Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_011735425.1 PPRO_RS07560 histidinol-phosphate transaminase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >NCBI__GCF_000015045.1:WP_011735425.1 Length = 375 Score = 237 bits (604), Expect = 4e-67 Identities = 135/365 (36%), Positives = 209/365 (57%), Gaps = 7/365 (1%) Query: 7 PSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGR- 65 P YVR Y+ +P + RE+G + +L +NENPLG P +A R +A EL Sbjct: 8 PDYVRCFQAYVPSRPDHLLMREYGAP--LLYRLNNNENPLGPPPAASREIASFPPELAAV 65 Query: 66 YPDANAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQYSFAVYAL 125 YP ++FEL+ AL R G+ + + +GNGS +++ AF + G +IV A +FAVY Sbjct: 66 YPSGDSFELREALGNRLGISPERILVGNGSCEVISSVIKAFCQPGDNIVTADKTFAVYEW 125 Query: 126 ATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKV 185 + G +A +VP + D ML + + T++IFV NPNNPTG++ G L FL++V Sbjct: 126 VAEFSGIQAHLVPLRDHAFDPQGMLDRIDNRTKIIFVCNPNNPTGSYWTGQLLTDFLERV 185 Query: 186 PRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPEL 245 +VV+DEAY E++ E+ D ++ + R+PNL+V RTFSK + LAGLR G+ + + Sbjct: 186 GSERIVVVDEAYREFVEDEEYPDGVSLMERFPNLVVFRTFSKMYALAGLRTGYLVGSDRV 245 Query: 246 TDLLNRVRQPFNVNTLAQAAAIAALNDK-AFLEKSAALNAQGYRRLTEAFDKLGLEYVPS 304 +++ R ++VN AQ AA+AAL+D + + AL + L A D LGLE V Sbjct: 246 VEVVRRTSVVYSVNVQAQRAALAALSDDGGHIAATRALVRESRAYLRTACDDLGLETVIG 305 Query: 305 DGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGLPEENEAFIAALE 364 +GN++++RV +D R L+K+G++VR + + P W+R+T+ E F AL Sbjct: 306 EGNYLMIRVPINDMLMYR---RLMKRGMMVRSMTGFRYPGWIRVTLKEMEVMTRFAQALG 362 Query: 365 RTLAA 369 +AA Sbjct: 363 AEIAA 367 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: 383 Number of extensions: 16 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: 375 Length adjustment: 30 Effective length of query: 340 Effective length of database: 345 Effective search space: 117300 Effective search space used: 117300 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: 50 (23.9 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