Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_054557498.1 I595_RS00860 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_001306415.1:WP_054557498.1 Length = 219 Score = 132 bits (333), Expect = 7e-36 Identities = 75/220 (34%), Positives = 126/220 (57%), Gaps = 10/220 (4%) Query: 17 LVQLAGIRKCFDGKEVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGR--- 73 ++ I+K + +V+ + ++I GE ++++GPSG GKTT+L+L+ L+T + + Sbjct: 1 MITATNIKKNYGDLKVLKGVSISIKKGEVISIVGPSGAGKTTLLQLVGTLDTPSNPKDSS 60 Query: 74 IMLDNEDITHVPAE------NRYVNTVFQSYALFPHMTVFENVAFGLRMQKTPAAEITPR 127 IM++ D+T + + N + +FQ + L P T ENV ++KTP A+ R Sbjct: 61 IMINGVDVTDLRDKQLAKFRNENIGFIFQFHQLLPEFTALENVCIPAFIKKTPKAKAEVR 120 Query: 128 VMEALRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQ 187 E L + L +P +LSGG+QQRVA+ARA++N P ++ DE LD + + + Sbjct: 121 GRELLDFLGLSQRYDHRPRELSGGEQQRVAVARALINNPSVIFADEPSGNLDSESAENLH 180 Query: 188 NELKALQRKLGITFVFVTHDQEEALTMSDRIVVMRDGRIE 227 L+ + G TFV VTH++E A M+DR ++M DG+I+ Sbjct: 181 QLFFKLREEFGQTFVIVTHNKELA-NMADRKLIMVDGQIQ 219 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: 191 Number of extensions: 8 Number of successful extensions: 3 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: 219 Length adjustment: 26 Effective length of query: 352 Effective length of database: 193 Effective search space: 67936 Effective search space used: 67936 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: 47 (22.7 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