Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_041098942.1 SUTH_RS09875 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000828635.1:WP_041098942.1 Length = 362 Score = 399 bits (1024), Expect = e-116 Identities = 199/361 (55%), Positives = 266/361 (73%), Gaps = 6/361 (1%) Query: 7 PSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRY 66 P+Y+RAI+PYI GKPI+E+AR+ G+ IVKLASNENPLGM A++A+ A + + RY Sbjct: 8 PAYIRAISPYIPGKPITELARQMGIPVEKIVKLASNENPLGMSPKARKAVEAALAGVERY 67 Query: 67 PDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALA 126 PD F+L AAL+ER+GV V LGNGSND+L++AA F+ G+S V+++++FAVY LA Sbjct: 68 PDQ--FDLIAALAERHGVATGQVVLGNGSNDVLDLAARVFLAPGRSAVFSRHAFAVYPLA 125 Query: 127 TQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVP 186 + GA IV PA YGHD AMLAA+ DTR++++ANPNNPTG F+ +L AF+DK+P Sbjct: 126 SMAAGAECIVAPAKHYGHDPAAMLAAIRPDTRIVWIANPNNPTGNFLPQAELRAFIDKIP 185 Query: 187 RHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELT 246 + VVLDEAYTEYL R D++AW++ PNL+V+RTFSK +GLAGLR+G+A+A+ ++ Sbjct: 186 ADIAVVLDEAYTEYLAPADRADTVAWIKDLPNLIVTRTFSKIYGLAGLRIGYAVARADVA 245 Query: 247 DLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDG 306 DLLNRVRQPFNVN LA A A+AAL+D F+ +S LN +G ++ +LGLE++PS G Sbjct: 246 DLLNRVRQPFNVNNLALAGALAALDDHGFVAESFELNRRGMEQIVAGLKRLGLEHIPSHG 305 Query: 307 NFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERT 366 NFV V + G VN +LL+QGVIVRP+G YGLP LR+TIGL EN F+ ALE++ Sbjct: 306 NFVTFEVKD----GAAVNGKLLQQGVIVRPIGGYGLPNHLRVTIGLETENARFLEALEKS 361 Query: 367 L 367 L Sbjct: 362 L 362 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: 433 Number of extensions: 13 Number of successful extensions: 3 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: 362 Length adjustment: 30 Effective length of query: 340 Effective length of database: 332 Effective search space: 112880 Effective search space used: 112880 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 09 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