Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Pf1N1B4_4890 Cystathionine gamma-lyase (EC 4.4.1.1)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4890 Length = 393 Score = 540 bits (1390), Expect = e-158 Identities = 258/377 (68%), Positives = 309/377 (81%) Query: 18 ATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVAALE 77 AT IH GQ+PDPSTGA+MPPIYA STY Q SPG H+GF+Y R+HNPTRFA ERCVA LE Sbjct: 14 ATRVIHAGQTPDPSTGALMPPIYANSTYLQQSPGVHKGFDYGRSHNPTRFALERCVADLE 73 Query: 78 GGTRAFAFASGMAATSTVMELLDAGSHVVAMDDLYGGTFRLFERVRRRTAGLDFSFVDLT 137 GGTRAFAFASG+AA + V+ELLDAG+H+V+ +DLYGGTFRLF++VRRR+AG FSFVDLT Sbjct: 74 GGTRAFAFASGLAAIANVLELLDAGAHIVSGNDLYGGTFRLFDKVRRRSAGHRFSFVDLT 133 Query: 138 DPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVVDNTFASPMLQRPL 197 D AAF+AA+ DT+MVW+ETP+NP+L L D+ A+A I R+ G++ V DNTFASP +QRPL Sbjct: 134 DLAAFEAALEDDTRMVWVETPSNPLLSLTDLDAVARICRQRGIICVADNTFASPWIQRPL 193 Query: 198 SLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFLQNSIGGVQGPFDSFLALRG 257 LG D+V+HS TKYLNGHSD++GGIAVVG NAELAE++ FLQN++G + GPFD+FL LRG Sbjct: 194 ELGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELAERLGFLQNAVGAIAGPFDAFLTLRG 253 Query: 258 LKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSGFGGIVSIVL 317 +KTL LRM HC NAL LAQWLE P + +V YPGL SHPQH LA+RQM GFGG++S+ L Sbjct: 254 VKTLALRMERHCSNALELAQWLERQPQVARVYYPGLPSHPQHELARRQMRGFGGMISLDL 313 Query: 318 KGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSV 377 AKRF E +F LAESLGGVESL+ HPA+MTHASIPV R QLGI DALVRLSV Sbjct: 314 NSDLAGAKRFLESVRIFALAESLGGVESLIEHPAIMTHASIPVETRAQLGIGDALVRLSV 373 Query: 378 GIEDLGDLRGDLERALV 394 G+ED+ DLR DL +AL+ Sbjct: 374 GVEDVEDLRADLAQALM 390 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: 558 Number of extensions: 23 Number of successful extensions: 1 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: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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