Align cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate WP_041245581.1 GURA_RS20075 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= BRENDA::Q1K8G0 (457 letters) >NCBI__GCF_000016745.1:WP_041245581.1 Length = 417 Score = 174 bits (441), Expect = 5e-48 Identities = 125/396 (31%), Positives = 200/396 (50%), Gaps = 44/396 (11%) Query: 59 GASSIPIYQSATFKQSSSNGGSEYD--------YTRSGNPTRTHLERHLAKIMNANRCLS 110 GA+++PI QS++F Q+++ + YTR GNPT LE+ LA + ++ Sbjct: 25 GATTVPIVQSSSFAQATAEELEDIFRGRKVGQVYTRVGNPTTESLEKRLALLEGGQAAIA 84 Query: 111 VSSGMGALDV-ITRLLKPGDEVITGDDLYGGTNRLLTYLKNNQGVIVHHVDTTNVESVRQ 169 +SGM A+ + +++ GDE++ L+GGT L + G+ VD T++ +VR Sbjct: 85 TASGMAAITTAVMTIVRSGDEILASSSLFGGTFSLFRDTLSGYGISTTFVDPTDLAAVRN 144 Query: 170 IISPKTTMVLLETPTNPLIKICDIPTIARITHEANEKAVVVVDNTMLSPMLFNPLDVGAD 229 I+ +T +V +ET NP + + DIP IA I A ++VD T+ +P L D+GAD Sbjct: 145 GINDRTRLVFVETIGNPKMDVPDIPAIALIARAAG--IPLLVDATVTTPCLARGSDLGAD 202 Query: 230 IVYESGTKYLSGHHDIMAGVIAVNDTELG------DK-------------LYFTINAT-- 268 IV S +K+++G + GVI +LG DK FT A Sbjct: 203 IVIHSTSKFINGTGSAIGGVI----IDLGRFDWQSDKFPHFEPFHKKYRAFAFTARARKL 258 Query: 269 -----GCGLSPNDSFLLMRGVKTLAIRMEKQQANAQRIAEFLESHGFK--VRYPGLKSHP 321 G +P +SFLL GV+TL++RME+ ANAQ++A+FL++H V YPGL+ P Sbjct: 259 IHKDFGACAAPMNSFLLAEGVETLSLRMERHCANAQKLAQFLKAHDRVRWVNYPGLEDSP 318 Query: 322 QYDLHWSM-ARGAGAVLSFETGDVALSERIVEAARLWGISVSFGCVNSLISMPCRMSHAS 380 + + + G VL+F D A + R + RL + G +L+ P Sbjct: 319 HHQVAKKLYGDKFGGVLTFGLADKAAAFRFINGVRLAKNLANIGDAKTLVIHPASTICCD 378 Query: 381 IDAKTRAERQMPEDIIRLCVGIEDADDLIDDLSRAL 416 + + + E+++R+ VGIE +D+I+D AL Sbjct: 379 YGPEEKGLMGVGEEMVRVSVGIEAINDIIEDFDSAL 414 Lambda K H 0.316 0.131 0.375 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: 389 Number of extensions: 21 Number of successful extensions: 6 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: 457 Length of database: 417 Length adjustment: 32 Effective length of query: 425 Effective length of database: 385 Effective search space: 163625 Effective search space used: 163625 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: 51 (24.3 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