Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate PP_1297 PP_1297 putative amino-acid ABC transporter-binding protein YhdW
Query= uniprot:Q31RP1 (359 letters) >FitnessBrowser__Putida:PP_1297 Length = 342 Score = 311 bits (798), Expect = 1e-89 Identities = 152/334 (45%), Positives = 222/334 (66%), Gaps = 4/334 (1%) Query: 28 LAACRSLGGNET-ESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIA 86 L A +LG T ++ + L+ V+ +G + CGV LPGFS D+QG G+D D+C+A+A Sbjct: 11 LTAAAALGAVSTAQAGATLDAVKKKGFVQCGVSDGLPGFSVPDAQGKIVGIDADVCRAVA 70 Query: 87 AALFNDPKAIEYRSLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDG 146 AA+F D +++ L++ ERF AL SGEVD+LSRNTTWT SRDA G L FA T+YDG Sbjct: 71 AAVFGDATKVKFSQLNAKERFTALQSGEVDVLSRNTTWTSSRDA--GMGLVFAGVTYYDG 128 Query: 147 QGLMVRRNSGIQSLQDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAY 206 G +V + G+ S ++ G +IC++ GTT+ELN++D R G++Y I F SD + + Sbjct: 129 VGFLVNKKLGVSSAKELDGATICIQAGTTTELNVSDFFRANGLKYTPITFDTSDESAKSL 188 Query: 207 AQGRCEGVTSDRSQLAARRTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVN 266 GRC+ +TSD+SQL A+R+ L+ ++ +L ISKEPL P D WF +VKW + Sbjct: 189 ESGRCDVLTSDKSQLFAQRSKLAAPTEYVVLPETISKEPLGPVVRKGDEEWFSIVKWTLF 248 Query: 267 ATIQAEEFGITQANID-QFKTSKNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGE 325 A + AEE GIT N++ + K +KNP++ R LG +GE G+ L L D+ + +K VGNYGE Sbjct: 249 AMLNAEEAGITSKNVEAEAKATKNPDVARLLGADGEYGKDLKLPKDWVVQIVKQVGNYGE 308 Query: 326 IYERNVGQQSPLKLNRGLNQLYKNGGLLYSPPFR 359 ++E+N+GQ + LK++RG+N L+ NGG+ Y+PP R Sbjct: 309 VFEKNLGQSTDLKIDRGMNALWNNGGIQYAPPVR 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: 293 Number of extensions: 8 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