Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate HSERO_RS14995 HSERO_RS14995 cystathionine beta-lyase
Query= SwissProt::P9WGB7 (388 letters) >FitnessBrowser__HerbieS:HSERO_RS14995 Length = 392 Score = 175 bits (444), Expect = 2e-48 Identities = 125/388 (32%), Positives = 179/388 (46%), Gaps = 23/388 (5%) Query: 14 PATRAIHAGYRPDPATGAVNVPIYASSTFAQDGVGGLRG-------GFEYARTGNPTRAA 66 P T +H+ YR A V I+ +ST V +R G+ Y G PT Sbjct: 11 PQTSLVHSSYRAPDGFEAFPVGIHHASTVLFPDVAAMRSRDWREKLGYTYGLHGTPTSFV 70 Query: 67 LEASLAAVEEGAFARAFSSGMAATDCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTRW- 125 LEA LA +E G + R SG+AA A L+ GD V++PD+ YG + K +W Sbjct: 71 LEARLAEIEGGKYCRVTPSGLAAIAMVNFAFLKSGDDVLLPDNVYGPS-----KDLGQWL 125 Query: 126 --DVQYTPVRLADLDAVGAA--ITPRTRLIWVETPTNPLLSIADITAIAELGTDRSAKVL 181 D Q T + G A I P TRL+W E P + + + DI A+ + V Sbjct: 126 ERDFQITARFYDPMIGEGLAELIRPTTRLVWTEAPGSVSMEVPDIPALCRAAHAKGVLVA 185 Query: 182 VDNTFASPALQQPLRLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDEEFAFLQNGAGA 241 +DNT+++ + G D+V+ + TKY G SDV+ GA++ D+ L+E+ G Sbjct: 186 IDNTWSAGIAFKAFEHGVDIVMQAVTKYQSGGSDVLMGAVIVRDQALNEKLELAHMRLGF 245 Query: 242 VPGPFDAYLTMRGLKTLVLRMQRHSENACAVAEFLADHPSVSSVLYPGLPSHPGHEIAAR 301 G D Y+ +R L ++ LR + H A VA +L P + +VL+P PGH R Sbjct: 246 GVGMDDVYMVLRSLSSMRLRFEAHDAAARKVAAWLKQRPEIVAVLHPAFEDCPGHAHWKR 305 Query: 302 QMRGFGGMVSVRMRAGRRAAQD--LCAKTRVFILAESLGGVESLIEHPSAMTHASTAGSQ 359 G GG+ SV AQ R+F + S GG SL P M A + Sbjct: 306 DFSGAGGLFSVIFDPRYVEAQTDRFVDSLRLFKIGYSWGGAHSLCV-PYRMKGMRRAWMR 364 Query: 360 LEVPDDLVRLSVGIEDIADLLGDLEQAL 387 LVR ++G+E DL+ D+EQAL Sbjct: 365 ---EGQLVRFNIGLESPEDLIADIEQAL 389 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: 379 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: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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 09 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