Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_084931761.1 HA51_RS02830 hypothetical protein
Query= uniprot:D8J112 (347 letters) >NCBI__GCF_002095475.1:WP_084931761.1 Length = 323 Score = 233 bits (593), Expect = 7e-66 Identities = 127/303 (41%), Positives = 191/303 (63%), Gaps = 9/303 (2%) Query: 43 LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAV 102 LL++++ FSF SP F V NL++ILQ +++N ++A+ T VII+ GIDLSVG AV Sbjct: 30 LLIIVVTFSFLSPVFFTVPNLLNILQQSSINALIALGMTLVIISGGIDLSVGPTAALSAV 89 Query: 103 MAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLSLVI 162 + G L G+P+P+ I A + GAL G SGM++A + PFI TLG + L + ++L+ Sbjct: 90 L-GATLMVAGVPVPVAILATLGIGALCGVFSGMLVAYAGLQPFIVTLGGLSLFRAIALIY 148 Query: 163 SGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYTF 222 +G P++ E F +I + G IP ++I+ ++A+ +++NKT G Y Sbjct: 149 TGGNPVFGIPME-FRSIINSDVFG-------IPTPIIIVAVIALVLWLVMNKTPLGEYIL 200 Query: 223 ALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIAA 282 A+G NEEA R++GV V KV V+ SG + +A LI+ RL +A+P +G +ELDAIAA Sbjct: 201 AVGGNEEAARVAGVPVKRTKVTVFIISGTLASLASLILIGRLGAAEPTIGNLWELDAIAA 260 Query: 283 VVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDILR 342 IGG SL GG G+I+GTIIGA I+ L NGL ++++ +Q + TG+III+A+ +D Sbjct: 261 AAIGGASLMGGKGSIVGTIIGAIILGALRNGLTLLNIQAFYQLLATGLIIIIAMLIDRAT 320 Query: 343 RRR 345 R R Sbjct: 321 RGR 323 Lambda K H 0.326 0.139 0.398 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: 242 Number of extensions: 14 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: 347 Length of database: 323 Length adjustment: 28 Effective length of query: 319 Effective length of database: 295 Effective search space: 94105 Effective search space used: 94105 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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