Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13); alanine racemase (EC 5.1.1.1); glutamate racemase (EC 5.1.1.3) (characterized)
to candidate SMc01976 SMc01976 hypothetical protein
Query= BRENDA::Q9X0Z7 (379 letters) >FitnessBrowser__Smeli:SMc01976 Length = 390 Score = 257 bits (656), Expect = 4e-73 Identities = 155/379 (40%), Positives = 212/379 (55%), Gaps = 26/379 (6%) Query: 12 EEDIPLKALSFPIFETTNFYFDSFDEMSKALRNGDYEFVYKRGSNPTTRLVEKKLAALEE 71 +E A+ PI +T+ F F +DEM + R +Y RG NPT R E+ LA LE Sbjct: 18 DESNAFDAVVPPIVQTSLFTFKDYDEMVASYRGERVRPIYTRGLNPTVRHFEEMLAKLEG 77 Query: 72 CEDARLVASGMSAISLSILHFLSSGDHVVCVDEAYSWAKKFFNYLSKKFDIEVSYVPPDA 131 EDA ASGMSAIS ++L F+ GD +V V Y A + F K+ +EV+YV Sbjct: 78 AEDAIGFASGMSAISSTVLSFVEPGDRIVAVKHVYPDAFRLFGTHLKRMRVEVTYVDGRD 137 Query: 132 ERIVEAITKKTKLIYLESPTSMRMKVIDIRKVTEAAGELKIKTVIDNTWASPIFQKPKLL 191 E V KL Y+ESPTS M D+ + A I TVIDN+WASP+FQ+P L Sbjct: 138 EEAVAKALPGAKLFYMESPTSWVMDTHDVAALAALARRQGIVTVIDNSWASPVFQQPVSL 197 Query: 192 GVDVVVHSATKYISGHGDVMAGVIAGDVEDMKNIFVDEYKNIGPVLSPIEAWLILRGLRT 251 GVD+V+HSA+KY+ GH DV+AGV+AG E + I + Y +G LSP +AWL++RG+RT Sbjct: 198 GVDLVIHSASKYLGGHSDVVAGVVAGSGELIGRIRSEAYPYLGGKLSPFDAWLLIRGMRT 257 Query: 252 LELRMKKHYENALVVSDFLMDHPKVLEVNYP-MNPRSPQYELASSQMSGGSGLMSFRLKT 310 L +RMK H +AL V+ L +HP V V +P + P +SG SGL SF + Sbjct: 258 LPVRMKAHERSALAVARRLAEHPLVETVCHPGLGNHLP------PGLSGTSGLFSFIFR- 310 Query: 311 DSAEKVKEFVESLRVFRMAVSWGSHENLVVP-------------RVAYGDCPKKDVNLIR 357 V+ F + L++F++ VSWG HE+L+VP A+G P+ +R Sbjct: 311 -EGVDVRRFADHLKLFKLGVSWGGHESLIVPGEVVLAQKAEPNSAAAFGISPRS----VR 365 Query: 358 IHVGLGDPEKLVEDLDQAL 376 +HVGL E L DL+ A+ Sbjct: 366 LHVGLEGTEALWSDLEAAM 384 Lambda K H 0.318 0.136 0.391 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: 16 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: 379 Length of database: 390 Length adjustment: 30 Effective length of query: 349 Effective length of database: 360 Effective search space: 125640 Effective search space used: 125640 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 Apr 09 2024. The underlying query database was built on Apr 09 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