Align cystathionine gamma-lyase (subunit 2/2) (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_007472892.1 CMTB2_RS00355 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::B3TNN8 (394 letters) >NCBI__GCF_000170735.1:WP_007472892.1 Length = 418 Score = 232 bits (591), Expect = 2e-65 Identities = 144/418 (34%), Positives = 215/418 (51%), Gaps = 43/418 (10%) Query: 1 MEFDTKLIHGGISEDKATGAVSVPIYMASTFHQQ---------KIGENQYEYSRSGNPTR 51 M+ T +H G +DK + VPIYM+S + Q + E Y+R GNPT Sbjct: 1 MKDSTLALHYGYEKDKEK-TMQVPIYMSSAYEYQDTDHAARLFNLQEEGNIYTRIGNPTT 59 Query: 52 EAVEKLIAELEGGTAGFAFASGSAAID-TVFSMFSAGDHFVIGNDVYGGTFRLIDAVLKR 110 EK IA LE G A ASG +AI ++ ++ GD+ +I N +YGG+ L LK+ Sbjct: 60 RVFEKRIAALENGIDALATASGMSAIFYSIANLVKNGDNVIISNKLYGGSITLSTQTLKQ 119 Query: 111 FGMTFTVVDTRDLAAVEEAITPNTKAIYLETPTNPLLRVTDIAAVAKIAKSHQILSIIDN 170 FG+ D ++ +EE I NTKAI E+ NP L V D +++IA I++I DN Sbjct: 120 FGIKAKYFDIKNPEMLEELIDENTKAILFESIANPALNVADFEIISEIANKRGIITICDN 179 Query: 171 TFSSPYVQRPLEQGVDIVLHSASKYLGGHSDVIAGLVV-----------------TKDDQ 213 T ++PY +P+ G+DIV+HSASKYL G+ VI G ++ K D Sbjct: 180 TIATPYSLKPINLGIDIVVHSASKYLSGNGTVIGGCIIESKSAKEKLKGDRYPQFNKPDD 239 Query: 214 LAEKIGY---------------LQNAIGGILAPQESWLLQRGIKTLSLRMRAHLANAEAV 258 + Y L G +++P SWLL G++TL LR+ H NA + Sbjct: 240 SYHGLIYNEKFDNPFIARSRLALLRDYGAVISPFNSWLLILGLETLHLRIERHSYNALEI 299 Query: 259 FNYLSNQPLVSKIYYPGDPNNPDYEVAKKQMHGFGAMISFELQDGLDPKQFVEQLHVITL 318 +LS+ V K+ YP N+ +Y +AKK + ++SFEL + K FV++L + L Sbjct: 300 AKFLSSHKKVKKVSYPFLNNDENYNLAKKYLKYGSGILSFELSSYEEAKNFVKKLKIFKL 359 Query: 319 AESLGALESLIEIPALMTHGSIPRDIRLKNGIKDELIRLSVGVEDQKDLLADLERGFN 376 ++ +S++ PA TH + ++ GI + LIRLSVG+ED +DL+ DL+ N Sbjct: 360 VTNIADTKSIVTHPASTTHQQLNKEELKNAGISEGLIRLSVGIEDVEDLIKDLDEALN 417 Lambda K H 0.317 0.134 0.376 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: 417 Number of extensions: 22 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 394 Length of database: 418 Length adjustment: 31 Effective length of query: 363 Effective length of database: 387 Effective search space: 140481 Effective search space used: 140481 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 (21.6 bits) S2: 50 (23.9 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