Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate CCNA_03271 CCNA_03271 methionine gamma-lyase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Caulo:CCNA_03271 Length = 401 Score = 320 bits (821), Expect = 4e-92 Identities = 184/391 (47%), Positives = 232/391 (59%), Gaps = 10/391 (2%) Query: 12 DRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSP--------GEHQGFEYSRTHN 63 D +T AIH G P GA+ PP++ TST+A S G +G YSR N Sbjct: 3 DDQTGFSTRAIHAGYDPADEHGALTPPLHLTSTFAFESAEAGGEMFAGTREGHFYSRISN 62 Query: 64 PTRFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERV 122 PT ER +A+LEG A A ASGM A T+T+ L AG V+ LYG TF F R Sbjct: 63 PTTDLLERRLASLEGAEAAVATASGMGAITATLWSFLRAGDEVITDQTLYGCTFA-FLRD 121 Query: 123 RRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLT 182 G+ VD+T P AAI T++V+ ETP NP ++LVDIAAI IA G Sbjct: 122 GLTRFGVTVKQVDMTRPETLAAAISDQTRIVYFETPANPNMRLVDIAAITRIAHAAGAKV 181 Query: 183 VVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSI 242 VVDNT+A+P L RPL+LGAD+VVHSATKYL GH D+VGGIA G ++ +++ Sbjct: 182 VVDNTYATPCLTRPLALGADIVVHSATKYLGGHGDLVGGIAAGGIEDMARVRLCGVKDMT 241 Query: 243 GGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLA 302 G V PF +FL LRGLKTL LRM H ++A A+A+WLE HPA+E+V YPGL S PQ LA Sbjct: 242 GAVMSPFTAFLVLRGLKTLSLRMARHSQSAQAVARWLEDHPAVEQVFYPGLQSFPQRDLA 301 Query: 303 KRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVAR 362 RQM+ GG+++ LKGG A + L A SLG E+L+ HPA MTH+ Sbjct: 302 ARQMAAGGGMMAFELKGGHAAGVAMMNRLALIRRAVSLGDAETLIQHPASMTHSPYTPEE 361 Query: 363 REQLGISDALVRLSVGIEDLGDLRGDLERAL 393 R GI + +VRLSVG+ED+ D+ DL AL Sbjct: 362 RAAAGIGEGMVRLSVGLEDVADILADLAMAL 392 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: 491 Number of extensions: 24 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: 397 Length of database: 401 Length adjustment: 31 Effective length of query: 366 Effective length of database: 370 Effective search space: 135420 Effective search space used: 135420 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