Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 224 bits (571), Expect = 3e-63 Identities = 120/291 (41%), Positives = 181/291 (62%), Gaps = 11/291 (3%) Query: 4 SLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEG 63 S++I GINK F K + L +++ + G+ L+GPSG GK+TLL IIAGL+ P EG Sbjct: 2 SIEIQGINKFFDK----FQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEG 57 Query: 64 EIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEM----RKMPKPERQKRI 119 IR GK+V + RDR + VFQ YAL+ ++VA+N+ F L + + KPE +KR+ Sbjct: 58 RIRFSGKDVTDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRV 117 Query: 120 DEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRA 179 ++ M+Q+ HL DR P+QLSGGQ+QR+A+ RA+A +P++ L DEP LDAK+R ++R Sbjct: 118 KDLLEMVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRR 177 Query: 180 EIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFI 239 ++ LH TSV+VTHDQ EA+ L ++ VM G ++Q+ TP E+Y RP + +V F+ Sbjct: 178 WLRSLHDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFL 237 Query: 240 GSPTMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETA 290 G +N+L G + G QG A P ++ L +RP + + ++A Sbjct: 238 GQ--VNVLSGKIRDGVMR-QGDAWIRLPEGCENDDAQLYLRPHEVRLTQSA 285 Lambda K H 0.318 0.135 0.388 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: 356 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: 355 Length of database: 362 Length adjustment: 29 Effective length of query: 326 Effective length of database: 333 Effective search space: 108558 Effective search space used: 108558 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