Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_011307957.1 MBAR_RS16035 aminotransferase class V-fold PLP-dependent enzyme
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000195895.1:WP_011307957.1 Length = 394 Score = 344 bits (883), Expect = 2e-99 Identities = 183/387 (47%), Positives = 253/387 (65%), Gaps = 13/387 (3%) Query: 5 TKLIHGGISEDATTGAVSVPIYQTSTY-----RQDAI---GHHKGYEYSR--SGNPTRFA 54 TK +H D GA + PI+QTST+ RQ A G GY Y+R PT Sbjct: 9 TKCVHAAEKPDPIFGAHTTPIFQTSTFIFENARQGAARFAGEESGYVYARIPPNTPTHAV 68 Query: 55 LEELIADLEGGVKGFAFASGLAGIHAV-FSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNG 113 L E A LEGG G FASG+A + A+ + L+ GDH++ D VYG T+ LF++VL G Sbjct: 69 LAEKFAALEGGEAGQTFASGMAAVTAIALTALKQGDHLISTDVVYGCTYSLFSQVLPGLG 128 Query: 114 LSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTF 173 + + +DTS +K+A KP TK ++LE+P+NP L + D+ + A +A+++ L +VDNTF Sbjct: 129 IEVSFVDTSKTENVKRAFKPETKMVFLESPANPTLNVCDIPEIARIARENEALCVVDNTF 188 Query: 174 ATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQ 233 ATPY+Q PL LGAD+ + S TKY+GGH+D++ G+V NN+ + ++ GG++GP Sbjct: 189 ATPYFQRPLELGADLSLSSCTKYIGGHADLLGGIVAGNNDFI-DRMSEVVGYTGGIMGPH 247 Query: 234 DSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGF 293 ++WL RG+KTL +RM+ H +NA+ VAEFLE P+VE V YPGLP HP YELA+KQM GF Sbjct: 248 EAWLCIRGLKTLHIRMERHAENAMKVAEFLESRPEVEWVRYPGLPGHPQYELARKQMSGF 307 Query: 294 SGMLSFTLKNDSEA-TPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIR 352 SGMLSF +K EA ++++KL L SLG ++L+ PA MTHAC+P R++ GI Sbjct: 308 SGMLSFEVKGGIEAGRKLMDNVKLCSLAVSLGATDTLIQHPASMTHACVPHEVRKSVGIT 367 Query: 353 DGLVRLSVGIEHEQDLLEDLEQAFAKI 379 DGLVRLSVGIE +D++ DL+QA I Sbjct: 368 DGLVRLSVGIEDPEDIIADLKQALEVI 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: 436 Number of extensions: 21 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: 394 Length adjustment: 30 Effective length of query: 350 Effective length of database: 364 Effective search space: 127400 Effective search space used: 127400 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