Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_012536942.1 AFE_RS09520 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000021485.1:WP_012536942.1 Length = 404 Score = 267 bits (683), Expect = 4e-76 Identities = 165/404 (40%), Positives = 228/404 (56%), Gaps = 21/404 (5%) Query: 1 MSNRTTHSHDGDRALSLATLAIHGG----QSPDPSTGAVMPPIYATSTYAQSSP------ 50 M+ + T+ DR L T+AI G Q + S I+ TS++ S Sbjct: 1 MNTKNTNPDWADR-LRPETIAIRAGIHRTQEQEHSEA-----IFPTSSFVFDSAEEAADR 54 Query: 51 --GEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTV-MELLDAGSHVVA 107 G G Y+R NPT +E +AALEG A ASGMAA T M +L AG HVVA Sbjct: 55 FAGRVPGNIYARFTNPTVRTFEERLAALEGAEACVATASGMAACLTAFMGILKAGDHVVA 114 Query: 108 MDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVD 167 ++G T +L + R G++ SFV L D A++AA+R +T+M+++ETP+NP+ ++ D Sbjct: 115 SRSIFGTTVQLLGNILSRF-GVETSFVPLADVPAWRAALRPNTRMLFLETPSNPLTEIGD 173 Query: 168 IAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGD 227 + A+A +A H VVDN F +P LQ+PL GADLV+HSATKYL+G +GG AV G Sbjct: 174 MQALADLAHVHDAWLVVDNCFCTPALQQPLKFGADLVIHSATKYLDGQGRTLGG-AVCGS 232 Query: 228 NAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEK 287 L + G PF++++ L+GL+TL LRM HC NA +A+WLE P + + Sbjct: 233 TELLNSGPRNFVRTAGPSLSPFNAWVQLKGLETLGLRMERHCANAQKIAEWLEARPEVAR 292 Query: 288 VIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLV 347 V YPGL SHPQ LA RQ G I+S L GG AA F + L +L +LG ++ + Sbjct: 293 VYYPGLDSHPQQALAARQQRLPGAILSFDLHGGQKAAWAFVDALRLLSLTANLGDAKTTI 352 Query: 348 NHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLER 391 HPA TH+ + R G+ D L+R+SVG+E DLR D+ER Sbjct: 353 THPASTTHSRVSPEARAAAGVGDGLLRISVGLEHADDLREDMER 396 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: 439 Number of extensions: 22 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: 404 Length adjustment: 31 Effective length of query: 366 Effective length of database: 373 Effective search space: 136518 Effective search space used: 136518 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