Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 236 bits (601), Expect = 1e-66 Identities = 146/344 (42%), Positives = 198/344 (57%), Gaps = 23/344 (6%) Query: 4 VRLVDVWKVFGEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIG 63 +R + K FG+ TAV + L + GEF LLG SGCGKTT LRM+AG E P+ G+I I Sbjct: 23 IRFEGISKRFGDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILID 82 Query: 64 DKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREV 123 + V + VPP +R + M+FQSYAL+PHM+V DNIAF LK + + I +V Sbjct: 83 GQDVTE------VPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAA 136 Query: 124 AELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELK 183 EL+ + RKP +LSGGQRQRVAL R + ++P+V L+DEPL+ LD KLR + EL Sbjct: 137 LELVQMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELV 196 Query: 184 KLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGSP 243 +Q ++G+T + VTHDQ EAMTM RI VMN G ++QVGSP ++Y+ P FVA FIG+ Sbjct: 197 NIQDRVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAA 256 Query: 244 PMNFLDAIVTEDGFVDFGEFRLKLLPDQFE---VLGELGYV--GREVIFGIRPEDLYDAM 298 M G V GE L + + E + E G V G V +RPE + M Sbjct: 257 NM--------FQGSVRGGEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKV---M 305 Query: 299 FAQVR-VPGENLVRAVVEIVENLGSERIVHLRVGGVTFVGSFRS 341 A+ + G N VV + LG I H+R+ + + R+ Sbjct: 306 IARDKPASGLNWAEGVVSDIAYLGDVSIYHVRLASGRKIQALRT 349 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: 314 Number of extensions: 10 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: 379 Length adjustment: 30 Effective length of query: 342 Effective length of database: 349 Effective search space: 119358 Effective search space used: 119358 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: 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