Align ABC transporter for L-Fucose, ATPase component (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= reanno::Smeli:SM_b21106 (365 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 244 bits (623), Expect = 3e-69 Identities = 127/283 (44%), Positives = 184/283 (65%), Gaps = 4/283 (1%) Query: 4 VTLKKLVKRYGALEVVHGIDLEVKDREFIALVGPSGCGKSTTLRMIAGLEEVSGGAIEIG 63 + L+ + K + V+H + L+++ EF+ ++GPSGCGK+T LR++AG E S G I + Sbjct: 8 IRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILD 67 Query: 64 GRKVNDLPPRARNISMVFQSYALYPHMTVAENMGFSLKIAGRPAEEIKTRVAEAAAILDL 123 GR + D+PP R ++ VFQSYAL+PHM+V +N+ F L+++G P EI RVA+A ++ L Sbjct: 68 GRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMVGL 127 Query: 124 AHLLERRPSQLSGGQRQRVAMGRAIVRQPDVFLFDEPLSNLDAKLRTQVRTEIKKLHARM 183 A RRP+ LSGGQ+QRVA+ RA+V +P V L DEPLS LD KLR Q+RTE+K+L M Sbjct: 128 AGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRREM 187 Query: 184 QATMIYVTHDQVEAMTLSDRIVIMRDGHIEQVGTPEDVFRRPATKFVAGFIGSPPMNMEE 243 T I+VTHDQ EA ++SDR+V+M +G + QVGTP +V+ +P FVA F+G + Sbjct: 188 GITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGETNVFEGV 247 Query: 244 AVLTDGKL--AFASGATLPLPPRFRSLVREGQKVTFGLRPDDV 284 A +DG + A G T L + G ++ LRP+D+ Sbjct: 248 AGQSDGGILQALVEGRTCELSS--HRGFQPGDRIRVLLRPEDL 288 Lambda K H 0.320 0.137 0.397 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: 363 Number of extensions: 11 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: 365 Length of database: 370 Length adjustment: 30 Effective length of query: 335 Effective length of database: 340 Effective search space: 113900 Effective search space used: 113900 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 (21.8 bits) S2: 49 (23.5 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