Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_057508383.1 ABB28_RS09425 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_001431535.1:WP_057508383.1 Length = 392 Score = 320 bits (821), Expect = 3e-92 Identities = 175/369 (47%), Positives = 232/369 (62%), Gaps = 19/369 (5%) Query: 13 GNRSDEVTGTVSAPIYLSTAYRHRGIGESTGFDYVRTKNPTRQLVEDAIANLENGARGLA 72 G D TG V PIY ++ Y GE GF+Y RT NPTR E +A+LE G+RG A Sbjct: 23 GQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVASLEGGSRGFA 82 Query: 73 FSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKY-GLTFHYDDFSDEDCLRS 131 F+SGMAA T+M L +G ++ D+YGGT+RLFE ++ GL F + D +D + Sbjct: 83 FASGMAATSTVMELLDAGSHVVAMDDIYGGTFRLFERVRRRTAGLDFSFVDLTDLAAFEA 142 Query: 132 KITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPLELGADIV 191 ITP TK V++ETPTNP+++ DI +A I K+HGL+++VDNTF +P+LQRPLELGAD+V Sbjct: 143 AITPATKMVWIETPTNPMLKIVDIAAVAAIAKQHGLIIVVDNTFASPMLQRPLELGADLV 202 Query: 192 IHSATKYLGGHNDLLAGLVVVKDER-LGEEMFQHQNAIGAVLPPFDSWLLMRGMKTLSLR 250 +HSATKYL GH+D++ G+VVV D L E+M QN+IGAV PFDS+L +RG+KTL LR Sbjct: 203 LHSATKYLNGHSDMVGGMVVVGDNTGLAEQMAFLQNSIGAVQGPFDSFLALRGLKTLPLR 262 Query: 251 MRQHQANAQELAAFLEEQEEISDVLYP----------------GKGGMLSFRLQKE-EWV 293 M+ H ANA LA +LE Q + V+YP G GG++S L+ E Sbjct: 263 MKAHCANALALAQWLETQPSVEKVIYPGLTSHPQHELATRQMNGYGGIVSIVLKGGFEAA 322 Query: 294 NPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSVGIEHAED 353 F + + AESLGGVES + +PA TH IP E R G+ L+R SVG+E D Sbjct: 323 KRFCERTELFTLAESLGGVESLVNHPAVMTHASIPVERRENLGISEGLVRLSVGVEELGD 382 Query: 354 LKEDLKQAL 362 L DL++AL Sbjct: 383 LMVDLERAL 391 Lambda K H 0.319 0.135 0.392 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: 388 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 373 Length of database: 392 Length adjustment: 30 Effective length of query: 343 Effective length of database: 362 Effective search space: 124166 Effective search space used: 124166 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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