Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate AZOBR_RS10240 AZOBR_RS10240 L-threonine-O-3-phosphate decarboxylase
Query= curated2:A7MJP4 (360 letters) >FitnessBrowser__azobra:AZOBR_RS10240 Length = 339 Score = 94.7 bits (234), Expect = 3e-24 Identities = 87/295 (29%), Positives = 134/295 (45%), Gaps = 32/295 (10%) Query: 31 LNANEYPLPVEFQLTAQTLNRYPECQPKRVI-ERYAQYAGVKPEQVLVSRGADEGIELLI 89 +N YPLP + A R P + + E A GV + + G + + ++ Sbjct: 38 INPWPYPLP---PIPADAWARLPGRAAETALREAAAACYGVPSADRVAAAGGSQALIQIL 94 Query: 90 RAFCEPGRDAVLYCPPTYGMYSVSAETSGVECRTVQATDGWQLDLPAIAEQLDGVKVIFV 149 PG AVL PTY ++ +G V++ +G D V+ V Sbjct: 95 PRLRRPGTVAVL--GPTYAEHAAGWAKAGHRVAEVESLEGCDAD------------VVVV 140 Query: 150 CSPNNPTGQLINPQDLRTLLEM--ARGKAIVVADEAYIEFCPQATLAGWLGEYPHLVVLR 207 +PNNP G+++ P+ L L E ARG +VV DEA+ E P+ ++A G LV+LR Sbjct: 141 VNPNNPDGRIVPPETLLALAERQAARGGWLVV-DEAFAEVTPECSVASEAGR-AGLVILR 198 Query: 208 TLSKAFALAGLRCGFTLANEEVINLLLKVIAPYPLSTPVADIAAQALSPEG-ITAMRERV 266 + K F LAG+R GF L ++ L + P+ +S P IA ALS I A R R+ Sbjct: 199 SFGKFFGLAGVRLGFLLGEPALVRDLRAAVGPWAVSGPALTIATAALSDSAWIAATRRRL 258 Query: 267 AQVLANRD--VLIAGLRETPCVEAVFDSETNYVLARITASSAVFKSLWDQGIILR 319 A A D ++ AG+R V + + L S+ ++K L G+++R Sbjct: 259 ADAAARFDARLMEAGVR-------VAGGTSLFRLIDDPQSAGLYKELGLAGVLVR 306 Lambda K H 0.320 0.136 0.402 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: 315 Number of extensions: 17 Number of successful extensions: 3 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: 360 Length of database: 339 Length adjustment: 29 Effective length of query: 331 Effective length of database: 310 Effective search space: 102610 Effective search space used: 102610 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 (21.8 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