Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate PfGW456L13_3549 pyridoxal phosphate-dependent deaminase, putative
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3549 Length = 343 Score = 179 bits (455), Expect = 7e-50 Identities = 121/339 (35%), Positives = 180/339 (53%), Gaps = 24/339 (7%) Query: 1 MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGAD-----VYIKRDDLTGLGIGGNKI 55 M ++ L+ F R +L+ TPIQ + + +G D +++KRDD +G GGNK+ Sbjct: 1 MQTQLDKSLSVFARADLLQGPTPIQRAARLEQLLGLDKQGIGLFLKRDDHMLIGAGGNKL 60 Query: 56 RKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVL-------RGKEEL 108 RKLE+ +G AL G D +ITVG + SNHA +T +LG+ L+L EL Sbjct: 61 RKLEFHIGAALQAGIDTIITVGGIQSNHARLTAAVCARLGIACELLLTRAVAKAEVDYEL 120 Query: 109 KGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYV 168 GN LLD++ G + +V+ A + L K AE A L+ G K V+P GG++P+G+LGY Sbjct: 121 NGNVLLDQLFGAQMQVF-AGGTDSLAK-AEARAALLRDSGHKVMVLPTGGSTPLGSLGYA 178 Query: 169 RAVGEIATQS---EVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPV-GIAVGRFGEVMT 224 R EIA Q ++ F+ +VV GS GT AGL+ G +L V +V E Sbjct: 179 RCAAEIAQQEAELQLTFNQVVVPNGSAGTHAGLAAGFRLLGRGTSMVKSFSVLSDQESSI 238 Query: 225 SKLDNLIKEAAELLGVKVEVRPELYDYSFGE----YGKITGEVAQIIRKVGTREGIILDP 280 ++ L +E LL +VR + + YG T + +R + EG+++DP Sbjct: 239 ARTLQLTRETLALLDSNAQVRADELVVDGSQLGTGYGLPTAAMQDAVRLMARAEGLLVDP 298 Query: 281 VYTGKAFYGLVDLARKGEL--GEKILFIHTGGISGTFHY 317 VY+GKAF GL+ ++G G+ +LFI TGG G + Y Sbjct: 299 VYSGKAFAGLLADLQQGRFVPGDNVLFIMTGGTPGLYAY 337 Lambda K H 0.319 0.142 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: 266 Number of extensions: 16 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: 325 Length of database: 343 Length adjustment: 28 Effective length of query: 297 Effective length of database: 315 Effective search space: 93555 Effective search space used: 93555 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 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