Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate Pf6N2E2_3856 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3856 Length = 251 Score = 119 bits (297), Expect = 9e-32 Identities = 79/265 (29%), Positives = 130/265 (49%), Gaps = 26/265 (9%) Query: 16 VLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKLQCN 75 +L AA A + + + +E Y P+N G++ GF+ ++ LC ++K++C Sbjct: 8 LLAAAVSLVFSTSAMAVEKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMKVECE 67 Query: 76 LVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVLPKAA 135 +V +WDG+IP L A KFD L+ ++S+ ER++ + F+ PY + F + PK Sbjct: 68 VVTSNWDGIIPALMAKKFDFLISSLSVNDERKQAVDFTDPYYSNKLQF------IAPK-- 119 Query: 136 PGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIATIRVYKTSP 195 + D K D ++ LKGK IG Q T+ ++ D T ++Y T Sbjct: 120 --------NVDFKVD-------KESLKGKVIGAQRSTLAGTWLEDELGSDITAKLYDTQE 164 Query: 196 ERDLDLANGRIDASFDDVTYYAANIDKKETASIVMAGPKIGGPIWGPGEGLAFRKQDADL 255 LDL +GR+DA D N D +T + K + G +A RK + +L Sbjct: 165 NAYLDLTSGRVDAILAD---KYVNYDWLKTEAGRAYEFKGDPVVEGDKIAIAVRKGNDEL 221 Query: 256 KAKFDTAISAALADGTVKKLSNKWF 280 + K + A+ LADGT KK+++K+F Sbjct: 222 RNKLNAALKEILADGTYKKINDKYF 246 Lambda K H 0.316 0.134 0.396 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: 161 Number of extensions: 7 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: 286 Length of database: 251 Length adjustment: 25 Effective length of query: 261 Effective length of database: 226 Effective search space: 58986 Effective search space used: 58986 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