Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ga0059261_3874 Ga0059261_3874 ABC-type antimicrobial peptide transport system, ATPase component
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Korea:Ga0059261_3874 Length = 243 Score = 125 bits (314), Expect = 1e-33 Identities = 74/228 (32%), Positives = 121/228 (53%), Gaps = 7/228 (3%) Query: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 +++D ++K + G ++L V + V PGE ++VGPSGCGKSTLL I++GL P + Sbjct: 7 AAIDAREVSKSYTVGQVRTQILFGVSVSVMPGELTLVVGPSGCGKSTLLAILSGLTLPDQ 66 Query: 63 GEIRIGGKNVVGMPPRDRDI------AMVFQSYALYPTLSVADNIGFALEMRKMPKPERQ 116 GE+ G + M RD VFQ + L+ L+ + + + L+ K+ E + Sbjct: 67 GEVDALGNPICRMKAGARDAFRLANTGFVFQGFNLFNALTAEEQVAYVLQCMKVKPAEAR 126 Query: 117 KRIDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVE 176 +R + + + RP +LSGG++QRVA+ RALA+QP++ DEP S LD+ Sbjct: 127 QRARAALEAVGLGPRMRLRPFELSGGEKQRVAIARALAKQPRILFADEPTSALDSHNGHA 186 Query: 177 MRAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPD 224 + A ++ + G + VTHD ++ RI M+ G + + PD Sbjct: 187 VIALLRDIAHNQGAAVLCVTHDP-RLLSFADRIIHMEDGRIIRDERPD 233 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: 195 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: 355 Length of database: 243 Length adjustment: 26 Effective length of query: 329 Effective length of database: 217 Effective search space: 71393 Effective search space used: 71393 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: 48 (23.1 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