Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate GFF2301 PS417_11735 methionine gamma-lyase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__WCS417:GFF2301 Length = 411 Score = 318 bits (816), Expect = 1e-91 Identities = 185/392 (47%), Positives = 241/392 (61%), Gaps = 15/392 (3%) Query: 14 ALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSP--------GEHQGFEYSRTHNPT 65 A +T AIH G P GA++PPIY ++T+A + GE G Y+R NPT Sbjct: 7 AFGFSTRAIHHGYDPKDHHGALVPPIYLSATFAFPTAEYGAACFAGEASGHFYTRISNPT 66 Query: 66 RFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRR 124 E +A LE G A AF+SGM A +T LL G V+ LYG TF L Sbjct: 67 LALLESRMATLENGDAAVAFSSGMGAIAATFWTLLRPGDEVIVSQTLYGCTFALLHHGIG 126 Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLT-V 183 G+ VDLTD A +AA+ T+M++ ETP NP L+LVDIAA+A +A + +T V Sbjct: 127 EF-GIKVRHVDLTDLTALQAALTPATRMIYCETPANPNLRLVDIAAVAALAHQQPNVTLV 185 Query: 184 VDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAF--LQNS 241 VDNT+ +P LQRPL LGAD+VVHSATKYL+GH D+ GIAV N LA+++ L++ Sbjct: 186 VDNTYCTPYLQRPLELGADVVVHSATKYLSGHGDITAGIAV--SNQALAQRIRLQGLKDL 243 Query: 242 IGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVL 301 G V P D+ L +RGLKTL LRM HC NA A+A+ L+ HPA++ V YPGL S PQ+ L Sbjct: 244 TGAVMSPQDASLLMRGLKTLALRMDRHCSNAQAVAEALQAHPAVQSVTYPGLRSFPQYEL 303 Query: 302 AKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVA 361 A +QM GG+++ LKGG + +RF +LFT A SLG ESL HPA MTH++ Sbjct: 304 ATQQMKMPGGMIAFELKGGIETGRRFMNALKLFTRAVSLGDAESLAQHPASMTHSTYTPQ 363 Query: 362 RREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 R GIS+ LVRLSVG+ED+ DL D+++AL Sbjct: 364 ERAAHGISEGLVRLSVGLEDVADLLADVQQAL 395 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: 473 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: 411 Length adjustment: 31 Effective length of query: 366 Effective length of database: 380 Effective search space: 139080 Effective search space used: 139080 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