Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate WP_090218896.1 CV091_RS11630 PLP-dependent transferase
Query= SwissProt::O31631 (373 letters) >NCBI__GCF_002796795.1:WP_090218896.1 Length = 438 Score = 230 bits (587), Expect = 5e-65 Identities = 144/387 (37%), Positives = 203/387 (52%), Gaps = 27/387 (6%) Query: 2 SQHVETKLAQIGNRSDEVTGTVSAPIYLSTAY-----RHRGIGESTGFD---YVRTKNPT 53 S + TK G D TG V PIY ++ + + I E G D Y R NP+ Sbjct: 43 SMGMSTKAVHAGTHDDPRTGAVGTPIYQASTFILQEETYGSIEEGFGRDRFIYTRYGNPS 102 Query: 54 RQLVEDAIANLENGARGLAFSSGMAAIQT-IMALFKSGDELIVSSDLYGGTYRLFENEWK 112 + V++ +A LE + FSSGMAAI +MAL G ++ +SDLYGGTY LF E+ Sbjct: 103 QWAVQEKLATLEGAESAIVFSSGMAAITAAVMALVDKGAHVVAASDLYGGTYNLFNQEFP 162 Query: 113 KYGLTFHYDDFSDEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVD 172 G++ D D + + + I PNT+ ++ E TNP+++ D+ + I K H L LIVD Sbjct: 163 SLGMSATLVDSYDLEAIEAAIQPNTQILYFEVITNPVLKVVDLPALVDIAKRHNLRLIVD 222 Query: 173 NTFYTPVLQRPLELGADIVIHSATKYLGGHNDLLAGLVVVKDERLGEEMFQHQNAIGAVL 232 +TF P + +PLELG D+V+HSA+KYL GH+DL+AG VV +L + ++ G L Sbjct: 223 STFAPPPVMKPLELGVDLVVHSASKYLNGHSDLIAG-VVCGPRKLVDMIWPRLLNYGGSL 281 Query: 233 PPFDSWLLMRGMKTLSLRMRQHQANAQELAAFLEEQEEISDVLYP--------------- 277 P +LL RG+KTL +RM+ H+A+A LA FLE + VLYP Sbjct: 282 DPHACFLLERGLKTLDIRMKAHEASATALAEFLETHPAVEKVLYPMLPSHPDHARAKELM 341 Query: 278 --GKGGMLSFRLQKEEWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIAN 335 G G + F ++ + LK A SLGG+ES I+ P + + R Sbjct: 342 KMGTGNVTFFVKGGDQAALALMDHLKLPKQATSLGGIESLISLPFNSSQATMTARQRADI 401 Query: 336 GVCNRLLRFSVGIEHAEDLKEDLKQAL 362 G+ +R SVGIE A+DL D QAL Sbjct: 402 GIYPGCVRLSVGIEDAKDLIADFDQAL 428 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: 377 Number of extensions: 13 Number of successful extensions: 5 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: 438 Length adjustment: 31 Effective length of query: 342 Effective length of database: 407 Effective search space: 139194 Effective search space used: 139194 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