Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_011385946.1 AMB_RS18160 ABC transporter ATP-binding protein
Query= uniprot:P0DTT6 (251 letters) >NCBI__GCF_000009985.1:WP_011385946.1 Length = 265 Score = 116 bits (290), Expect = 5e-31 Identities = 76/246 (30%), Positives = 136/246 (55%), Gaps = 13/246 (5%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +LE+RDV +FG V+AL VS ++NKGE+ +++G NGAGK++++ +SG +KP G + Sbjct: 8 VLEVRDVSLAFGGVRALTEVSFQVNKGELFSIIGPNGAGKTSMLNCVSGRYKPTSGRVFM 67 Query: 64 EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLARE-------VTNKIFL---N 113 +G+ V SPN +LG+ +Q+LAL + + NI + R T ++ Sbjct: 68 DGRDVTGLSPNVRATLGLGRTFQNLALFGHMSVLDNIMVGRHHLLGNNAATGALYWLSGA 127 Query: 114 KKKMMEESKKLLDSLQ-IRIPDINMKVE-NLSGGQRQAVAVARAVYFSAKMILMDEPTAA 171 +K+ + +K+ D + + I I V L G R+ V +ARA+ K+IL+DEP A Sbjct: 128 RKEELAHRRKVEDIIDFLEIAHIRKAVAGTLPYGLRKRVELARAMAVEPKVILLDEPMAG 187 Query: 172 LSVVEARKVLELARNLKKK-GLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNV 230 +++ E + +L ++ G+ V++I H++ +++ R+ VL+ G+ I +E Sbjct: 188 MNLEEKEDMARYIVDLNEEWGMTVIMIEHDMGVVMDISHRVMVLEFGRKIAEGLPDEVMN 247 Query: 231 EEITEV 236 E +V Sbjct: 248 NERVKV 253 Lambda K H 0.318 0.137 0.371 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: 153 Number of extensions: 7 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: 251 Length of database: 265 Length adjustment: 24 Effective length of query: 227 Effective length of database: 241 Effective search space: 54707 Effective search space used: 54707 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 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