Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_012565752.1 RC1_RS02465 PLP-dependent transferase
Query= SwissProt::P9WGB7 (388 letters) >NCBI__GCF_000016185.1:WP_012565752.1 Length = 383 Score = 301 bits (771), Expect = 2e-86 Identities = 173/377 (45%), Positives = 223/377 (59%), Gaps = 9/377 (2%) Query: 14 PATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRGGFEYARTGNPTRAALEASLAA 73 P T A DPAT V ++ ++TF + G GG YAR NPT E LA Sbjct: 8 PDTLLARAQGAHDPATHGVVPAVHPATTFLRAGDLSYPGGHSYARPFNPTFDGAETLLAT 67 Query: 74 VEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDVQYTPVR 133 +E A A FSSGM+A +A L PGDHV+ P Y G + +W + V Sbjct: 68 LEGAAQALLFSSGMSAATAVFQA-LEPGDHVIAPQVMYWGLRNWLKGFAAQWGLGLDLVD 126 Query: 134 LADLDAVGAAITP-RTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDNTFASPALQ 192 + D AV AA+ P RTRLIW ETP NP + D+ A AE+ A++ VDNT +P L Sbjct: 127 MRDPAAVAAAVRPGRTRLIWAETPANPTWEVTDLAACAEIAHRAGARLAVDNTVPTPLLT 186 Query: 193 QPLRLGADVVLHSTTKYIGGHSDVVGGALVT-NDEELDEEFAFLQNGAGAVPGPFDAYLT 251 +P+ GAD+V+HS TKY+ GHSDV+GGAL T + E A ++ GA+PGPF+A+L Sbjct: 187 RPVEHGADIVMHSATKYLNGHSDVLGGALATARADGFWERIAAIRANQGAIPGPFEAWLL 246 Query: 252 MRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAARQMR-GFGGMV 310 +RG++TL LR++R A +AE A HP + +VLYPGLP+HPGH +AARQMR GFGGM+ Sbjct: 247 LRGMRTLGLRVERACATAQRLAEHFAGHPKLEAVLYPGLPTHPGHAVAARQMRGGFGGML 306 Query: 311 SVRMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQLEVPDDLVRLS 370 SVR++ G A A R++ A SLGGVESL+EH S G P DL+RLS Sbjct: 307 SVRVKGGAAGAVAASAALRIWTRATSLGGVESLVEH-----RGSIEGPDSPCPQDLLRLS 361 Query: 371 VGIEDIADLLGDLEQAL 387 GIE DL+ DLEQAL Sbjct: 362 CGIEHADDLIADLEQAL 378 Lambda K H 0.319 0.135 0.393 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: 557 Number of extensions: 36 Number of successful extensions: 7 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: 383 Length adjustment: 30 Effective length of query: 358 Effective length of database: 353 Effective search space: 126374 Effective search space used: 126374 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 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