Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_017178050.1 A1QA_RS0106175 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000295095.1:WP_017178050.1 Length = 375 Score = 305 bits (780), Expect = 2e-87 Identities = 173/345 (50%), Positives = 218/345 (63%), Gaps = 16/345 (4%) Query: 22 IDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFIDGERVNDVPPSKRGIAMVF 81 ++L+I +GEF+V VGPSGCGKST LRM+AGLE++ G + I V DV P R IAMVF Sbjct: 24 LNLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNSGRILIGDRDVTDVQPKDRDIAMVF 83 Query: 82 QSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQLTPYLDRLPKALSGGQRQR 141 Q+YALYPHM+V+DNM F ++IA KEEID+RVR AA +L LT YLDR PKALSGGQRQR Sbjct: 84 QNYALYPHMSVHDNMGFALKIAGTPKEEIDKRVREAAKILGLTEYLDRKPKALSGGQRQR 143 Query: 142 VAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSERMSDTTMIYVTHDQVEAMTL 201 VA+GRAI R PKVFL DEPLSNLDA LRV TR +IA L + TT +YVTHDQ EA+T+ Sbjct: 144 VAMGRAIVRKPKVFLMDEPLSNLDAKLRVQTRTQIASLQRSLGVTT-VYVTHDQTEALTM 202 Query: 202 ADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNVIPATITATGQQTAVSLAGG 261 DRI VL G ++QVG P E+Y++PAN FVA FIGSPAMN+ T +G ++ A Sbjct: 203 GDRIAVLKDGLLQQVGTPREMYDKPANEFVAGFIGSPAMNL--GHFTVSGDVASIGSAKI 260 Query: 262 KSVTLDVPTNASENGKTASFGVRPEDLRVTEA-DDFLFEGTVSIVEALGEVTLLYIEGL- 319 + + E+G + G RPE L V A D+ VS VE LG +Y E + Sbjct: 261 QLSRATLDAIKPEDGGKVAIGFRPESLEVVSASDEHSIPVRVSFVEELGSDAYIYGELVG 320 Query: 320 -----------VENEPIIAKMPGIARVGRGDKVRFTADKAKLHLF 353 ++ II ++P G G+ V + H+F Sbjct: 321 AEGSEDKLGSGEDSSQIIVRVPPRTAPGAGETVYVRIKPGQEHIF 365 Lambda K H 0.320 0.137 0.387 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: 358 Number of extensions: 16 Number of successful extensions: 3 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: 362 Length of database: 375 Length adjustment: 30 Effective length of query: 332 Effective length of database: 345 Effective search space: 114540 Effective search space used: 114540 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 24 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