Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_011190189.1 DP_RS14915 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_000025945.1:WP_011190189.1 Length = 386 Score = 283 bits (723), Expect = 8e-81 Identities = 149/372 (40%), Positives = 223/372 (59%), Gaps = 9/372 (2%) Query: 23 AVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSLQQAMCELEGGAGCVL 82 ++N I +AS+L+F S A + G L YG + ++A+C+LEGG C Sbjct: 24 SINPPIHKASTLLFASYADLALANEGKYPG-LTYGTDRLPAQRAFEEALCQLEGGEICRA 82 Query: 83 FPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLGVTTSWFDPLIGADIVK 142 F G A+ +++ AF + GDH+++ + Y P+ +FC+K+LSK GV S+ +GADI Sbjct: 83 FQSGINAIVHTLQAFTKAGDHIVVCDNVYWPTSNFCNKVLSKFGVEISYAPSAVGADIAD 142 Query: 143 HLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDNTWAAGVLFKALDFGID 202 +L+ NT ++F+ESPGS T E+ D+ AI R+ D + ++D TW + +AL FG+D Sbjct: 143 YLRDNTSLIFMESPGSNTFEIQDIEAITQIARA--RDIVTILDGTWGTPLYHRALSFGVD 200 Query: 203 VSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDADTAYITSRGLRTLGVR 262 VSIQ+ATKY+ GHSD ++GTA N + + L + Y RGL+TL VR Sbjct: 201 VSIQSATKYISGHSDILLGTATVNHKYADILARYYQSLELFAPPADCYAALRGLKTLHVR 260 Query: 263 LRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLKKKLNNE 322 L+ H +S+L++A+WL PQ R+ HPA P H WK+ FTGS GLF+F KK+ + + Sbjct: 261 LKHHEQSALQIADWLESQPQTGRIIHPARPDHPQHSRWKKYFTGSCGLFAFTFKKEPSEK 320 Query: 323 ELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEIDFSGTLIRLHIGLEDVDD 382 EL +++ LF + YSWGGY+SLI A + +R +++ S T+IRL+IGLE V+D Sbjct: 321 ELGEFINALQLFGIGYSWGGYKSLITAGK-----YVRNGSDLNGS-TVIRLNIGLEAVED 374 Query: 383 LIADLDAGFARI 394 L DL AR+ Sbjct: 375 LCHDLAQALARL 386 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: 363 Number of extensions: 12 Number of successful extensions: 4 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: 386 Length adjustment: 31 Effective length of query: 364 Effective length of database: 355 Effective search space: 129220 Effective search space used: 129220 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