Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_093427355.1 BM272_RS03610 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_900112605.1:WP_093427355.1 Length = 373 Score = 343 bits (881), Expect = 3e-99 Identities = 181/362 (50%), Positives = 240/362 (66%), Gaps = 8/362 (2%) Query: 10 VRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 VR +APY GKP++E+ RE+G+ +A +KLASNENPLG A+ A A E G YPD Sbjct: 12 VRGLAPYKPGKPVAELQREYGVADA--IKLASNENPLGASPRAREAAAATLDEAGIYPDG 69 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYALATQG 129 F L+ +++ +GV A+ VTLGNGS+D L A FV G +VY+ ++FA+Y L TQ Sbjct: 70 GGFALRGRIADHHGVAAEQVTLGNGSSDPLAFAVEVFVTPGDEVVYSAHAFALYPLLTQA 129 Query: 130 LGARAIVVPAVK-YGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRH 188 GAR + VP YGHDL+AM AA++D TR++FVANPNNPTGT + L FL++VP H Sbjct: 130 AGARGVEVPTTAGYGHDLEAMAAAITDRTRVVFVANPNNPTGTRVGASALRNFLERVPGH 189 Query: 189 VVVVLDEAYTEYLPQ-EKRY-DSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELT 246 + V+DEAY EY + Y D+ AW+ +PNLLV+RTFSK GLAGLRVG+ ++ P + Sbjct: 190 TLAVVDEAYFEYARDLDSDYPDASAWLAEFPNLLVTRTFSKLHGLAGLRVGYGLSSPAVA 249 Query: 247 DLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLGLEYVPSDG 306 DLLNRVR PFNVN AQAAA+AA++D L S N +G +L + GL+++PS G Sbjct: 250 DLLNRVRPPFNVNAPAQAAALAAMDDAEHLAASLEANREGMAQLEAGLRERGLDWIPSVG 309 Query: 307 NFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALERT 366 NF+ G D V+ LL+QGVI+RP+G YGLP+ LR TIG +NE + AL+R Sbjct: 310 NFLTFDTGGD---AGEVHEALLRQGVILRPMGEYGLPRHLRATIGRTADNERLLTALDRA 366 Query: 367 LA 368 LA Sbjct: 367 LA 368 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: 413 Number of extensions: 25 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: 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 Jul 25 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