Align Cystathionine gamma-synthase; CGS; EC 2.5.1.48; O-succinylhomoserine (thiol)-lyase (uncharacterized)
to candidate WP_011383705.1 AMB_RS06585 cystathionine beta-lyase
Query= curated2:Q1M0P5 (380 letters) >NCBI__GCF_000009985.1:WP_011383705.1 Length = 390 Score = 203 bits (517), Expect = 6e-57 Identities = 131/391 (33%), Positives = 208/391 (53%), Gaps = 16/391 (4%) Query: 1 MHMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGH--------HKGYEYSRSGNPTR 52 M T+++H G +A GAV+ P+Y ST ++ +G Y R G PT Sbjct: 1 MKKSTRILHAGRKPEAFHGAVNPPVYHASTILHPSVAAMEKSGKTPFEGVRYGRFGTPTT 60 Query: 53 FALEELIADLEGGVKGFAFASGLAGIH-AVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVK 111 FALEE +A+LEGG + A +SGLA I A+ + L++GDH+L+ D Y T + + VL Sbjct: 61 FALEEAVAELEGGHRTVATSSGLAAITGALLAFLKAGDHLLMVDTTYFPTRKFCDSVLGG 120 Query: 112 NGLSCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDN 171 G+ T D + I ++PNT+ ++ E+P + ++ D+ A A G + ++DN Sbjct: 121 LGIETTYYDPLVGAGITALMRPNTRVVFTESPGSLTFEVQDIPAIAEAAHAGGAVVMMDN 180 Query: 172 TFATPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLG 231 T+ ++Q P G DI + + TKY+ GH+D + G +T L ++ A G G Sbjct: 181 TWGVLHFQ-PFTKGIDISIQAATKYIVGHADAMLGTITAATPELWLQVKTSLAAFGASPG 239 Query: 232 PQDSWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMR 291 ++ +L RG++TL +R++ H ++AL + +LE P+V+RV YP L + P +EL K+ Sbjct: 240 TEEMYLGLRGLRTLPVRLRQHAESALRLTRWLEARPEVDRVLYPPLASDPGHELWKRDFT 299 Query: 292 GFSGMLSFTLKNDSEAT--PFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAA 349 G G+ LK S+A ++ F LG S GG ESLV +P H+ I +T Sbjct: 300 GGCGLFGVILKPASKAAVDAMLDGYSHFKLGFSWGGFESLV-IPT-SGHSII-RTATPWT 356 Query: 350 GIRDGLVRLSVGIEHEQDLLEDLEQAFAKIS 380 + L R G+E DL EDLE+ F +++ Sbjct: 357 PVGPSL-RFHAGLEDADDLEEDLERGFERLA 386 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: 395 Number of extensions: 26 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: 390 Length adjustment: 30 Effective length of query: 350 Effective length of database: 360 Effective search space: 126000 Effective search space used: 126000 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 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