Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_050463906.1 AKL27_RS16305 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_001189915.1:WP_050463906.1 Length = 368 Score = 566 bits (1459), Expect = e-166 Identities = 280/367 (76%), Positives = 321/367 (87%) Query: 1 MTASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAA 60 M+ FGP YVRA+APY AGKPI+EVAREFGL+E++IVKLASNENPLGMPESAQRA+ QA Sbjct: 1 MSIQFGPDYVRALAPYQAGKPIAEVAREFGLEESSIVKLASNENPLGMPESAQRALQQAV 60 Query: 61 SELGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSF 120 ++LGRYPDAN F+LKAA+S RYGVP DW+TLGNGSNDILE+AAHAFV+ GQS++YAQY F Sbjct: 61 ADLGRYPDANGFDLKAAISARYGVPQDWITLGNGSNDILELAAHAFVQPGQSVMYAQYGF 120 Query: 121 AVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEA 180 VY LATQ +GARAI VPA +GHDL AMLAA++DDTRLIF+ANPNNPTGTF+ +LEA Sbjct: 121 LVYPLATQAVGARAIEVPAKDFGHDLPAMLAAIADDTRLIFIANPNNPTGTFVPAAELEA 180 Query: 181 FLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAI 240 FL VP HVVVVLDEAY EYL E +Y+S+ WVR +PNLLVSRT SKA+GLAGLRVGFAI Sbjct: 181 FLRAVPSHVVVVLDEAYNEYLNAELQYESVEWVRAFPNLLVSRTMSKAYGLAGLRVGFAI 240 Query: 241 AQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLE 300 AQP +TDLLNR+RQPFNVN+LAQAAAIAALNDKAFL+KSA LNA+GY +LT+AFD LGLE Sbjct: 241 AQPGVTDLLNRIRQPFNVNSLAQAAAIAALNDKAFLQKSADLNARGYAQLTQAFDALGLE 300 Query: 301 YVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFI 360 YVPS GNFVLV+VG DD AG RVNL LLK+G+IVRPV NY LPQWLRI+IGLPEEN AF+ Sbjct: 301 YVPSFGNFVLVKVGADDGAGARVNLALLKRGIIVRPVANYKLPQWLRISIGLPEENVAFL 360 Query: 361 AALERTL 367 AL+ L Sbjct: 361 DALKTVL 367 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: 546 Number of extensions: 18 Number of successful extensions: 1 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 Sep 24 2021. The underlying query database was built on Sep 17 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