Align ABC transporter (characterized, see rationale)
to candidate Ga0059261_3653 Ga0059261_3653 phosphate ABC transporter ATP-binding protein, PhoT family (TC 3.A.1.7.1)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 111 bits (277), Expect = 3e-29 Identities = 75/239 (31%), Positives = 124/239 (51%), Gaps = 20/239 (8%) Query: 3 KLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICG----- 57 K+ VN G + +RDVS+++ F+GPSGCGKST LR + ++ Sbjct: 28 KMAARGVNVFYGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMNDTVASARVE 87 Query: 58 GDLLIDGRRVND-----LEPRERGVGMVFQSYALYPHMSVYDNISF-----GLKLAKTDK 107 G++ +DG + D ++ R R VGMVFQ +P S+Y+N+++ GL AK D Sbjct: 88 GEITLDGENIYDKSMDVVQLRAR-VGMVFQKPNPFP-KSIYENVAYGPRIHGLARAKGDM 145 Query: 108 TSLRERVLKTAQIL-QLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDA 166 + ER LK A + ++ L LSGGQ+QR+ + RA+A +P+++L DEP S LD Sbjct: 146 DQIVERSLKRAGLWEEVKDRLNDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDP 205 Query: 167 SLRVQMRNEIARLHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERP 225 ++ I L R ++ VTH+ +A ++ + + G + + G +++ P Sbjct: 206 IATAKIEELIHELRGRY--AIVIVTHNMQQAARVSQRTAFFHLGTLVEYGETDQIFTAP 262 Lambda K H 0.320 0.137 0.394 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: 187 Number of extensions: 6 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: 381 Length of database: 276 Length adjustment: 28 Effective length of query: 353 Effective length of database: 248 Effective search space: 87544 Effective search space used: 87544 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: 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