Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate BWI76_RS24285 BWI76_RS24285 cystathionine beta-lyase
Query= BRENDA::P06721 (395 letters) >FitnessBrowser__Koxy:BWI76_RS24285 Length = 395 Score = 694 bits (1790), Expect = 0.0 Identities = 337/395 (85%), Positives = 369/395 (93%) Query: 1 MADKKLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRG 60 MADK LDT LV+AGRSKKYT G+VNSVIQRASSLVFD+VEAKKHATRNRA GELFYGRRG Sbjct: 1 MADKHLDTALVHAGRSKKYTQGSVNSVIQRASSLVFDTVEAKKHATRNRAKGELFYGRRG 60 Query: 61 TLTHFSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSK 120 TLTHFSLQ+AMCELEGGAGC LFPCGAAAVAN+ILAF+EQGDH+L+TNTAYEP+QDFC+K Sbjct: 61 TLTHFSLQEAMCELEGGAGCALFPCGAAAVANTILAFVEQGDHILVTNTAYEPTQDFCTK 120 Query: 121 ILSKLGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDA 180 IL+KLGVTT WFDPLIG DI + +QPNT++VFLESPGSITMEVHDVPAIVAAVR V P+A Sbjct: 121 ILAKLGVTTGWFDPLIGGDIARLVQPNTRVVFLESPGSITMEVHDVPAIVAAVRRVAPEA 180 Query: 181 IIMIDNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLM 240 IIMIDNTWAAGVLFKAL+FGID+SIQA TKYL+GHSDAM+GTAV N RCW QLRENAYLM Sbjct: 181 IIMIDNTWAAGVLFKALEFGIDISIQAGTKYLIGHSDAMVGTAVSNERCWAQLRENAYLM 240 Query: 241 GQMVDADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFW 300 GQMVDADTAY+TSRGLRTL VRLRQHHESSL++AEWLA+HPQVARVNHPALPGSKGHEFW Sbjct: 241 GQMVDADTAYMTSRGLRTLAVRLRQHHESSLQIAEWLAQHPQVARVNHPALPGSKGHEFW 300 Query: 301 KRDFTGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRP 360 +RDFTGSSGLFSFVL K+L + EL+ YLD+FSLFSMAYSWGG+ESLILANQPEHIAAIRP Sbjct: 301 QRDFTGSSGLFSFVLNKRLTDAELSAYLDHFSLFSMAYSWGGFESLILANQPEHIAAIRP 360 Query: 361 QGEIDFSGTLIRLHIGLEDVDDLIADLDAGFARIV 395 E+DFSGTLIRLHIGLE+V DL DL AGFARIV Sbjct: 361 DAEVDFSGTLIRLHIGLENVTDLQDDLAAGFARIV 395 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: 579 Number of extensions: 13 Number of successful extensions: 1 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: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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