Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 255 bits (651), Expect = 2e-72 Identities = 135/292 (46%), Positives = 191/292 (65%), Gaps = 12/292 (4%) Query: 4 VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63 +RL V K F T + ++ L+++ GEF+ +LGPSGCGKTT LR++AG E PS G+I + Sbjct: 8 IRLEHVAKEFDGETVLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEIILD 67 Query: 64 DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123 + + D VPP R + VFQSYAL+PHM+V+DN+AF L++ +P+ EI +RV + Sbjct: 68 GRSMRD------VPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKA 121 Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183 ++GL R+P LSGGQ+QRVA+ RA+V +P V L+DEPLS LD KLRV+MR ELK Sbjct: 122 LRMVGLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELK 181 Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243 +L+R++G+T I+VTHDQ EA +M DR+ VMN G + QVG+P EVY++P N FVA F+G Sbjct: 182 QLRREMGITFIFVTHDQEEAFSMSDRVVVMNEGCVAQVGTPVEVYEQPVNMFVARFVGE- 240 Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLGELGY-VGREVIFGIRPEDL 294 N + + G D G + + E+ G+ G + +RPEDL Sbjct: 241 -TNVFEGVA---GQSDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPEDL 288 Lambda K H 0.323 0.142 0.406 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: 386 Number of extensions: 24 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: 372 Length of database: 370 Length adjustment: 30 Effective length of query: 342 Effective length of database: 340 Effective search space: 116280 Effective search space used: 116280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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