Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate GFF2246 HP15_2196 glutamate/glutamine/aspartate/asparagine ABC transporter, periplasmic substrate-binding protein
Query= uniprot:Q31RP1 (359 letters) >FitnessBrowser__Marino:GFF2246 Length = 347 Score = 336 bits (861), Expect = 6e-97 Identities = 159/315 (50%), Positives = 216/315 (68%), Gaps = 2/315 (0%) Query: 45 LNQVQARGKLLCGVEGRLPGFSFLDSQGNYSGLDVDICKAIAAALFNDPKAIEYRSLDSV 104 L V+ +G L CGV LPGFS D +GN++G+DVD C+A+AAA+F D A+E+ L + Sbjct: 35 LENVKEKGHLQCGVTSGLPGFSQPDEKGNWTGIDVDTCRAVAAAIFGDANAVEFTPLTAK 94 Query: 105 ERFPALASGEVDLLSRNTTWTLSRDAKGGNNLEFAPTTFYDGQGLMVRRNSGIQSLQDFQ 164 ERF AL SGE+D+LSRNTTWTL+RDA G L FA +YDGQG ++ + G+ Sbjct: 95 ERFTALQSGEIDMLSRNTTWTLTRDASLG--LNFAGVNYYDGQGFLINKGIGVDDATQLD 152 Query: 165 GKSICVETGTTSELNLADTMRELGVQYQEIKFPNSDANYAAYAQGRCEGVTSDRSQLAAR 224 G +IC++ GTT+ELNL+D R G++++ I F S+ +A GRC+ +TSDRSQLAA Sbjct: 153 GATICIQAGTTTELNLSDYFRAKGMEFKPIVFDTSEQTVQGFAAGRCDVLTSDRSQLAAL 212 Query: 225 RTTLSDADQHQLLDAVISKEPLSPATLNNDSPWFDVVKWVVNATIQAEEFGITQANIDQF 284 R+ LSD ++L ISKEPL P D WF++VKWV+ A I AEE G+T AN D Sbjct: 213 RSKLSDPSSAKILPNTISKEPLGPVVRQGDDQWFNIVKWVLFAQINAEELGVTSANADDM 272 Query: 285 KTSKNPEIRRFLGLEGELGQQLGLSNDFAYRAIKAVGNYGEIYERNVGQQSPLKLNRGLN 344 S NP I+R LG +G++G +LGL +DF Y+A+K VGNYGE+Y+RNVG +PL L+RG+N Sbjct: 273 LKSDNPNIQRLLGTDGDMGAKLGLPDDFGYQAVKLVGNYGEMYDRNVGPDTPLGLDRGIN 332 Query: 345 QLYKNGGLLYSPPFR 359 L+ GG++Y+PP R Sbjct: 333 ALWTEGGIMYAPPVR 347 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: 301 Number of extensions: 10 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: 359 Length of database: 347 Length adjustment: 29 Effective length of query: 330 Effective length of database: 318 Effective search space: 104940 Effective search space used: 104940 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