Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_019896009.1 A377_RS0109055 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000384235.1:WP_019896009.1 Length = 399 Score = 295 bits (754), Expect = 2e-84 Identities = 165/387 (42%), Positives = 251/387 (64%), Gaps = 10/387 (2%) Query: 15 LSLATLAIHGGQ---SPDPSTGAVMPP----IYATSTYAQSSPGEHQGFEYSRTHNPTRF 67 L +ATLAI G + ++ A+ P ++ A G+ G YSR NPT Sbjct: 6 LDMATLAIRAGYQQTAEQENSEAIFPTSSFRYHSAQQAADRFSGDEPGNVYSRFTNPTVQ 65 Query: 68 AYERCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRLFERVRRRT 126 A+ER +AA+E G A ASGM+A +++M LL AG H+V ++G T LF++ R+ Sbjct: 66 AFERRLAAMEEGEACVATASGMSAILASMMGLLQAGDHLVCSQSVFGTTRVLFDQYLRKF 125 Query: 127 AGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDN 186 G++ ++V LTD AA++ A++ +T+++++ETP+NP+ ++ DIA + +AR + VVDN Sbjct: 126 -GIEVTYVPLTDYAAWQNALQDNTRLLFLETPSNPLSEIADIARLGELARANQAWLVVDN 184 Query: 187 TFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQ 246 F +P LQ+PL+LGADLVVHSATK+L+G +VGG AVVG A + E++ + + G Sbjct: 185 CFCTPALQKPLTLGADLVVHSATKFLDGQGRVVGG-AVVGPAALVDEKIRGVMRTAGPSM 243 Query: 247 GPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQM 306 PF++++ L+GL+TL LRM+AH E A ALA WL PA+++V +PGLASHPQ L RQ Sbjct: 244 SPFNAWVFLKGLETLALRMKAHSEQAQALADWLVAQPAVKQVYFPGLASHPQRALIARQQ 303 Query: 307 SGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQL 366 SG GG+++ + GG +AA ++T + ++ +LG V++ + HPA THA + A RE Sbjct: 304 SGPGGLLAFEVAGGREAAWTVIDQTRMISITANLGDVKTSITHPATTTHARVSQADREAS 363 Query: 367 GISDALVRLSVGIEDLGDLRGDLERAL 393 GIS++LVR+SVG+E + D++ DL R L Sbjct: 364 GISESLVRVSVGLEAIEDIQADLARGL 390 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: 416 Number of extensions: 17 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: 399 Length adjustment: 31 Effective length of query: 366 Effective length of database: 368 Effective search space: 134688 Effective search space used: 134688 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 10 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