Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 231 bits (590), Expect = 2e-65 Identities = 140/349 (40%), Positives = 200/349 (57%), Gaps = 18/349 (5%) Query: 4 LELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGAIL 63 +ELRNV K +G + NI L I G+ + L+GPSGCGK+T++ +AGLE S G I Sbjct: 7 VELRNVTKRFGSNT--VIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIF 64 Query: 64 VDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVSKLL 123 +D D++ S + RDI MVFQSYAL+P MS+ +N+ +GLK+ +P AE+ V ++ Sbjct: 65 IDGEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMV 124 Query: 124 QIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 +E R Q+SGGQQQRVA+ RAL +PK+ LFDEPLSNLDA LR MR +++ + + Sbjct: 125 DLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQK 184 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPPMNF 243 + T++YVTHDQ EA + D V VM G I Q G+P+D+Y PA+ F+ASF+G N Sbjct: 185 QFDITSLYVTHDQSEAFAVSDTVLVMNKGHIMQIGSPQDLYRQPASRFMASFMGD--ANL 242 Query: 244 IPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANGLPT 303 P DG +D PL G E ++G+RPE I L++ G + Sbjct: 243 FPATF--SDG----YVDIYGYHLPRPLHFGTQG----EGMVGVRPEAITLSD---RGEES 289 Query: 304 IRAEVQVTEPTGPDTLVFVNLNDTKVCCRL-APDVAPAVGETLTLQFDP 351 R ++ GP V V + ++ ++ A + P VGE L+ P Sbjct: 290 QRCVIRHVAYMGPQYEVTVEWHGQEILLQVNATRLQPDVGEQYYLEIHP 338 Lambda K H 0.319 0.138 0.393 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: 342 Number of extensions: 13 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: 386 Length of database: 348 Length adjustment: 30 Effective length of query: 356 Effective length of database: 318 Effective search space: 113208 Effective search space used: 113208 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 (21.7 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