Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate GFF4561 PS417_23345 amino acid ABC transporter substrate-binding protein
Query= uniprot:Q31RP1 (359 letters) >FitnessBrowser__WCS417:GFF4561 Length = 342 Score = 306 bits (783), Expect = 7e-88 Identities = 146/321 (45%), Positives = 210/321 (65%), Gaps = 3/321 (0%) Query: 40 ESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYR 99 E+ + L+ +Q +G + CGV LPGF DS+G +G+DVD+C A+AAA+F D +++ Sbjct: 24 EAGTTLDAIQKKGFIQCGVSDGLPGFGVPDSKGKMTGIDVDVCHAVAAAVFGDASKVKFT 83 Query: 100 SLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNSGIQS 159 L + ERF AL SGE+DL+SRNTTWT SRD+ G L F T+YDG G +V G+ + Sbjct: 84 QLTAKERFTALQSGEIDLISRNTTWTSSRDS--GMGLVFTGVTYYDGIGFLVNNKLGVTA 141 Query: 160 LQDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDRS 219 + G ++C++ GTT+ELN++D R G++Y I F +D + GRC+ +T+D+S Sbjct: 142 AKQLDGATVCIQAGTTTELNVSDYFRTHGMKYTPITFDTADESAKGLEAGRCDVLTTDQS 201 Query: 220 QLAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQA 279 L A+R ++ D+ +L VISKEPL P D WF +VKW + A + AEE GIT Sbjct: 202 GLYAQRIKMAQPDEFVVLPEVISKEPLGPLVRKGDDEWFSIVKWTLFAMLNAEEMGITSQ 261 Query: 280 NI-DQFKTSKNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPLK 338 N+ +Q KT+KNP++ R LG +GE G+ L L D+ + +K VGNYGE++ERN+GQ S LK Sbjct: 262 NVEEQAKTTKNPDVARLLGADGEYGKDLKLRKDWVVQIVKQVGNYGEVFERNIGQGSVLK 321 Query: 339 LNRGLNQLYKNGGLLYSPPFR 359 + RGLN L+ NGG+ Y+PP R Sbjct: 322 IKRGLNALWNNGGIQYAPPVR 342 Lambda K H 0.317 0.134 0.391 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: 299 Number of extensions: 12 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: 359 Length of database: 342 Length adjustment: 29 Effective length of query: 330 Effective length of database: 313 Effective search space: 103290 Effective search space used: 103290 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: 49 (23.5 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