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 Echvi_4510 Echvi_4510 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::Q55DV9 (387 letters) >FitnessBrowser__Cola:Echvi_4510 Length = 403 Score = 284 bits (727), Expect = 3e-81 Identities = 165/402 (41%), Positives = 233/402 (57%), Gaps = 17/402 (4%) Query: 1 MTQPNNYKIG--TNVIHAGQSADKNTGAVIVPISLSTTFLQPSPGVL----HSEYD---Y 51 M +P+ +G T IHAG+ D TGA + +STT+L + H E D Y Sbjct: 1 MEKPDFKNLGEQTRAIHAGELPDPVTGASSPNLVMSTTYLAEAGTGFSVEGHDEEDPWIY 60 Query: 52 SRSGNPTRKAFEECIAACENAKYALSFASGLATLTTIT-HLLKSGDEVISIDDVYGGTRR 110 +R GNPT EE +A E A+ A++FASG+ +T + HLLK+GD I D Y Sbjct: 61 TRWGNPTVHQLEEKLAVLEEAETAVAFASGMGAITVLFFHLLKAGDHAIVSDVAYAALSE 120 Query: 111 YFTRVAANFDLKFSFVDLSTLDDLKNAFTDKTRLVWIETPTNPLLKVADIKAVADYVHSR 170 + + +++ + VD S L +K A + TRL++IETP NP+L++ DI+AVA Sbjct: 121 MTNEMVPSLNIQITKVDTSDLSAVKAAVKNNTRLIYIETPCNPILRLTDIEAVAGIARGA 180 Query: 171 GATLVVDNTFMSPYFQNPLDLGADIVMHSVTKYINGHSDCVMGVLATNNDELYAKLKFLQ 230 GA L VD+TF +P PL LGAD ++HS+TKY+ GH D + G + +L K Sbjct: 181 GARLAVDSTFATPAATKPLQLGADFIVHSLTKYLGGHGDALGGAILGRKADLAPLRKKTA 240 Query: 231 NSIGAVPSPFDCFLALRGLKTLHVRMEAHQKNAFAICNFLEKHPKVERVIYPGLPSHPQH 290 +GAV SPF+ +L LRGL T +RM AH+KNA + FLEKHPKV+RVIYPGLPSHPQH Sbjct: 241 IRMGAVISPFNAWLILRGLATFPIRMRAHEKNALKVAAFLEKHPKVKRVIYPGLPSHPQH 300 Query: 291 EICKRQMKGYGGMVVFFVKGSIDQSRSFLENIKLFALAESLGGVESLIEL-------PSV 343 E+ K+QMK + GM+ F V+ +S F + +++ A SLG SLI S Sbjct: 301 ELAKKQMKNFSGMLTFQVENGKKRSGIFADKLRIVHYAVSLGHHRSLIFYLDSADLKESS 360 Query: 344 MTHASVPAEERAKLGISDTLIRLSVGIEDINDLLADISQALD 385 A+ +E ++ D + RLSVG+ED D++ D+++ALD Sbjct: 361 FKFATGKQDESWEIYAGDGIFRLSVGLEDSKDIIDDLNRALD 402 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: 399 Number of extensions: 18 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: 387 Length of database: 403 Length adjustment: 31 Effective length of query: 356 Effective length of database: 372 Effective search space: 132432 Effective search space used: 132432 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