Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_036260610.1 DL86_RS08955 cystathionine beta-lyase
Query= BRENDA::P43623 (340 letters) >NCBI__GCF_000746085.1:WP_036260610.1 Length = 395 Score = 399 bits (1024), Expect = e-116 Identities = 197/339 (58%), Positives = 246/339 (72%), Gaps = 5/339 (1%) Query: 3 DRTELSKFGITTQLSVIGRNPDEQSGFVNPPLYKGSTIILKKLSDLEQRKGRF-YGTAGS 61 DRT L T+L GR P +Q GFVN P+Y+GST++ D+ K RF YGT G+ Sbjct: 8 DRTRLKN---RTKLVHAGRRPSDQHGFVNTPIYRGSTVLYPTFEDIRAHKARFTYGTKGT 64 Query: 62 PTIDNLENAWTHLTGGAGTVLSASGLGSISLALLALSKAGDHILMTDSVYVPTRMLCDGL 121 PT + LE AWT L+G AGTVL+ SGL +++LAL A KAGDHIL+TDSVY PTR+ C + Sbjct: 65 PTTEALEGAWTELSGAAGTVLAPSGLAAVTLALFAAVKAGDHILVTDSVYGPTRLFCGTV 124 Query: 122 LAKFGVETDYYDPSIGKDIEKLVKPNTTVIFLESPGSGTMEVQDIPALVSVAKKHGIKTI 181 LA+ GVET YYDP IG IE L++PNT+VIFLE+PGS + E+QD+PA+ + A+ GI I Sbjct: 125 LARMGVETTYYDPLIGASIEALIRPNTSVIFLETPGSQSFELQDVPAIAAAAQARGICAI 184 Query: 182 LDNTWATPLFFDAHAHGIDISVEAGTKYLGGHSDLLIGLASANEECWPLLRSTYDAMAML 241 LDNTWATPLFF HA G+D+++EAGTKYL GHSDLL+GL SAN +P LR+TYDA AM Sbjct: 185 LDNTWATPLFFPPHARGMDMAIEAGTKYLSGHSDLLLGLVSANARWFPRLRATYDAFAMC 244 Query: 242 PGAEDCQLALRGMRTLHLRLKEVERKALDLAAWLGNRDEVEKVLHPAFEDCPGHEYWVRD 301 PG ED LALRG+RTL LRL+E ER+ LDLA WL R E+ +VLHPA CPGH W RD Sbjct: 245 PGPEDVFLALRGLRTLDLRLREAERQGLDLARWLAGRPEIVQVLHPALPSCPGHALWKRD 304 Query: 302 YKGSSGLFSIVLKNGFTRAGLEKMVEGMKVLQLGFSWGG 340 + GSSGLFS +L + A L M++G+K+ +G+SWGG Sbjct: 305 FLGSSGLFSALLA-PCSDAALAAMLDGLKLFGMGYSWGG 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: 392 Number of extensions: 18 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