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_041277999.1 DP_RS12690 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::B3TNN8 (394 letters) >NCBI__GCF_000025945.1:WP_041277999.1 Length = 427 Score = 208 bits (529), Expect = 3e-58 Identities = 138/421 (32%), Positives = 213/421 (50%), Gaps = 45/421 (10%) Query: 1 MEFDTKLIHGGISEDKATGAVSVPIYMAS--TFHQQKIGENQYE-------YSRSGNPTR 51 M+ ++ +H G DKAT A +VPIY S TF + G + ++ Y+R NPT Sbjct: 1 MKLESLALHHGYEADKATRAATVPIYQTSSYTFENSQHGADLFDLKTPGNIYTRIMNPTT 60 Query: 52 EAVEKLIAELEGGTAGFAFASGSAAID-TVFSMFSAGDHFVIGNDVYGGTFRLIDAVLKR 110 + +EK IA +EGG A A ASG AAI + ++ GD+ V + +YGGT+ L +L Sbjct: 61 DVLEKRIAAMEGGLAALALASGMAAITCAIHNICLLGDNIVSTSQLYGGTYNLFKYLLPA 120 Query: 111 FGMTFTVVDTRDLAAVEEAITPNTKAIYLETPTNPLLRVTDIAAVAKIAKSHQILSIIDN 170 G+ + + D A+ EAI T+AIY E+ NP V DI +A+IA H I I+DN Sbjct: 121 RGIEVRMAECDDYQAIAEAIDIKTRAIYCESIANPAGNVADIKKLAEIAHEHGIPLIVDN 180 Query: 171 TFSSPYVQRPLEQGVDIVLHSASKYLGGHSDVIAGLVV-----------------TKDDQ 213 T ++PY+ RP+E G D+V+HS +KY+GGH + G++V T+ D Sbjct: 181 TVATPYLCRPIELGADVVVHSLTKYIGGHGTSLGGIIVDSGKFGWAKEAGKFPTLTEPDP 240 Query: 214 LAEKIGY----------------LQNAIGGILAPQESWLLQRGIKTLSLRMRAHLANAEA 257 + Y L G ++P S+ + +G++TL LRM H NAE Sbjct: 241 SYHGLVYTEALGATAYIGRCRVALLRDTGAAISPMNSFQILQGLETLGLRMERHCENAEK 300 Query: 258 VFNYLSNQPLVSKIYYPGDPNNPDYEVAKKQMHG-FGAMISFELQDGLDPK-QFVEQLHV 315 + YL V+ + Y +P YE +K G ++SF L G FV+ L + Sbjct: 301 LALYLGEHKEVAWVRYAALSASPYYESCQKITGGRASGILSFGLVGGFAAGIAFVDALKM 360 Query: 316 ITLAESLGALESLIEIPALMTHGSIPRDIRLKNGIKDELIRLSVGVEDQKDLLADLERGF 375 I ++G +SL PA TH + +G+ +LIR+SVG+E+ +D++ D+ + Sbjct: 361 ILRLVNIGDAKSLACHPASTTHRQLSDSDMKASGVSSDLIRISVGIENIEDIILDVSQAL 420 Query: 376 N 376 + Sbjct: 421 D 421 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: 414 Number of extensions: 21 Number of successful extensions: 5 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: 427 Length adjustment: 31 Effective length of query: 363 Effective length of database: 396 Effective search space: 143748 Effective search space used: 143748 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