Align lysine racemase (EC 5.1.1.5) (characterized)
to candidate BWI76_RS17730 BWI76_RS17730 alanine racemase
Query= BRENDA::Q04HB7 (371 letters) >FitnessBrowser__Koxy:BWI76_RS17730 Length = 356 Score = 127 bits (320), Expect = 4e-34 Identities = 114/372 (30%), Positives = 177/372 (47%), Gaps = 26/372 (6%) Query: 7 RSTRIEFSKSSLAYNVQYTKQVSGAKTLWLAVKSNAYGHGLLQVSKIARECGVDGLAVSV 66 R + S+L N Q ++ + A LW VK+NAYGHGL +V DG A+ Sbjct: 3 RPVKASIDMSALRQNQQIVRRAAPASRLWAVVKANAYGHGLARVWNALS--AADGFAMLN 60 Query: 67 LDEGIAIRQAGIDDFILIL-GPIDVKYAPIASKYHFLTTVSSLDWLKSADKILGKEKLSV 125 L+E I +R+ G IL+L G + KY T+V S +K+ + L + Sbjct: 61 LEEAILLRELGWKGPILMLEGFFHADELALFDKYRLTTSVHSNWQIKALQQAKLHAPLDI 120 Query: 126 NLAVDTGMNRIGVRSKKDLKDEIEFLQEHSDH-FSYDGIFTHFASSDNPDDHYFQRQKNR 184 + V++GMNR+G + I + Q S H S + +HFA ++NPD R Sbjct: 121 YVKVNSGMNRLGFMPDRL---HIVWQQLRSLHNVSEMTLMSHFAEAENPDG--IVEPMRR 175 Query: 185 WYELIDGLIMPRYVHVMNSGAAMYHSKELPGCNSIARVGTVVYGVEPSEGVLGPIDK--L 242 + +GL PR + NS A ++H + + R G V+YG PS G+ + L Sbjct: 176 IEQAAEGLDCPR--SLANSAATLWHPESH---FNWVRPGIVLYGASPS-GLWQDVANTGL 229 Query: 243 KPVFELKSALTFVKKIPAGEGISYGSKFVTSRDTWIGTLPIGYGDGW--LAEYQDFQLLI 300 KPV L S + V+ + AGE + YG+ + T+ + IG + GY DG+ LA +L+ Sbjct: 230 KPVMTLSSEIIAVQNLKAGEAVGYGATWRTAEERRIGIVACGYADGYPRLAP-SGTPVLV 288 Query: 301 DGQKCRQVGQIAMDQMMVALP--HEYPIGTEVTLIGKSGKYENTLYDLHKHSGVPPWKIT 358 DG + VG+I+MD + V L + IG V L GK K + D+ G +++ Sbjct: 289 DGVRTATVGRISMDMLAVDLTPCPQAGIGAPVELWGKEIKID----DVASACGTVGYELM 344 Query: 359 VAFSDRLKRMVV 370 A + R+ + V Sbjct: 345 CALAPRVPVVTV 356 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: 328 Number of extensions: 21 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: 356 Length adjustment: 29 Effective length of query: 342 Effective length of database: 327 Effective search space: 111834 Effective search space used: 111834 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