Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_011022500.1 MA_RS13170 PLP-dependent transferase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000007345.1:WP_011022500.1 Length = 406 Score = 339 bits (870), Expect = 7e-98 Identities = 181/387 (46%), Positives = 251/387 (64%), Gaps = 13/387 (3%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTY-----RQDAI---GHHKGYEYSR--SGNPTRFA 54 TK +H G D GA + PI+QTST+ Q A G GY Y+R PT Sbjct: 9 TKCVHAGEEPDPVFGAHTTPIFQTSTFIFKNVEQGAARFAGEESGYVYTRIPPNTPTHAV 68 Query: 55 LEELIADLEGGVKGFAFASGLAGIHAV-FSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNG 113 L E +A LEGG G FASG+A I AV S L+ GDH++ D VYG T+ LF+++L G Sbjct: 69 LAEKVAVLEGGEAGQTFASGMAAITAVVLSTLKQGDHLISTDVVYGCTYSLFSEILPGFG 128 Query: 114 LSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTF 173 + + +DTSD+ +++ A KP T+ ++LETP+NP + + D+ + + +AK G + IVDNTF Sbjct: 129 IDVSFVDTSDIKKVRAAFKPETRMVFLETPANPTITVCDIREISKLAKAQGAICIVDNTF 188 Query: 174 ATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQ 233 ATPY+Q PL LGADI + S TKY+GGH+D++ G+V + + + + + GG++G Sbjct: 189 ATPYFQKPLELGADISLSSCTKYIGGHADLLGGIVVGSRDFM-KSLGKVVGYTGGIMGLH 247 Query: 234 DSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGF 293 ++WL RG+KTL +RM+ H +NAL VA FLE HP VE V YPGL HP +E+AKKQM G+ Sbjct: 248 EAWLCIRGLKTLHIRMERHAENALTVANFLEAHPTVEWVRYPGLSNHPQHEVAKKQMSGY 307 Query: 294 SGMLSFTLKNDSEA-TPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIR 352 GMLSF ++ EA ++S++L L SLG ++L+ PA MTHACIP R GI+ Sbjct: 308 GGMLSFEIRGGVEAGRRLMDSVRLCSLAVSLGATDTLIQHPASMTHACIPGHIRNKVGIK 367 Query: 353 DGLVRLSVGIEHEQDLLEDLEQAFAKI 379 DGLVRLSVGIE +D++ DLEQA +K+ Sbjct: 368 DGLVRLSVGIEDPEDIIADLEQALSKV 394 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: 444 Number of extensions: 26 Number of successful extensions: 5 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: 406 Length adjustment: 31 Effective length of query: 349 Effective length of database: 375 Effective search space: 130875 Effective search space used: 130875 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