Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_011318199.1 AVA_RS06945 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase
Query= BRENDA::O57809 (325 letters) >NCBI__GCF_000204075.1:WP_011318199.1 Length = 307 Score = 129 bits (324), Expect = 9e-35 Identities = 98/305 (32%), Positives = 152/305 (49%), Gaps = 12/305 (3%) Query: 23 PIQYLPN-ISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSKGADVVITVGAVHS 81 PIQ + + I+ G ++ + R DL + GNK KL+Y L +A KG ++T G +S Sbjct: 9 PIQKINSEIANNAGVEIDVLRLDLMHPWVNGNKWYKLKYNLLEAKEKGYTTLLTFGGAYS 68 Query: 82 NHAFVTGLAAKKLGLDAILVLRGKEELKGNYLLD--KIMGIETRVYDAKDSFELMKYAEE 139 NH F T A LG I V+RG+E L N L G++ VY ++++ A Sbjct: 69 NHIFATAAAGNLLGFQTIGVIRGEETLPLNPTLSFATKQGMQL-VYVDRETYRQRNSATL 127 Query: 140 IAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSEVKFDSIVVAAGSGGTLAGLS 199 A+ KR G + ++IP GG++ L VR EI + + F+ + VA G+ TLAG++ Sbjct: 128 HADLRKRFG-EVFIIPEGGSN----LNGVRGCLEIISAATQAFNIVCVACGTATTLAGIA 182 Query: 200 LGLSILNEDIR-PVGIAVGRFGEVMTSKLDNLIKEAAELLGVKVEVRPELYDYSFGEYGK 258 L L I PV G E +T ++N + + + DY FG Y K Sbjct: 183 LALEAKQRVIGFPVLKNGGFLAEEITQFMNNYVAAGLPISSSSPAHWELVCDYHFGGYAK 242 Query: 259 ITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLARKGEL--GEKILFIHTGGISGTFH 316 + ++ ++ G+ LD VYT K FYG++DL ++ G++IL IHTGG+ G Sbjct: 243 VKDDLIVFSQQFTQTHGVPLDYVYTAKMFYGVMDLLKQRYFTKGDRILMIHTGGLQGNIG 302 Query: 317 YGDKL 321 ++L Sbjct: 303 MSERL 307 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: 203 Number of extensions: 10 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: 325 Length of database: 307 Length adjustment: 27 Effective length of query: 298 Effective length of database: 280 Effective search space: 83440 Effective search space used: 83440 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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