Align cystathionine gamma-lyase (EC 4.4.1.1); cysteine-S-conjugate beta-lyase (EC 4.4.1.13) (characterized)
to candidate GFF1649 PGA1_c16720 putative pyridoxal phosphate-dependent transferase
Query= BRENDA::A2RM21 (380 letters) >FitnessBrowser__Phaeo:GFF1649 Length = 383 Score = 204 bits (520), Expect = 3e-57 Identities = 129/369 (34%), Positives = 199/369 (53%), Gaps = 19/369 (5%) Query: 19 TGAVSVPIYQTS--------TYKQNGLGQPKEYEYSRSGNPTRHALEELIADLEGGVQGF 70 +GA++ PI QTS ++ G+ Y+R NPT A E L+A E G Sbjct: 19 SGAITPPIVQTSLFSFDSYEAFEDRMAGRSNAAIYTRVQNPTVAAFESLMAKAEQGEAAV 78 Query: 71 AFSSGLAGIHAVLSLF-SAGDHIILADDVYGGTFRLMDKVLTKTGIIYDLVDLSNLDDLK 129 AF+SG+A I + L F GD I + VY ++R M+++L G+ D L++ + Sbjct: 79 AFASGMAAISSTLLAFVKPGDRIACVEHVYPDSYRFMERMLRPFGVEIDYYAPHQLEE-E 137 Query: 130 AAFKEETKAIYFETPSNPLLKVLDIKEISAIAKAHDALTLVDNTFATPYLQQPIALGADI 189 + Y E+PS+ + + L++K+++A AK H LT++DN++A+P Q+P+ G DI Sbjct: 138 PELLNGVRLAYLESPSSVVFQPLNLKKVTAHAKRHGVLTMIDNSWASPVFQKPLTQGVDI 197 Query: 190 VLHSATKYLGGHSDVVAGLVTTNSKELASEIGFLQNSIGAVLGPQDSWLVQRGIKTLALR 249 VLHSA+KY+ GHSD VAG+V + + +GA L P +++L+ RG++TL+ R Sbjct: 198 VLHSASKYISGHSDTVAGVVVAAQQHIDRIRDLTLPLLGAKLAPFEAFLLTRGLRTLSAR 257 Query: 250 MEAHSANAQKIAEFLETSKAVSKVYYPGLNSHPGHEIAKKQMSAFGGMISFELTDENAVK 309 M H A A + L V +V+ PG N PG ++ G+++ E D + Sbjct: 258 MRQHQATATLFIDRLSALPQVRRVHSPGPNEVPG-------LTGRSGLMAVEFDDSVDIP 310 Query: 310 DFVENLSYFTLAESLGGVESLIEVPAVMTHASIPKE-LREEIGIKDGLIRLSVGVEAIED 368 F LS+F L S GG ESLI +PA + A I +E + G+ L+RL++G+E ED Sbjct: 311 AFSNALSHFRLGVSWGGFESLI-LPARVGLAQIGEENSMQRFGVSPNLVRLNLGLEEAED 369 Query: 369 LLTDIKEAL 377 L DI AL Sbjct: 370 LWADITSAL 378 Lambda K H 0.315 0.133 0.366 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: 290 Number of extensions: 17 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: 383 Length adjustment: 30 Effective length of query: 350 Effective length of database: 353 Effective search space: 123550 Effective search space used: 123550 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: 42 (22.0 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