Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 213 bits (541), Expect = 8e-60 Identities = 116/283 (40%), Positives = 169/283 (59%), Gaps = 15/283 (5%) Query: 4 IQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISID 63 I+ I K F L I+L I G+ L+GPSG GK+TLLR +AGLE+ + G I Sbjct: 3 IEIQGINKFFDKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFS 62 Query: 64 GKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKL----KNLAAAEITKRVNEISE 119 GK + D+ ++R + VFQ YAL+ HMTVAEN+ FGL + + EI KRV ++ E Sbjct: 63 GKDVTDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLE 122 Query: 120 LLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIKRL 179 ++Q++HL DR P +LSGGQ+QR+AL RA++ + ++L DEP LDA +R +R ++ L Sbjct: 123 MVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSL 182 Query: 180 HHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSPEM 239 H T ++VTHDQ EA L D++ V+ +G IEQ+ TP E+Y RP + F+ F+G ++ Sbjct: 183 HDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLG--QV 240 Query: 240 NFLEGAVLEKI-----PW---PEARKADQI-LGIRPDAFALNQ 273 N L G + + + W PE + D L +RP L Q Sbjct: 241 NVLSGKIRDGVMRQGDAWIRLPEGCENDDAQLYLRPHEVRLTQ 283 Lambda K H 0.318 0.136 0.383 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: 282 Number of extensions: 9 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: 347 Length of database: 362 Length adjustment: 29 Effective length of query: 318 Effective length of database: 333 Effective search space: 105894 Effective search space used: 105894 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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