Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 3607593 Dshi_1002 Cystathionine gamma-synthase (RefSeq)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Dino:3607593 Length = 380 Score = 276 bits (705), Expect = 9e-79 Identities = 176/383 (45%), Positives = 221/383 (57%), Gaps = 22/383 (5%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATST------YAQSSPGEHQGFEYSRTHNPTRFAYERC 72 TLA HGG + D ++G V+PPI +T YA +P YSR + A E Sbjct: 11 TLAAHGGGAVDTASGGVVPPIQPATTFRRGPDYAPLNPDNI----YSRDDSEALRAVETL 66 Query: 73 VAALEGGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFS 132 +AALEGG A AF SGMAAT+ V L AG+ VV +Y GT + R G+ Sbjct: 67 LAALEGGAGALAFPSGMAATAAVFRTLPAGARVVLQSGIYWGTTKWVRDFCARR-GVTLV 125 Query: 133 FVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPM 192 VD D A +A A T +V++ETP+NP LK VDI A A A G L VVD+T A+P+ Sbjct: 126 EVDAADAHALGSACAAPTALVFVETPSNPWLKTVDIRAAAAAAHGAGALLVVDSTAATPV 185 Query: 193 LQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGD-NAELAEQMAFLQNSIGGVQGPFDS 251 L RPL LGADLV+HSATK LNGHSD++ G V D E ++A ++ G V GPF++ Sbjct: 186 LTRPLGLGADLVMHSATKGLNGHSDVLAGALVTADAGHETWARIATDRHDAGAVLGPFEA 245 Query: 252 FLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMS-GFG 310 +L LRG++TLPLR+ AL LAQ L T + V YPGL H H +A QM+ GFG Sbjct: 246 WLLLRGMRTLPLRVARMSATALELAQRLSTDTRVADVFYPGLPGHAGHDIAVAQMTGGFG 305 Query: 311 GIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISD 370 G++S ++ G A + ELF A SLGGVESLV H A + S GI + Sbjct: 306 GLMSFLVHGDRQTALEVVGRLELFQRATSLGGVESLVEHRATIEPDS---------GIPE 356 Query: 371 ALVRLSVGIEDLGDLRGDLERAL 393 LVRLSVGIED GDL DL+RAL Sbjct: 357 TLVRLSVGIEDAGDLWADLDRAL 379 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: 436 Number of extensions: 28 Number of successful extensions: 6 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: 380 Length adjustment: 30 Effective length of query: 367 Effective length of database: 350 Effective search space: 128450 Effective search space used: 128450 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