Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_068462251.1 APY04_RS09740 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_001541235.1:WP_068462251.1 Length = 405 Score = 248 bits (634), Expect = 2e-70 Identities = 142/357 (39%), Positives = 213/357 (59%), Gaps = 4/357 (1%) Query: 39 IYATSTYAQSS-PGEHQGFEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATST-VM 96 +YA + A++ E GF+YSR NPT +E + LEG A A ASGMAA + V+ Sbjct: 44 VYANAEQAEARFKNEDPGFQYSRFGNPTVAMFEERIRLLEGAEEARATASGMAAVNAAVL 103 Query: 97 ELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIE 156 L AG H+V+ L+G + + + R G+ + VD D A+K AI+ +TK+ + E Sbjct: 104 SCLKAGDHIVSARALFGACRYIVDTLAPRY-GIGCTLVDGRDLNAWKKAIQPNTKLFFFE 162 Query: 157 TPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHS 216 TP+NP L+LVDIAA++ IA G + VVDN FA+PMLQRP++LGAD+VV+SATK+++G Sbjct: 163 TPSNPTLELVDIAAVSEIAHSIGAIVVVDNVFATPMLQRPMALGADVVVYSATKHIDGQG 222 Query: 217 DMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALA 276 +GG + + +L+ + G PF++++ L+G++T+ LR+ A + A +A Sbjct: 223 RCLGGAVLCSSDYMAGGLQEYLRQT-GPTMSPFNAWVMLKGMETMSLRVNAQVQTAGRIA 281 Query: 277 QWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTL 336 L P ++ V+Y G HPQ +AKRQMSG G +++ ++GG AA L + Sbjct: 282 DHLAKQPGVKSVLYCGRDDHPQAEIAKRQMSGGGQMIAFEVEGGKAAAFALQNALGLIKI 341 Query: 337 AESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 + +LG +SL+ HPA TH I R +LGI D L+RLS+G+E DL DL+ L Sbjct: 342 SNNLGDAKSLITHPATTTHFRIGPEARAELGIGDGLMRLSIGLEAFEDLAADLDAGL 398 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: 424 Number of extensions: 18 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: 405 Length adjustment: 31 Effective length of query: 366 Effective length of database: 374 Effective search space: 136884 Effective search space used: 136884 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 Jul 25 2024. The underlying query database was built on Jul 25 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