Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate CCNA_02112 CCNA_02112 D-cysteine desulfhydrase
Query= BRENDA::O57809 (325 letters) >FitnessBrowser__Caulo:CCNA_02112 Length = 333 Score = 223 bits (569), Expect = 4e-63 Identities = 132/324 (40%), Positives = 180/324 (55%), Gaps = 17/324 (5%) Query: 9 LAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSK 68 LA+FPR TP++ +P + E+G D+++KRDD TGL GGNK RKLE+LLG+AL + Sbjct: 3 LARFPRARFAHLPTPLEPMPRLGAELGIDLWVKRDDCTGLAGGGNKTRKLEFLLGEALIQ 62 Query: 69 GADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKEELK-------GNYLLDKIMGIE 121 GAD ++T GAV SNH T A + GL ++L + K GN LLDK+MG Sbjct: 63 GADTLVTQGAVQSNHVRQTIAAGARFGLKTEVILEERTGSKASDYMGNGNVLLDKLMGAS 122 Query: 122 TRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEI---ATQS 178 R +++ + AE +++ G KPYVIP GG++ +G LGYV E+ A Q Sbjct: 123 LRY--VPGGTDMVAELDSTAENVRQRGGKPYVIPGGGSNTVGALGYVDCARELVVQADQM 180 Query: 179 EVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELL 238 ++K D +V A GS GT AGL G + L+ DI +G V + NL AE + Sbjct: 181 DLKIDRLVTATGSAGTHAGLVAGFAALSVDIPILGFGVRAPKPKQEENVYNLAVATAETI 240 Query: 239 GVKVEVRPELY----DYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLA 294 G VR E DY YG + V + EG++LDPVY+GKA GL+D A Sbjct: 241 GAGGRVRREAVVADCDYVGEGYGLVDQGVIDALALAARTEGLLLDPVYSGKAMKGLIDQA 300 Query: 295 RKGEL-GEKILFIHTGGISGTFHY 317 RKG GE+++F+HTGG G F Y Sbjct: 301 RKGAFKGERVVFLHTGGAQGLFGY 324 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: 303 Number of extensions: 11 Number of successful extensions: 5 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: 333 Length adjustment: 28 Effective length of query: 297 Effective length of database: 305 Effective search space: 90585 Effective search space used: 90585 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