Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate SM_b21375 SM_b21375 sugar uptake ABC transporter permease
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Smeli:SM_b21375 Length = 320 Score = 216 bits (551), Expect = 5e-61 Identities = 122/308 (39%), Positives = 194/308 (62%), Gaps = 11/308 (3%) Query: 40 FASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTF 99 F SL+++ + FSF +P FM V N ++ILQ AV + A T+VI+ IDLSVG+++ Sbjct: 22 FLSLVMLCIVFSFFNPRFMTVVNFMNILQQVAVVAIAAFGMTWVILLGEIDLSVGSIIAV 81 Query: 100 CAVMAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGL- 158 A M G +GM IA + GAL G ++G++ AKL +P FI T+ M + +G+ Sbjct: 82 -AGMVGAQCFAFGMGFAPAIALTLAAGALMGMLNGVLTAKLLLPSFIVTVATMGIYRGMV 140 Query: 159 SLVISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFG 218 SL +G + N+T ++AI +S +G +P + ++ ++ + I+L+KT FG Sbjct: 141 SLPTNGAPAMIENET--WTAIGTESFLG-------LPIIIWVVAVLFVINQIVLSKTSFG 191 Query: 219 RYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELD 278 R + G N EA SG+KVD K+ ++ SG + I+G++++SRL SAQ G YELD Sbjct: 192 RRAYLTGGNREAAVYSGIKVDRLKILIFMISGVMAAISGVLLSSRLFSAQTNAGMSYELD 251 Query: 279 AIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYL 338 AIAA V+GGTSL+GG GT++GT+IGA I+ V+ NG+ ++SV +Q +V G++I++AV+L Sbjct: 252 AIAAAVLGGTSLAGGVGTMVGTLIGALIIGVMNNGMNMLSVPYFYQLIVKGLVILVAVWL 311 Query: 339 DILRRRRR 346 D+ ++ + Sbjct: 312 DVRAKQAK 319 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: 286 Number of extensions: 12 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: 320 Length adjustment: 28 Effective length of query: 319 Effective length of database: 292 Effective search space: 93148 Effective search space used: 93148 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 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