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_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 219 bits (559), Expect = 8e-62 Identities = 140/362 (38%), Positives = 211/362 (58%), Gaps = 28/362 (7%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 ++ + I KR+ + +VE+ +L IH EF +G SGCGK+T LRM+AG E T G + Sbjct: 23 IRFEGISKRFGDFT--AVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRIL 80 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 ID + + + P +R + M+FQ+YAL+PHMSV +N+AFGLK K I +V A E++ Sbjct: 81 IDGQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELV 140 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 + F RKP LSGGQRQRVA+ R + ++ KV L+DEPL+ LD KLR A + E+ I Sbjct: 141 QMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQD 200 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 R+G T + VTHDQ EAMT++ RI +M+A G IEQ+G+P ++Y P +FVA Sbjct: 201 RVGITFVMVTHDQGEAMTMSSRIGVMNA----------GCIEQVGSPVDIYEYPGTRFVA 250 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKI-LEEKGYL--GKKVTLGIRPEDI 300 FIG A N F+ +V + L++A P+ + + + E G + G VT+ +RPE + Sbjct: 251 DFIG--AANMFQGSVRG----GEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKV 304 Query: 301 SSDQIVHETFPNASVTADILVSEL--LGSESMLYVKFGSTEFTARVNARDSHSPGEKVQL 358 I + + A+ +VS++ LG S+ +V+ S + H GE+ +L Sbjct: 305 ---MIARDKPASGLNWAEGVVSDIAYLGDVSIYHVRLASGRKIQALRTNLHH--GEESRL 359 Query: 359 TF 360 T+ Sbjct: 360 TW 361 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: 315 Number of extensions: 13 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: 379 Length adjustment: 30 Effective length of query: 347 Effective length of database: 349 Effective search space: 121103 Effective search space used: 121103 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 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