Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate WP_085218094.1 B9N75_RS06660 cystathionine gamma-synthase family protein
Query= BRENDA::Q5H4T8 (397 letters) >NCBI__GCF_900177405.1:WP_085218094.1 Length = 434 Score = 217 bits (552), Expect = 6e-61 Identities = 147/410 (35%), Positives = 212/410 (51%), Gaps = 29/410 (7%) Query: 11 GDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSS---------------PGEHQG 55 G R L ATL + G P S G++ PI+ TST+ + PG +G Sbjct: 24 GGRKLKPATLMMGHGFDPALSEGSLKAPIFLTSTFVFENAAAGKRHFEGVTGKRPGGAEG 83 Query: 56 FEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVM-ELLDAGSHVVAMDDLYGG 114 YSR + P + E +AA E + F+SGM+A +T++ + G +V LY Sbjct: 84 LVYSRFNGPNQEILEDRLAAWEDAEDSLTFSSGMSAIATLLLTFVQPGDVIVHSGPLYAA 143 Query: 115 TFRLFERVRRR--TAGLDF---SFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIA 169 T L R+ R LDF + D KA + ++++E+P NP LVD+ Sbjct: 144 TETLIGRILGRFGVTWLDFPAGATGDEISAVLEKAKAQGRVSLIYLESPANPTNALVDVE 203 Query: 170 AIA-----VIARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV 224 A+A V +DNTF P+ +PL GADL V+S TKY GHSD+V G + Sbjct: 204 AVAASRDAVFGGDEKPPIAIDNTFLGPLWSKPLEHGADLSVYSLTKYAGGHSDLVAG-GI 262 Query: 225 VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPA 284 VG A L + + ++N+IG + P +++ LR L+TL LRM ENA + + HP Sbjct: 263 VGSKA-LLDPIRMMRNTIGTITDPNTAWMLLRSLETLELRMSRAGENAEKVCAFFRDHPK 321 Query: 285 IEKVIYPG-LASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGV 343 +E V Y G L Q + +R +G G S+ LKGG A F + ++ LA SLGG Sbjct: 322 VESVGYLGFLKDGRQADIYRRHCTGAGSTFSLYLKGGEREAFAFLDALKIAKLAVSLGGT 381 Query: 344 ESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 E+L + PA MTH S+P R++ LGI+D LVR+S+G+ED DL D ++AL Sbjct: 382 ETLASAPAAMTHLSVPDERKQALGITDNLVRISIGVEDADDLIADFDQAL 431 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: 466 Number of extensions: 25 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: 434 Length adjustment: 31 Effective length of query: 366 Effective length of database: 403 Effective search space: 147498 Effective search space used: 147498 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 26 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