Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate WP_008510542.1 BIBO1_RS17490 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >NCBI__GCF_000182725.1:WP_008510542.1 Length = 333 Score = 345 bits (884), Expect = 1e-99 Identities = 197/366 (53%), Positives = 242/366 (66%), Gaps = 38/366 (10%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M L LK + K YGA +V+ I+L++ +GEF++FVGPSGCGKSTLLR IAGLE+++ G + Sbjct: 1 MGSLQLKSVHKRYGAQEVLKDINLEVNDGEFIIFVGPSGCGKSTLLRSIAGLEDVSAGQV 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 I+GE V PPS+RGIAMVFQSYALYPH+TV NM G++ A K+EI+ RV A+ M Sbjct: 61 LINGEDVTVTPPSRRGIAMVFQSYALYPHLTVKANMGLGLKQAGAPKDEIEGRVAKASAM 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L L PYL R P LSGGQRQRVAIGRA+ RNP++FLFDEPLSNLDAALRV TR+EIAKL Sbjct: 121 LALEPYLARRPAELSGGQRQRVAIGRALVRNPELFLFDEPLSNLDAALRVQTRLEIAKLH 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 + TMIYVTHDQVEAMTLADRIVVL+AG IEQ+G+P+ELY RP NLFVA FIGSP M Sbjct: 181 RELK-ATMIYVTHDQVEAMTLADRIVVLNAGRIEQIGSPMELYNRPDNLFVAGFIGSPQM 239 Query: 241 NVIPAT-ITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299 N I A I ATG +T G+RPE L V+ + ++ Sbjct: 240 NFIEAARIGATGART--------------------------IGIRPEHLSVSR-ESGTWK 272 Query: 300 GTVSIVEALGEVTLLYIE----GLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDT 355 G V E LG T+LY+E GLV A++ G D + T ++ K H FD Sbjct: 273 GKVIHAEHLGADTILYVETETAGLV-----TARLFGEQHYNEDDVIFLTPEEGKTHYFDE 327 Query: 356 NGQSYR 361 G++ R Sbjct: 328 AGKAIR 333 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: 356 Number of extensions: 14 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: 362 Length of database: 333 Length adjustment: 29 Effective length of query: 333 Effective length of database: 304 Effective search space: 101232 Effective search space used: 101232 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