Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 217 bits (553), Expect = 4e-61 Identities = 135/341 (39%), Positives = 191/341 (56%), Gaps = 15/341 (4%) Query: 15 GGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPAR 74 G V+ ++L I G+ V LLGPSGCGK+T+LR++AGLE S G + I G V + Sbjct: 17 GSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIFIDGEDVTHRSIQ 76 Query: 75 ERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRA 134 +R++ MVFQ+YAL+PHMS+ +N+ +GL+ L P AE+ RV+E A+++LE +R Sbjct: 77 QRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMVDLEGFEDRFVDQ 136 Query: 135 MSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHD 194 +SGGQQQR A+ARA+I P V LFDEPLSNLDA LR +R I+ L ++ T++YVTHD Sbjct: 137 ISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQKQFDITSLYVTHD 196 Query: 195 QLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQL 254 Q EA ++D V++M G I+Q GSP +LYR P + F A F+G N T DG + Sbjct: 197 QSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGD--ANLFPATF--SDGYV 252 Query: 255 FIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGA 314 I H L F M + VRP+ + ++ E + + V +G Sbjct: 253 DIYGYHLPRPL---HFGTQGEGM---VGVRPEAITLSDRGEESQRCV----IRHVAYMGP 302 Query: 315 DALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVF 355 +T Q + V A RL QP L+ H +F Sbjct: 303 QYEVTVEWHGQEILLQVNATRL-QPDVGEQYYLEIHPYGMF 342 Lambda K H 0.321 0.137 0.403 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: 329 Number of extensions: 8 Number of successful extensions: 1 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: 406 Length of database: 348 Length adjustment: 30 Effective length of query: 376 Effective length of database: 318 Effective search space: 119568 Effective search space used: 119568 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: 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