Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate BWI76_RS18365 BWI76_RS18365 cystine ABC transporter substrate-binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__Koxy:BWI76_RS18365 Length = 266 Score = 116 bits (290), Expect = 6e-31 Identities = 81/258 (31%), Positives = 125/258 (48%), Gaps = 28/258 (10%) Query: 28 QAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKLQCNLVAQDWDGMIPG 87 Q K+ T+ + LEG Y P++ GKL GFE + L + + ++ +L WDGM+ Sbjct: 36 QVKERGTLRVGLEGTYPPFSYQGDDGKLTGFEVDFANELAKHLGVKADLKPTKWDGMLAS 95 Query: 88 LQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVLPKAAPGAGVVKLSGDP 147 L + + DV+++ ++I+ +R+K FS PY ++ + L K GV+K + D Sbjct: 96 LDSKRIDVVINQVTISDQRKKKYDFSTPY-------TISGIQALVKKG-NEGVIKTAAD- 146 Query: 148 KADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIATIRVYKTSPERDLDLANGRID 207 LKGK +G+ GT Y +++ + + IR Y P + DL GRID Sbjct: 147 -------------LKGKKVGVGLGTNYEEWLRQNVQGV-DIRTYDDDPTKYQDLRVGRID 192 Query: 208 ASFDDVTYYAANIDKKETASIVMAGPKIGGPIWGPGEGLAFRKQDADLKAKFDTAISAAL 267 A D A ++ KK ++ + G G+A RK + DL D AI+ Sbjct: 193 AILVD-RLAALDLVKKTGNTLAVTGEAFS----RQESGVALRKGNEDLLKAVDGAIADMQ 247 Query: 268 ADGTVKKLSNKWFKTDVT 285 DGT+K LS KWF DVT Sbjct: 248 KDGTLKALSEKWFGADVT 265 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: 162 Number of extensions: 6 Number of successful extensions: 4 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: 266 Length adjustment: 25 Effective length of query: 261 Effective length of database: 241 Effective search space: 62901 Effective search space used: 62901 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