Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011385004.1 AMB_RS13205 polyamine ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000009985.1:WP_011385004.1 Length = 379 Score = 207 bits (528), Expect = 3e-58 Identities = 125/297 (42%), Positives = 171/297 (57%), Gaps = 4/297 (1%) Query: 4 IHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRI 63 I + ++K + V H +DL I GEF LLG SGCGK+T+LRM+AG E + G + I Sbjct: 23 IRFEGISKRFGDFTAVEH-VDLAIHKGEFFSLLGASGCGKTTLLRMLAGFEIPTTGRILI 81 Query: 64 GGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLN 123 G V ++P ER V M+FQ+YAL+PHMSV DNIAFGL++ I +V L+ Sbjct: 82 DGQDVTEVPPYERPVNMMFQSYALFPHMSVADNIAFGLKQDGLAKPVIKDKVAAALELVQ 141 Query: 124 LEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQR 183 + RKP +SGGQ+QR A+AR + K P V L DEPL+ LD KLR + ++ + R Sbjct: 142 MGRFSGRKPHQLSGGQRQRVALARCLAKEPKVVLLDEPLAALDKKLREATQLELVNIQDR 201 Query: 184 LRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFL 243 + T V VTHDQ EAMT++ R+ +M G I Q GSP ++Y YP F A FIG A N Sbjct: 202 VGITFVMVTHDQGEAMTMSSRIGVMNAGCIEQVGSPVDIYEYPGTRFVADFIG--AANMF 259 Query: 244 SGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300 G+V+ +G L I L+ + V + VRP+ V IA ++ PA+ L Sbjct: 260 QGSVRGGEGALAIACPELEHDLSVTEAGAVAAGTPVTVMVRPEKVMIARDK-PASGL 315 Lambda K H 0.321 0.137 0.403 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: 343 Number of extensions: 14 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: 406 Length of database: 379 Length adjustment: 31 Effective length of query: 375 Effective length of database: 348 Effective search space: 130500 Effective search space used: 130500 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: 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