Align cystathionine gamma-lyase (subunit 1/2) (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_004514768.1 GMET_RS12040 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::B3TNN9 (394 letters) >NCBI__GCF_000012925.1:WP_004514768.1 Length = 428 Score = 222 bits (566), Expect = 1e-62 Identities = 137/423 (32%), Positives = 230/423 (54%), Gaps = 43/423 (10%) Query: 1 MEFDTKLIHGGISEDKYTGATSVPIYMASTF------HQQKI-GENEYE--YSRSGNPTR 51 + FDT +H G D T + +VPIY +++ H + G E+ Y+R NPT Sbjct: 6 ISFDTLALHAGQEPDPTTLSRAVPIYQTASYAFKSSEHAANLFGLKEFGNIYTRLMNPTS 65 Query: 52 EAVEKLIADLEDGTAGFAFASGSAAID-TVFSLFSAGDHFVIGNDVYGGTFRLIDAVLKR 110 + +EK +A+L+ G A ASG AAI V ++ AG + V + +YGGT+ L L + Sbjct: 66 DVLEKRLAELDGGVGALAVASGQAAITYAVLNIAQAGQNIVSTSYLYGGTYNLFHYTLPK 125 Query: 111 FGMTFTVVDTRDLQAVKAAITPATKAIYLETPTNPLLRVTDIAAVAKIAKDRGILSIIDN 170 G+T VDT D + V+ AI T+ +Y E+ NP V D A+A+IA + GI ++DN Sbjct: 126 LGITVKFVDTSDPENVRRAIDDKTRLVYTESVGNPKNNVDDFEAIARIAHEAGIPFVVDN 185 Query: 171 TFSSPYVQRPLDLGVDIVLHSASKYLGGHSDLVAGLVVTKD------------------- 211 T ++ Y+ +PL+ G DIV++S +K++GGH + G VV Sbjct: 186 TVTTSYLFKPLEHGADIVVYSLTKFIGGHGTSIGGAVVDGGKFPWNNGRFPEMTEPDPSY 245 Query: 212 ------QALGEKIGYLQNAI------GGILAPQESWLLQRGMKTLSLRMRAHLANAEAIF 259 +ALG L+ I G ++P S+L +G++TL +RM H+ NA A+ Sbjct: 246 HGLCYWEALGNLSYILKMRITLLRDMGACISPFNSFLFLQGLETLPVRMARHVENARAVA 305 Query: 260 NYLKNQPLVSKIYYPGDPNNPDYEVAQKQM-HGFGAMISFELQAGLDP-KQFVEQLQVIT 317 +L+ PLVS + YPG ++ D+ A+K + G GA+I F + GL+ ++F++ ++++ Sbjct: 306 QWLEKHPLVSWVNYPGLASHKDHGNARKYLPKGEGAIIGFGINGGLEAGRRFIDSAKLLS 365 Query: 318 LAESLGALESLIEIPALMTHGSIPHDIRLKNGIKDELIRLSVGVEDQKDLLADLERGFDQ 377 ++G +SL+ PA TH + + +L +G+ + IRLS+G+E+ D++AD+++ Sbjct: 366 HLANIGDAKSLVIHPASTTHQQLSEEEQLASGVTQDYIRLSIGIEEVADIIADIDQALAA 425 Query: 378 LKG 380 +G Sbjct: 426 SQG 428 Lambda K H 0.318 0.135 0.381 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: 422 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: 428 Length adjustment: 31 Effective length of query: 363 Effective length of database: 397 Effective search space: 144111 Effective search space used: 144111 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 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