Align Cystathionine beta-lyase PatB; CBL; Beta-cystathionase PatB; Cysteine lyase PatB; Cysteine-S-conjugate beta-lyase PatB; EC 4.4.1.13 (characterized)
to candidate 209104 DVU0171 hemolysin-related protein
Query= SwissProt::Q08432 (387 letters) >MicrobesOnline__882:209104 Length = 393 Score = 299 bits (765), Expect = 1e-85 Identities = 155/387 (40%), Positives = 222/387 (57%), Gaps = 4/387 (1%) Query: 3 FDKREERLGTQSVKWDKTGELFGVT--DALPMWVADMDFRAPEAITEALKERLDHGIFGY 60 FD +R GT S+KWD +FG +A+P+WVADMDF APEA+ A+K+ GI+GY Sbjct: 9 FDTLIDRTGTGSLKWDDMERIFGPVPQNAIPLWVADMDFHAPEAVQNAVKDVAAQGIYGY 68 Query: 61 TTPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYT 120 ++A W+ +RHGW ES+ PGVV +++ ++ T PGD V VQPPVY Sbjct: 69 PAESSAPREAAATWLADRHGWAPGKESLVTVPGVVPGMALLIRELTAPGDGVAVQPPVYP 128 Query: 121 PFYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRE 180 P + V GR ++ NPL+E DG + +D LE + V L +LC+PHNP GR W+R+ Sbjct: 129 PLFDCVRAAGRRVVENPLVETDGRWGMDLGGLEG-IFKGGVRLLLLCSPHNPVGRVWTRD 187 Query: 181 DLLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAG 240 +L L +LC +GV VV+DEIH DL+L GH HT FASL D VTC + SK+FN+ G Sbjct: 188 ELSALADLCQRYGVMVVADEIHHDLVLPGHTHTVFASLPQCQPDRVVTCVSASKSFNLGG 247 Query: 241 LQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNMN 300 L + ++ D R + + ++ GL + F + A EAA+ G PWLD L YI N Sbjct: 248 LPHAYVVATDGALRQRIAHAVVGRGLAHGDLFGMVAQEAAHRHGAPWLDALRMYIADNAA 307 Query: 301 EAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGG 360 + L + LP V+M + +YL WLD A G+ + + +R++ G V+ G +G GG Sbjct: 308 MLQDRLHSHLPWVRMATLEGTYLAWLDCRASGMDETTMMRRLVAAG-VVPSGGRFFGTGG 366 Query: 361 EGFMRLNAGCSLATLQDGLRRIKAALS 387 EG +R+N L + R+ L+ Sbjct: 367 EGHLRVNLATPRTRLSAAIARMIVGLA 393 Lambda K H 0.318 0.135 0.408 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: 442 Number of extensions: 20 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: 387 Length of database: 393 Length adjustment: 31 Effective length of query: 356 Effective length of database: 362 Effective search space: 128872 Effective search space used: 128872 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: 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