Align Cystathionine gamma-lyase; CGL; CSE; Cysteine desulfhydrase; Cysteine-protein sulfhydrase; Gamma-cystathionase; Homocysteine desulfhydrase; EC 4.4.1.1; EC 4.4.1.2 (characterized)
to candidate CA265_RS06375 CA265_RS06375 cystathionine gamma-synthase
Query= SwissProt::Q55DV9 (387 letters) >FitnessBrowser__Pedo557:CA265_RS06375 Length = 379 Score = 424 bits (1089), Expect = e-123 Identities = 203/378 (53%), Positives = 273/378 (72%), Gaps = 2/378 (0%) Query: 8 KIGTNVIHAGQSADKNTGAVIVPISLSTTFLQPSPGVLHSEYDYSRSGNPTRKAFEECIA 67 K T IHAGQ D TGAV+ PI ++T+ Q SPG + Y+YSR NPTRKA E+C+A Sbjct: 2 KFATKAIHAGQEPDPTTGAVMTPIYQTSTYWQKSPGD-NKGYEYSRGTNPTRKALEDCLA 60 Query: 68 ACENAKYALSFASGLATLTTITHLLKSGDEVISIDDVYGGTRRYFTRVAANFDLKFSFVD 127 A ENAKY L+F+SG+ + LL+ GDEVI+ +D+YGG+ R FT++ + +KF F+D Sbjct: 61 ALENAKYGLAFSSGMGATDAVLKLLQPGDEVITGNDLYGGSYRIFTKIFTKYGIKFHFLD 120 Query: 128 LSTLDDLKNAFTDKTRLVWIETPTNPLLKVADIKAVADYVHSRGATLVVDNTFMSPYFQN 187 LS +++ DKT+LVWIETPTNP +++ DI+ VA + L VDNTF SPY QN Sbjct: 121 LSKPENILPYINDKTKLVWIETPTNPTMQIIDIEGVAKITKEKNLILTVDNTFASPYLQN 180 Query: 188 PLDLGADIVMHSVTKYINGHSDCVMGVLATNNDELYAKLKFLQNSIGAVPSPFDCFLALR 247 P+DLGADIVMHSVTKYI GHSD VMG L TN+++LY L F+ N+ GA P P D FL LR Sbjct: 181 PIDLGADIVMHSVTKYIGGHSDVVMGALVTNDEQLYKDLWFIYNACGATPGPQDAFLVLR 240 Query: 248 GLKTLHVRMEAHQKNAFAICNFLEKHPKVERVIYPGLPSHPQHEICKRQMKGYGGMVVFF 307 G+KTLH+RM+AH +N I ++L+ HPKV+++ +PG HP H+I K+QM+G+GGM+ Sbjct: 241 GIKTLHLRMKAHCENGERIAHYLKTHPKVDKIYWPGFEDHPNHDIAKKQMRGFGGMISIT 300 Query: 308 VKGS-IDQSRSFLENIKLFALAESLGGVESLIELPSVMTHASVPAEERAKLGISDTLIRL 366 +KG+ ++++ N K+F LAESLGGVESLI P+ MTH S+P EER K+G++D L+RL Sbjct: 301 LKGADLEETFRISSNFKVFTLAESLGGVESLINHPATMTHGSIPKEEREKVGVTDNLLRL 360 Query: 367 SVGIEDINDLLADISQAL 384 SVG+EDI+DLL D++ AL Sbjct: 361 SVGVEDIDDLLEDLANAL 378 Lambda K H 0.320 0.135 0.394 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: 492 Number of extensions: 20 Number of successful extensions: 3 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: 387 Length of database: 379 Length adjustment: 30 Effective length of query: 357 Effective length of database: 349 Effective search space: 124593 Effective search space used: 124593 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 (21.8 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