Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_066917961.1 ACG33_RS00985 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::P43623 (340 letters) >NCBI__GCF_001579945.1:WP_066917961.1 Length = 424 Score = 122 bits (306), Expect = 2e-32 Identities = 94/316 (29%), Positives = 150/316 (47%), Gaps = 37/316 (11%) Query: 53 GRFYGTAGSPTIDNLENAWTHLTGGAGTVLSASGLGSISLALLALSKAGDHILMTDSVYV 112 G Y +PT D LE L GG G++ ++G+ ++ A++ L++AGD+I+ +Y Sbjct: 49 GNIYTRIMNPTCDVLEKRVAMLEGGVGSLALSAGMAAVHYAIINLAEAGDNIVSVPQLYG 108 Query: 113 PTRMLCDGLLAKFGVETDYYDPSIGKDIEKLVKPNTTVIFLESPGSGTMEVQDIPALVSV 172 T L +L K G+ET + IEKL+ T IF ES G+ + D+ A+ + Sbjct: 109 GTYTLFAHMLPKMGIETRFAADDSAAAIEKLIDAKTKAIFFESIGNPAGNIVDVEAVAKM 168 Query: 173 AKKHGIKTILDNTWATPLFFDAHAHGIDISVEAGTKYLGGHSDLLIGLA--------SAN 224 A+ HG+ TI+DNT ATP +GIDI V A TKY+GGH L GL + + Sbjct: 169 ARGHGVATIVDNTVATPSLLKPIDYGIDIVVHALTKYMGGHGTTLGGLIVDSGNFPWADH 228 Query: 225 EECWPLLRSTYDAM-------AMLPGAE-------------------DCQLALRGMRTLH 258 ++ +P+ +A A+ P A + L+G+ TL Sbjct: 229 QQRYPMFNEPEEAYHGVVYVDALGPAAYIGRARTVPLRNTGAALSPFNAFQLLQGIETLP 288 Query: 259 LRLKEVERKALDLAAWLGNRDEVEKVLHPAFEDCPGHEYWVRDYKG-SSGLFSIVLKNGF 317 LR++ A +A L VE V + ++ P H + KG +SG+ + +K GF Sbjct: 289 LRMERHCENAQRVAEHLQEHAMVEWVSYAGLKNHPHHALAQKYMKGRASGILTFGVKGGF 348 Query: 318 TRAGLEKMVEGMKVLQ 333 AG+ K + +K+ + Sbjct: 349 D-AGV-KFYDALKLFK 362 Lambda K H 0.318 0.137 0.411 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: 354 Number of extensions: 21 Number of successful extensions: 2 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: 340 Length of database: 424 Length adjustment: 30 Effective length of query: 310 Effective length of database: 394 Effective search space: 122140 Effective search space used: 122140 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