Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (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:A0A1N7U8S3 (276 letters) >FitnessBrowser__Korea:Ga0059261_3653 Length = 276 Score = 130 bits (327), Expect = 3e-35 Identities = 96/268 (35%), Positives = 145/268 (54%), Gaps = 25/268 (9%) Query: 18 AQPVTAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQ 77 A+P A K+ G++ YGE + ++ VS++ +V + IG SG GKST LR +N + Sbjct: 21 ARPAEHA-KMAARGVNVFYGEKQAIRDVSIDVDMENVTAFIGPSGCGKSTFLRTLNRMND 79 Query: 78 PDA-----GVITLDGISIEMRQGRAGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLEN 132 A G ITLDG +I + D +Q LR R+ MVFQ N + ++ EN Sbjct: 80 TVASARVEGEITLDGENIYDKS---------MDVVQ-LRARVGMVFQKPNPFPK-SIYEN 128 Query: 133 ITMAPR-RVLDVSAAEAEKRARMYLDKVGLPSRVADQYP---AFLSGGQQQRVAIARALA 188 + PR L + + ++ L + GL V D+ LSGGQQQR+ IARA+A Sbjct: 129 VAYGPRIHGLARAKGDMDQIVERSLKRAGLWEEVKDRLNDSGTALSGGQQQRLCIARAIA 188 Query: 189 MEPEIILFDEPTSALDPELVGEVLKVIQTLAEEGR-TMLMVTHEMGFARQVSSQVLFLHQ 247 ++PE+IL DEP SALDP ++ ++I L GR +++VTH M A +VS + F H Sbjct: 189 VDPEVILMDEPCSALDPIATAKIEELIHEL--RGRYAIVIVTHNMQQAARVSQRTAFFHL 246 Query: 248 GRVEEHGDA-RILDQPNSERLQQFLSNR 274 G + E+G+ +I P ER + +++ R Sbjct: 247 GTLVEYGETDQIFTAPRQERTKDYITGR 274 Lambda K H 0.319 0.133 0.372 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: 168 Number of extensions: 14 Number of successful extensions: 3 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: 276 Length of database: 276 Length adjustment: 25 Effective length of query: 251 Effective length of database: 251 Effective search space: 63001 Effective search space used: 63001 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: 47 (22.7 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