Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_074201059.1 BUQ81_RS03740 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_900141795.1:WP_074201059.1 Length = 391 Score = 301 bits (770), Expect = 3e-86 Identities = 168/384 (43%), Positives = 238/384 (61%), Gaps = 12/384 (3%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSP--------GEHQGFEYSRTHNPTRFAYE 70 T AIHGG P G I+ TS++A S G+ G YSR NPT +E Sbjct: 7 TFAIHGGYRRTPE-GENSEAIFPTSSFAFDSAAQAAARFSGDEPGNIYSRFTNPTVRTFE 65 Query: 71 RCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGL 129 + +AA+EGG ASGM+A S ++ +L++G H+V+ ++G T LF + + G+ Sbjct: 66 QRLAAMEGGEACVGTASGMSAILSLMLGMLESGDHIVSSQSIFGTTKVLFSKYLGKL-GI 124 Query: 130 DFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFA 189 D ++V LTD A+ AAIR +T+M+++ETP+NPM + DI +A IA H L VVDN F Sbjct: 125 DTTYVPLTDYDAWAAAIRPETRMLFLETPSNPMTDVADIQRLAEIAHAHDCLLVVDNCFC 184 Query: 190 SPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPF 249 +P LQ+PL LGADLV+HSATK+L+G VGG AVVG + + E + + G PF Sbjct: 185 TPALQQPLKLGADLVIHSATKFLDGQGRCVGG-AVVGPESLVEEHVRGFLRTCGPSMSPF 243 Query: 250 DSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGF 309 ++++ +GL+TL +RM+AH NALALAQWL HPA+E+V YPGL SHPQH LA RQ Sbjct: 244 NAWVFFKGLETLHVRMQAHSANALALAQWLSDHPAVEQVFYPGLPSHPQHELAMRQQKAG 303 Query: 310 GGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGIS 369 GG+VS +KGG A + + E+ + +LG ++L+ HPA TH+ + R GI+ Sbjct: 304 GGLVSFRIKGGRGDAWKVVDSLEMIHITANLGDTKTLITHPATTTHSRVEPEARLAAGIT 363 Query: 370 DALVRLSVGIEDLGDLRGDLERAL 393 D L+R+SVG+E + D++ DL R L Sbjct: 364 DNLLRVSVGLESIEDIKADLGRGL 387 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: 464 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: 391 Length adjustment: 31 Effective length of query: 366 Effective length of database: 360 Effective search space: 131760 Effective search space used: 131760 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