Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 281 bits (720), Expect = 2e-80 Identities = 151/328 (46%), Positives = 210/328 (64%), Gaps = 7/328 (2%) Query: 16 PLVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM 75 P V+L G+ K F + + DLTI GE +TLLGPSGCGKTT+LR+IAGLET G I Sbjct: 43 PAVRLQGLMKRFGKTVAVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIY 102 Query: 76 LDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMV 135 + I P R + +FQ+YALFPH T+FENVAFGL+ + E+ +V +AL MV Sbjct: 103 IKGRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMV 162 Query: 136 QLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQR 195 +L +R QLSGGQQQR+A+ARA+V +P +LL+DE LSALD KLR++M+ E+ +Q+ Sbjct: 163 RLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQ 222 Query: 196 KLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFN 255 +L +T +FVTHDQ EAL+MS++IVVM+DGR +Q+GTP ++Y+ P N FVA F+G N F+ Sbjct: 223 QLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGHANFFD 282 Query: 256 ATVIERLDEQRVRANV-EGRECNIYVNFAVEPGQKLHVLLRPEDLRV------EEINDDN 308 A V+E LD +VR + EG E GQ +H+++R + + V +E + Sbjct: 283 ARVLEVLDNDQVRVRIAEGLEFTADHVGRWRQGQDVHLVMRAQKINVTSPDLADEELEST 342 Query: 309 HAEGLIGYVRERNYKGMTLESVVELENG 336 G + +R+Y G VEL NG Sbjct: 343 DLNYYPGKIYDRSYMGGETSYFVELANG 370 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: 391 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: 378 Length of database: 406 Length adjustment: 31 Effective length of query: 347 Effective length of database: 375 Effective search space: 130125 Effective search space used: 130125 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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