Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate BPHYT_RS22760 BPHYT_RS22760 sugar ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__BFirm:BPHYT_RS22760 Length = 384 Score = 355 bits (912), Expect = e-103 Identities = 190/372 (51%), Positives = 254/372 (68%), Gaps = 16/372 (4%) Query: 1 MTGLLLKDIRKSYG-AVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59 M + L+ ++K+YG VI +DL+I E EF VF+GPSGCGKSTLLRMIAGLE++T GD Sbjct: 1 MASISLRGVQKAYGEGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60 Query: 60 MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119 + I G+ +NDVP ++RG+AMVFQSYAL+PHM+V++NMAFG+++A+ K+E+DR+VR AA Sbjct: 61 LSIGGKLMNDVPAAQRGVAMVFQSYALFPHMSVFENMAFGLKLAKTPKDEVDRKVREAAR 120 Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179 +LQL L+R PKALSGGQRQRVAIGRAI R P VFLFDEPLSNLDA LR TRIEIA+L Sbjct: 121 ILQLEALLERKPKALSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDATLRGQTRIEIARL 180 Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSA-------GHIEQVGAPLELYERPANLFVA 232 ++ + +++YVTHDQ+EAMTLAD+IV+L A G I Q+GAPLELY RP + FVA Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPKSRFVA 240 Query: 233 RFIGSPAMNVIPATITATGQQTAVSLAGGKSVTLDVPTNAS--ENGKTASFGVRPEDLRV 290 FIGSP MN +P + + Q T+ VP N + + + + GVRPE L Sbjct: 241 GFIGSPRMNFLPGRVASLDAQGVTITLDHTQETVRVPVNGAGLQTSQAVTLGVRPEHLEF 300 Query: 291 TE-----ADDFLFEGTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTA 345 + DD + TVS+VE LGE + ++++ ++AK PG R+ G++ Sbjct: 301 VDPSSVAPDDAVLTRTVSLVEQLGEHSYVHLD-QPGGAALVAKAPGNTRLAPGERASLRV 359 Query: 346 DKAKLHLFDTNG 357 +A HLF +G Sbjct: 360 PRAACHLFTEDG 371 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: 392 Number of extensions: 17 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: 384 Length adjustment: 30 Effective length of query: 332 Effective length of database: 354 Effective search space: 117528 Effective search space used: 117528 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: 50 (23.9 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