Align phenylpyruvate decarboxylase (EC 4.1.1.43) (characterized)
to candidate RR42_RS10655 RR42_RS10655 pyruvate dehydrogenase
Query= BRENDA::A0A222AKA3 (368 letters) >FitnessBrowser__Cup4G11:RR42_RS10655 Length = 340 Score = 133 bits (335), Expect = 6e-36 Identities = 104/329 (31%), Positives = 152/329 (46%), Gaps = 17/329 (5%) Query: 29 AAAPAAAGVPPDR--QLLMYRAMVVGRAFNRQATAFSRQGRLAVYPSSR-GQEACQVGSA 85 A AP + VP D+ L + R M+ R + G++ + G+EA VG Sbjct: 8 APAPPSGPVPYDKVVALDLLRDMLRIRRLEEKCAELYDAGKIRGFLHLYIGEEAVGVGVL 67 Query: 86 LAVRPTDWLFPTYRESVALLTRGIDP-VQVLTLFRGDQHCG---------YDPVTEHTAP 135 A+ P D + TYRE L RG+D V + ++ Q C +D T Sbjct: 68 HALAPEDNVVATYREHGHALVRGMDMGVLMAEMYGKQQGCARGRGGSMHLFDRATRLFGG 127 Query: 136 QCTPLATQCLHAAGLADAARMAGDPIVALAYIGDGATSEGDFHEALNYAAVRRAPVVFLV 195 L A GLA A +M V + GDGA +EG FHE++N A++ + PV+F Sbjct: 128 NAIVGGGLPL-AVGLALAEKMQAGQRVTACFFGDGAVAEGAFHESMNLASLWKLPVLFCC 186 Query: 196 QNNQYAISVPLAKQTAARTLADKAAGYGMPGVRIDGNDVLQVYRAVHDAAERARAGHGPT 255 +NN YA+ L + + L KAA Y M V +DG D++ V+ A DAA R+G GP Sbjct: 187 ENNLYAMGTALERHESQTDLCAKAASYNMTAVAVDGMDIVAVHEAARDAAAHVRSGAGPV 246 Query: 256 LIEAVTYRIDAHTNADDDTRYRPAGEADVWAAQDPVDRLERDLLAAGVLDRAAADGIAAA 315 +E TYR AH+ D + YR E + W P+ L A G L + AA Sbjct: 247 FLELRTYRFRAHSMYDAEL-YRQKAEVEAWEECGPIHTFTARLKAGGKLAEEEFLALDAA 305 Query: 316 ADAFAGELSARFSAPPTGDPMQ-MFRHVY 343 A+A + A F+ T +P++ + + VY Sbjct: 306 ANAEVAKAEA-FAEAGTWEPVEDLLKDVY 333 Lambda K H 0.319 0.132 0.395 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: 246 Number of extensions: 16 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: 368 Length of database: 340 Length adjustment: 29 Effective length of query: 339 Effective length of database: 311 Effective search space: 105429 Effective search space used: 105429 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 Sep 17 2021. The underlying query database was built on Sep 17 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