Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_020176501.1 A3OQ_RS0116385 cystathionine beta-lyase
Query= BRENDA::P43623 (340 letters) >NCBI__GCF_000385335.1:WP_020176501.1 Length = 395 Score = 405 bits (1042), Expect = e-118 Identities = 201/328 (61%), Positives = 247/328 (75%), Gaps = 2/328 (0%) Query: 14 TQLSVIGRNPDEQSGFVNPPLYKGSTIILKKLSDLEQRKGRF-YGTAGSPTIDNLENAWT 72 T+L GR P EQSGFVN P+Y+GST++ L DL R+ F YGT GSPT + L+ AWT Sbjct: 16 TKLVHAGRKPSEQSGFVNTPIYRGSTVLFPTLDDLLNRRMPFTYGTQGSPTTEALQTAWT 75 Query: 73 HLTGGAGTVLSASGLGSISLALLALSKAGDHILMTDSVYVPTRMLCDGLLAKFGVETDYY 132 L+G GTV+ +GL +I++ALLA+ KAGDHIL++DSVY P R CD +L + GVET YY Sbjct: 76 ELSGAKGTVIVPTGLAAIAIALLAVVKAGDHILVSDSVYRPNRNFCDTILKRMGVETTYY 135 Query: 133 DPSIGKDIEKLVKPNTTVIFLESPGSGTMEVQDIPALVSVAKKHGIKTILDNTWATPLFF 192 +P IG IE L++PNT+VIFLE+PGS T EVQDIPA+V+VA+ GI TILDNTWATPLFF Sbjct: 136 EPLIGAGIEALIRPNTSVIFLETPGSQTFEVQDIPAIVAVARAKGICTILDNTWATPLFF 195 Query: 193 DAHAHGIDISVEAGTKYLGGHSDLLIGLASANEECWPLLRSTYDAMAMLPGAEDCQLALR 252 AHAHG+DIS+EAGTKYL GHSDLL+GL +ANE +P L +TYDA AM PG ED LALR Sbjct: 196 QAHAHGVDISLEAGTKYLSGHSDLLLGLVTANEVWYPALHATYDAFAMCPGPEDVFLALR 255 Query: 253 GMRTLHLRLKEVERKALDLAAWLGNRDEVEKVLHPAFEDCPGHEYWVRDYKGSSGLFSIV 312 GMRTL LRL E +R+ L +A WLG R EV KVLHPA CPGHE W RD+ GSSGLFSI+ Sbjct: 256 GMRTLELRLNEAQRQGLAMAQWLGGRKEVLKVLHPALPSCPGHEIWKRDFLGSSGLFSIL 315 Query: 313 LKNGFTRAGLEKMVEGMKVLQLGFSWGG 340 L ++ L ++G+++ +GFSWGG Sbjct: 316 LA-PCSQQALAAFLDGLELFGMGFSWGG 342 Lambda K H 0.318 0.137 0.411 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: 397 Number of extensions: 13 Number of successful extensions: 3 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: 340 Length of database: 395 Length adjustment: 30 Effective length of query: 310 Effective length of database: 365 Effective search space: 113150 Effective search space used: 113150 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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