Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate CA265_RS08180 CA265_RS08180 O-acetylhomoserine aminocarboxypropyltransferase
Query= SwissProt::Q83A83 (387 letters) >FitnessBrowser__Pedo557:CA265_RS08180 Length = 443 Score = 228 bits (581), Expect = 3e-64 Identities = 145/422 (34%), Positives = 222/422 (52%), Gaps = 48/422 (11%) Query: 12 DTRVIHAGQKPDPLTGAVMTPIYTASTYAQKSP--GVHQ------GYEYSRSQNPTRFAY 63 +T +HAGQ+ DP TG+ PIY ++Y K+ G + G Y+R NPT + Sbjct: 8 ETLQLHAGQEIDPTTGSRAVPIYQTTSYGFKNAEHGANLFALKEFGNIYTRIMNPTNDVF 67 Query: 64 ERCVADLESGQHGFAFASGMAATATILE-LLQPGDHVVVMDDVYGGSYRLFENVRKRSAG 122 E+ +A LE G A ASG AA L +L+ GD +V +YGG+Y F+ KR G Sbjct: 68 EKRIAALEGGVAALAVASGQAAQFIALNNILEAGDSIVSSSHIYGGTYNQFKVAFKR-LG 126 Query: 123 LSFSFVDFTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTF 182 + F + + +T KTK +++E+ NP + D KIA IAK+ ++ V DNTF Sbjct: 127 IHVDFANPDVPEEFENKITDKTKAIFLETIGNPAFSVPDFEKIAAIAKKYDLPLVVDNTF 186 Query: 183 -ATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAE-------------- 227 A + +PLE G +IV SATK++ GH IGGV V G N Sbjct: 187 GAGGYLFKPLEHGANIVVESATKWIGGHGTSIGGVIVDGGNYNWGNGKFPQFSEPSEGYH 246 Query: 228 ---------------QLKYLQNA-------IGAIAAPFDSFMVLRGLKTLAIRMERHCEN 265 ++++ A +G +PF+SF++L+GL+TL++R++RH +N Sbjct: 247 GLVFSDVFGIGGPFGNIQFIIRARVEGLRDLGPALSPFNSFLLLQGLETLSLRVQRHVDN 306 Query: 266 AMQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQM-RYFGGMISVELKCDLNETKKVLER 324 A++LA WLE HP VK V YPGL S +++AKK + FG ++S EL +V++ Sbjct: 307 ALELATWLENHPLVKEVQYPGLASSKYNNLAKKYLSNGFGAVLSFELTGSKENATQVVDN 366 Query: 325 CQLFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVGIEAITDLRHDLE 384 +L + ++G ++LI P+ TH + + E+ G+ +R+SVGIE I D++ D E Sbjct: 367 LKLVSHLANVGDAKTLIIQPSATTHQQLSETEQLAAGVKPNALRVSVGIEHIDDIKADFE 426 Query: 385 AA 386 A Sbjct: 427 QA 428 Lambda K H 0.319 0.134 0.385 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: 423 Number of extensions: 26 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 387 Length of database: 443 Length adjustment: 31 Effective length of query: 356 Effective length of database: 412 Effective search space: 146672 Effective search space used: 146672 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 (21.8 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