Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate HSERO_RS01355 HSERO_RS01355 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__HerbieS:HSERO_RS01355 Length = 381 Score = 360 bits (923), Expect = e-104 Identities = 195/366 (53%), Positives = 249/366 (68%), Gaps = 10/366 (2%) Query: 1 MTGLLLKDIRKSYG-AVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59 M + L+ +K+YG A VI +DLDI E EF VF+GPSGCGKSTLLR IAGLE++T GD Sbjct: 1 MASITLRAAQKAYGDAPPVIRNVDLDIGEHEFCVFLGPSGCGKSTLLRSIAGLEDLTSGD 60 Query: 60 MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119 +FI G+RVNDVP ++R +AMVFQSYAL+PHMTVY+NM+FG+ +A+ K EI+++VR AA Sbjct: 61 LFIGGKRVNDVPSAQRSVAMVFQSYALFPHMTVYENMSFGLTLAKLPKAEIEQKVREAAR 120 Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179 +LQL L R PK LSGGQRQRVAIGRAI R P VFLFDEPLSNLDA LR TRIEIA+L Sbjct: 121 ILQLEELLQRKPKELSGGQRQRVAIGRAIVRRPGVFLFDEPLSNLDATLRSQTRIEIARL 180 Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSA-------GHIEQVGAPLELYERPANLFVA 232 + +++YVTHDQVEAMTLADRIV+L A G I QVG P+ELY P N FVA Sbjct: 181 HRQFEQASVVYVTHDQVEAMTLADRIVLLHAGADTQRFGSIAQVGTPMELYHHPRNRFVA 240 Query: 233 RFIGSPAMNVIPATITATGQQ-TAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVT 291 FIGSP MN +PA + + V L+G + L A + G+ + GVRPE + + Sbjct: 241 GFIGSPRMNFLPAQVAGVQENGILVRLSGSEETLLVAAQGALQPGQMVTVGVRPEHMEIG 300 Query: 292 EADDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLH 351 + V +VE LGE T ++++ +P++AK G AR+ RG++VR A + Sbjct: 301 SQGQYGIHREVVLVERLGEQTYVHLDE-PAGQPLVAKAAGDARITRGERVRVAIAPACAY 359 Query: 352 LFDTNG 357 LFD +G Sbjct: 360 LFDQDG 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: 406 Number of extensions: 16 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: 381 Length adjustment: 30 Effective length of query: 332 Effective length of database: 351 Effective search space: 116532 Effective search space used: 116532 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