Align Cystathionine gamma-synthase; CGS; O-succinylhomoserine (thiol)-lyase; EC 2.5.1.48 (characterized)
to candidate SMc01666 SMc01666 methionine gamma-lyase
Query= SwissProt::P00935 (386 letters) >FitnessBrowser__Smeli:SMc01666 Length = 427 Score = 218 bits (555), Expect = 3e-61 Identities = 140/406 (34%), Positives = 214/406 (52%), Gaps = 37/406 (9%) Query: 7 TIAVRSGLNDDEQYGCVVPPIHLSSTYNF-------------TGFNEPRAHD-----YSR 48 T+ + G + + G V PPI L+ST+ F +G EP A YSR Sbjct: 20 TLMLNYGYDPELSEGAVKPPIFLTSTFVFHSAEEGRDFFDFVSGRREPPAGVGAGLVYSR 79 Query: 49 RGNPTRDVVQRALAELEGGAGAVLTNTGMSAIHLVTTVFLKPGDLLVAPHDCYGGSYRLF 108 +P ++V+ LA E L ++GMSAI F++PGD ++ YGG+ L Sbjct: 80 FNHPNSEIVEDRLAIFERAEAGALFSSGMSAIATTLLAFVRPGDSILHSQPLYGGTETLL 139 Query: 109 -DSLAKRGCYRVLFVDQGDEQALRAALAE-----KPKLVLVESPSNPLLRVVDIAKICHL 162 + G V F D DE A+ AA E + ++L+E+P+NP +VD+A + + Sbjct: 140 AKTFLNLGVSAVGFADGTDEAAVNAAAEEAMSKGRVSVILIETPANPTNSLVDVALVRRI 199 Query: 163 AREVGA------VSVVDNTFLSPALQNPLALGADLVLHSCTKYLNGHSDVVAGVVIAKDP 216 A +G + DNT L P Q+P+ GADL L+S TKY+ GHSD++AG V+ Sbjct: 200 AERIGERQAHRPIVACDNTLLGPVFQHPIEHGADLSLYSLTKYVGGHSDLIAGAVLGSKA 259 Query: 217 DVVTELAWWANNIGVTGGAFDSYLLLRGLRTLVPRMELAQRNAQAIVKYLQTQPLVKKLY 276 ++ ++ +IG +++ R L TL RME A NA+ + ++L+ P V++++ Sbjct: 260 -LIRQVKALRGSIGTQLDPHSCWMIGRSLETLSVRMEKANDNARIVAEFLRDHPKVERIH 318 Query: 277 HPSLPENQGH----EIAARQQKGFGAMLSFELDGDEQTLRRFLGGLSLFTLAESLGGVES 332 + LP + + A Q G G+ SF++ G ++ RFL L +F LA SLGG ES Sbjct: 319 Y--LPFHDADTPVGRVFATQCTGAGSTFSFDIAGGQEAAFRFLNALQIFKLAVSLGGTES 376 Query: 333 LISHAATMTHAGMAPEARAAAGISETLLRISTGIEDGEDLIADLEN 378 L SH A MTH+G+ E RA G+ E+ +R+S GIE +DL+AD+ N Sbjct: 377 LASHPAAMTHSGVPIEVRARIGVLESTIRLSIGIEHPDDLVADVAN 422 Lambda K H 0.319 0.136 0.394 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: 371 Number of extensions: 28 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: 386 Length of database: 427 Length adjustment: 31 Effective length of query: 355 Effective length of database: 396 Effective search space: 140580 Effective search space used: 140580 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 (21.7 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