Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate WP_028312315.1 H566_RS0116635 ABC transporter ATP-binding protein
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >NCBI__GCF_000482785.1:WP_028312315.1 Length = 358 Score = 233 bits (593), Expect = 8e-66 Identities = 140/329 (42%), Positives = 208/329 (63%), Gaps = 17/329 (5%) Query: 4 LKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTIELD 63 L + +L+ + I+KG+ ++++ E + +GPSG GK+TLLR +AGLE+ G I + Sbjct: 7 LTVTDLKLSYGDNPILKGVSMDLHRGEVISLLGPSGSGKTTLLRAVAGLEQPHEGRISIA 66 Query: 64 GRDI------TEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEA 117 G+++ EV +R+L +VFQ+YAL+PH +V N+++ L L + A ++ +V++A Sbjct: 67 GKNVFDGAAGVEVPAEQRNLGLVFQSYALWPHKTVFDNVAYGLKLRKTDSATIKDRVSDA 126 Query: 118 ARILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELA 177 + L LG + ER P QLSGGQ+QRVAI RA+V NP + L DEPLSNLDA LR + R L Sbjct: 127 LKNLGLGHLGERYPHQLSGGQQQRVAIARALVYNPPVILLDEPLSNLDAKLREEARAWLR 186 Query: 178 RLHKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTP 237 L LQ + + VTHDQ EAM ++D++++LNGGRIEQ GSP E+Y +PA+LF AGF+GT Sbjct: 187 ELIVRLQLSALVVTHDQGEAMAMSDRILLLNGGRIEQQGSPTEMYLKPASLFAAGFMGTN 246 Query: 238 KMGFLKGKVTRVERQNC-EVLLDAGTRITLPLS---GANLSIGGAVTLGIRPEHLNLA-L 292 LKG R+E++N ++LLD G + GA ++GG T +R E + LA Sbjct: 247 NT--LKG---RIEQRNADDILLDIGEHKLWGRACGQGAPATVGGEATAVVRVEGVKLADG 301 Query: 293 PGDCTLQVTADVSERLGSDTFCHVLTASG 321 PG + + S LG D + +VL ++G Sbjct: 302 PGPNRMPMDLVTSMYLG-DRWEYVLDSAG 329 Lambda K H 0.321 0.137 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: 325 Number of extensions: 9 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: 367 Length of database: 358 Length adjustment: 29 Effective length of query: 338 Effective length of database: 329 Effective search space: 111202 Effective search space used: 111202 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