Align ABC transporter for D-Glucose-6-Phosphate, periplasmic substrate-binding component (characterized)
to candidate GFF3014 HP15_2958 extracellular solute-binding protein family 1
Query= reanno::WCS417:GFF4324 (428 letters) >FitnessBrowser__Marino:GFF3014 Length = 416 Score = 428 bits (1100), Expect = e-124 Identities = 219/420 (52%), Positives = 271/420 (64%), Gaps = 16/420 (3%) Query: 8 AVAISIASLFPLSAFAADSKGTVEVVHWWTSGGEKAAVDVLKAQVEKDGFVWKDGAVAGG 67 A A+S A+L P A A G VEV+HWWT+GGE A LK +E G WKD AVAGG Sbjct: 12 AAAVS-AALLPAQALQA---GEVEVLHWWTAGGEARAAVALKEMMEDQGHTWKDFAVAGG 67 Query: 68 GGATAMTVLKSRAVAGNPPGVAQIKGPDIQEWASTGLLDTDVLKDVAKEEKWDSLLDKKV 127 GG AMTVLK+RAV+GNPP AQIKG DI+EWA G L + L DVA+ W L+ + Sbjct: 68 GGEAAMTVLKTRAVSGNPPAAAQIKGLDIREWAKLGFLTS--LDDVAEANNWGQLIPPVI 125 Query: 128 SDTVKYEGDYVAVPVNIHRVNWLWINPEVFKKAGITKNPTTLQEFYAAGDKLKAAGFIPL 187 +D ++YE YVAVPVN+HRVNWLW NPE K G+ P TL EFY A +KLKAAG PL Sbjct: 126 ADVMQYEDSYVAVPVNVHRVNWLWANPETLNKVGVGV-PKTLDEFYQAAEKLKAAGITPL 184 Query: 188 AHGGQPWQDSTVFEAVVLSVMGADGYKKALVDLDNGALTGPEMVKALTELKKVATYMDVD 247 AHGGQPWQD+TVFEAV L+VMG D + A V+ D + +M + E KV +Y+D + Sbjct: 185 AHGGQPWQDATVFEAVALAVMGPDDFASAFVEHDMDVINSAQMEEVFAEFAKVMSYVDDN 244 Query: 248 GKGQDWNLEAGKVINGKAGMQIMGDWAKSEWTAAKKVAGKDYECVAFPGTDKAFTYNIDS 307 G+DWN G VI G+A MQIMGDWAK E+TAA G+DY C A PGT FT+N+DS Sbjct: 245 AAGRDWNTATGMVIRGEAAMQIMGDWAKGEFTAAGLTPGEDYVCAAAPGTGGQFTFNVDS 304 Query: 308 LAVFKQKDKGTAAGQQDIAKVVLGENFQKVFSINKGSIPVRNDMLNKMDSYGFDSCAQTA 367 A+F D+ Q+D+A+ ++ FQ VF+ KGSIPVR D FD+CAQ + Sbjct: 305 FAMFSLSDEDNTKAQKDLARTIMEPEFQAVFNKAKGSIPVRTD---------FDTCAQAS 355 Query: 368 AKDFLADAKTGGLQPSMAHNMATTLAVQGAFFDVVTNYINDPKADPADTAKKLGAAIKSA 427 F + A+ GGL PS AH +ATT VQG FDVVTN++N DPA +L AAI++A Sbjct: 356 MDTFKSSAEDGGLVPSFAHGLATTSYVQGQIFDVVTNFVNSDNKDPARATDQLAAAIQAA 415 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: 529 Number of extensions: 17 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: 416 Length adjustment: 32 Effective length of query: 396 Effective length of database: 384 Effective search space: 152064 Effective search space used: 152064 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