Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate AO356_27130 AO356_27130 cystathionine gamma-lyase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27130 Length = 400 Score = 234 bits (597), Expect = 3e-66 Identities = 148/390 (37%), Positives = 207/390 (53%), Gaps = 16/390 (4%) Query: 15 LSLATLAIHGGQSPDPSTGAVMPPIYATSTY------AQSSPGEHQGFEYSRTHNPTRFA 68 LS ATLA+HGG D ++GAV P+ ++Y A G Y+R + Sbjct: 11 LSAATLAVHGGNVADVTSGAVRTPLVMANSYLLPEDPATMDWSSPDGLVYTRNQGHNQVC 70 Query: 69 YERCVAALEGGTRAFAFASGMAATSTVM-ELLDAGSHVVAMDDLYGGTFRLFERVRRRTA 127 E+ +AALEG A FA+G+AA +V L +G HV+ D Y +RLF + Sbjct: 71 LEKKLAALEGCEDAVVFATGVAALHSVFFSFLKSGDHVIVSDITYQAVWRLFAELLPERY 130 Query: 128 GLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNT 187 G++ +FVD+ D + + AIR +TK++ ET NP K+ DIAA+A IA HG L VD T Sbjct: 131 GIEATFVDVGDLESVRNAIRPNTKLIHTETIANPTTKVADIAALAEIAHAHGALISVDAT 190 Query: 188 FASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQG 247 F P R G D V+HS TKY+NGH D +GG+ V+G N + + +G Sbjct: 191 FTPPPFFRASQHGVDFVIHSLTKYINGHGDAMGGV-VIGSNPLINKIKNDALVDLGATIS 249 Query: 248 PFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMS 307 PF++++ +RG TLPLR++ A LAQ+L++ I V YPGL SHPQH LA+RQ + Sbjct: 250 PFNAWMIMRGSVTLPLRLKQLLNTAEKLAQFLDSDDRIAYVYYPGLPSHPQHKLARRQFA 309 Query: 308 --GFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARRE- 364 G+G +++ ++G D RF + T A SLG ESL+ H E Sbjct: 310 GKGYGAVMAFAVEGDPDTQNRFVSNLRIITSAVSLGHDESLIVHVGAEGRGGFDKYPEEF 369 Query: 365 -QLGISDALVRLSVGIEDLGDLRGDLERAL 393 Q G +R SVG+ED DL D+ AL Sbjct: 370 RQYG----HLRFSVGLEDPEDLIKDITFAL 395 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: 446 Number of extensions: 22 Number of successful extensions: 6 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: 400 Length adjustment: 31 Effective length of query: 366 Effective length of database: 369 Effective search space: 135054 Effective search space used: 135054 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 09 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