Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate 349730 BT0202 histidinol-phosphate aminotransferase (NCBI ptt file)
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Btheta:349730 Length = 346 Score = 147 bits (370), Expect = 6e-40 Identities = 110/352 (31%), Positives = 182/352 (51%), Gaps = 30/352 (8%) Query: 20 KPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDANAFELKAALS 79 KP S E+ A++ L +NENP +P + RYPD +ELK LS Sbjct: 16 KPYSSARDEYKGAVASVF-LDANENPYNLPHN-------------RYPDPMQWELKTLLS 61 Query: 80 ERYGVPADWVTLGNGSNDILEIAAHAFVE-KGQSIVYAQYSFAVYALATQ--GLGARAIV 136 + V + LGNGS++ +++ AF E + ++V ++ +Y + + R ++ Sbjct: 62 KIKKVSPQHIFLGNGSDEAIDLVFRAFCEPEKDNVVAIDPTYGMYQVCADVNNVEYRKVL 121 Query: 137 VPAVKYGHDLDAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDKVPRHVVVVLDEA 196 + + + +LAA + T+LIF+ +PNNPTG + ++E L + +V+LDEA Sbjct: 122 LDE-NFQFSAEKLLAATDERTKLIFLCSPNNPTGNDLLRSEIEKILREFEG--LVILDEA 178 Query: 197 YTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPELTDLLNRVRQPF 256 Y ++ + + +YPNL+V +TFSKA+G A +R+G A A + +L++++ P+ Sbjct: 179 YNDFSEAPSFLEELD---KYPNLVVFQTFSKAWGCAAIRLGMAFASEAIIGILSKIKYPY 235 Query: 257 NVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKLG--LEYVPSDGNFVLVRVG 314 NVN L Q AIA L+ +E+ + L E F KL + PSD NF L +V Sbjct: 236 NVNQLTQQQAIAMLHKYYEIERWIKTLKEERDYLEEEFAKLSCTVRMYPSDSNFFLAKV- 294 Query: 315 NDDAAGNRVNLELLKQGVIVRPVGNYGL-PQWLRITIGLPEENEAFIAALER 365 DA ++ L+ +G+IVR + L LR+T+G EN +AAL++ Sbjct: 295 -TDAV--KIYNYLVGEGIIVRNRHSISLCCNCLRVTVGTRVENNTLLAALKK 343 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: 304 Number of extensions: 22 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: 346 Length adjustment: 29 Effective length of query: 341 Effective length of database: 317 Effective search space: 108097 Effective search space used: 108097 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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