Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS00415 BPHYT_RS00415 sugar ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__BFirm:BPHYT_RS00415 Length = 422 Score = 404 bits (1037), Expect = e-117 Identities = 207/417 (49%), Positives = 263/417 (63%), Gaps = 10/417 (2%) Query: 10 AISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAGGGG 69 A+ +A++ A A VEV+H+WTSGGE + VLK +++ G WKD AVAGGGG Sbjct: 15 ALGVAAVL---ACGAARSAEVEVLHYWTSGGEAKSAQVLKQMLDEKGDTWKDFAVAGGGG 71 Query: 70 ATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDKKVSD 129 AMT LK+R +AGNPP AQIKGP IQEW G+L + + DVAK E WD L+ ++S Sbjct: 72 GNAMTALKTRVIAGNPPAAAQIKGPAIQEWGDEGVLVS--INDVAKREGWDKLIPPQISG 129 Query: 130 TVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFIPLAH 189 +KY+G YVA PVN+HRVN LWIN + KK + P T EF+ + L+ AG P+A Sbjct: 130 IMKYKGQYVAAPVNVHRVNRLWINADALKKVN-AQPPATWDEFFRTAEALQKAGITPVAI 188 Query: 190 GGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMDVDGK 249 GGQ WQD+ FE V L V GA Y+KA V LD L GP MVKAL KK+ Y D Sbjct: 189 GGQQWQDAETFETVALGVGGAAFYEKAFVQLDQSTLRGPTMVKALETFKKIKAYTDKAQT 248 Query: 250 GQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNIDSLA 309 G+DWNL G VI+GKA MQ MGDWAK E++ A KV GKDY CV PG+ A+T+N+DS A Sbjct: 249 GRDWNLATGMVISGKAAMQFMGDWAKGEFSVAGKVPGKDYLCVPAPGSQNAYTFNVDSFA 308 Query: 310 VFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSCAQTAAK 369 FK + GQ+D+A ++L FQ++F++NKGSIPVR MD FD+CAQ +A Sbjct: 309 FFKVRSADVEKGQKDLASLLLSPKFQEIFNLNKGSIPVRQG----MDLSKFDTCAQRSAA 364 Query: 370 DFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAAIKS 426 DF + G L PS AH+M T AV+GAF+DV+ N+ ND A KL A K+ Sbjct: 365 DFTSAQAKGTLVPSWAHDMVDTPAVEGAFYDVIGNFWNDDNESAQQAADKLAVAAKT 421 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: 549 Number of extensions: 22 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: 422 Length adjustment: 32 Effective length of query: 396 Effective length of database: 390 Effective search space: 154440 Effective search space used: 154440 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