Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_013518386.1 ALIDE2_RS16910 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_000204645.1:WP_013518386.1 Length = 404 Score = 275 bits (702), Expect = 2e-78 Identities = 159/370 (42%), Positives = 222/370 (60%), Gaps = 17/370 (4%) Query: 39 IYATSTYAQSS--------PGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMA 90 +Y TS++ QS E G+ YSRT NPT ++ER +AA+EG A A A+GM+ Sbjct: 33 LYLTSSFVQSDCASAARRFANEEAGYTYSRTSNPTVTSFERRLAAMEGTECAVATATGMS 92 Query: 91 ATSTV-MELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRAD 149 A V + L AG HV+ ++G T +L R G++ SFV TD A+KAA+R + Sbjct: 93 AILLVALTALKAGDHVICSQSMFGSTIKLLGTEMARF-GVETSFVSQTDVQAWKAAMRPN 151 Query: 150 TKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSAT 209 T++++ ETPTNP+ L DIAA+A +A HG L VDN+FASP+LQ+P+ GADLVVHS T Sbjct: 152 TRLLFAETPTNPLTDLCDIAALAELAHAHGALLAVDNSFASPVLQQPVRFGADLVVHSGT 211 Query: 210 KYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHC 269 K L+G ++ G AV G A + + M S G PF++++ L+GL+TL LR++A Sbjct: 212 KLLDGQGRVMAG-AVCGTVALVDKVMGTFLRSGGLNLAPFNAWVVLKGLETLGLRVKAES 270 Query: 270 ENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDA------ 323 AL LA WLE HP + +V YPGL SHPQH LA RQ +G GG V G A Sbjct: 271 AAALELATWLEAHPKVARVYYPGLKSHPQHELAMRQQNGMGGTVLAFDVAGQGAQQLRAN 330 Query: 324 AKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLG 383 A + T + ++ +LG V++ + HPA +H + +R+ GI L+R+SVG+E LG Sbjct: 331 AFHVVDSTRVCSITANLGDVKTTITHPASTSHGRLTEEQRQAAGIGQGLIRISVGLEHLG 390 Query: 384 DLRGDLERAL 393 DL+ DL R L Sbjct: 391 DLQNDLARGL 400 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: 433 Number of extensions: 23 Number of successful extensions: 5 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