Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate HSERO_RS02210 HSERO_RS02210 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__HerbieS:HSERO_RS02210 Length = 372 Score = 361 bits (927), Expect = e-104 Identities = 196/360 (54%), Positives = 248/360 (68%), Gaps = 3/360 (0%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M + ++++ K Y +V+ I+L+I++GEFVVFVGPSGCGKSTLLRMIAGLEEI+ GD+ Sbjct: 1 MAAVSIRNLAKRYDDNEVMRDINLEIEDGEFVVFVGPSGCGKSTLLRMIAGLEEISDGDL 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 I R+N+VP SKRG+AMVFQSYALYPHM++YDNMAFG++IA +SK EID V+ AA + Sbjct: 61 DIGARRMNEVPASKRGVAMVFQSYALYPHMSLYDNMAFGLKIAGKSKAEIDAAVQHAAKI 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L + LDR P+ALSGGQRQRVAIGRAI R P VFLFDEPLSNLDAALRV R+E AKL Sbjct: 121 LHIDHLLDRKPRALSGGQRQRVAIGRAITRQPSVFLFDEPLSNLDAALRVKMRLEFAKLH 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 + + TTMIYVTHDQ+EAMTLAD+IVVLS G IEQVG+P +LY PAN FVA FIGSP M Sbjct: 181 DDLK-TTMIYVTHDQIEAMTLADKIVVLSEGRIEQVGSPQQLYHHPANRFVAGFIGSPKM 239 Query: 241 NVIPATITA-TGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299 N I T+ A V L GG V + + G+ + GVRPE L + + L + Sbjct: 240 NFIDGTVAAIQADGVQVQLPGGGLQWAAVDGSTLQVGQKVTLGVRPEHLNIAQGQAAL-Q 298 Query: 300 GTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQS 359 + +E LG+ + LY + +I ++P G + AD A+ HLF +GQ+ Sbjct: 299 ARCTALELLGDFSYLYAAYEGSEDALILRVPDSLDAPHGSVLPLAADPARCHLFGADGQA 358 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: 391 Number of extensions: 13 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: 372 Length adjustment: 30 Effective length of query: 332 Effective length of database: 342 Effective search space: 113544 Effective search space used: 113544 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