Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate Echvi_2458 Echvi_2458 histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__Cola:Echvi_2458 Length = 354 Score = 149 bits (377), Expect = 9e-41 Identities = 115/369 (31%), Positives = 187/369 (50%), Gaps = 32/369 (8%) Query: 11 RAIAPYIAG-KPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASELGRYPDA 69 + + P+IA KP S E+ E V L +NENP G + A RYPD Sbjct: 7 KLLRPHIAQLKPYSSARDEYTGKEG--VFLDANENPFG---------SITAESFNRYPDP 55 Query: 70 NAFELKAALSERYGVPADWVTLGNGSNDILEIAAHAFVEKGQ-SIVYAQYSFAVYALATQ 128 LK +S VP + + +GNGS++ +++ AF G+ +I+ ++ +Y ++ Sbjct: 56 YQHALKEKISAIKQVPVEQIFIGNGSDEAIDLLMRAFCRPGKDNIIILPPTYGMYEVSAD 115 Query: 129 GLGARAIVVPAVKYGHDL----DAMLAAVSDDTRLIFVANPNNPTGTFIEGPKLEAFLDK 184 I + V D DA+L AV ++T++IF+ +PNNP+G + + + Sbjct: 116 ---INDISIKRVNLSADFQLRPDAILEAVDENTKIIFICSPNNPSGNKVRRKDILKII-- 170 Query: 185 VPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLRVGFAIAQPE 244 V +VV+DEAY ++ + A + ++PNLLV +TFSKA+GLA LR+G A A Sbjct: 171 VGFDGLVVVDEAYIDFSDEPS---FTAELPQHPNLLVMQTFSKAWGLAALRLGMAFASLP 227 Query: 245 LTDLLNRVRQPFNVNTLAQAAAIAALNDKAFLEKSAALNAQGYRRLTEAFDKL-GLEYV- 302 + +LN+++ P+N++ L Q + AL D + +++ Q L A K+ G++ + Sbjct: 228 IIRILNKIKPPYNISGLTQETVLKALQDTSKMKQMVKEMLQERDYLLHALSKMDGIKKIH 287 Query: 303 PSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGL-PQWLRITIGLPEENEAFIA 361 P+ NFVLV V A L++Q +IVR L Q LRI++G EEN+ I Sbjct: 288 PTHANFVLVEV----PAAKETYDHLIEQQIIVRDRSKVVLCDQCLRISVGTREENDQLIG 343 Query: 362 ALERTLAAA 370 L +A + Sbjct: 344 KLSEFIATS 352 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: 293 Number of extensions: 16 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: 354 Length adjustment: 29 Effective length of query: 341 Effective length of database: 325 Effective search space: 110825 Effective search space used: 110825 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