Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012383319.1 BIND_RS01560 histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000019845.1:WP_012383319.1 Length = 378 Score = 235 bits (600), Expect = 1e-66 Identities = 133/355 (37%), Positives = 204/355 (57%), Gaps = 8/355 (2%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 V I PY+ GK + A I KL+SNE PLG AQ+A A +A +L YPD Sbjct: 21 VLGIEPYVPGKSAAPGV-------AKIHKLSSNETPLGPSPEAQKAFAASAEKLALYPDG 73 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 A L+ A++ R+G+ + G GS+++L + A ++ G+ ++ ++ F VY +A Sbjct: 74 AATLLRTAIASRHGLDPARIVCGAGSDELLSLLAAVYLGPGEEGIFTEHGFLVYKIAILT 133 Query: 130 LGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHV 189 G IVVP D+DA+LAAV+ TR++++ANPNNPTGT++ +++ +P +V Sbjct: 134 AGGTPIVVPEKDLTTDVDAILAAVTPRTRIVYIANPNNPTGTYLPFAEVKRLATSLPPNV 193 Query: 190 VVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLL 249 ++VLD AY EY+ + + V + N++++RTFSK +GLA LR+G+ A + D L Sbjct: 194 LLVLDAAYGEYVTRNDYSAGLELVSTHENVVMTRTFSKIYGLAALRLGWCYAPLAVADAL 253 Query: 250 NRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDGNFV 309 NRVR PFN + A A +AAL D+A ++++ A N L E KLG + PS NF+ Sbjct: 254 NRVRGPFNTSGPAIATGVAALADQAHIDRAIAHNETWLSWLGEEIGKLGFKVTPSVANFL 313 Query: 310 LVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364 L+ D A V+ L +G+I+R V +YGLP LR+T+G E N + L+ Sbjct: 314 LLHF-EDQAEAQAVDAFLSSRGLILRAVASYGLPNCLRLTVGTEEANRLVVDGLK 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: 349 Number of extensions: 10 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: 378 Length adjustment: 30 Effective length of query: 340 Effective length of database: 348 Effective search space: 118320 Effective search space used: 118320 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