Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 161 bits (408), Expect = 2e-44 Identities = 94/281 (33%), Positives = 156/281 (55%), Gaps = 19/281 (6%) Query: 24 SLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQPSHGRILFDGKDVTNLSTQSRNI 83 +++ VD + G ++LLG SGCGKTTLL +++G P+ GRIL DG+DVT + R + Sbjct: 37 AVEHVDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILIDGQDVTEVPPYERPV 96 Query: 84 AQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRVRDILEMIDLASWARRKAQGLTAD 143 +FQ ++ M+V DN+AF L+ G+A+ + +V LE++ + ++ RK L+ Sbjct: 97 NMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQMGRFSGRKPHQLSGG 156 Query: 144 QKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLRSQLKRLHKQFGFTMVYVTHDQTE 203 Q+Q+++L R L + + +L DEPL +D ++ + +L + + G T V VTHDQ E Sbjct: 157 QRQRVALARCLAK-EPKVVLLDEPLAALDKKLREATQLELVNIQDRVGITFVMVTHDQGE 215 Query: 204 ALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYFIGSPGMNFMPARIEGSTVKVGDE 263 A+T + ++ VM G I Q+G+P +++E P FV FIG+ M +GS V+ G+ Sbjct: 216 AMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIGAANM------FQGS-VRGGEG 268 Query: 264 TLTLEYAPKTSGTAKTELG-----------IRPEFIRLGRE 293 L + + TE G +RPE + + R+ Sbjct: 269 ALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARD 309 Lambda K H 0.321 0.137 0.405 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: 301 Number of extensions: 16 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: 356 Length of database: 379 Length adjustment: 30 Effective length of query: 326 Effective length of database: 349 Effective search space: 113774 Effective search space used: 113774 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 (21.8 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