Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_086509774.1 BZY95_RS09910 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_002151265.1:WP_086509774.1 Length = 424 Score = 231 bits (589), Expect = 3e-65 Identities = 147/418 (35%), Positives = 221/418 (52%), Gaps = 46/418 (11%) Query: 19 TLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEH---------QGFEYSRTHNPTRFAY 69 T+A+H G +PD AV PI+ T++++ S +H +G YSR NPT Sbjct: 5 TIALHHGYAPDDQH-AVAVPIHQTTSFSFDS-AQHAADLFDLKVEGNIYSRIMNPTCAVL 62 Query: 70 ERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAG 128 E+ VAALEGG A ASGMAA T + + +AG ++V++ +LYGGT+ LF R G Sbjct: 63 EQRVAALEGGIAGLAVASGMAAITYAIQTIAEAGDNIVSISELYGGTYNLFAHTLPRQ-G 121 Query: 129 LDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTF 188 ++ F D D ++ I A TK V+ E+ NP +VD+A +A +A +HG+ +VDNT Sbjct: 122 IEVRFADKDDIDGIESLIDARTKAVFCESVGNPSGSVVDMARLAEVAHRHGVPVIVDNTV 181 Query: 189 ASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV------------------------ 224 +P L RP+ GAD+V+HSATKY+ GH VGG+ V Sbjct: 182 PTPFLWRPIEHGADIVIHSATKYIGGHGTTVGGVIVDSGRFPWADHPQRFPLLNEPDVSY 241 Query: 225 --------VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALA 276 +G+ A +A ++G ++ L+GL+TL LR+ C+NAL +A Sbjct: 242 HGVCYTRDIGEAAFIARARVVPLRNMGAALSAQAAWNLLQGLETLALRIERICDNALKVA 301 Query: 277 QWLETHPAIEKVIYPGLASHPQHVLAKRQMSG-FGGIVSIVLKGGFDAAKRFCEKTELFT 335 ++LE H A+ V Y GL H H LA+R M G GI+S ++GG +A RF + + Sbjct: 302 EYLEAHDAVTWVQYAGLPGHKDHQLAQRYMGGRASGILSFGIQGGREAGARFYDALGMIL 361 Query: 336 LAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 ++G ++ + PA TH + ++ +VRLS+GIE + D+ DLE+AL Sbjct: 362 RLVNIGDAKTCSSIPASTTHRQLSDEELAAASVTPDMVRLSIGIEHVDDIIADLEQAL 419 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: 489 Number of extensions: 30 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 397 Length of database: 424 Length adjustment: 31 Effective length of query: 366 Effective length of database: 393 Effective search space: 143838 Effective search space used: 143838 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