Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate AZOBR_RS08655 AZOBR_RS08655 amino acid ABC transporter substrate-binding protein
Query= uniprot:Q31RP1 (359 letters) >FitnessBrowser__azobra:AZOBR_RS08655 Length = 340 Score = 339 bits (870), Expect = 6e-98 Identities = 169/321 (52%), Positives = 220/321 (68%), Gaps = 3/321 (0%) Query: 40 ESNSRLNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYR 99 ++ L+ V+ RG + CGV LPGF DS GN++GLDVD C+A+A ALFNDP +++ Sbjct: 22 QAGPTLDAVKGRGFVQCGVNAGLPGFGNPDSSGNWTGLDVDYCRAVAVALFNDPNKVKFT 81 Query: 100 SLDSVERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNSGIQS 159 L + +RFPA+ SGEVDLLSRNTT TL+RD G L FAP T+YDGQG MV + G++S Sbjct: 82 PLSAQQRFPAIQSGEVDLLSRNTTVTLTRDTSVG--LNFAPVTYYDGQGFMVNKKLGVKS 139 Query: 160 LQDFQGKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDRS 219 ++ G ++CV+ GTT+ELNLAD R + Y + ++D AAY GRC+ +T+D S Sbjct: 140 AKELNGATVCVQAGTTTELNLADYFRTNNMSYNPVVIESNDEVNAAYFAGRCDVLTTDAS 199 Query: 220 QLAARRTTLSDA-DQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQ 278 LA R ++ D H +L +ISKEPL+PA + D WFDVVKW V ATIQAEE GIT Sbjct: 200 GLAGTRAGVAPVPDDHIILPEIISKEPLAPAVRHGDDQWFDVVKWTVYATIQAEEMGITS 259 Query: 279 ANIDQFKTSKNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPLK 338 N+D+F SKNPEI+R LG +G+ LGL +AY IK +GNYGEI+ERNVG ++PLK Sbjct: 260 KNVDEFVNSKNPEIQRILGTSPGMGKALGLDEKWAYNIIKTMGNYGEIFERNVGTKTPLK 319 Query: 339 LNRGLNQLYKNGGLLYSPPFR 359 L RGLN L+ NGGL Y+ P R Sbjct: 320 LERGLNALWTNGGLQYAMPIR 340 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: 361 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: 340 Length adjustment: 29 Effective length of query: 330 Effective length of database: 311 Effective search space: 102630 Effective search space used: 102630 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