Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Keio:15248 Length = 378 Score = 214 bits (546), Expect = 2e-60 Identities = 120/285 (42%), Positives = 174/285 (61%), Gaps = 3/285 (1%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 ++L G+ K + +V+ ++L I GE + +GPSGCGK+T+LR+IAGLE + G + +D Sbjct: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 Query: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123 + VP R + VFQSYAL+PHMTV EN++F L++ K AEI V A +QL Sbjct: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137 Query: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183 + R P LSGGQ+QRVAI R++V P++ L DE LS LD LR + E+ L+ + Sbjct: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197 Query: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243 T V+VTHDQ EA+T++ RIVV+ G I Q G+P E+YE+P+N FVA FIG ++N+ Sbjct: 198 -GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIG--EINMF 254 Query: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDM 288 +I + V GR + Y + G ++V +RPED+ Sbjct: 255 NATVIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDL 299 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: 313 Number of extensions: 11 Number of successful extensions: 2 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: 378 Length adjustment: 30 Effective length of query: 343 Effective length of database: 348 Effective search space: 119364 Effective search space used: 119364 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: 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