Align O-phosphoserine sulfhydrylase monomer (EC 2.5.1.65) (characterized)
to candidate Synpcc7942_B2623 Synpcc7942_B2623 cysteine synthase A
Query= metacyc::MONOMER-20565 (273 letters) >FitnessBrowser__SynE:Synpcc7942_B2623 Length = 329 Score = 94.4 bits (233), Expect = 3e-24 Identities = 81/252 (32%), Positives = 120/252 (47%), Gaps = 15/252 (5%) Query: 5 KLEFFNPFSRSIKDRAVFNLVMKALKRGDINGTRRLFEATSGNVGIAMAAISNIFNVEFR 64 KLE+ NP S+KDR +L+ A +G I L E T+GN GI +A + + Sbjct: 36 KLEYLNPLG-SVKDRTALSLIQSARSQGLITAGTTLIEPTTGNTGIGLAFAAAAEQLRLI 94 Query: 65 AYLPKPTPDATVTLLKVLGAEVVKTD-FEVIDREMIEFVRDEAEKAGAVNLNQFENDDNF 123 +P + L K+LGA+VV T E + + + + + +V L QF+N N Sbjct: 95 LVMPDRVSAERIRLAKLLGAKVVLTPAAEAMLGCIAKAQALQQQIPDSVILQQFQNPANP 154 Query: 124 EAHYRYTAREIDEQLRSIGVSPDVIVAGVGTSGHIAGIAKYFKE-RYDTKVIGVVPAKNE 182 H T EI R D++VAGVGT G + GI++Y K R + I V PA++ Sbjct: 155 SIHQATTGPEI---WRDTDGEVDIVVAGVGTGGTLMGISRYLKPLRPRLQSIAVQPARSP 211 Query: 183 KI----PGIKRLETRPKWFFD-----AGIDEVVEVTQREAIEGSIQVARREGILIGLSSG 233 + G +L F + IDE++ + +AI A REGI +G+SSG Sbjct: 212 VLSGGAAGSHQLTGMGPNFVSPLVDRSLIDEILSAYEEDAIAVIRTCAAREGIPLGVSSG 271 Query: 234 AVVSALEKVRDR 245 A+V A +V R Sbjct: 272 AIVWAALQVAKR 283 Lambda K H 0.320 0.138 0.388 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: 201 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: 273 Length of database: 329 Length adjustment: 27 Effective length of query: 246 Effective length of database: 302 Effective search space: 74292 Effective search space used: 74292 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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