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 Dsui_3257 Dsui_3257 bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__PS:Dsui_3257 Length = 381 Score = 258 bits (659), Expect = 2e-73 Identities = 150/383 (39%), Positives = 216/383 (56%), Gaps = 13/383 (3%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 +FD ER G+ S KW + + D LP+WVADMDF AP A+ E L++R+DHG+FGY Sbjct: 4 DFDTPVERRGSDSFKWGR----YAGRDVLPLWVADMDFAAPPAVLEVLRQRVDHGVFGYG 59 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 + +V + +GW+V E + + PG+VT L++A + PG+ V+ PVY P Sbjct: 60 GATPEVTGSVLQALDRDYGWQVQAEWLVWLPGLVTGLNVACRGLAGPGETVLSAVPVYPP 119 Query: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKL-SDPSVTLFILCNPHNPSGRSWSRE 180 F + R + PL ++G + DF LE L +DP +L +LC+PHNP GR+WSR Sbjct: 120 FLSAPALSERCLATVPLHCQEGRWCWDFAALEAALQADPRPSLLLLCHPHNPVGRAWSRS 179 Query: 181 DLLKLGELCLEHGVTVVSDEIHSDLMLY-GHKHTPFASLSDDFADISVTCAAPSKTFNIA 239 +L + ELC + V V SDEIH+DL L G +H PFA L + A SVT APSKT+NI Sbjct: 180 ELETVAELCGRYDVLVCSDEIHADLQLEPGVRHLPFACLDAEAARRSVTLMAPSKTYNIP 239 Query: 240 GLQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNM 299 GL + +IPD R +F+ ++ + +N + A AAY+ G PW + L+ Y+ +N Sbjct: 240 GLSCAFAVIPDSTIRRRFTRAM-AGIVPHVNVLGLAACGAAYAHGEPWREALLAYLRQN- 297 Query: 300 NEAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPG 359 E P ++M+ P+A+YL W+D GL E R + V L G ++ G Sbjct: 298 RERVVQAVAGWPGLEMVAPEATYLAWIDARQSGL---EEPARAFEAAGVGLSDGREF--G 352 Query: 360 GEGFMRLNAGCSLATLQDGLRRI 382 GF+RLN GC ATL+ L R+ Sbjct: 353 APGFVRLNFGCPGATLEAALERM 375 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: 462 Number of extensions: 21 Number of successful extensions: 7 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: 381 Length adjustment: 30 Effective length of query: 357 Effective length of database: 351 Effective search space: 125307 Effective search space used: 125307 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