Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_028311054.1 H566_RS0108150 polyamine ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_000482785.1:WP_028311054.1 Length = 365 Score = 231 bits (588), Expect = 3e-65 Identities = 138/339 (40%), Positives = 202/339 (59%), Gaps = 18/339 (5%) Query: 23 VLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVGMPPRDRDI 82 ++R +D+ + GEFL L+GPSG GK+T L ++AG + PT GEIR+GGK + +PP R+I Sbjct: 23 IVRDLDLDIERGEFLTLLGPSGSGKTTCLMMLAGFETPTAGEIRLGGKVINKLPPWRRNI 82 Query: 83 AMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGG 142 +VFQ+YAL+P ++V +NI F L +RK+P E +++ + AM+++ +R P QLSGG Sbjct: 83 GVVFQNYALFPHMTVRENIRFPLAVRKLPAHEIDQKVKQALAMVKLDAFGERYPQQLSGG 142 Query: 143 QRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEA 202 Q+QR+A+ RAL P+L L DEPL LD +LR M+ EIK LH + GIT V+VTHDQ EA Sbjct: 143 QQQRIALARALVFSPELVLMDEPLGALDKQLREHMQMEIKHLHDSLGITFVFVTHDQSEA 202 Query: 203 MTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAVT---GGQFGIQ 259 +T+ RIAV G +QQL D +Y RPAN +VA FIG N L V G + ++ Sbjct: 203 LTMSDRIAVFDKGRIQQLDRADALYERPANAFVAGFIGE--SNALAATVEQHHGAECSLR 260 Query: 260 ---GAALNLAPPPSSA-NEVLLGVRPEHLVMQ---ETAPWRGRVSVVEPT--GPDTYVMV 310 G+ L + A N + +RPE +++ E AP R +V E G + + Sbjct: 261 LADGSLLRASVGDLGAENTATVSIRPERVLIDQAAEAAPNRFTATVKELVYLGDHLRLRL 320 Query: 311 DTAA-GSVTLRTDA---QTRVQPGEHVGLALAPAHAHWF 345 D A G+ ++ A +V P + + + + P HA F Sbjct: 321 DLAGNGNFMVKLPAGALDRQVLPEQTIAVGIRPEHARAF 359 Lambda K H 0.318 0.135 0.388 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: 333 Number of extensions: 14 Number of successful extensions: 1 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: 355 Length of database: 365 Length adjustment: 29 Effective length of query: 326 Effective length of database: 336 Effective search space: 109536 Effective search space used: 109536 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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