Align spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein
Query= CharProtDB::CH_024626 (378 letters) >NCBI__GCF_000526715.1:WP_024851725.1 Length = 282 Score = 151 bits (382), Expect = 2e-41 Identities = 90/221 (40%), Positives = 136/221 (61%), Gaps = 16/221 (7%) Query: 20 LAGIRKCFDGK----EVIPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIM 75 ++G+ K F K EV+ +DLT+ EF+ L+G SGCGK+T+LR+I GLE + G+++ Sbjct: 7 ISGLNKTFITKKGAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKGQVL 66 Query: 76 LDNEDITHVPAENRYVNTVFQSYALFPHMTVFENVAFGLRMQKT-------PAAEITPRV 128 +D E+I + P ++R + VFQ Y+L+P +TV EN+ F ++ + R Sbjct: 67 VD-EEIVNKPGKDRAM--VFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMVDRS 123 Query: 129 MEALRMVQLETFAQRKPHQLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQN 188 L ++ LE P+QLSGG +QRVAIARA+++KP +LL+DE ALD + R+ M + Sbjct: 124 YALLDLMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREVMHD 183 Query: 189 ELKALQRKLGITFVFVTHDQEEALTMSDRIVVM--RDGRIE 227 + L T VFVTHD EEA+ ++DR+VVM GRI+ Sbjct: 184 LILHLFEIEKSTIVFVTHDVEEAIYLADRVVVMAPNPGRID 224 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: 232 Number of extensions: 13 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: 282 Length adjustment: 28 Effective length of query: 350 Effective length of database: 254 Effective search space: 88900 Effective search space used: 88900 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: 48 (23.1 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