Align Aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate HSERO_RS23520 HSERO_RS23520 histidinol-phosphate aminotransferase
Query= reanno::BFirm:BPHYT_RS14905 (370 letters) >FitnessBrowser__HerbieS:HSERO_RS23520 Length = 360 Score = 159 bits (403), Expect = 9e-44 Identities = 127/375 (33%), Positives = 186/375 (49%), Gaps = 29/375 (7%) Query: 3 ASFGPSYVRAIAPYIAGKPISEVAREFGLDEATIVKLASNENPLGMPESAQRAMAQAASE 62 + F V + PY G+ ++AR +VKL +NE+P G A +A+A+ S+ Sbjct: 2 SKFWSPIVSRLTPYTPGEQ-PKIAR--------LVKLNTNESPYGPSPLALQAIAREVSD 52 Query: 63 -LGRYPDANAFELKAALSERY---GVPADWVTLGNGSNDILEIAAHAFVEKGQSIVYAQY 118 L YP+ +A LK A++ R+ GV V +GNGS+++L A HA ++ G+ I++ Sbjct: 53 SLRLYPNPDAEPLKQAIARRHAADGVSVREVFVGNGSDEVLAHAFHALLQHGKPILFPDI 112 Query: 119 SFAVYALATQGLGARAIVVPAVKYGHDLDAMLAAVSDDTRLI---FVANPNNPTGTFIEG 175 +++ Y G + AV D + I NPN PTG + Sbjct: 113 TYSFYPTYA---GLYQVEYRAVPLAEDFTLRSEDYLGHGQAIGGIIFPNPNAPTGCLLGL 169 Query: 176 PKLEAFLDKVPRHVVVVLDEAYTEYLPQEKRYDSIAWVRRYPNLLVSRTFSKAFGLAGLR 235 +E L P VVVV DEAY ++ Q +I V+RYPNLLV +T SK+ LAG+R Sbjct: 170 ADVERILQGNPERVVVV-DEAYIDFGGQS----AIPLVQRYPNLLVVQTLSKSRALAGMR 224 Query: 236 VGFAIAQPELTDLLNRVRQPFNVNTL---AQAAAIAALNDKAFLEKSAALNAQGYRRLTE 292 VGFA+ +L D L RV+ FN L A A A AA+ D+ + K+ + L Sbjct: 225 VGFAVGHADLIDALERVKNSFNSYPLDRPAIAGATAAIEDEDYFRKTCNMVIASRTALAA 284 Query: 293 AFDKLGLEYVPSDGNFVLVRVGNDDAAGNRVNLELLKQGVIVRPVGNYGLPQWLRITIGL 352 LG + +PS NF+ VR DAA ++ L G+IVR + + Q+LRITIG Sbjct: 285 QLAGLGFQVLPSAANFLFVRHPQHDAA--QLAAALRADGIIVRHFKSERISQFLRITIGT 342 Query: 353 PEENEAFIAALERTL 367 E+ + AL R L Sbjct: 343 DEDCGVLVEALRRHL 357 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: 331 Number of extensions: 19 Number of successful extensions: 6 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: 360 Length adjustment: 30 Effective length of query: 340 Effective length of database: 330 Effective search space: 112200 Effective search space used: 112200 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