Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate Ga0059261_1388 Ga0059261_1388 cystathionine beta-lyase, bacterial
Query= BRENDA::P06721 (395 letters) >FitnessBrowser__Korea:Ga0059261_1388 Length = 411 Score = 343 bits (879), Expect = 7e-99 Identities = 176/388 (45%), Positives = 258/388 (66%), Gaps = 9/388 (2%) Query: 8 TQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTHFSL 67 T++V AGR ++T G VN+ + RAS++++D+V + + + + LFYGRRG+ T +SL Sbjct: 26 TRVVGAGRRPEWTQGIVNAPVWRASTILYDTVADLRASAGSDTHHRLFYGRRGSPTQWSL 85 Query: 68 QQAMCELEGGAGCV-LFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSKLG 126 +A+ ELE GA L+P G AAV+ ++L+ + GD +L+ ++ Y+P++ F + L + G Sbjct: 86 AEALTELEPGAEATFLYPSGVAAVSAALLSVLSPGDELLLADSVYDPTRSFATGFLKRFG 145 Query: 127 VTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMIDN 186 V T ++DP+IGA I + + T+ +F+E+PGS+T EV DVPAIVAA ++ + ++DN Sbjct: 146 VITRFYDPMIGAGIAELITDKTRAIFMETPGSLTFEVQDVPAIVAAAKA--RGVVTLLDN 203 Query: 187 TWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMVDA 246 TWA +LF A++ GID+SI A TKY+VGHSD M+G+ A W+QLR ++ +GQ Sbjct: 204 TWATPLLFPAIEKGIDLSILACTKYVVGHSDVMLGSVTATAEHWQQLRATSFALGQTASP 263 Query: 247 DTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDFTG 306 D A++ SRGLRT+ +RL+QH E++L++A WL P+VARV HPALP GH+ + RDF G Sbjct: 264 DDAWLGSRGLRTMALRLKQHGEAALEIARWLETRPEVARVLHPALPSCPGHDLFVRDFKG 323 Query: 307 SSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRP-QGEID 365 +GLFSFVL+ N A +D+ LF + YSWGG+ESL + P+ I + P Q E Sbjct: 324 PAGLFSFVLRGG-NEAGRAALIDSLELFGIGYSWGGFESLAIPVDPDRIRTVIPWQAE-- 380 Query: 366 FSGTLIRLHIGLEDVDDLIADLDAGFAR 393 G +RL IGLED DLIADL AG R Sbjct: 381 --GPAVRLQIGLEDPADLIADLAAGLDR 406 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: 391 Number of extensions: 17 Number of successful extensions: 5 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: 411 Length adjustment: 31 Effective length of query: 364 Effective length of database: 380 Effective search space: 138320 Effective search space used: 138320 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 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