Align cystathionine gamma-lyase (EC 4.4.1.1) (characterized)
to candidate 3609021 Dshi_2410 O-succinylhomoserine sulfhydrylase (RefSeq)
Query= BRENDA::Q5H4T8 (397 letters) >FitnessBrowser__Dino:3609021 Length = 392 Score = 266 bits (680), Expect = 8e-76 Identities = 151/341 (44%), Positives = 222/341 (65%), Gaps = 7/341 (2%) Query: 56 FEYSRTHNPTRFAYERCVAALEGGTRAFAFASGMAATSTVM-ELLDAGSHVVAMDDLYGG 114 F Y+R NPT +E +AA+EG AFA ASGMAA + + +L AG HVV+ L+G Sbjct: 53 FIYARYGNPTVRMFEDRIAAVEGTEDAFATASGMAAVNGALASMLRAGDHVVSARALFGS 112 Query: 115 TFRLFERVRRRTAGLDFSFVDLTDPAAFKAAIRADTKMVWIETPTNPMLKLVDIAAIAVI 174 + E V R G++ +FVD TD AA++AAIR DTK V+ ET +NP L+++DI A+A + Sbjct: 113 CLYILEEVLTRY-GVEVTFVDGTDLAAWRAAIRPDTKAVFFETISNPTLEVIDIEAVAKL 171 Query: 175 ARKHGLLTVVDNTFASPMLQRPLSLGADLVVHSATKYLNGHSDMVGGIAVVGDNAELAEQ 234 A G L +VDN FA+P+ R GAD++V+SATK+++G +GG V+ + + Sbjct: 172 AHAVGALVIVDNVFATPIFSRAKDQGADVIVYSATKHIDGQGRCLGG--VICGTRDFVRK 229 Query: 235 MA--FLQNSIGGVQGPFDSFLALRGLKTLPLRMRAHCENALALAQWLETHPAIEKVIYPG 292 +A +L+++ GG PF++++ L+ ++TL LR+RA E A ALA+ LE H A+EKVI+P Sbjct: 230 VAEPYLKHT-GGSLSPFNAWVMLKSMETLDLRVRAQAETAQALAETLEGHAALEKVIFPH 288 Query: 293 LASHPQHVLAKRQMSGFGGIVSIVLKGGFDAAKRFCEKTELFTLAESLGGVESLVNHPAV 352 L SHPQ+ LA+ QM+ G ++++ +KGG A RF E+ T++ +LG +S+ HPA Sbjct: 289 LPSHPQYDLARAQMAAGGTVLALDIKGGKAGAFRFLNALEIVTISNNLGDAKSIATHPAT 348 Query: 353 MTHASIPVARREQLGISDALVRLSVGIEDLGDLRGDLERAL 393 TH + +R LGI+D L+RLSVG+ED GDL DL+ AL Sbjct: 349 TTHQRLTPEQRAGLGITDGLIRLSVGLEDAGDLLRDLQTAL 389 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: 394 Number of extensions: 19 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: 392 Length adjustment: 31 Effective length of query: 366 Effective length of database: 361 Effective search space: 132126 Effective search space used: 132126 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