Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_004511499.1 GMET_RS07870 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::A0A0M3VI47 (457 letters) >NCBI__GCF_000012925.1:WP_004511499.1 Length = 414 Score = 199 bits (506), Expect = 1e-55 Identities = 129/407 (31%), Positives = 215/407 (52%), Gaps = 32/407 (7%) Query: 80 LSTVVMNFENEFDPYEAVSTPIYQTATFKQPSATV--------NGPYDYTRSGNPTRDAL 131 L T++++ E P A + PI Q+++F +A + YTR NPT ++L Sbjct: 7 LDTLLIHGGLEPGPAGATTVPIVQSSSFAHETAEDLEDIFRGRKAGHVYTRINNPTTESL 66 Query: 132 ERLLAKLDKADRAFCFGSGMAALS-AVSQLFENGDEIIAGDDIYGGSDRLLSSVIPRTGV 190 ER LA L+ A SGMAA++ AV + GDEI++ ++GG+ L + G+ Sbjct: 67 ERRLALLEGGISAIATSSGMAAITLAVLSIVRCGDEILSSASLFGGTFSLFRDTLSNYGI 126 Query: 191 VVKRVNTSDLEEVASAFGPATKLVWLESPTNPRLQISDIGKIAEMAHARGVLVLVDNSIM 250 + V+ SDL + +A T+L+++E+ NPRL + D+ +A +A GV ++VD ++ Sbjct: 127 ATRFVDPSDLAAMRAAVTERTRLIFVETMGNPRLDVPDLAALAAIAREAGVPLVVDATVT 186 Query: 251 SPVLCQPLELGADIVMHSATKFIGGHSYIMAGVIA------------------VKGER-- 290 +PVL + ELGADI++HS +K+I G + G I VK R Sbjct: 187 TPVLGRVKELGADIIVHSTSKYINGTGSAIGGAIIDCGTFDWRRESYPHFEPYVKKFRQF 246 Query: 291 --LAKEMYFLQNAVGSGLAPFDCWLCLQGIKTMELRVEKQQKSAQKIAEFLAFHPRVKKV 348 A+ + +G+ AP + +L +GI+TM LR+E+ +AQ++AEFLA HP+V V Sbjct: 247 AFSARARKLIHKDLGACPAPMNSYLLSEGIETMALRMERNCANAQRLAEFLAAHPKVAWV 306 Query: 349 NYAGLPGHPGRDLHYSQAKGA-GSVLSFLTGSLALSKHVVESTKYFSITVSFGSVKSLIS 407 NY GL P + +Q G G++L+F A + H ++ + + G K+L+ Sbjct: 307 NYPGLTSSPWHETAKAQFGGRYGALLTFGLADKAAAFHCIDGLRLAKNLANIGDTKTLVI 366 Query: 408 MPCFMSHASIPVAVREARGLTEDLVRISVGIENVDDLIADLDQALSS 454 P A + G++E+++R+SVGIE +DD+I D ++L++ Sbjct: 367 HPASTICADFGPEEKALMGVSEEMIRVSVGIEAIDDIIEDFAESLNA 413 Lambda K H 0.318 0.134 0.386 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: 382 Number of extensions: 11 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: 457 Length of database: 414 Length adjustment: 32 Effective length of query: 425 Effective length of database: 382 Effective search space: 162350 Effective search space used: 162350 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 (21.7 bits) S2: 51 (24.3 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