Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate GFF776 PGA1_c07900 alpha-glucoside transport ATP-binding protein AglK
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__Phaeo:GFF776 Length = 363 Score = 445 bits (1144), Expect = e-129 Identities = 233/360 (64%), Positives = 279/360 (77%), Gaps = 2/360 (0%) Query: 1 MTGLLLKDIRKSYGA-VDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGD 59 M L L ++ K+YG V+V+ I+LDIK+GE +VFVGPSGCGKSTLLRMIAGLE I+GG Sbjct: 1 MANLKLTNVAKTYGGGVEVLRDINLDIKQGELIVFVGPSGCGKSTLLRMIAGLERISGGT 60 Query: 60 MFIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAAD 119 + ID +ND+PP++RGIAMVFQSYALYPHMTV DNMAF ++IA++SK+EID + AA Sbjct: 61 LEIDNAVMNDIPPAQRGIAMVFQSYALYPHMTVRDNMAFALKIAKKSKDEIDAAIDRAAK 120 Query: 120 MLQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKL 179 +LQL PYLDRLPKALSGGQRQRVAIGR+I R+PKV+LFDEPLSNLDAALRVATRIEIA+L Sbjct: 121 ILQLEPYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRIEIAQL 180 Query: 180 SERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPA 239 E M D+TMIYVTHDQVEAMTLA RIVVL+ I QVG PL+LY+RP N FVA+FIGSPA Sbjct: 181 KEAMPDSTMIYVTHDQVEAMTLASRIVVLADKGIAQVGTPLDLYQRPENEFVAQFIGSPA 240 Query: 240 MNVIPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299 MN+IP T+ ATG +T V L G+ V ++PT ++ G + GVRPEDL L + Sbjct: 241 MNLIPGTVVATGPRTTVRLTSGEEVVAEIPTTDADQGLAVNVGVRPEDLVEEGTGGALID 300 Query: 300 GTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNGQS 359 V IVEALGEVT+LYI +P+IAK+PGI + RG VR AD A+LHLF NGQS Sbjct: 301 SRVDIVEALGEVTVLYIAAGEGKDPLIAKLPGIHKGLRGSSVRLYADPARLHLFH-NGQS 359 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: 442 Number of extensions: 19 Number of successful extensions: 1 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: 363 Length adjustment: 29 Effective length of query: 333 Effective length of database: 334 Effective search space: 111222 Effective search space used: 111222 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