Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF1380 HP15_1347 sulfate/thiosulfate transporter subunit
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Marino:GFF1380 Length = 362 Score = 206 bits (525), Expect = 6e-58 Identities = 119/313 (38%), Positives = 186/313 (59%), Gaps = 14/313 (4%) Query: 3 ALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILI 62 ++EI+ I K + + + L I++ + G+ LLG SG GK+TLL IIAGL P G I Sbjct: 2 SIEIQGINKFFDKFQALHDINLTIPDGQLTALLGPSGSGKTTLLRIIAGLETPEEGRIRF 61 Query: 63 GERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEM----RRVPQAEHDKAVRDTA 118 + V +H +DR + VFQ YAL+ +++VA N+ FGL + R + E K V+D Sbjct: 62 SGKDVTDLHVRDRRVGFVFQHYALFRHMTVAENVAFGLNVLPRKERPGKPEIRKRVKDLL 121 Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 ++Q+E+L DR P+QLSGGQ+QR+A+ RA+ P++ L DEP LDAK+R ++R L+ Sbjct: 122 EMVQLEHLADRYPAQLSGGQKQRIALARAMAMRPEILLLDEPFGALDAKVRKDLRRWLRS 181 Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238 LH L T V+VTHDQ EA+ L+ ++ VM +GRIEQ+ P E+Y RP + +V F+G Sbjct: 182 LHDELHFTSVFVTHDQEEALELSDQVVVMSNGRIEQVDTPLELYGRPDSRFVFEFLGQ-- 239 Query: 239 MNILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLA-AGSEAQRLT 297 +N+L ++ +G+ +G + + LP ++ +RP +RL + S+ L Sbjct: 240 VNVLSGKI-RDGVMRQG-DAWIRLPEGCE-----NDDAQLYLRPHEVRLTQSASDDAHLP 292 Query: 298 ASVEVVELTGPEL 310 +E + L G E+ Sbjct: 293 FRIEAINLIGAEV 305 Lambda K H 0.320 0.136 0.385 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: 354 Number of extensions: 13 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: 360 Length of database: 362 Length adjustment: 29 Effective length of query: 331 Effective length of database: 333 Effective search space: 110223 Effective search space used: 110223 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