Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS04180 BPHYT_RS04180 sugar ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__BFirm:BPHYT_RS04180 Length = 415 Score = 365 bits (936), Expect = e-105 Identities = 195/420 (46%), Positives = 254/420 (60%), Gaps = 12/420 (2%) Query: 7 LAVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAG 66 L A +AS SA A + ++ V+HWWTSGGE A+ VLK ++K G+ WKD AVAG Sbjct: 5 LMSAAIVASTLATSAQVASAAESLSVLHWWTSGGESKAIRVLKDDMDKQGYEWKDFAVAG 64 Query: 67 GGGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDKK 126 G GA AMT LK++ ++GN P AQIKGP IQ+WA G+L D+ K W + L + Sbjct: 65 GAGAAAMTALKTQVMSGNAPSAAQIKGPLIQDWADQGVL-VDIDKSATD---WKAQLPAQ 120 Query: 127 VSDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFIP 186 ++ T+ +G YVA P ++HR+NWLWIN K G K PTT EF+A DK +AAG P Sbjct: 121 INKTMMSKGHYVAAPFSVHRINWLWINKAALDKVG-GKPPTTWPEFFALADKFRAAGITP 179 Query: 187 LAHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMDV 246 +A GGQPWQD T++E VVLS GAD Y+KA++DLD LT P+M++ +K+ Y D Sbjct: 180 VARGGQPWQDMTIWETVVLS-QGADFYRKAMIDLDQKTLTSPQMLQVFQTARKIQGYFDK 238 Query: 247 DGKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNID 306 G+DWNL VING GMQ MGDWAK E+ A K A DY C A PGT AFTY +D Sbjct: 239 GSTGRDWNLATAMVINGSGGMQFMGDWAKGEFANANKKADVDYICAAAPGTSNAFTYTVD 298 Query: 307 SLAVFKQKDKGTAA-GQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSCAQ 365 S F+Q K A GQ +AK ++ FQ+ FS+ KGSIPVR D+ MD FD+CA+ Sbjct: 299 SFVFFQQNGKKEATLGQLALAKTIMSPAFQEQFSLYKGSIPVRQDV--SMDK--FDACAK 354 Query: 366 TAAKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAAIK 425 + D K+ PS A + A +GA DVVT ++N DP + +K+ AA K Sbjct: 355 KSYADEQTTIKSNTFFPSFAFGDVQSSATEGAITDVVTGFMNS-NEDPQEAMRKVAAAAK 413 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: 511 Number of extensions: 24 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: 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: 42 (22.0 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