Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate Echvi_1734 Echvi_1734 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= BRENDA::Q1M0P5 (380 letters) >FitnessBrowser__Cola:Echvi_1734 Length = 369 Score = 310 bits (794), Expect = 4e-89 Identities = 177/381 (46%), Positives = 236/381 (61%), Gaps = 15/381 (3%) Query: 1 MHMQTKLIHGGISEDATTGAVSVPIYQTSTYRQDAIGHHKGYEYSRSGNPTRFALEELIA 60 M +T IHGG + A AV PI ++T+ H + YSRS NP R ALEEL+A Sbjct: 1 MKFETLAIHGGEKKSAPHRAVVQPITLSTTFEH----HEESLIYSRSQNPNRMALEELLA 56 Query: 61 DLEGGVKGFAFASGLAGIHAVFSLLQSGDHVLLGDDVYGGTFRLFNKVLVKNGLSCTIID 120 LE G AF+SG A AVF L G H++ D+Y G + + L K+ L T D Sbjct: 57 QLEKGSAAAAFSSGNAAGMAVFQALPLGSHIVAPSDMYHGLKKQLVE-LFKDKLEVTFTD 115 Query: 121 TSDLSQIKKAIKPNTKALYLETPSNPLLKITDLAQCASVAKDHGLLTIVDNTFATPYYQN 180 SD ++KAI+PNTK L++ETPSNP+LKI+D+ + +AK+ + + DNTFATP +QN Sbjct: 116 LSDPENLEKAIQPNTKLLWIETPSNPMLKISDIRRLTKMAKEDDIRVVCDNTFATPVFQN 175 Query: 181 PLLLGADIVVHSGTKYLGGHSDVVAG-LVTTNNEALAQEIAFFQNAIGGVLGPQDSWLLQ 239 PL LGAD+V+HS TKY GGHSD++ G L+T ++ ++I Q G VL P D +LL Sbjct: 176 PLELGADLVMHSATKYFGGHSDILGGALITKKSDEFWKQIVNVQQTGGAVLSPFDCYLLV 235 Query: 240 RGIKTLGLRMQAHQKNALCVAEFLEKHPKVERVYYPGLPTHPNYELAKKQMRGFSGMLSF 299 R IKTL RM+ H ++A +A FL++HPKVERV+YPGL HP +++AK QM GF G+LSF Sbjct: 236 RSIKTLAYRMRGHAEHAGMIATFLDQHPKVERVFYPGLTAHPGHDVAKSQMTGFGGILSF 295 Query: 300 TLKNDSE-ATPFVESLKLFILGESLGGVESLVGVPAFMTHACIPKTQREAAGIRDGLVRL 358 +K E A + SLK + SLGGVESL+ A + P T+ L+RL Sbjct: 296 LVKGKPEDADKLISSLKYYTNATSLGGVESLIERRAAVEG---PDTKTP-----QNLIRL 347 Query: 359 SVGIEHEQDLLEDLEQAFAKI 379 SVG+EH DLLED+E+AF I Sbjct: 348 SVGLEHLDDLLEDMEKAFYSI 368 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: 411 Number of extensions: 15 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: 369 Length adjustment: 30 Effective length of query: 350 Effective length of database: 339 Effective search space: 118650 Effective search space used: 118650 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