Align ABC transporter for D-Galactose and D-Glucose, periplasmic substrate-binding component (characterized)
to candidate H281DRAFT_00166 H281DRAFT_00166 carbohydrate ABC transporter substrate-binding protein, CUT1 family
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1894 (432 letters) >FitnessBrowser__Burk376:H281DRAFT_00166 Length = 415 Score = 394 bits (1011), Expect = e-114 Identities = 217/424 (51%), Positives = 271/424 (63%), Gaps = 12/424 (2%) Query: 6 RLATVISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFTWKDGA 65 + ++ + L V A ++ SVEV+HWWTSGGE AV VLK + K G+TWKD A Sbjct: 2 KFRAIMGALCAAGLMCGVSAVQAAESVEVLHWWTSGGESKAVGVLKDDMTKQGYTWKDFA 61 Query: 66 VAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAENWDGLL 125 VAGG G+ AMT LK++ ++GN P AQIKGP IQ+W S G+L + S A +W L Sbjct: 62 VAGGAGAAAMTALKTQVISGNAPSAAQIKGPLIQDWASQGVL----VPIDSVAGDWKKNL 117 Query: 126 SKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDKLKAAG 185 ++ + +G YVA P ++HRVNWL+IN KAG K PTT EF+A DK+KAAG Sbjct: 118 PPEIDKIMHADGHYVAAPFSVHRVNWLYINKAALDKAG-GKVPTTWPEFFAVADKMKAAG 176 Query: 186 FIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELKKITGY 245 +A GGQPWQD T++EDVVLS GAD YKKALVDLD+KTL+ +M F ++KI GY Sbjct: 177 IQPIAMGGQPWQDLTLWEDVVLS-QGADFYKKALVDLDEKTLTSDKMVGVFDTVRKIQGY 235 Query: 246 MDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTEKAFTY 305 D R GRDWN+A A VI+GKAGMQ MGDWAK E+ A K +G DY C A PGTEKA+T+ Sbjct: 236 FDAGRTGRDWNLATAMVINGKAGMQFMGDWAKGEFANAGKKSGSDYVCAAVPGTEKAYTF 295 Query: 306 NIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMDKLGFD 365 N+DS F+ K +K Q LAK + +FQ+ FS+NKGSIPVR + M K FD Sbjct: 296 NVDSFVFFQQKG-QKAATPGQLALAKTIMSPEFQEQFSLNKGSIPVRLGV--SMAK--FD 350 Query: 366 ECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKASAQLA 425 +CA+KS D K+GG PS+AH MA A GAI DVVT FMN + D A A LA Sbjct: 351 DCAKKSYADEQVAIKSGGYVPSLAHGMAQPDAAAGAISDVVTKFMNSQQ-DSKSAVAALA 409 Query: 426 SAVK 429 A K Sbjct: 410 KAAK 413 Lambda K H 0.314 0.129 0.377 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: 611 Number of extensions: 33 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: 432 Length of database: 415 Length adjustment: 32 Effective length of query: 400 Effective length of database: 383 Effective search space: 153200 Effective search space used: 153200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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