Align GtsA (GLcE), component of Glucose porter, GtsABCD (characterized)
to candidate GFF1857 Psest_1896 ABC-type sugar transport system, periplasmic component
Query= TCDB::Q88P38 (428 letters) >FitnessBrowser__psRCH2:GFF1857 Length = 415 Score = 517 bits (1332), Expect = e-151 Identities = 267/428 (62%), Positives = 316/428 (73%), Gaps = 13/428 (3%) Query: 1 MNSTLRLAAAISFASLIPLGAQAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFIWK 60 MN+ RLA ++S A +P+ A A G VEV+HWWTSGGEK A D L+ VE+ G WK Sbjct: 1 MNAFHRLALSVSLA--LPVLAHA----GEVEVLHWWTSGGEKRAADTLQKLVEQKGHSWK 54 Query: 61 DGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQDWAATGLLDADVLKDVAKEGKWD 120 D AVAGGGG AMTVLK+RAV+GNPP AQIKGPDIQ+W GLL L D AK +WD Sbjct: 55 DFAVAGGGGEAAMTVLKTRAVSGNPPSAAQIKGPDIQEWGELGLLAN--LDDTAKAERWD 112 Query: 121 SLLDKKVADTVKYDGDYVAVPVNIHRINWLWINPEVFKKAGIDKAPTTLDEFYAAADKLK 180 +LL ++V ++YDG YVAVPVN+HR+NWLWINPEVF+KAG K P TLDEF+AAADKLK Sbjct: 113 ALLPEQVRKIMQYDGSYVAVPVNVHRVNWLWINPEVFEKAGA-KPPKTLDEFFAAADKLK 171 Query: 181 AAGFIPLAHGGQPWQDSTVFESVVLSVMGVDGYKKALVDLDSATLTGPQMVKALTELKKV 240 AAGFIP+AHGGQPWQD TVFE VLS++G D Y KA V+LD+ TLTG +MV+A T LKK+ Sbjct: 172 AAGFIPVAHGGQPWQDGTVFEGFVLSILGPDDYHKAFVELDNDTLTGDKMVQAFTALKKL 231 Query: 241 ATYMDPDGKGQDWNLEAAKVINGKAGMQIMGDWAKSEWTLAKKTAGKDYQCVPFPGTDKS 300 Y+D D G++WN VI+GKAGMQIMGDWAKSE+T A K AGK+YQC+PFPGT S Sbjct: 232 RDYIDADAAGREWNRATGMVIDGKAGMQIMGDWAKSEFTAANKVAGKNYQCLPFPGTQGS 291 Query: 301 FLYNIDSLVVFKQNNAGTSAGQQDIARKVLGEDFQKVFSINKGSIPVRNDMLADMGKYGF 360 F +NIDSL +FK ++ Q+D+AR VL +FQ F+ NKGSIPVR D DM + F Sbjct: 292 FAFNIDSLAMFKLSSDDNRKAQEDLARTVLEPEFQTFFNQNKGSIPVRQDQ--DMSE--F 347 Query: 361 DACAQTSAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADAAKKL 420 DACAQ S DF AK GLQPS+ H MA + VQGA FDVVTN+ NDPKADP AAK+L Sbjct: 348 DACAQQSMTDFKEAAKGSGLQPSLTHGMAASSYVQGAVFDVVTNFFNDPKADPQKAAKQL 407 Query: 421 AAAIKAAQ 428 AAAIKA Q Sbjct: 408 AAAIKAVQ 415 Lambda K H 0.315 0.131 0.392 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: 556 Number of extensions: 21 Number of successful extensions: 4 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: 41 (21.6 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