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_011382978.1 AMB_RS02755 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000009985.1:WP_011382978.1 Length = 553 Score = 140 bits (352), Expect = 1e-37 Identities = 83/233 (35%), Positives = 134/233 (57%), Gaps = 13/233 (5%) Query: 4 LKLDNIYKRYPNAKH--YSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGN 61 ++ + K YP K V+ F+L +H EFI +G SGCGKST L M AGL D++EG Sbjct: 293 VEFSRVKKIYPTPKGPLTVVDGFDLKMHQGEFISLIGHSGCGKSTVLTMTAGLTDVSEGG 352 Query: 62 LYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA- 120 + +D + +++A P D A+VFQ +L+P ++ +N+A G+ R Y +R+ + Sbjct: 353 VILDGREVSEAGP---DRAVVFQAPSLFPWLTALQNVALGVD-RVYPHASPAERLDIVSY 408 Query: 121 --EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178 E +GL + +++K +D+S G RQRV + RA K+ L+DEP LD+ R ++ + Sbjct: 409 YLERVGLGDSMDKKASDMSNGMRQRVGIARAFALSPKLLLLDEPFGMLDSLTRWELQEVL 468 Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQ 231 ++ R T I VTHD EA+ LAD++V+M+ PN IG++ + P+ Sbjct: 469 MEVWTRTRVTAICVTHDVDEAILLADKVVMMTNGPN----ARIGKVLNVDIPR 517 Score = 120 bits (302), Expect = 7e-32 Identities = 78/215 (36%), Positives = 122/215 (56%), Gaps = 7/215 (3%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M L+L + K Y + + + +L+I D EFI +G SG GK+T + ++AGL G Sbjct: 1 MPILELKGVAKSYGASS--VLRDIDLEIEDGEFIAILGFSGSGKTTLVSLMAGLIKPDAG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLK--LRKYKKDDINKRVHE 118 + + K + D DR + VFQ+Y+L P ++V N+A + + K + RV + Sbjct: 59 EVLLRGKPV-DGPGADRGV--VFQSYSLMPWLTVEGNIALAVDAVMPDASKAERKARVAK 115 Query: 119 AAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178 ++GL+ ER+P++LSGG RQRVA+ RA+ + L+DEPLS LDA R ++ EI Sbjct: 116 YIGMVGLSHAAERRPSELSGGMRQRVAVARALAMSPDILLLDEPLSALDALTRAKLQDEI 175 Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATP 213 I + T I +T+D EA+ LADRI+ ++ P Sbjct: 176 EAIWEQEKKTVILITNDVDEALLLADRIIPLNPGP 210 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: 466 Number of extensions: 24 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 553 Length adjustment: 33 Effective length of query: 344 Effective length of database: 520 Effective search space: 178880 Effective search space used: 178880 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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