Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_052666181.1 NITAL_RS10435 cystathionine gamma-synthase
Query= SwissProt::P9WGB7 (388 letters) >NCBI__GCF_000969705.1:WP_052666181.1 Length = 383 Score = 439 bits (1129), Expect = e-128 Identities = 229/387 (59%), Positives = 278/387 (71%), Gaps = 6/387 (1%) Query: 1 MSEDRTGHQGISGPATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRGGFEYARTG 60 M++ R QG S TRAIH G PDP TGAV VPIY +STFAQ VG G+EYARTG Sbjct: 1 MTDSRGSDQGFS---TRAIHVGQEPDPRTGAVIVPIYQTSTFAQPAVGQ-HLGYEYARTG 56 Query: 61 NPTRAALEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDK 120 NPTR AL+ LA++E A F+SG+AA D +R +L PGDH+V +D YGGT+R +D+ Sbjct: 57 NPTRTALQECLASLEGTEAAVCFASGLAAEDAVIR-LLTPGDHIVCANDVYGGTWRQLDQ 115 Query: 121 VFTRWDVQYTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKV 180 V R+ ++ TPV + DLDAV AA P TR +W ETP+NPLL I D+ A+A+L +R A + Sbjct: 116 VHRRFGIESTPVDMTDLDAVAAAFRPTTRYLWAETPSNPLLKILDLAALAQLAHERGAWL 175 Query: 181 LVDNTFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNGAG 240 + DNTFA+P LQQP LGAD+++HSTTKY+GGHSDVVGGA+ T D + AFLQN G Sbjct: 176 VADNTFATPYLQQPTALGADIIIHSTTKYLGGHSDVVGGAVCT-DAATASDLAFLQNAVG 234 Query: 241 AVPGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAA 300 AVPGPFD +LT+RG+KTL +RM RH NA +AE L P V +V YPGLPS PGH++A Sbjct: 235 AVPGPFDNFLTLRGIKTLGVRMDRHVVNAMRIAEVLEADPRVEAVHYPGLPSDPGHDLAK 294 Query: 301 RQMRGFGGMVSVRMRAGRRAAQDLCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQL 360 RQM G GGMVS R G A +C T +F LAESLGGVESLIE P MTHAS AG+ L Sbjct: 295 RQMTGAGGMVSFRPTGGAETAARVCQGTELFFLAESLGGVESLIEVPGIMTHASVAGTPL 354 Query: 361 EVPDDLVRLSVGIEDIADLLGDLEQAL 387 EVPDDLVRLSVGIED+ DLL DL++AL Sbjct: 355 EVPDDLVRLSVGIEDVDDLLADLDRAL 381 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: 555 Number of extensions: 23 Number of successful extensions: 4 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