Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_059153468.1 V474_RS22510 cystathionine beta-lyase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_001046635.1:WP_059153468.1 Length = 411 Score = 146 bits (368), Expect = 1e-39 Identities = 122/403 (30%), Positives = 191/403 (47%), Gaps = 41/403 (10%) Query: 1 MSQHVETKLAQIGNRSDEVTGTVSAPI-------YLSTAYRHRG--IGESTGFDYVRTKN 51 + Q T++ G RS+ V+ P+ Y TA +G E F Y R Sbjct: 15 LPQAPATRIVGAGRRSEWTGPVVNPPVWRASTHLYADTAALAQGPRTNEDGRFFYGRRGA 74 Query: 52 PTRQLVEDAIANLENGARG-LAFSSGMAAIQTIM-ALFKSGDELIVSSDLYGGTYRLFEN 109 PT+ + DA+ +E GA G + + SG+AAI +M L + GD +++S + Y T Sbjct: 75 PTQWALADALTAIEPGAAGTVLYPSGLAAIAGVMLTLLRPGDIVLISDNAYDPTRATGTG 134 Query: 110 EWKKYGLTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLL 169 +G+ + D D T+AV +E P + M+ D+ +ARI +E G + Sbjct: 135 LLTDFGIEPRFFDPLDIAAYERLFCKRTRAVLLEAPGSLSMEMCDLPELARIAREKGAVS 194 Query: 170 IVDNTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIG 229 ++DNT+ P+ LE G DI + + TK++GGH+D++ G E L ++ Q +G Sbjct: 195 VLDNTWAGPLGFPALERGIDITLMALTKHVGGHSDVMMGSASAGPE-LYAKLRQRAQQLG 253 Query: 230 AVLPPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYP------------ 277 V+ P D+ L +RG++TL LR+R +A +A +L E+ E++ VL P Sbjct: 254 TVVSPDDAALTLRGLRTLHLRLRHEADSALAIARWLNERPEVAQVLCPMLPGAPGHDIWS 313 Query: 278 ----GKGGMLSFRLQKEEWV--NPFLKALKTICFAESLGGVESF---ITYPATQTHM--- 325 G G+ SF + N F+ AL S GG ES I A ++ M Sbjct: 314 RDFSGGCGLFSFTFKGGTAAARNRFVDALTLFGIGYSWGGFESLVVPIDPSACRSRMAWP 373 Query: 326 DIPEEIRIANGVCNRLLRFSVGIEHAEDLKEDLKQALCQVKEG 368 P E ++GV R ++G+E A DL DL+QAL +EG Sbjct: 374 PHPHEAGDSHGV-----RLAIGLEDAGDLIADLEQALAAWREG 411 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: 329 Number of extensions: 25 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: 411 Length adjustment: 31 Effective length of query: 342 Effective length of database: 380 Effective search space: 129960 Effective search space used: 129960 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 Jul 26 2024. The underlying query database was built on Jul 25 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