Align Glucose/galactose transporter (characterized, see rationale)
to candidate WP_083189367.1 BLR17_RS03160 L-fucose:H+ symporter permease
Query= uniprot:A0KXM0 (423 letters) >NCBI__GCF_900100165.1:WP_083189367.1 Length = 433 Score = 290 bits (741), Expect = 8e-83 Identities = 172/422 (40%), Positives = 245/422 (58%), Gaps = 20/422 (4%) Query: 15 SEAGNG-NYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYF 73 +E G G NY + +TSLFF+WG L+ ILIPHLK LN Q+ LI F AYF Sbjct: 15 TEKGQGPNYVLPFILITSLFFLWGMAHNLDSILIPHLKKACQLNNRQSTLIDTSVFLAYF 74 Query: 74 LVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQ 133 L++IPAG ++K++GY+ I+ GL++ + G LF PAA+ Y LFL ALF++ G+TIL+ Sbjct: 75 LMAIPAGMIIKKVGYKNSIIIGLLVFATGAFLFVPAANTQAYELFLVALFIIGCGLTILE 134 Query: 134 VAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILS---------VAASVSS 184 +ANPY LG E++S RLNL +FN L VAP GS+ ILS A + Sbjct: 135 TSANPYAAILGPPESSSKRLNLAASFNGLAAMVAPIVGSMFILSGKSFTPEQMAAMPEAE 194 Query: 185 ELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIR-EHSQAAAEEVQTHLGKTSAL 243 L EA VKLPY++L L ++A++F + LP ++ EH+ EV+ G S L Sbjct: 195 RLTYLAGEAAAVKLPYIILGTILVLVAVLFYFMHLPSMKPEHT-----EVEVKPGFFSVL 249 Query: 244 QSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFI 303 + HL V F YVGA+V + SF + + M E AA+Y+ Y M GRFI Sbjct: 250 KHRHLSWAVVAQFFYVGAQVCVTSFFIRMAEQG--ANMDEITAAYYLGLYGVLFMAGRFI 307 Query: 304 GSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALR 363 G+ ++ + +L+ A ++A+L VA+ SG ++A+ +G F SIMFPTIFSL L Sbjct: 308 GTFFLKYVKDYVLLSIYAVLSAILCAVAIYGSGIYVIYALGAIGFFMSIMFPTIFSLGLV 367 Query: 364 DLGPHTSQGSGILCLAIVGGAIVPLLQGVLAD--NLGIQLAFILPVVCYGFILFYGAKGS 421 L +T GS L ++IVGGAI+P G L D + IQ +++P+VC+ IL++G G Sbjct: 368 GLKSNTETGSSWLVMSIVGGAILPYGMGTLIDMNHDDIQSGYLIPLVCFLIILYFGVFGH 427 Query: 422 KM 423 K+ Sbjct: 428 KV 429 Lambda K H 0.326 0.138 0.402 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: 536 Number of extensions: 34 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: 423 Length of database: 433 Length adjustment: 32 Effective length of query: 391 Effective length of database: 401 Effective search space: 156791 Effective search space used: 156791 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 24 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