Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate RR42_RS12250 RR42_RS12250 sulfate ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >FitnessBrowser__Cup4G11:RR42_RS12250 Length = 374 Score = 218 bits (554), Expect = 3e-61 Identities = 125/312 (40%), Positives = 184/312 (58%), Gaps = 12/312 (3%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELD 63 +++KN+QK F F + + L+ ++ + +GPSGCGK+TLLR+IAGLE AG I L+ Sbjct: 3 IQVKNVQKHFGNFVALDDVTLDFDEGQLTALLGPSGCGKTTLLRIIAGLERADAGQILLE 62 Query: 64 GRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAG----VNKAEVEKKVNEAAR 119 GRD + +R + VFQ YAL+ HM+V +N++F L + +A++ KV Sbjct: 63 GRDASHQHVRQRQVGFVFQHYALFKHMTVFENVAFGLRVKPRAERPGEAQIRDKVRALLE 122 Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179 +++L + +R P QLSGGQRQR+A+ RA+ P++ L DEP LDA +R ++R L RL Sbjct: 123 LVQLDWLADRYPPQLSGGQRQRIALARALAVEPRVLLLDEPFGALDAKVRKELRRWLRRL 182 Query: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239 H EL T ++VTHDQ EA+ +AD+VV++N G +EQ G+P +Y+ PA FV GFLG + Sbjct: 183 HDELHVTSVFVTHDQEEALEVADQVVLMNRGHVEQAGTPEAVYNHPATPFVFGFLG--NV 240 Query: 240 GFLKGKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLA--LPGDCT 297 G++ ER LL G I LP+ G+ G +RP L+L PG Sbjct: 241 NLFHGRLEVGERGG---LLHTGDSI-LPVIGSGHETAGDAVAYVRPHDLDLERYSPGTDG 296 Query: 298 LQVTADVSERLG 309 + VT + LG Sbjct: 297 IAVTLRRALTLG 308 Lambda K H 0.321 0.137 0.390 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: 351 Number of extensions: 18 Number of successful extensions: 2 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: 367 Length of database: 374 Length adjustment: 30 Effective length of query: 337 Effective length of database: 344 Effective search space: 115928 Effective search space used: 115928 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: 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