 307 +NRVRQPFN N LAQA A AAL+D+ F+ ++ G L ++GLE +P+ N Sbjct: 245 YMNRVRQPFNANALAQAGATAALDDRDFVARTLDTTRAGLAFLHAGLREMGLEALPTQTN 304 Query: 308 FVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERTL 367 + L+RV G RV +L +GVI+R + +YGLP+++RI +GLPEENE F+ A+++ L Sbjct: 305 YFLIRV---PIPGKRVFERMLHEGVIIRAMDSYGLPEFIRINVGLPEENERFLNAMKKVL 361 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: 385 Number of extensions: 15 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: 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