Align Putative amino-acid binding periplasmic protein (characterized, see rationale)
to candidate GFF3832 PGA1_262p02360 putative histidine-binding periplasmic protein
Query= uniprot:Q92PA9 (260 letters) >FitnessBrowser__Phaeo:GFF3832 Length = 259 Score = 210 bits (534), Expect = 3e-59 Identities = 108/256 (42%), Positives = 154/256 (60%), Gaps = 2/256 (0%) Query: 3 ISRRLAATASAAVFVLMAGVAMAEGEKVVIGTEGAYPPFNNLESDGTLTGFDIDIAKALC 62 IS + +AA VA AE K+ + E YPPF +L+S G G++ID+ A+C Sbjct: 4 ISNLKSTVLAAATVAATCAVAQAEPVKIGVAAE-PYPPFASLDSSGQWVGWEIDVINAVC 62 Query: 63 EEMKAECTFVTQDWDGIIPALIAKKFDAIVASMSITEERKQQVDFTNKYYNTPPAIVVPK 122 + +C WDGIIP+L ++ DAI+ASMSITEER + +DF++ YYNTP IV K Sbjct: 63 AAAELDCVITPVAWDGIIPSLTGQQVDAIMASMSITEERLKTIDFSDPYYNTPAVIVADK 122 Query: 123 DSPITEATAAALSGKALGAQGSTTHSNYAEAHMKESEVKLYPTADEYKLDLANGRIDAAI 182 I EAT +L+GK +G Q ST H YA+ H K+SE+++Y T DE DL GRIDA Sbjct: 123 SMDI-EATPESLAGKVVGIQASTIHQAYAQEHFKDSELRVYQTQDEANQDLFAGRIDATQ 181 Query: 183 DDVVVLSEWLKTEDGACCKLLGTLPIDPVINGEGAGIAIRKGDDALREKLNKAIEAIRAN 242 D + +++++ ++ G CC++ G + D I G+G G +RKGD + LNK I AI A+ Sbjct: 182 ADSIAMADFVGSDAGGCCEIKGAVANDEAILGKGVGAGVRKGDSDVLAALNKGIAAILAD 241 Query: 243 GKYKQINEKYFPFDVY 258 G + +I KYF +Y Sbjct: 242 GTHAEITSKYFTTSIY 257 Lambda K H 0.315 0.132 0.377 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: 189 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: 260 Length of database: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 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: 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