Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_085217314.1 B9N75_RS02160 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_900177405.1:WP_085217314.1 Length = 407 Score = 344 bits (882), Expect = 3e-99 Identities = 189/394 (47%), Positives = 250/394 (63%), Gaps = 11/394 (2%) Query: 2 ADKKLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGT 61 +D++ DT +V AGR +++ AVN AS+++FD+V + A A+G +YGR GT Sbjct: 20 SDRRRDTTIVQAGRRREWIGAAVNPPTWHASTILFDTVAEMEAAAP--ADGTFYYGRHGT 77 Query: 62 LTHFSLQQAMCELEGGA-GCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSK 120 T ++L +A+ LE GA G LFP GAAAVA ++LA + GD +LM ++AY P++ C Sbjct: 78 PTTWALSEALTALEPGAVGTRLFPSGAAAVAMALLAVLRPGDELLMVDSAYGPTRAICDS 137 Query: 121 ILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDA 180 L +LG+TT ++DPLIGADI + T+ +FLESPGS+T EV DVPAIVA R Sbjct: 138 ELKRLGITTRYYDPLIGADIAALIGDKTRAIFLESPGSLTFEVQDVPAIVAVARE--RGI 195 Query: 181 IIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLM 240 +IDNTWA + F A+ G+D+SI A TKY+ GHSD M+G+ + R W++LR+ + Sbjct: 196 ATLIDNTWATPLFFPAIAAGVDISILACTKYIGGHSDLMMGSVTVSERWWDRLRQVFRMY 255 Query: 241 GQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFW 300 GQ V D A +RGLRTLGVR+ +H ++L VA WLA PQVARV HPAL GH W Sbjct: 256 GQAVGPDDAAACARGLRTLGVRMERHQANALTVANWLANQPQVARVLHPALADCPGHALW 315 Query: 301 KRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRP 360 RDF GSSGLFS +L + A +D F++ YSWGGYESL + PE + + P Sbjct: 316 SRDFKGSSGLFSIILNGG-DAAARAALIDGLEHFAIGYSWGGYESLAVPADPERLRSATP 374 Query: 361 -QGEIDFSGTLIRLHIGLEDVDDLIADLDAGFAR 393 Q E G L+RLHIGLED DDLI DL G AR Sbjct: 375 WQAE----GPLVRLHIGLEDPDDLIEDLARGLAR 404 Lambda K H 0.321 0.135 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: 431 Number of extensions: 20 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: 395 Length of database: 407 Length adjustment: 31 Effective length of query: 364 Effective length of database: 376 Effective search space: 136864 Effective search space used: 136864 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
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