Align glucose transporter, permease component (characterized)
to candidate SM_b20903 SM_b20903 sugar uptake ABC transporter permease
Query= reanno::Phaeo:GFF3640 (433 letters) >FitnessBrowser__Smeli:SM_b20903 Length = 453 Score = 461 bits (1186), Expect = e-134 Identities = 231/424 (54%), Positives = 306/424 (72%), Gaps = 8/424 (1%) Query: 11 EHSKRGLFQQLELDVRLLGMIGAFVILCIGFNILT----DGRFLTPRNIFNLTIQTVSVA 66 E+ + F+ E+D RLLGM+GA +I+ +GF ++T DG FL PRN++NLT+QT SVA Sbjct: 30 ENPVKRFFRATEIDTRLLGMVGALIIIWLGFQVMTGGLFDGLFLKPRNLWNLTVQTSSVA 89 Query: 67 IMATGMVFVIVTRHIDLSVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGL 126 +MATGMV VIVTR+IDLSVG++L C +M V+Q VLP GLG HPATW IT+A G+ Sbjct: 90 VMATGMVLVIVTRNIDLSVGSVLGFCGMIMGVLQAQVLPQYLGLG--HPATWAITLACGI 147 Query: 127 AIGTLIGAFQGWMVGFLTIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTF-LVFGGTS 185 A+G IGA G ++ FL +PAFIVTLGG LVWR W++T GQT+ P+D+TF L+ GGT Sbjct: 148 AVGGAIGALHGSIIAFLNVPAFIVTLGGLLVWRGATWFVTSGQTVAPMDATFRLMGGGTE 207 Query: 186 GTLGTTLSWVVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVAI 245 G++G T SW+VG +A + + A+ NSR+ ++ GFP++P WAE ++ A +LG VA+ Sbjct: 208 GSIGATASWIVGSLACIAIVGAILNSRKQRKRFGFPLRPVWAEYFLSILGCALVLGAVAV 267 Query: 246 LNAYQIPARRLKRMMEAQGETMPEG-LVVGYGLPISVLILIATAVVMTIIARRTRLGRYI 304 N Y P +R +A G P+G L + +G+ I VL+ I +VMT IA R R GRY+ Sbjct: 268 ANHYYWPVNIARRYADANGIAWPDGGLQISHGIAIPVLVAIVVGIVMTFIATRLRFGRYV 327 Query: 305 FATGGNPDAAELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIA 364 FA GGNP+AAEL+GI TR +TVKIF LMG LCA++A +++ARL +N G LDEL IA Sbjct: 328 FALGGNPEAAELAGIKTRWVTVKIFTLMGVLCAIAAAISTARLNAATNAQGELDELYTIA 387 Query: 365 AAVIGGTALSGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDIL 424 AAVIGGT+L+GG GTI GA++GAL+MQSLQSGM ++G+D PFQ IVVG VLV AVW+D + Sbjct: 388 AAVIGGTSLAGGVGTIAGAMIGALVMQSLQSGMVLLGIDTPFQRIVVGVVLVTAVWLDTV 447 Query: 425 YRKR 428 YR R Sbjct: 448 YRAR 451 Lambda K H 0.327 0.141 0.419 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: 722 Number of extensions: 41 Number of successful extensions: 5 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: 433 Length of database: 453 Length adjustment: 32 Effective length of query: 401 Effective length of database: 421 Effective search space: 168821 Effective search space used: 168821 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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