Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 199 bits (507), Expect = 7e-56 Identities = 114/320 (35%), Positives = 190/320 (59%), Gaps = 17/320 (5%) Query: 4 IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 I ++ ++K F K + AL ++N+ I +G+ +LGPSG+GKTT +RIIAGL+ P G + Sbjct: 3 IEIQGINKFFDKFQ--ALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIR 60 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNM----KMSKEEIRK 119 F + V + DR++G VFQ +AL+ ++T EN+AF L + + K EIRK Sbjct: 61 FSGKDVTD-----LHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRK 115 Query: 120 RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSA 179 RV+++ +++ + H+ + +P +LSGGQ+QR+ALARA+ P +LLLDEPF LDA++R Sbjct: 116 RVKDLLEMVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDL 175 Query: 180 RALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVAS 239 R ++ + L T + V+HD + ++D+V V+ G++ QV P +LY P S V Sbjct: 176 RRWLRSLHDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFE 235 Query: 240 LIGEINELEGKVTNEGVVIGS--LRFPVSVSSDRAIIGIRPEDVKLSKDVIKDDSWILVG 297 +G++N L GK+ + + G +R P +D A + +RP +V+L++ DD+ + Sbjct: 236 FLGQVNVLSGKIRDGVMRQGDAWIRLPEGCENDDAQLYLRPHEVRLTQSA-SDDAHL--- 291 Query: 298 KGKVKVIGYQGGLFRITITP 317 +++ I G RI + P Sbjct: 292 PFRIEAINLIGAEVRIELKP 311 Lambda K H 0.319 0.139 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: 328 Number of extensions: 15 Number of successful extensions: 4 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: 353 Length of database: 362 Length adjustment: 29 Effective length of query: 324 Effective length of database: 333 Effective search space: 107892 Effective search space used: 107892 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