Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_055437263.1 ASC41_RS13945 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_001418085.1:WP_055437263.1 Length = 343 Score = 155 bits (392), Expect = 2e-42 Identities = 113/353 (32%), Positives = 180/353 (50%), Gaps = 37/353 (10%) Query: 20 KPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALS 79 KP S EF V L +NENP G +L RYPD E+K L+ Sbjct: 17 KPYSSARDEF--KGTADVFLDANENPFG--------------DLNRYPDPQQQEIKEKLA 60 Query: 80 ERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYA-QYSFAVYALATQGLGARAIVVP 138 V + + +GNGS++++++A F E G+ V ++ +Y ++ I P Sbjct: 61 ALKTVEKNQIFIGNGSDEVIDLAFRIFCEPGKDKVLTFSPTYGMYDVSANINNIEIIKQP 120 Query: 139 AVKYGHDLDAMLAAVS-----DDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVL 193 + +D L + +D ++IF+ +PNNPTG I +E L+ +V++ Sbjct: 121 LI---NDFQISLNQLQPYLDFEDIKIIFICSPNNPTGNSINPEDIEYVLENFEG--IVIV 175 Query: 194 DEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVR 253 DEAY ++ Q +I +Y NL+VS+TFSKA+GLAG+RVG A A + L NRV+ Sbjct: 176 DEAYIDFSAQTSFIKNI---NKYNNLIVSQTFSKAWGLAGVRVGVAYANEAIIKLYNRVK 232 Query: 254 QPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGL--EYVPSDGNFVLV 311 P+NV+TL Q A + +LN+ + ++ + + +L +A KL + P+D NF+L+ Sbjct: 233 PPYNVSTLNQEAVLKSLNNFEAVTENIQIILKERTKLKDALSKLSIVKNIHPTDANFLLI 292 Query: 312 RVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364 V N N+ L+++ VI+R N + +RITIG EEN+ I L+ Sbjct: 293 EVDN----ANKTYQYLIEEKVIIRN-RNTQVDNCVRITIGTSEENDRLIKVLK 340 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: 290 Number of extensions: 18 Number of successful extensions: 5 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: 343 Length adjustment: 29 Effective length of query: 341 Effective length of database: 314 Effective search space: 107074 Effective search space used: 107074 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 Jul 26 2024. The underlying query database was built on Jul 25 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