Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate Pf1N1B4_596 Glucose ABC transport system, periplasmic sugar-binding protein
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_596 Length = 435 Score = 699 bits (1805), Expect = 0.0 Identities = 348/435 (80%), Positives = 380/435 (87%), Gaps = 7/435 (1%) Query: 1 MNAINRLAVAISIASL-----FPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKD 55 MNAI+RLA IS+ASL FP+SA AAD+KG+VEVVHWWTSGGEKAAVDVLKAQVEKD Sbjct: 1 MNAISRLATVISLASLLPVAAFPVSALAADAKGSVEVVHWWTSGGEKAAVDVLKAQVEKD 60 Query: 56 GFVWKDGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAK 115 GF WKDGAVAGGGG+TAMTVLKSRAVAGNPPGVAQIKGPDIQEW STGLL TD LK+V+K Sbjct: 61 GFTWKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDTLKEVSK 120 Query: 116 EEKWDSLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAA 175 E WD+LL KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGI K PTTL+EFYAA Sbjct: 121 SEGWDNLLIKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIDKAPTTLEEFYAA 180 Query: 176 GDKLKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALT 235 GDKLKAAGFI LAHGGQPWQDSTVFE VVLSVMGADGYKKALVDLD L+GPEM KA T Sbjct: 181 GDKLKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMAKAFT 240 Query: 236 ELKKVATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFP 295 ELKKV YMD + G+DWN+ A VINGKAGMQ+MGDWAKSEWTAAKKVAGKDY+CV FP Sbjct: 241 ELKKVTGYMDPNRAGRDWNIAAADVINGKAGMQMMGDWAKSEWTAAKKVAGKDYQCVPFP 300 Query: 296 GTDKAFTYNIDSLAVFKQK--DKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLN 353 GT+KAFTYNIDS+AVFK K KG A QQD+AKV LG++FQKVFSINKGSIPVR DMLN Sbjct: 301 GTEKAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGKDFQKVFSINKGSIPVRTDMLN 360 Query: 354 KMDSYGFDSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADP 413 M GFD+CAQ +AKDFLAD KTGGLQPSMAHNMAT+LAVQGA FDVVTN++ND ADP Sbjct: 361 DMSGLGFDACAQASAKDFLADEKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKNADP 420 Query: 414 ADTAKKLGAAIKSAK 428 A + +L +A+K+A+ Sbjct: 421 AKASAQLASAVKAAQ 435 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: 723 Number of extensions: 24 Number of successful extensions: 3 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: 435 Length adjustment: 32 Effective length of query: 396 Effective length of database: 403 Effective search space: 159588 Effective search space used: 159588 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: 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