Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate WP_013402806.1 CALHY_RS04440 alanine racemase
Query= BRENDA::Q04HB7 (371 letters) >NCBI__GCF_000166355.1:WP_013402806.1 Length = 390 Score = 167 bits (424), Expect = 3e-46 Identities = 119/372 (31%), Positives = 201/372 (54%), Gaps = 20/372 (5%) Query: 12 EFSKSSLAYNVQYTKQVSGAKTLWLAV-KSNAYGHGLLQVSKIARECGVDGLAVSVLDEG 70 E +L YN++ K+ +T +AV K++AYGHG +++S++ + GV LAV+++DE Sbjct: 13 EIDLDNLVYNLENIKKKILPQTHIMAVVKADAYGHGAVEISRVLVKNGVSMLAVAIIDEA 72 Query: 71 IAIRQAGIDDFILILG--PIDVKYAPIASKY-HFLTTVSSLDWLKSADKILGKEKLSVNL 127 + +R D ILILG P ++ + ++ + T +L A + +GK K +++ Sbjct: 73 LQLRHFNFDVPILILGFTPFELSEQVVENEISQTVYTYEQAYYLSQAAQKVGK-KAKIHI 131 Query: 128 AVDTGMNRIGVRSKKDLKDEIEFLQEHSDHFSYDGIFTHFASSDNPDDHYFQRQK----- 182 VDTGM RIG + + + + + +GIF+HF+S+D+PD F ++ Sbjct: 132 KVDTGMGRIGFLCCDESIQTVLNIAK-LPNIELEGIFSHFSSADDPDSDNFTHEQFMKFE 190 Query: 183 NRWYELIDGLIMPRYVHVMNSGAAM-YHSKELPGCNSIARVGTVVYGVEPSEGVLGPIDK 241 N EL + +Y H+ NS AA+ + +L + R+G ++YG+ P+ + I Sbjct: 191 NFVKELNKNGVYFKYKHIANSSAAIRFPQYQL----DVVRLGLILYGLYPNSSLKEHIS- 245 Query: 242 LKPVFELKSALTFVKKIPAGEGISYGSKFVTSRDTWIGTLPIGYGDGWL-AEYQDFQLLI 300 +KPV +K+ + VK++P G ISY +++T+R + I T+PIGY DG+ +LI Sbjct: 246 IKPVMSVKARVINVKEVPEGFPISYNRRYITTRKSKIATIPIGYADGFTRVGSSQRHVLI 305 Query: 301 DGQKCRQVGQIAMDQMMVALP--HEYPIGTEVTLIGKSGKYENTLYDLHKHSGVPPWKIT 358 G+ + VG I MDQ MV + + IG EV +IGK GK E L + G ++I Sbjct: 306 KGEFAKVVGSICMDQCMVDVTDIEDVKIGDEVVIIGKQGKNEILADHLAEQIGTINYEIV 365 Query: 359 VAFSDRLKRMVV 370 +FS R+ R+ + Sbjct: 366 CSFSKRIPRVYI 377 Lambda K H 0.319 0.137 0.410 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: 345 Number of extensions: 18 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: 371 Length of database: 390 Length adjustment: 30 Effective length of query: 341 Effective length of database: 360 Effective search space: 122760 Effective search space used: 122760 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: 50 (23.9 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