Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_018231479.1 THITHI_RS0102420 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000378965.1:WP_018231479.1 Length = 373 Score = 335 bits (859), Expect = 1e-96 Identities = 178/366 (48%), Positives = 242/366 (66%), Gaps = 11/366 (3%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 V+ + PY GKPI E+ RE G+ E+ VKLASNENPLG A A S + YPD Sbjct: 13 VQNLTPYQPGKPIDELERELGIRES--VKLASNENPLGPGVRALDAARAQLSGVALYPDG 70 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 N F LK L+E V A +TLGNGSN+ILE+ A AF+ G++ V++ ++FAVY + Q Sbjct: 71 NGFALKRRLAEYLNVDATRITLGNGSNEILELIARAFLAPGRNAVFSAHAFAVYPIVVQA 130 Query: 130 LGARAIVVPA------VKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLD 183 +GA A V A + +GHDLDAM A + DTR++FVANPNNPTGT+++ + AFL Sbjct: 131 VGAEARVAVANGPDHVLPWGHDLDAMAALIDGDTRVVFVANPNNPTGTWLDEASVHAFLK 190 Query: 184 KVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQP 243 +VP + V+DEAY EY + D+ W+ +PNL+V+RTFSK GLAGLR+G+ ++ Sbjct: 191 RVPEDTLAVMDEAYFEYAEVDGYPDATRWLDAFPNLIVTRTFSKIHGLAGLRIGYGVSGE 250 Query: 244 ELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVP 303 + D+LNRVRQPFN N+LAQAAA+AAL+D + +S +N +G R+LT A + GL ++P Sbjct: 251 AVADILNRVRQPFNTNSLAQAAALAALDDADHVRRSVQVNREGLRQLTAACGQRGLGFIP 310 Query: 304 SDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAAL 363 S GNF+ + VG + A V LL+QGVIVRP+ YGLP LR+T+G EN FI AL Sbjct: 311 SVGNFLSIDVGREAAP---VYEALLRQGVIVRPIAGYGLPNHLRVTVGREHENRRFIDAL 367 Query: 364 ERTLAA 369 ++ LA+ Sbjct: 368 DKVLAS 373 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: 444 Number of extensions: 19 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: 373 Length adjustment: 30 Effective length of query: 340 Effective length of database: 343 Effective search space: 116620 Effective search space used: 116620 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