Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate 208681 DVU3161 ABC transporter, ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >MicrobesOnline__882:208681 Length = 349 Score = 235 bits (599), Expect = 2e-66 Identities = 124/269 (46%), Positives = 174/269 (64%), Gaps = 7/269 (2%) Query: 33 IPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDITHVPAENRYVN 92 + + + G+ L LLGPSGCGK+T LRLIAGLE+V SGRI++ D+T++P R + Sbjct: 19 VDDVSFEVEQGDMLVLLGPSGCGKSTTLRLIAGLESVTSGRILIGGRDVTNLPPAQRQLA 78 Query: 93 TVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPHQLSGGQ 152 VFQSYALFPH+TV +N+ FGL ++K PAAE R+ A+ ++ L +RKP +LSGGQ Sbjct: 79 MVFQSYALFPHLTVRDNILFGLVVRKVPAAERQKRLDRAVEILGLGKLLERKPGELSGGQ 138 Query: 153 QQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTHDQEEAL 212 QQRVA+ RA+V + + L+DE LS LD KLR++M+ E++ALQ+ LG+T V+VTHDQ EA+ Sbjct: 139 QQRVALGRALVAEAAVCLMDEPLSNLDAKLRQEMRREIRALQQTLGMTMVYVTHDQTEAM 198 Query: 213 TMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNATVIERLDEQRVRANVE 272 +M+DRI++M+ GRI Q+ TP E+Y P F FIG M + D RV + Sbjct: 199 SMADRIILMQGGRIVQNATPTEMYSRPATAFAGSFIGTPPMNLVRLQGNDDGIRVAGSRS 258 Query: 273 GRECNIYVNFAVEPGQKLHVLLRPEDLRV 301 GR G + +RPE +R+ Sbjct: 259 GR-------VTCHAGADCMLGIRPEHIRI 280 Lambda K H 0.319 0.136 0.385 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: 283 Number of extensions: 7 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: 378 Length of database: 349 Length adjustment: 29 Effective length of query: 349 Effective length of database: 320 Effective search space: 111680 Effective search space used: 111680 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 (21.7 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