Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_086512005.1 BZY95_RS21850 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_002151265.1:WP_086512005.1 Length = 372 Score = 264 bits (675), Expect = 3e-75 Identities = 149/321 (46%), Positives = 200/321 (62%), Gaps = 16/321 (4%) Query: 6 KLNKQPSSLSPLVQLAGIRKCFDGKE-VIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIA 64 K N+ PL+ G++K +DG+ V+ L+LTI GEF+TLLGPSG GKTT L ++A Sbjct: 5 KTNESHPHPPPLITFTGVQKTYDGEHLVVKDLNLTIRQGEFVTLLGPSGSGKTTCLMMLA 64 Query: 65 GLETVDSGRIMLDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEI 124 G E SG I L ++ + VP R VFQ+YALFPHMTV EN+ + L+ ++ PAAE Sbjct: 65 GFEVPTSGDIFLRDQRLNSVPPHKRNFGMVFQNYALFPHMTVEENIRYPLKTRRMPAAEA 124 Query: 125 TPRVMEALRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRK 184 +V L M+QL FA+R+P QLSGGQQQRVA+AR++V +P+L+L+DE L ALD +LR+ Sbjct: 125 DRKVAHILDMIQLRDFARRRPTQLSGGQQQRVALARSLVFEPQLVLMDEPLGALDKQLRE 184 Query: 185 QMQNELKALQRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFV 244 QMQ E+K L +LG+T VFVTHDQ EALTMSDR+ V DG I+Q +P +YE P N FV Sbjct: 185 QMQLEIKHLHERLGLTVVFVTHDQSEALTMSDRVAVFNDGVIQQIDSPSNLYEHPANAFV 244 Query: 245 AGFIGEINMFNATVIERLDEQRVRANVEGRECNIYVNFAVEPGQKLHVLLRPED-----L 299 A FIGE N T+ R+ +VEGR C + G + L D + Sbjct: 245 AQFIGE----NNTLAGRIQ------SVEGRHCRVSFGDGCSTGALIGTGLAVGDATRLSI 294 Query: 300 RVEEINDDNHAEGLIGYVRER 320 R E + + A+GL ++ R Sbjct: 295 RPERVKLNGSAQGLPNRLQAR 315 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: 354 Number of extensions: 19 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: 372 Length adjustment: 30 Effective length of query: 348 Effective length of database: 342 Effective search space: 119016 Effective search space used: 119016 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