Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012850579.1 TCUR_RS00945 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000024385.1:WP_012850579.1 Length = 360 Score = 246 bits (629), Expect = 5e-70 Identities = 145/327 (44%), Positives = 194/327 (59%), Gaps = 13/327 (3%) Query: 38 KLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALSERYGVPADWVTLGNGSND 97 KL+SNE+P G S A+ +AA + RYPD NA L A+SER+ VPAD + +G GS Sbjct: 34 KLSSNESPFGPLPSVLEAIGEAARRVNRYPDNNATALIEAISERFAVPADHIAVGCGSVG 93 Query: 98 ILEIAAHAFVEKGQSIVYAQYSFAVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDT 157 + ++ A E G ++YA SF Y + GA+A+ VP + HDL AM A+++ T Sbjct: 94 VTQMLLEAVAEPGAEVLYAWRSFEAYPVLVALSGAQAVQVPLREETHDLAAMAEAITERT 153 Query: 158 RLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYP 217 RLIFV NPNNPTGT + +LE+FLD+VP +VVLDEAY EY+ E+ D + P Sbjct: 154 RLIFVCNPNNPTGTAVRRAELESFLDRVPADCLVVLDEAYREYIRDEQVPDGLTLYGDRP 213 Query: 218 NLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLE 277 NL V RTFSKA+GLAGLRVGF +A P + + + PF+VN+LAQAAAIA+L + L Sbjct: 214 NLAVLRTFSKAYGLAGLRVGFLVAHPVVAGAVRKTMLPFSVNSLAQAAAIASLAAEDELL 273 Query: 278 KSAALNAQGYRRLTEAFDKLGLEYVPSDGNFVLVRVGN---DDAAGNRVNLELLKQGVIV 334 + + R+ A G P++ NFV +R+G D AA QGV V Sbjct: 274 ERVEGTVKERHRVVSALRDQGWSVPPTEANFVWLRLGERTLDFAAACEA------QGVSV 327 Query: 335 RPVGNYGLPQWLRITIGLPEENEAFIA 361 RP G R++IGLPEEN+AF+A Sbjct: 328 RPFAGEG----ARVSIGLPEENDAFLA 350 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: 341 Number of extensions: 9 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: 360 Length adjustment: 30 Effective length of query: 340 Effective length of database: 330 Effective search space: 112200 Effective search space used: 112200 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