Align [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized)
to candidate CCNA_03740 CCNA_03740 cysteine synthase
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Caulo:CCNA_03740 Length = 328 Score = 201 bits (511), Expect = 2e-56 Identities = 125/313 (39%), Positives = 172/313 (54%), Gaps = 15/313 (4%) Query: 4 YDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAE 63 YDS++ +G+TPLV L RLS + P + AKLE NP S+KDR V MIE E Sbjct: 22 YDSIIDTIGDTPLVRLPRLSAELN-----PKAEVLAKLEFFNPIASVKDRIGVSMIESLE 76 Query: 64 ADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFS 123 A G+L+PGATI+EPTSGNTGI+LA A KGY+L VMPE+ S+ERR++L L GA++ + Sbjct: 77 AQGVLKPGATIIEPTSGNTGIALAFVAAAKGYKLTLVMPESMSIERRKMLLLLGAKLELT 136 Query: 124 AAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAG 182 AE G AV A+EL P VM Q+ N AN H T E+ D + V+G Sbjct: 137 PAEKGMRGAVTRAQELIEATPGAVMPQQFENSANPLIHRVSTAEEIWNDTAGAVDAVVSG 196 Query: 183 LGTTGTLMGTGRFLREHVANVKIVAAEPRY-------GEGVYALRNMDEGFVPELYDPEI 235 +GT GT+ G G+ L+ ++K+VA EP G + ++ + GFVP + D + Sbjct: 197 VGTGGTITGVGQALKARKPSLKMVAVEPEASPVLSGGAPGPHKIQGIGAGFVPGVLDRGV 256 Query: 236 LTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVAD 295 + V DA R TEG+ GIS+GA L AA + G+ I +++ Sbjct: 257 IDDIVQVSNDDAFAMARRAAATEGLPVGISSGAALTAAFDLALRDAYKGK--TIVVIIPS 314 Query: 296 AGWKYLSTGAYAG 308 +YLST + G Sbjct: 315 FAERYLSTALFDG 327 Lambda K H 0.317 0.134 0.398 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: 262 Number of extensions: 11 Number of successful extensions: 3 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: 323 Length of database: 328 Length adjustment: 28 Effective length of query: 295 Effective length of database: 300 Effective search space: 88500 Effective search space used: 88500 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 (21.6 bits) S2: 48 (23.1 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