Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= BRENDA::Q97UY8 (353 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 195 bits (495), Expect = 2e-54 Identities = 119/342 (34%), Positives = 196/342 (57%), Gaps = 22/342 (6%) Query: 7 KNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDD 66 + +SK F G A+++V++ I GE F +LG SG GKTT +R++AG ++P+TG + D Sbjct: 26 EGISKRF--GDFTAVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDG 83 Query: 67 RLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAK 126 + V VPP +R + M+FQ++AL+P+++ +NIAF L ++K I+ +V + Sbjct: 84 QDVTE-----VPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALE 138 Query: 127 ILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEV 186 ++ + P +LSGGQ+QRVALAR L K+P ++LLDEP + LD ++R++ + + + Sbjct: 139 LVQMGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNI 198 Query: 187 QSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINE 246 Q R+G+T ++V+HD + ++ R+GV+ G + QVG P D+Y+ P + VA IG N Sbjct: 199 QDRVGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAANM 258 Query: 247 LEGKVT-NEG---VVIGSLRFPVSVSSDRAI-------IGIRPEDVKLSKDVIKDDSWIL 295 +G V EG + L +SV+ A+ + +RPE V +++D K S + Sbjct: 259 FQGSVRGGEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARD--KPASGLN 316 Query: 296 VGKGKVKVIGYQGGLFRITITPLDSEEEIFTYSDHPIHSGEE 337 +G V I Y G + I L S +I + +H GEE Sbjct: 317 WAEGVVSDIAYLGDV-SIYHVRLASGRKIQALRTN-LHHGEE 356 Lambda K H 0.319 0.139 0.390 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: 286 Number of extensions: 7 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: 353 Length of database: 379 Length adjustment: 30 Effective length of query: 323 Effective length of database: 349 Effective search space: 112727 Effective search space used: 112727 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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