Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_086005351.1 RHSP_RS08730 sugar ABC transporter ATP-binding protein
Query= ecocyc::YTFR-MONOMER (500 letters) >NCBI__GCF_000359745.1:WP_086005351.1 Length = 477 Score = 350 bits (897), Expect = e-101 Identities = 191/474 (40%), Positives = 293/474 (61%), Gaps = 3/474 (0%) Query: 28 VDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGIG 87 ++ +RRG + LLGENGAGKSTL+K L GVY G I L G+A P+N A+ GI Sbjct: 1 MNLKVRRGRVHTLLGENGAGKSTLMKILAGVYKPTSGEILLAGKAYQPQNPRDARGHGIS 60 Query: 88 TVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATELMASYGFSLDVREPLNRFS 147 V+QE++L N+SVA N+F EP RFG +R + + +A L+ G ++V + S Sbjct: 61 IVFQELSLCRNLSVAQNIFASHEPSRFGFVRDRVLVAKAEALIEDLGLPVNVHAKVGDLS 120 Query: 148 VAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIFVTHFLDQ 207 +A +Q+V I + + L A V+ILDEPT+SL E E+LF ++ +L+ RG ++I+++H +++ Sbjct: 121 IAQRQLVEIAKGLSLPADVIILDEPTSSLSDSEAEILFSIIERLKARGKAIIYISHRMEE 180 Query: 208 VYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGREL-DTHALQRAGRTLLSDKPVAA 266 + ++SD ITV+R+G +V E E +L+ +M+GRE+ D + + A R S PV A Sbjct: 181 IMRLSDDITVIRDGEYVTTTEKSETSIDKLIALMVGREMQDIYPPRVAPRPAESTAPVLA 240 Query: 267 FKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNL 326 KN G ++V+PGE+VGL GL+GSGR++ + +FG++ + G + GKP L Sbjct: 241 TKNLTVPGKFHEVSIDVKPGEVVGLFGLIGSGRSDIMKALFGMERPE-GQIFLDGKPLTL 299 Query: 327 RSPHQASVLGIGFCPEDRKTDGIIAAASVRENI-ILALQAQRGWLRPISRKEQQEIAERF 385 SP A GI F E+RK +G++ A SV N+ ++AL+ G + ++ A+ Sbjct: 300 ASPSDAIRHGIAFVTENRKEEGLVLAHSVERNVNMVALKQLAGPFGLMRGSAERAAAKAE 359 Query: 386 IRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLI 445 + +L I+ S + LSGGNQQK++L++WL RP+ LILDEPTRG+DVGA EI R+I Sbjct: 360 VLRLAIKAASIDTSTGSLSGGNQQKIVLAKWLQIRPRVLILDEPTRGVDVGAKFEIYRII 419 Query: 446 ETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIMNAIA 499 L A+G A+L++SSEL E++G +DRV +M +R A + L+ +M A Sbjct: 420 RELAAEGAAILMVSSELPEVLGLSDRVAVMHNRSLAAVLDAEGLTPETVMTYAA 473 Lambda K H 0.321 0.138 0.391 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: 576 Number of extensions: 22 Number of successful extensions: 7 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: 500 Length of database: 477 Length adjustment: 34 Effective length of query: 466 Effective length of database: 443 Effective search space: 206438 Effective search space used: 206438 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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