Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate GFF2490 PS417_12700 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__WCS417:GFF2490 Length = 367 Score = 340 bits (871), Expect = 5e-98 Identities = 178/358 (49%), Positives = 239/358 (66%), Gaps = 3/358 (0%) Query: 1 MTGLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDM 60 M L +K+++K + +I GIDL++ + EFVVFVGPSGCGKSTLLR+IAGLEE++ G + Sbjct: 1 MANLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTI 60 Query: 61 FIDGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADM 120 +DG + +V P+KR +AMVFQ+YALYPHM+V NM+F + +A K+ ++ +V AA + Sbjct: 61 ELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARI 120 Query: 121 LQLTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLS 180 L+L P L+R PK LSGGQRQRVAIGRAI RNPK+FLFDEPLSNLDAALRV R+E+A+L Sbjct: 121 LELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 Query: 181 ERMSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAM 240 + + TMIYVTHDQVEAMTLAD++VVL++G IEQVG+PLELY +PANLFVA F+G+P M Sbjct: 181 KEL-QATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239 Query: 241 NVIPATITATGQQTA-VSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTEADDFLFE 299 + +T Q+ V L G + L + G + G+RPE L + Sbjct: 240 GFLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQTTLT 299 Query: 300 GTVSIVEALGEVTLLYIEGLVENEPIIAKMPGIARVGRGDKVRFTADKAKLHLFDTNG 357 T + E LG T ++ EP+ ++ G G+ + D A HLFDT+G Sbjct: 300 VTADVGERLGSDTFCHVI-TANGEPLTMRIRGDMASQYGETLHLHLDPAHCHLFDTDG 356 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: 375 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: 367 Length adjustment: 29 Effective length of query: 333 Effective length of database: 338 Effective search space: 112554 Effective search space used: 112554 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