Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_057507534.1 ABB28_RS04735 ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >NCBI__GCF_001431535.1:WP_057507534.1 Length = 229 Score = 134 bits (338), Expect = 2e-36 Identities = 73/220 (33%), Positives = 122/220 (55%), Gaps = 6/220 (2%) Query: 1 MASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEP 60 M++ + + I K + +G + V+VL +D+ + G+F+ L+GPSG GK+TLLN+I GLD P Sbjct: 1 MSTLVSLRSITKTYQRGPEQVKVLHGIDLDIETGDFVALMGPSGSGKTTLLNLIGGLDSP 60 Query: 61 TEGEIRIGGKNVVGMPP------RDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPE 114 + GEI I G+ + M R + VFQ Y L P L+ N+ L + + + Sbjct: 61 SGGEITIEGERIDQMGGGQLSTWRSHHVGFVFQFYNLMPMLTAQKNVELPLLLTHLGAAQ 120 Query: 115 RQKRIDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLR 174 R++ + ++ ++ RP++LSGGQ+QRVA+ RA+ P + DEP +LD + Sbjct: 121 RRRNAEIALTLVGLADRRSHRPNELSGGQQQRVAIARAIVSDPTFLICDEPTGDLDRQSA 180 Query: 175 VEMRAEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKG 214 E+ +++L++ G T + VTHD A + + KG Sbjct: 181 EEILQLLQQLNREHGKTIIMVTHDPKAAEYATHTVHLDKG 220 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: 213 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: 355 Length of database: 229 Length adjustment: 26 Effective length of query: 329 Effective length of database: 203 Effective search space: 66787 Effective search space used: 66787 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: 47 (22.7 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