Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate Echvi_4510 Echvi_4510 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= BRENDA::Q1M0P5 (380 letters) >FitnessBrowser__Cola:Echvi_4510 Length = 403 Score = 284 bits (727), Expect = 3e-81 Identities = 163/392 (41%), Positives = 235/392 (59%), Gaps = 23/392 (5%) Query: 4 QTKLIHGGISEDATTGAVSVPIYQTSTYRQDA------IGHHKG--YEYSRSGNPTRFAL 55 QT+ IH G D TGA S + ++TY +A GH + + Y+R GNPT L Sbjct: 12 QTRAIHAGELPDPVTGASSPNLVMSTTYLAEAGTGFSVEGHDEEDPWIYTRWGNPTVHQL 71 Query: 56 EELIADLEGGVKGFAFASGLAGIHAVF-SLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGL 114 EE +A LE AFASG+ I +F LL++GDH ++ D Y + N+++ + Sbjct: 72 EEKLAVLEEAETAVAFASGMGAITVLFFHLLKAGDHAIVSDVAYAALSEMTNEMVPSLNI 131 Query: 115 SCTIIDTSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFA 174 T +DTSDLS +K A+K NT+ +Y+ETP NP+L++TD+ A +A+ G VD+TFA Sbjct: 132 QITKVDTSDLSAVKAAVKNNTRLIYIETPCNPILRLTDIEAVAGIARGAGARLAVDSTFA 191 Query: 175 TPYYQNPLLLGADIVVHSGTKYLGGHSDVVAGLVTTNNEALAQEIAFFQNAIGGVLGPQD 234 TP PL LGAD +VHS TKYLGGH D + G + LA +G V+ P + Sbjct: 192 TPAATKPLQLGADFIVHSLTKYLGGHGDALGGAILGRKADLAPLRKKTAIRMGAVISPFN 251 Query: 235 SWLLQRGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFS 294 +WL+ RG+ T +RM+AH+KNAL VA FLEKHPKV+RV YPGLP+HP +ELAKKQM+ FS Sbjct: 252 AWLILRGLATFPIRMRAHEKNALKVAAFLEKHPKVKRVIYPGLPSHPQHELAKKQMKNFS 311 Query: 295 GMLSFTLKNDSEATP-FVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIR- 352 GML+F ++N + + F + L++ SLG SL+ ++ A + ++ + A + Sbjct: 312 GMLTFQVENGKKRSGIFADKLRIVHYAVSLGHHRSLI---FYLDSADLKESSFKFATGKQ 368 Query: 353 ---------DGLVRLSVGIEHEQDLLEDLEQA 375 DG+ RLSVG+E +D+++DL +A Sbjct: 369 DESWEIYAGDGIFRLSVGLEDSKDIIDDLNRA 400 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: 403 Number of extensions: 23 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: 403 Length adjustment: 31 Effective length of query: 349 Effective length of database: 372 Effective search space: 129828 Effective search space used: 129828 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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