Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Echvi_4510 Echvi_4510 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Cola:Echvi_4510 Length = 403 Score = 271 bits (692), Expect = 3e-77 Identities = 166/393 (42%), Positives = 228/393 (58%), Gaps = 22/393 (5%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTY-AQSSPG-------EHQGFEYSRTHNPTRFAYE 70 T AIH G+ PDP TGA P + ++TY A++ G E + Y+R NPT E Sbjct: 13 TRAIHAGELPDPVTGASSPNLVMSTTYLAEAGTGFSVEGHDEEDPWIYTRWGNPTVHQLE 72 Query: 71 RCVAALEGGTRAFAFASGMAATSTVM-ELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 +A LE A AFASGM A + + LL AG H + D Y L E L Sbjct: 73 EKLAVLEEAETAVAFASGMGAITVLFFHLLKAGDHAIVSDVAYAA---LSEMTNEMVPSL 129 Query: 130 DFSF--VDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNT 187 + VD +D +A KAA++ +T++++IETP NP+L+L DI A+A IAR G VD+T Sbjct: 130 NIQITKVDTSDLSAVKAAVKNNTRLIYIETPCNPILRLTDIEAVAGIARGAGARLAVDST 189 Query: 188 FASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQG 247 FA+P +PL LGAD +VHS TKYL GH D +GG A++G A+LA +G V Sbjct: 190 FATPAATKPLQLGADFIVHSLTKYLGGHGDALGG-AILGRKADLAPLRKKTAIRMGAVIS 248 Query: 248 PFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMS 307 PF+++L LRGL T P+RMRAH +NAL +A +LE HP +++VIYPGL SHPQH LAK+QM Sbjct: 249 PFNAWLILRGLATFPIRMRAHEKNALKVAAFLEKHPKVKRVIYPGLPSHPQHELAKKQMK 308 Query: 308 GFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNH--PAVMTHASIPVARREQ 365 F G+++ ++ G + F +K + A SLG SL+ + A + +S A +Q Sbjct: 309 NFSGMLTFQVENGKKRSGIFADKLRIVHYAVSLGHHRSLIFYLDSADLKESSFKFATGKQ 368 Query: 366 -----LGISDALVRLSVGIEDLGDLRGDLERAL 393 + D + RLSVG+ED D+ DL RAL Sbjct: 369 DESWEIYAGDGIFRLSVGLEDSKDIIDDLNRAL 401 Lambda K H 0.320 0.134 0.391 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: 418 Number of extensions: 24 Number of successful extensions: 5 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: 397 Length of database: 403 Length adjustment: 31 Effective length of query: 366 Effective length of database: 372 Effective search space: 136152 Effective search space used: 136152 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