Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate PfGW456L13_1894 Glucose ABC transport system, periplasmic sugar-binding protein
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1894 Length = 432 Score = 697 bits (1800), Expect = 0.0 Identities = 344/432 (79%), Positives = 378/432 (87%), Gaps = 4/432 (0%) Query: 1 MNAINRLAVAISIASL--FPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFV 58 MNAI+RLA IS+ASL PLS AA+SKG+VEVVHWWTSGGEKAAVDVLKAQVEKDGF Sbjct: 1 MNAISRLATVISLASLSALPLSVLAAESKGSVEVVHWWTSGGEKAAVDVLKAQVEKDGFT 60 Query: 59 WKDGAVAGGGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEK 118 WKDGAVAGGGG+TAMTVLKSRAVAGNPPGVAQIKGPDIQEW STGLL TD LKDV+K E Sbjct: 61 WKDGAVAGGGGSTAMTVLKSRAVAGNPPGVAQIKGPDIQEWGSTGLLSTDALKDVSKAEN 120 Query: 119 WDSLLDKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDK 178 WD LL KKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGI K PTTL+EFYAAGDK Sbjct: 121 WDGLLSKKVSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGIEKAPTTLEEFYAAGDK 180 Query: 179 LKAAGFIPLAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELK 238 LKAAGFI LAHGGQPWQDSTVFE VVLSVMGADGYKKALVDLD L+GPEM K+ ELK Sbjct: 181 LKAAGFIALAHGGQPWQDSTVFEDVVLSVMGADGYKKALVDLDQKTLSGPEMTKSFAELK 240 Query: 239 KVATYMDVDGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTD 298 K+ YMD + G+DWN+ A VI+GKAGMQ+MGDWAKSEWTAAKK+AGKDY+CVAFPGT+ Sbjct: 241 KITGYMDPNRAGRDWNIAAADVISGKAGMQMMGDWAKSEWTAAKKIAGKDYQCVAFPGTE 300 Query: 299 KAFTYNIDSLAVFKQK--DKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMD 356 KAFTYNIDS+AVFK K KG A QQD+AKV LG +FQKVFS+NKGSIPVRNDMLN+MD Sbjct: 301 KAFTYNIDSMAVFKLKADRKGDIAAQQDLAKVALGTDFQKVFSMNKGSIPVRNDMLNEMD 360 Query: 357 SYGFDSCAQTAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADT 416 GFD CAQ +AKDF+AD KTGGLQPSMAHNMAT+LAVQGA FDVVTN++ND ADPA Sbjct: 361 KLGFDECAQKSAKDFIADDKTGGLQPSMAHNMATSLAVQGAIFDVVTNFMNDKDADPAKA 420 Query: 417 AKKLGAAIKSAK 428 + +L +A+K+A+ Sbjct: 421 SAQLASAVKAAQ 432 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: 722 Number of extensions: 19 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: 432 Length adjustment: 32 Effective length of query: 396 Effective length of database: 400 Effective search space: 158400 Effective search space used: 158400 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