Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_010960192.1 MCA_RS04295 polyamine ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_000008325.1:WP_010960192.1 Length = 385 Score = 374 bits (959), Expect = e-108 Identities = 199/359 (55%), Positives = 247/359 (68%), Gaps = 4/359 (1%) Query: 15 SPLVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRI 74 S + + K + + +L + GE LTLLGPSGCGKTTVLRL+AGLE DSG I Sbjct: 24 STIASFRAVSKHYGSHCALRDFNLELREGELLTLLGPSGCGKTTVLRLLAGLEIPDSGEI 83 Query: 75 MLDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRM 134 LD + VP E R VNTVFQSYALFPH++V ENVAFGLRM+K +AEI R EALRM Sbjct: 84 FLDGRTLAGVPPEARNVNTVFQSYALFPHLSVAENVAFGLRMKKLGSAEIRARTAEALRM 143 Query: 135 VQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQ 194 V+L+ +P QLSGGQQQRVA+ARA+VN+PR+LLLDE LSALDY+LR++MQ ELK LQ Sbjct: 144 VRLDGLGGHRPLQLSGGQQQRVALARALVNRPRVLLLDECLSALDYQLRREMQLELKGLQ 203 Query: 195 RKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEINMF 254 R+ GITFVFVTHD+EEAL+MSDRI VMR GRIEQ G PR+IYE P NLFVA F GE N+ Sbjct: 204 RQTGITFVFVTHDREEALSMSDRIAVMRTGRIEQLGPPRDIYERPANLFVAQFAGESNVL 263 Query: 255 NATVIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPEDLRVEEINDDNHAE-GL 313 ATV + + G + + G +L ++LRPEDL V +DD AE GL Sbjct: 264 EATVTAITAPDSLIVELAGTPLTVRTDRRFRVGARLVLVLRPEDLHV---HDDAAAEGGL 320 Query: 314 IGYVRERNYKGMTLESVVELENGKMVMVSEFFNEDDPDFDHSLDQKMAINWVESWEVVL 372 G+V ER Y+G+TL++V+ L+ G + SEFF ED P DH Q++ ++W WE+VL Sbjct: 321 AGHVLERTYRGVTLDTVIALDAGPRIKTSEFFREDTPALDHPPGQRVRVSWTPGWEIVL 379 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: 382 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: 385 Length adjustment: 30 Effective length of query: 348 Effective length of database: 355 Effective search space: 123540 Effective search space used: 123540 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 Sep 24 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