Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate WP_013519368.1 ALIDE2_RS14220 cystathionine beta-lyase
Query= SwissProt::P9WGB7 (388 letters) >NCBI__GCF_000204645.1:WP_013519368.1 Length = 409 Score = 162 bits (410), Expect = 2e-44 Identities = 126/397 (31%), Positives = 175/397 (44%), Gaps = 29/397 (7%) Query: 16 TRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRG-------GFEYARTGNPTRAALE 68 TR IH YRP A ++ +ST V +R + Y G PT LE Sbjct: 11 TRLIHHDYRPPAGFEAPQPAVHKASTVIFPNVAAMRAREWKDKSSYTYGLHGTPTTYQLE 70 Query: 69 ASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRWDVQ 128 LA +E G SG+AA A+LR GD V+IPD+AYG L + + ++ Sbjct: 71 ERLATLEGGRQCLLAPSGLAAIATVSLALLRHGDEVLIPDNAYGPNKALAEVELRHYGIR 130 Query: 129 ---YTPVRLADLDAVGAAITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVLVDNT 185 Y P+ ADL A IT TRL+W+E P + L D+ + R +DNT Sbjct: 131 HQVYDPLDPADL---AARITDATRLVWLEAPGSVTLEFPDLPEQVRICRARGVTTALDNT 187 Query: 186 FASPALQQPL------RLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNGA 239 + + P +LG D+ +H+ TKY G DV+ G++ T DE L Sbjct: 188 WGAGLAFAPFDLAGDGQLGVDISVHALTKYPSGGGDVLMGSITTRDEALHLRMKLTHMRL 247 Query: 240 GAVPGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHE-- 297 G G D +R L ++ LR + H A A+A+++ V+ VL+P LP PGHE Sbjct: 248 GLGVGANDVEAVLRSLPSMALRYRAHDAAARALAQWMGTKAPVAQVLHPALPGSPGHEHW 307 Query: 298 -----IAARQMRGFGGMVSVRMRAGRRAAQ--DLCAKTRVFILAESLGGVESLIEHPSAM 350 A G+ SV + A AQ C R+F L S GG SL+ Sbjct: 308 RALCGSAGGPEGAAAGLFSVVIDARHTQAQVDAFCDGLRLFRLGYSWGGPMSLVVPYDLP 367 Query: 351 THASTAGSQLEVPDDLVRLSVGIEDIADLLGDLEQAL 387 A LE +VR +VG+E + DL DL QA+ Sbjct: 368 GMRERATPHLEA-GTVVRFAVGLEAVEDLRQDLAQAM 403 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: 396 Number of extensions: 21 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: 409 Length adjustment: 31 Effective length of query: 357 Effective length of database: 378 Effective search space: 134946 Effective search space used: 134946 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