Align alanine racemase (EC 5.1.1.1) (characterized)
to candidate 5209311 Shew_1789 cystathionine beta-lyase (RefSeq)
Query= BRENDA::P06721 (395 letters) >FitnessBrowser__PV4:5209311 Length = 395 Score = 421 bits (1083), Expect = e-122 Identities = 204/389 (52%), Positives = 282/389 (72%), Gaps = 5/389 (1%) Query: 5 KLDTQLVNAGRSKKYTLGAVNSVIQRASSLVFDSVEAKKHATRNRANGELFYGRRGTLTH 64 K +T++V+ GR KK++ G +N + RAS++VFD++E +HAT+NRANG +FYGRRGT TH Sbjct: 2 KKETKIVSVGRDKKWSKGVINPPVFRASTVVFDTIEDMRHATKNRANGAMFYGRRGTPTH 61 Query: 65 FSLQQAMCELEGGAGCVLFPCGAAAVANSILAFIEQGDHVLMTNTAYEPSQDFCSKILSK 124 F+ Q A+ ELEGG G L+P G+AA++ ++L+F++ GDH+LM +TAYEP++D C K+L Sbjct: 62 FAFQAAIAELEGGVGTALYPSGSAAISGALLSFLKAGDHLLMVDTAYEPTRDLCDKLLKG 121 Query: 125 LGVTTSWFDPLIGADIVKHLQPNTKIVFLESPGSITMEVHDVPAIVAAVRSVVPDAIIMI 184 G+ T+++DPLIG I ++PNTK++FLESPGSIT+EV DVP + A + ++M+ Sbjct: 122 FGIETTYYDPLIGDGIEALIRPNTKVLFLESPGSITLEVQDVPTLSAIAHR--HNLVVML 179 Query: 185 DNTWAAGVLFKALDFGIDVSIQAATKYLVGHSDAMIGTAVCNARCWEQLRENAYLMGQMV 244 DNTWA+ + + + G+D+SIQAATKY+VGHSD M+GTA N W+QLREN+YLMGQ Sbjct: 180 DNTWASPINCRPFELGVDISIQAATKYIVGHSDVMLGTATANQAHWDQLRENSYLMGQCT 239 Query: 245 DADTAYITSRGLRTLGVRLRQHHESSLKVAEWLAEHPQVARVNHPALPGSKGHEFWKRDF 304 AD Y+ SRGLRTLGVR+ QH ++ L+VA LA P+V + HPA GHEF+KRDF Sbjct: 240 SADDIYLASRGLRTLGVRMAQHEKNGLEVANLLATRPEVDHLRHPAFASCPGHEFFKRDF 299 Query: 305 TGSSGLFSFVLKKKLNNEELANYLDNFSLFSMAYSWGGYESLILANQPEHIAAIRPQGEI 364 + S+GLFSFVLK+ N + + +++ F M +SWGGYESLIL I +R + Sbjct: 300 SASNGLFSFVLKRG-NIKAITAFVEGMDHFKMGFSWGGYESLILG--VFGIDKLRTATQW 356 Query: 365 DFSGTLIRLHIGLEDVDDLIADLDAGFAR 393 D S LIRLH+GLE+ +DLI DL+AGFAR Sbjct: 357 DSSKPLIRLHVGLENPEDLIKDLEAGFAR 385 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: 435 Number of extensions: 17 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: 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