Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_00166 H281DRAFT_00166 carbohydrate ABC transporter substrate-binding protein, CUT1 family
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__Burk376:H281DRAFT_00166 Length = 415 Score = 371 bits (952), Expect = e-107 Identities = 201/407 (49%), Positives = 254/407 (62%), Gaps = 15/407 (3%) Query: 23 AADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAGGGGATAMTVLKSRAVA 82 A + +VEV+HWWTSGGE AV VLK + K G+ WKD AVAGG GA AMT LK++ ++ Sbjct: 21 AVQAAESVEVLHWWTSGGESKAVGVLKDDMTKQGYTWKDFAVAGGAGAAAMTALKTQVIS 80 Query: 83 GNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDKKVSDTVKYEGDYVAVPV 142 GN P AQIKGP IQ+WAS G+L + VA + W L ++ + +G YVA P Sbjct: 81 GNAPSAAQIKGPLIQDWASQGVLVP--IDSVAGD--WKKNLPPEIDKIMHADGHYVAAPF 136 Query: 143 NIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFIPLAHGGQPWQDSTVFEA 202 ++HRVNWL+IN KAG K PTT EF+A DK+KAAG P+A GGQPWQD T++E Sbjct: 137 SVHRVNWLYINKAALDKAG-GKVPTTWPEFFAVADKMKAAGIQPIAMGGQPWQDLTLWED 195 Query: 203 VVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMDVDGKGQDWNLEAGKVIN 262 VVLS GAD YKKALVDLD LT +MV ++K+ Y D G+DWNL VIN Sbjct: 196 VVLS-QGADFYKKALVDLDEKTLTSDKMVGVFDTVRKIQGYFDAGRTGRDWNLATAMVIN 254 Query: 263 GKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNIDSLAVFKQK-DKGTAAG 321 GKAGMQ MGDWAK E+ A K +G DY C A PGT+KA+T+N+DS F+QK K G Sbjct: 255 GKAGMQFMGDWAKGEFANAGKKSGSDYVCAAVPGTEKAYTFNVDSFVFFQQKGQKAATPG 314 Query: 322 QQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSCAQTAAKDFLADAKTGGLQ 381 Q +AK ++ FQ+ FS+NKGSIPVR + FD CA+ + D K+GG Sbjct: 315 QLALAKTIMSPEFQEQFSLNKGSIPVRLG----VSMAKFDDCAKKSYADEQVAIKSGGYV 370 Query: 382 PSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAAIKSAK 428 PS+AH MA A GA DVVT ++N + D+ + A K+AK Sbjct: 371 PSLAHGMAQPDAAAGAISDVVTKFMNSQQ----DSKSAVAALAKAAK 413 Lambda K H 0.314 0.131 0.388 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: 569 Number of extensions: 21 Number of successful extensions: 6 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: 428 Length of database: 415 Length adjustment: 32 Effective length of query: 396 Effective length of database: 383 Effective search space: 151668 Effective search space used: 151668 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: 42 (22.0 bits) S2: 50 (23.9 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