Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Dsui_2042 Dsui_2042 cystathionine beta-lyase/cystathionine gamma-synthase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__PS:Dsui_2042 Length = 392 Score = 480 bits (1236), Expect = e-140 Identities = 245/385 (63%), Positives = 299/385 (77%), Gaps = 10/385 (2%) Query: 18 ATLAIHGGQSPDPSTGAVMPPIYATSTYAQ---SSPGEHQG--FEYSRTHNPTRFAYERC 72 AT AIH GQ PDP+TGAV PIYATSTY Q + P ++ G F+Y+R+ NPTR A ERC Sbjct: 8 ATRAIHAGQEPDPTTGAVSIPIYATSTYVQPALNEPKQYAGATFDYARSANPTRLALERC 67 Query: 73 VAALEGGTRA----FAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAG 128 +A LEGG A FAFASG+AA++TV+ELL AGSHVVA DDLYGG+ RLF RVR +A Sbjct: 68 IADLEGGAFATATGFAFASGLAASATVLELLPAGSHVVASDDLYGGSVRLFNRVRSNSAD 127 Query: 129 LDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTF 188 L ++ D + + +AAI +TK++W+ETP+NP+LKLVD+ +A I + GLLTV DNTF Sbjct: 128 LKVTYADFSSRESIEAAITPETKLLWVETPSNPLLKLVDLDLVAAIGKDRGLLTVADNTF 187 Query: 189 ASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGP 248 ASP +QRPL G D+VVHSATKYLNGHSD++ G+AV A+LAE++AFLQN+ G V GP Sbjct: 188 ASPWIQRPLEHGFDIVVHSATKYLNGHSDVIAGVAVTA-RADLAERLAFLQNAAGAVLGP 246 Query: 249 FDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSG 308 FD+FLALRGLKTL LRM HC NA A+A+WLE HPAIEKV YPGLASHPQH LAKRQM G Sbjct: 247 FDAFLALRGLKTLALRMERHCANAEAIARWLEQHPAIEKVHYPGLASHPQHELAKRQMRG 306 Query: 309 FGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGI 368 FGG+VS V+KGG AAK+ E T++F LAESLGGVESL+ PA+MTHAS+P +R ++GI Sbjct: 307 FGGMVSAVVKGGLPAAKKLLENTKIFVLAESLGGVESLIELPALMTHASVPPEQRRRIGI 366 Query: 369 SDALVRLSVGIEDLGDLRGDLERAL 393 D LVRLSVG+ED+ DL DLE+AL Sbjct: 367 DDGLVRLSVGVEDVEDLLADLEQAL 391 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: 554 Number of extensions: 24 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: 397 Length of database: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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