Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011386328.1 AMB_RS20110 histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000009985.1:WP_011386328.1 Length = 363 Score = 239 bits (609), Expect = 1e-67 Identities = 141/373 (37%), Positives = 209/373 (56%), Gaps = 14/373 (3%) Query: 1 MTASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAA 60 MTA + I PY+ G+ E G+D I+KL+SNE LG A A+ A Sbjct: 1 MTAPAPRPGIMDIRPYVGGESAIE-----GVDR--ILKLSSNEGALGPSPKAMEALRAMA 53 Query: 61 SELGRYPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSF 120 E+ RYPD A +L+ A+ R+G+ A + G GS+++L I A+ G ++Y+ + F Sbjct: 54 PEMHRYPDGGAEDLRKAIGARFGLDASRIVCGAGSDELLGILCRAYAGPGDEVLYSAHGF 113 Query: 121 AVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEA 180 +YA+A + GA + P V ++D +LAAV+ T+++F+ANPNNPTGT++ ++ Sbjct: 114 LMYAIAAKACGATPVTAPEVDLTANVDNLLAAVTPRTKILFLANPNNPTGTYLPATEVAR 173 Query: 181 FLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAI 240 + +++V+D AYTE++ + I V N++V RTFSK + L GLR+G+A Sbjct: 174 LRAGLRADILLVIDAAYTEFVSRNDYSGGIELVEAGDNVVVCRTFSKMYALGGLRLGWAY 233 Query: 241 AQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLE 300 + +LNRVR PFNV A AA +AA ND A+ E + N L+ +LGL Sbjct: 234 CPENVAGVLNRVRNPFNVGAPALAAGLAAFNDTAYAELCKSHNDYWLPWLSGQLAELGLT 293 Query: 301 YVPSDGNFVLVR----VGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEEN 356 VPS NF+LVR G D A ++ L +G+IVR +G YGL LRITIG EEN Sbjct: 294 VVPSVCNFILVRFPKDAGKDAGAADKF---LRSKGIIVRAMGGYGLGDCLRITIGTGEEN 350 Query: 357 EAFIAALERTLAA 369 + +AAL+ + A Sbjct: 351 QLVVAALKEFVGA 363 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: 343 Number of extensions: 14 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: 363 Length adjustment: 30 Effective length of query: 340 Effective length of database: 333 Effective search space: 113220 Effective search space used: 113220 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