Align Uncharacterized protein (characterized, see rationale)
to candidate GFF925 Psest_0954 Fe-S oxidoreductase
Query= uniprot:E4PLR5 (279 letters) >FitnessBrowser__psRCH2:GFF925 Length = 273 Score = 413 bits (1062), Expect = e-120 Identities = 198/272 (72%), Positives = 229/272 (84%), Gaps = 1/272 (0%) Query: 1 MSQLFYDAAPNATRVSPEREADRHYPEKPEAVTLFGTCVVDLFFPEAGLDTIRLLEREGV 60 MS+LFYDAAPNATRV+P R YP KP V LFGTCVVDLF+PEAGLD IRLLEREG+ Sbjct: 1 MSELFYDAAPNATRVAPPLPKPREYPAKPSQVYLFGTCVVDLFYPEAGLDAIRLLEREGL 60 Query: 61 RVHFPQEQSCCGQPAWTSGYRDEAKAVARAQLDILDRSGLPVVVPSGSCAGMFRHHYPAL 120 VH+PQ Q+CCGQPA+TSGY DEA+ VARAQLD+ + PVVVPSGSCAGM RHHY L Sbjct: 61 TVHYPQGQTCCGQPAYTSGYTDEARNVARAQLDLF-ANDWPVVVPSGSCAGMLRHHYLDL 119 Query: 121 FADEPDTLKRVEALAERTFELTEFLLKVCRVQLADRGAPSKIALHTSCSARREMNTHLHA 180 F D+P TLK+ +ALAERTFEL EFLL VC+V+ D G P+K+ALHTSCSARREMNTHLH Sbjct: 120 FKDDPATLKKAQALAERTFELAEFLLNVCKVEFKDAGTPTKVALHTSCSARREMNTHLHG 179 Query: 181 RELLQQLEGVERIDHDHESECCGFGGTFSVRMPEVSGAMVKDKTRSLIDSGAVEMVTADG 240 R LL QL VER++HDHESECCGFGGTFSVRMP++SGAMV DKTR+L +SGA ++++AD Sbjct: 180 RALLAQLGQVERVEHDHESECCGFGGTFSVRMPDISGAMVLDKTRALKESGAHQVISADC 239 Query: 241 GCLMNINGSLEKQKESFRGRHLASFLWERTNG 272 GCLMNINGSLEKQ+E+ RG+HLASFLW+RT G Sbjct: 240 GCLMNINGSLEKQREALRGQHLASFLWQRTGG 271 Lambda K H 0.320 0.134 0.406 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: 355 Number of extensions: 8 Number of successful extensions: 2 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: 279 Length of database: 273 Length adjustment: 25 Effective length of query: 254 Effective length of database: 248 Effective search space: 62992 Effective search space used: 62992 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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