Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_234244490.1 BZY95_RS20650 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_002151265.1:WP_234244490.1 Length = 398 Score = 255 bits (652), Expect = 1e-72 Identities = 141/321 (43%), Positives = 208/321 (64%), Gaps = 17/321 (5%) Query: 18 VQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLD 77 ++L + K + + + + GEF+ LLGPSGCGK+T LR+IAGLE +GRI + Sbjct: 7 IRLEAVSKRWGDTAAVDAIGFDVAPGEFVILLGPSGCGKSTTLRMIAGLEQATAGRIEIG 66 Query: 78 NEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQL 137 D+TH+P +R ++ VFQSYALFPH++V +N+ FGLR +K P AE R+ ++V L Sbjct: 67 GRDVTHLPPGDRGISMVFQSYALFPHLSVADNIVFGLRSRKVPKAERRERLARVAQLVDL 126 Query: 138 ETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKL 197 E + +RKP QLSGGQ+QRVA+ARA++++ + L+DE LS LD +LR +M+ E+KALQ++L Sbjct: 127 EAYLERKPAQLSGGQRQRVALARAIISEHPICLMDEPLSNLDARLRGEMRREIKALQQRL 186 Query: 198 GITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMFNAT 257 G+T ++VTHDQ EA++M DR+++M+DGRI QD TP E+YE P + F AGFIG M T Sbjct: 187 GMTVIYVTHDQVEAMSMGDRVILMQDGRIVQDATPSELYERPASAFAAGFIGSPAMNLVT 246 Query: 258 VIERLDEQRVRANVEGR-ECNIYVNFAVEPGQKLHVL-LRPEDLRVEEINDDNHAEGLIG 315 + D A ++G C++ + A K H L LRPE++R+ + A G+ Sbjct: 247 LSAAAD----GAVIDGEPRCSVAPHEA-----KGHWLGLRPEEIRLLPAD----APGVPA 293 Query: 316 YVRERNYKGMTLESVVELENG 336 V + Y G +S+V L+ G Sbjct: 294 EVIDAEYLG--ADSIVRLKVG 312 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: 361 Number of extensions: 14 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: 398 Length adjustment: 30 Effective length of query: 348 Effective length of database: 368 Effective search space: 128064 Effective search space used: 128064 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