Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_011446196.1 SARO_RS12875 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_000013325.1:WP_011446196.1 Length = 410 Score = 271 bits (693), Expect = 2e-77 Identities = 164/401 (40%), Positives = 228/401 (56%), Gaps = 20/401 (4%) Query: 1 MADKKLDTQLVNAGRSKKYTL------GAVNSVIQRASSLVFDSVEAKKHATRNRANGEL 54 M+D T+ V AGR +++T VN + RAS+ ++ + A + N +G Sbjct: 7 MSDLGPGTRGVLAGRREEWTGTPDHPGAVVNPAVWRASTHLYPDMAALRAHPANE-DGRF 65 Query: 55 FYGRRGTLTHFSLQQAMCELE-GGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEP 113 +YGRRG T ++L +A+ ++E G AG VL+P G AA+A +L + GD +LMT+ AYEP Sbjct: 66 YYGRRGAPTQWALAEALTQIEPGAAGTVLYPSGVAAIAGVLLTMLRPGDVLLMTDNAYEP 125 Query: 114 SQDFCSKILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAV 173 S+ +L GV T WFDP TK V LESPGS+TMEV DVPA+ AA Sbjct: 126 SRVMARGLLRDFGVETRWFDPTSIGAFEAACCDRTKAVLLESPGSLTMEVQDVPALAAAA 185 Query: 174 RSVVPDAIIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQL 233 ++ + ++DNTWA+ + F L G+D+ + TK++ GHSD M+G+A + +L Sbjct: 186 KA--RGIVSVLDNTWASPLGFAGLSHGVDIVAMSLTKHVSGHSDCMMGSASAGPDWYRKL 243 Query: 234 RENAYLMGQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPG 293 R + +G +V D A + RGLRT+ +RL S+L +A WL P+VARV P LPG Sbjct: 244 RLRSQGLGLVVSPDDASLMLRGLRTMKMRLEAETASALAIAGWLEGRPEVARVLCPMLPG 303 Query: 294 SKGHEFWKRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPE 353 S GHE W RDF G GLFSFVLK + A +D +LF + YSWGG+ESL P Sbjct: 304 SPGHELWARDFAGGCGLFSFVLKGGSSAARDA-LIDALALFGIGYSWGGFESLATPVDP- 361 Query: 354 HIAAIRPQGEIDFSGTL------IRLHIGLEDVDDLIADLD 388 A+IR +G +RL IGLED DLIAD++ Sbjct: 362 --ASIRTASAWPLAGMAMEDRFGVRLSIGLEDTADLIADIE 400 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: 426 Number of extensions: 19 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: 410 Length adjustment: 31 Effective length of query: 364 Effective length of database: 379 Effective search space: 137956 Effective search space used: 137956 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 Apr 10 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