Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate AO356_29765 AO356_29765 ABC transporter substrate-binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29765 Length = 281 Score = 201 bits (511), Expect = 2e-56 Identities = 112/286 (39%), Positives = 163/286 (56%), Gaps = 9/286 (3%) Query: 1 MKVKRTTAAKTLIGAVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEP 60 M R A L+ +G A+ A P++ K +A EG Y PWN T G L G+E Sbjct: 1 MLKNRAWLALALMPMFVGIASAQALPSEIK------VATEGAYPPWNYTNADGSLTGYEI 54 Query: 61 ELVANLCERIKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATP 120 EL LCER+K++C +V+Q+W+G+IPGL GK+D ++ ++ +T ER+K+IAFSK YA P Sbjct: 55 ELTHVLCERMKVKCTIVSQEWNGIIPGLTVGKYDAIIASMGVTAERKKVIAFSKSYAKAP 114 Query: 121 ATFAVADAKVLPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFIND 180 F L A L+ P + Q +DAL+ +LKGK IG+Q+G+ + F+ + Sbjct: 115 NGFLTTSDNELKSLADAGNSYDLTDSPASAQAAIDALKAKLKGKVIGVQTGSTASNFVRE 174 Query: 181 GFKDIATIRVYKTSPERDLDLANGRIDASFDDVTYYAANIDKKETASIVMAGPKIGGPIW 240 FK + IR Y T + LDLANGR+D +VT + I+ + +V GP G + Sbjct: 175 YFKGL-DIRDYPTFEQLALDLANGRLDIGVANVTTFKPVIEVNK-GVLVATGPTFAGGVL 232 Query: 241 GPG-EGLAFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDVT 285 G G +A R+ D L+ FD AI+A +DGT K L+ KWF TD++ Sbjct: 233 GQGTTNIALRQGDEALRQAFDAAITAVNSDGTNKALTEKWFGTDIS 278 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: 186 Number of extensions: 13 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: 286 Length of database: 281 Length adjustment: 26 Effective length of query: 260 Effective length of database: 255 Effective search space: 66300 Effective search space used: 66300 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