Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate WP_012566352.1 RC1_RS05470 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >NCBI__GCF_000016185.1:WP_012566352.1 Length = 401 Score = 338 bits (868), Expect = 1e-97 Identities = 183/394 (46%), Positives = 252/394 (63%), Gaps = 11/394 (2%) Query: 3 DKKLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTL 62 D L T+L +AGR+ GAVN RAS+++ ++ A + + YGR GT Sbjct: 12 DLDLSTRLAHAGRAPGSHAGAVNIPPYRASTILHPTLAA--FLAPDPEYRSVRYGRMGTP 69 Query: 63 THFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKIL 122 + + ++AM ELEGG G V G A+ ++ AF+ GDH+L+T++ Y P++ FC ++L Sbjct: 70 SSHAFEEAMAELEGGCGAVAVGSGLQAITVALSAFVRAGDHILVTDSVYGPTRHFCDQML 129 Query: 123 SKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAII 182 ++LGV T ++DP IGA I ++ NT+++ LESPGS+T E+ DVPAIVAA R+ + Sbjct: 130 ARLGVETEFYDPGIGAGIAGLIRENTRLIMLESPGSLTFEMQDVPAIVAAARA--RGCLT 187 Query: 183 MIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNAR-CWEQLRENAYLMG 241 +IDNTWAAGV FK L G+DVSIQAATKY+ GHSDA +G V C ++++A ++G Sbjct: 188 LIDNTWAAGVFFKPLALGVDVSIQAATKYVCGHSDATLGVIVAREEACRMAVKQSAVMLG 247 Query: 242 QMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWK 301 AD ++ RGLRTL VRL +H E+ +++A W+A P+V RV HPALP GH W+ Sbjct: 248 AAAGADDLFLALRGLRTLPVRLARHQETGIRLARWMAGQPEVRRVLHPALPDDPGHALWQ 307 Query: 302 RDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRP- 360 RDFTG+ GLF+ L ++ + LA LD SLF M YSWGG+ESLIL P+ I P Sbjct: 308 RDFTGACGLFAVEL-DRIPQDALAAMLDGLSLFGMGYSWGGFESLILPAFPDRIRTAVPW 366 Query: 361 QGEIDFSGTLIRLHIGLEDVDDLIADLDAGFARI 394 +G GTLIRLH GLED +DLI DLD F R+ Sbjct: 367 RGR----GTLIRLHAGLEDAEDLIRDLDRAFDRL 396 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: 380 Number of extensions: 14 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: 401 Length adjustment: 31 Effective length of query: 364 Effective length of database: 370 Effective search space: 134680 Effective search space used: 134680 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