Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 223 bits (568), Expect = 7e-63 Identities = 133/367 (36%), Positives = 212/367 (57%), Gaps = 26/367 (7%) Query: 2 TTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGN 61 + ++L+++ K + + + LDI EF+ +GPSGCGK+T LR++AG E + G Sbjct: 6 SVIRLEHVAKEFDGET--VLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGE 63 Query: 62 LYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAE 121 + +D + M D P R + VFQ+YAL+PHMSV++N+AFGL++ K +I +RV +A Sbjct: 64 IILDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALR 123 Query: 122 ILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKI 181 ++GL R+P LSGGQ+QRVA+ RA+V V L+DEPLS LD KLRV MR E+ ++ Sbjct: 124 MVGLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQL 183 Query: 182 HRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKF 241 R +G T I+VTHDQ EA +++DR+V+M+ G + Q+GTP E+Y +P N F Sbjct: 184 RREMGITFIFVTHDQEEAFSMSDRVVVMNE----------GCVAQVGTPVEVYEQPVNMF 233 Query: 242 VAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQE-KILEEKGYL-GKKVTLGIRPED 299 VA F+G N FE + + G+ AL +G+ ++ +G+ G ++ + +RPED Sbjct: 234 VARFVGE--TNVFEGVAGQ----SDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPED 287 Query: 300 ISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGS------TEFTARVNARDSHSPG 353 + ++ E + I+ + GS + V+ S TEF + + G Sbjct: 288 LLVEREEPEDDDKLWLPGRIMETVYKGSTWDMVVQLDSGHEILVTEFFDEDADKMNFQAG 347 Query: 354 EKVQLTF 360 E+V +++ Sbjct: 348 ERVVVSW 354 Lambda K H 0.318 0.135 0.379 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: 331 Number of extensions: 21 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: 377 Length of database: 370 Length adjustment: 30 Effective length of query: 347 Effective length of database: 340 Effective search space: 117980 Effective search space used: 117980 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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