Align Cystathionine gamma-synthase/O-acetylhomoserine (thiol)-lyase; CGS/OAH thiolyase; O-acetylhomoserine sulfhydrylase; OAH sulfhydrylase; EC 2.5.1.- (characterized)
to candidate CA265_RS08190 CA265_RS08190 cystathionine gamma-synthase
Query= SwissProt::O31631 (373 letters) >FitnessBrowser__Pedo557:CA265_RS08190 Length = 371 Score = 222 bits (565), Expect = 1e-62 Identities = 142/376 (37%), Positives = 202/376 (53%), Gaps = 28/376 (7%) Query: 6 ETKLAQIGNRSDEVTGTVSAPIYLSTAY-RHRGIGESTGFDYVRTKNPTRQLVEDAIANL 64 ET N +TG V+ P+ LST + R G G Y R NP R +E+ +A L Sbjct: 4 ETLAIHASNLVKSITGDVTPPLNLSTTFFRDAEGGYPGGHMYSRVSNPNRSALENTVAKL 63 Query: 65 ENGARGLAFSSGMAAIQTIMALFKSGDELIVSSDLYGGTYRLFENEWKKYGLTFHYDDFS 124 E G AFSSG + K G +I D+Y G + + L F + D + Sbjct: 64 EYGEDAAAFSSGNTCGLVLFQALKPGSHIIAPDDMYWGIKKQLLTIFND-SLEFDFIDQT 122 Query: 125 DEDCLRSKITPNTKAVFVETPTNPLMQEADIEHIARITKEHGLLLIVDNTFYTPVLQRPL 184 D D +++ I NTK +++ETP+NPL++ DIE IA+I K + L D+TF +P+LQ P+ Sbjct: 123 DLDLIQASIRSNTKLIWIETPSNPLLKVTDIEEIAKIAKAKNITLACDSTFASPILQNPI 182 Query: 185 ELGADIVIHSATKYLGGHNDLLAG-LVVVKDERLGEEMFQHQNAIGAVLPPFDSWLLMRG 243 LGADIV+HS+TKYLGGH+D+L G LV K + L E++ Q GAV PFD +LL R Sbjct: 183 LLGADIVMHSSTKYLGGHSDVLGGILVTAKKDELWEKIKNIQQTGGAVPSPFDCFLLTRS 242 Query: 244 MKTLSLRMRQHQANAQELAAFLEEQEEISDVLYPGK----------------GGMLSFRL 287 +KTL+ RM+ H N + +A +L + V YPG GGM+SF + Sbjct: 243 IKTLAYRMKGHCENGKIIADYLNAHPNVEAVFYPGLESHPQHDIAKKQMKDFGGMMSFLV 302 Query: 288 QKE-EWVNPFLKALKTICFAESLGGVESFITYPATQTHMDIPEEIRIANGVCNRLLRFSV 346 + + E + + ++ A SLGGVES I + + ++ P+ N LLR SV Sbjct: 303 KGDVEAAHKVVNKVQLFAQATSLGGVESLIEH---RYSVEGPDSKTPKN-----LLRISV 354 Query: 347 GIEHAEDLKEDLKQAL 362 G+EHA+D+ DL QAL Sbjct: 355 GLEHADDIIADLAQAL 370 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: 340 Number of extensions: 19 Number of successful extensions: 6 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: 371 Length adjustment: 30 Effective length of query: 343 Effective length of database: 341 Effective search space: 116963 Effective search space used: 116963 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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