Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 213 bits (542), Expect = 7e-60 Identities = 127/303 (41%), Positives = 181/303 (59%), Gaps = 23/303 (7%) Query: 20 LHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVA 79 LH ++L I DG+ LLGPSG GK+T+LR+IAGLE G +R G V DL R+R V Sbjct: 18 LHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRFSGKDVTDLHVRDRRVG 77 Query: 80 MVFQNYALYPHMSVYDNIAFGLR---RLKRPAA-EIDRRVREVAALLNLEALLERKPRAM 135 VFQ+YAL+ HM+V +N+AFGL R +RP EI +RV+++ ++ LE L +R P + Sbjct: 78 FVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLLEMVQLEHLADRYPAQL 137 Query: 136 SGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQ 195 SGGQ+QR A+ARA+ P + L DEP LDAK+R LR ++ LH L T+V+VTHDQ Sbjct: 138 SGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRSLHDELHFTSVFVTHDQ 197 Query: 196 LEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLF 255 EA+ L+D+V++M +GRI Q +P ELY P + F F+G +N LSG + +DG + Sbjct: 198 EEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLG--QVNVLSGKI--RDGVM- 252 Query: 256 IETAHQRWALTGERFSRLRHAMA---VKLAVRPDHVRIAGEREPAASLTCPVSVELVEIL 312 G+ + RL +L +RP VR+ A L P +E + ++ Sbjct: 253 ---------RQGDAWIRLPEGCENDDAQLYLRPHEVRLTQSASDDAHL--PFRIEAINLI 301 Query: 313 GAD 315 GA+ Sbjct: 302 GAE 304 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: 364 Number of extensions: 11 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: 406 Length of database: 362 Length adjustment: 30 Effective length of query: 376 Effective length of database: 332 Effective search space: 124832 Effective search space used: 124832 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