Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate WP_029133561.1 A3GO_RS0111730 cystathionine gamma-synthase
Query= BRENDA::H7C6A2 (386 letters) >NCBI__GCF_000428045.1:WP_029133561.1 Length = 390 Score = 258 bits (660), Expect = 2e-73 Identities = 158/389 (40%), Positives = 227/389 (58%), Gaps = 15/389 (3%) Query: 6 NTQGFSTASIHAGYEPDDYYGSINTPIYASTTFAQNAPNEL-------RKGYEYTRVG-N 57 + +G +T +IH G D +GS +TPIY +TTFA + +L + G YTR G N Sbjct: 5 DARGLATRAIH-GSTQQDAHGSPHTPIYNTTTFAFPSTADLLYVVDGMKPGALYTRYGLN 63 Query: 58 PTIVALEQTVAALEGAKYGRAFSSGMAATDILFRIILKPGDHIVLGNDAYGGTYRLIDTV 117 P+I ALE+T+A LEGA+ AF SGMAA LF + D IV DAYGGT L+ Sbjct: 64 PSIFALEETLAGLEGAELSWAFCSGMAAETALF--LAYGQDGIVCIGDAYGGTLELLAAQ 121 Query: 118 FTAWGVEYTVVDTSVVEEVKAAIKDNTKLIWVETPTNPALGITDIEAVAKLTEGTNAKLV 177 G++ + S + + + + KL++ ETPTNPAL + DI A+A A++ Sbjct: 122 LPQLGIKTHFILGSELSRLDHLLAEGPKLVFFETPTNPALELFDIRAIAAKAHIYGARVA 181 Query: 178 VDNTFASPYLQQPLKLGAHAVLHSTTKYIGGHSDVVGGLVVTNDQEMDEELLFMQGGIGP 237 VD+TFASP Q+PL+LGA V+HS TKY+GGHSD+ G ++ +E+ + + +G Sbjct: 182 VDSTFASPVNQRPLELGADFVVHSATKYLGGHSDLTAGAIM-GSKELLLPIWNWRKNLGS 240 Query: 238 IPSVFDAYLTARGLKTLAVRMDRHCDNAEKIAEFLDSRPEVSTVLYPGLKNHPGHEVAAK 297 + + A L AR L+TL VR+ + +A+ +A+ + P+V VLYPGL + GH +A Sbjct: 241 MIAPETASLLARSLRTLVVRVRQQNASAQAVAQAMARHPKVERVLYPGLPDFAGHALAKA 300 Query: 298 QMKRFGGMISVRFAGGEEAAKKFCTSTKLICLAESLGGVESLLEHPATMTHQSAAGSQLE 357 QM FGGM+++ AGG E A + +L LA SLGG ESL+ P T TH + Sbjct: 301 QMHGFGGMLTIEVAGGGEEATRVADRLQLFALAPSLGGAESLVTQPCTTTHHGLTPEERA 360 Query: 358 ---VPRDLVRISIGIEDIEDLLADVEQAL 383 + ++R+SIG+ED DL+AD+EQAL Sbjct: 361 RRGISDAMLRLSIGLEDAADLIADLEQAL 389 Lambda K H 0.316 0.134 0.385 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: 423 Number of extensions: 32 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: 386 Length of database: 390 Length adjustment: 30 Effective length of query: 356 Effective length of database: 360 Effective search space: 128160 Effective search space used: 128160 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: 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