Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 7023651 Shewana3_0880 ABC transporter related (RefSeq)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__ANA3:7023651 Length = 241 Score = 149 bits (376), Expect = 8e-41 Identities = 89/237 (37%), Positives = 137/237 (57%), Gaps = 7/237 (2%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 + +T + K+YGD VL IN I+QGE++ +GPSG GKST LR I LEK T G +EI+ Sbjct: 2 INITNLHKSYGDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLEKPTQGDIEIE 61 Query: 64 GTVVND----VPPAQRGIAMVFQSYALYPHMTVRENMSFA-LKIAKKSQAEIDAAVEAAA 118 G + V ++ + MVFQ++ L+PH TV +N++ A + + +QAE D A Sbjct: 62 GQSITAKDACVDKLRQKVGMVFQNFNLFPHKTVLQNITLAPVSLKLMTQAEADNKALALL 121 Query: 119 EKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQ 178 ++ L + P +LSGGQ+QRVAI R++ +P + LFDEP S LD + V L++ + Sbjct: 122 TQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPEM-VGDVLDVMK 180 Query: 179 LKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235 A TMV VTH+ A ++ R++ + GG + + P EL+ +P+ F+ Sbjct: 181 -DLAQKGMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEELFTRPKEARTQSFL 236 Lambda K H 0.316 0.135 0.379 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: 219 Number of extensions: 9 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: 373 Length of database: 241 Length adjustment: 27 Effective length of query: 346 Effective length of database: 214 Effective search space: 74044 Effective search space used: 74044 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 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