Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 200276 SO1095 O-acetylhomoserine (thiol)-lyase, putative (NCBI ptt file)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__MR1:200276 Length = 430 Score = 219 bits (558), Expect = 1e-61 Identities = 145/427 (33%), Positives = 210/427 (49%), Gaps = 50/427 (11%) Query: 15 LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEH---------QGFEYSRTHNPT 65 + L +LA+H G + +T A PIY T++Y +H G Y+R NPT Sbjct: 1 MKLESLALHHGYESEATTKAAAVPIYQTTSYTFDDT-QHGADLFDLKVAGNIYTRIMNPT 59 Query: 66 RFAYERCVAALEGGTRAFAFASGMAA-TSTVMELLDAGSHVVAMDDLYGGTFRLFERVRR 124 E+ +AA+EGG A A ASGMAA T + L G ++V+ LYGGT+ LF Sbjct: 60 TSVLEQRLAAIEGGIGALAVASGMAAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTLP 119 Query: 125 RTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKHGLLTVV 184 R G++ D +A I A TK ++ E+ NP +VD+ +A IA KHG+ +V Sbjct: 120 RQ-GVEVRMAAFDDFEELEALIDAKTKALFCESIGNPAGNIVDLKRLAEIAHKHGVPLIV 178 Query: 185 DNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAV-------------------- 224 DNT A+P+L RP GAD+V+HS TKY+ GH +GGI + Sbjct: 179 DNTVATPVLCRPFEHGADIVIHSLTKYIGGHGTTIGGIIIDSGKFDWVANKERFSLLNQA 238 Query: 225 ------------VGDNAELAEQMAFLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENA 272 G A + + G P +FL L+GL+TL LRM HC NA Sbjct: 239 DPSYHGVVYTEAFGPAAFIGRCRVVPLRNTGAALSPHSAFLLLQGLETLSLRMERHCANA 298 Query: 273 LALAQWLETHPAIEKVIYPGLASHPQHVLAKRQMSG-FGGIVSIVLKG-----GFDAAKR 326 LALA++L HP++ V Y L S P ++ G GI+S +K G A + Sbjct: 299 LALAEYLILHPSVSWVNYGALPSSPFRENCEKITGGKASGIISFGIKAATPEEGKIAGGK 358 Query: 327 FCEKTELFTLAESLGGVESLVNHPAVMTHASIPVARREQLGISDALVRLSVGIEDLGDLR 386 F + ++ ++G +SL HPA TH + + G+S+ L+R+SVGIE + D+ Sbjct: 359 FIDALKMVLRLVNIGDAKSLACHPASTTHRQLDANELARAGVSEDLIRISVGIEHIDDII 418 Query: 387 GDLERAL 393 D+ +AL Sbjct: 419 ADVSQAL 425 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: 501 Number of extensions: 26 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: 430 Length adjustment: 31 Effective length of query: 366 Effective length of database: 399 Effective search space: 146034 Effective search space used: 146034 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