Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_057508383.1 ABB28_RS09425 cystathionine gamma-synthase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_001431535.1:WP_057508383.1 Length = 392 Score = 412 bits (1060), Expect = e-120 Identities = 212/378 (56%), Positives = 271/378 (71%), Gaps = 3/378 (0%) Query: 1 MHMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIA 60 + + T IHGG S D +TGAV PIY TSTY Q + G H+G+EYSR+ NPTRFA E +A Sbjct: 13 LSLATLAIHGGQSPDPSTGAVMPPIYATSTYAQSSPGEHQGFEYSRTHNPTRFAYERCVA 72 Query: 61 DLEGGVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKN-GLSCTII 119 LEGG +GFAFASG+A V LL +G HV+ DD+YGGTFRLF +V + GL + + Sbjct: 73 SLEGGSRGFAFASGMAATSTVMELLDAGSHVVAMDDIYGGTFRLFERVRRRTAGLDFSFV 132 Query: 120 DTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQ 179 D +DL+ + AI P TK +++ETP+NP+LKI D+A A++AK HGL+ +VDNTFA+P Q Sbjct: 133 DLTDLAAFEAAITPATKMVWIETPTNPMLKIVDIAAVAAIAKQHGLIIVVDNTFASPMLQ 192 Query: 180 NPLLLGADIVVHSGTKYLGGHSDVVAGLVTT-NNEALAQEIAFFQNAIGGVLGPQDSWLL 238 PL LGAD+V+HS TKYL GHSD+V G+V +N LA+++AF QN+IG V GP DS+L Sbjct: 193 RPLELGADLVLHSATKYLNGHSDMVGGMVVVGDNTGLAEQMAFLQNSIGAVQGPFDSFLA 252 Query: 239 QRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLS 298 RG+KTL LRM+AH NAL +A++LE P VE+V YPGL +HP +ELA +QM G+ G++S Sbjct: 253 LRGLKTLPLRMKAHCANALALAQWLETQPSVEKVIYPGLTSHPQHELATRQMNGYGGIVS 312 Query: 299 FTLKNDSEATP-FVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVR 357 LK EA F E +LF L ESLGGVESLV PA MTHA IP +RE GI +GLVR Sbjct: 313 IVLKGGFEAAKRFCERTELFTLAESLGGVESLVNHPAVMTHASIPVERRENLGISEGLVR 372 Query: 358 LSVGIEHEQDLLEDLEQA 375 LSVG+E DL+ DLE+A Sbjct: 373 LSVGVEELGDLMVDLERA 390 Lambda K H 0.318 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: 452 Number of extensions: 16 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: 380 Length of database: 392 Length adjustment: 30 Effective length of query: 350 Effective length of database: 362 Effective search space: 126700 Effective search space used: 126700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 10 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