Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate WP_005459142.1 SACCYDRAFT_RS20695 cystathionine gamma-synthase
Query= BRENDA::A0PKT3 (388 letters) >NCBI__GCF_000244975.1:WP_005459142.1 Length = 386 Score = 483 bits (1244), Expect = e-141 Identities = 243/376 (64%), Positives = 289/376 (76%), Gaps = 1/376 (0%) Query: 13 GLATRAIHSGYRPDPATGAVNAPIYASSTFAQDGVGGLR-GGYEYARTGNPTRTALEAAL 71 G TRAIH+G PDP TGAV PIY +ST+AQDGVGG R G YEY+RT NPTRTALE AL Sbjct: 8 GFETRAIHAGQEPDPRTGAVIVPIYQTSTYAQDGVGGTREGDYEYSRTANPTRTALEEAL 67 Query: 72 AAVEDAAFGRAFSSGMAAADCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTGWNVEYTP 131 AA+E AF+SGMAA+D LR LRPGDH+V+ +D YGGTFRLIDKV T W V Y+ Sbjct: 68 AALEGGRHALAFASGMAASDAVLRTTLRPGDHLVLGNDVYGGTFRLIDKVLTEWGVNYSV 127 Query: 132 VALADLDAVRAAIRPTTRLIWVETPTNPLLSIADIAGIAQLGADSSAKVLVDNTFASPAL 191 +L+DLD VR A+RP T+L+W E+PTNPLL IADIA +A+L AK++VDNTFA+P L Sbjct: 128 ASLSDLDEVREALRPETKLVWCESPTNPLLGIADIAALAELAHVGGAKLVVDNTFATPYL 187 Query: 192 QQPLSLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDQSFAFLQNGAGAVPGPFDAYLT 251 Q PL LGAD+V+HSTTKY+GGHSDVVGGA++T+ +EL + FL+N AGAVPG FDA+LT Sbjct: 188 QTPLELGADIVVHSTTKYLGGHSDVVGGAVITDSDELRERLFFLRNSAGAVPGAFDAWLT 247 Query: 252 MRGLKTLVLRMQRHSENAAAVAEFLAEHPAISTVLYPGLPSHPGHAVAARQMRGFGGMVS 311 +RGLKTL +RM+RH NA +AE LA HP + V YPGL HPGH++AA+QMR FGGMVS Sbjct: 248 LRGLKTLAVRMERHCGNAELIAEALAVHPKVERVYYPGLAEHPGHSLAAKQMRRFGGMVS 307 Query: 312 VRMRAGRTAAEQLCAKTNIFILAESLGSVESLIEHPSAMTHASTAGSQLEVPDDLVRLSV 371 G AA + A+T +FILAESLG VESLIEHP MTHAS AGS L+VP +LVRLSV Sbjct: 308 FTHVDGEQAALNVAARTKLFILAESLGGVESLIEHPGRMTHASVAGSLLQVPAELVRLSV 367 Query: 372 GIEDVADLLDDLKQAL 387 GIED DLL DL+ AL Sbjct: 368 GIEDAHDLLADLRYAL 383 Lambda K H 0.318 0.133 0.386 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: 524 Number of extensions: 18 Number of successful extensions: 2 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: 388 Length of database: 386 Length adjustment: 30 Effective length of query: 358 Effective length of database: 356 Effective search space: 127448 Effective search space used: 127448 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 (21.7 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