Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate Dsui_3185 Dsui_3185 O-succinylhomoserine sulfhydrylase
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__PS:Dsui_3185 Length = 395 Score = 295 bits (754), Expect = 2e-84 Identities = 173/395 (43%), Positives = 230/395 (58%), Gaps = 13/395 (3%) Query: 8 SHDGDRALSLATLAIHGGQSPDPSTGAVMPPIYATSTY--------AQSSPGEHQGFEYS 59 S D + L TLA+ GQ +Y TS++ A GE +G YS Sbjct: 2 SIDSNNDWQLETLAVRAGQERS-QFNEHSEALYLTSSFVFENAAQAAARFSGEEEGNVYS 60 Query: 60 RTHNPTRFAYERCVAALEGGTRAFAFASGMAAT-STVMELLDAGSHVVAMDDLYGGTFRL 118 R NPT ++ +AALEG A ASGM+A S VM L AG HVVA L+G T +L Sbjct: 61 RFSNPTLSLFQDRLAALEGAESAICTASGMSAIMSLVMAHLKAGDHVVASAGLFGATIQL 120 Query: 119 FERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVIARKH 178 F + R G+ ++ T P + AAIR +TK+ ++ETP+NP+ ++ DIAA+A IA Sbjct: 121 FNNILARF-GISTTYASQTRPEEWAAAIRPETKLFFLETPSNPLTEVADIAALAEIAHAK 179 Query: 179 GLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQMAFL 238 G+L VDN F +P LQRPL LGADLVVHSATKYL+G ++GG AVVG E FL Sbjct: 180 GILVAVDNCFCTPALQRPLELGADLVVHSATKYLDGQGRVLGG-AVVGSKKLTEEVFKFL 238 Query: 239 QNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPGLASHPQ 298 + + G F++++ +GL+TL +RM A NAL LA WLE HP + +V YPGLASHPQ Sbjct: 239 RTA-GPTLSAFNAWVLAKGLETLKIRMAAQSANALELATWLEAHPKVARVFYPGLASHPQ 297 Query: 299 HVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAVMTHASI 358 H LA RQ G IVS +KGG A + + L ++ +LG V++ + HPA TH I Sbjct: 298 HALAMRQQKSGGAIVSFEVKGGKPEAWKVVDNCRLLSITANLGDVKTTITHPATTTHGRI 357 Query: 359 PVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 R GI D L+R++VG+E + DL+ DLER L Sbjct: 358 SAEARATAGIGDGLLRIAVGLEAVPDLQADLERGL 392 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: 413 Number of extensions: 20 Number of successful extensions: 4 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: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 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