Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 5210736 Shew_3164 ABC transporter-related protein (RefSeq)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__PV4:5210736 Length = 241 Score = 115 bits (287), Expect = 1e-30 Identities = 68/221 (30%), Positives = 129/221 (58%), Gaps = 10/221 (4%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 +++I ++HK FG + L G+ I +GEVV+++G +G+GKST ++ I+ +P +G++V Sbjct: 1 MIKISNLHKYFGDNQVLKGIDESIARGEVVSVIGPSGSGKSTFLRCINLLEQPTQGEIVI 60 Query: 64 EGKKVIFNSPN---DARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE 120 +G+ + +P+ D + ++Q+ L P + NI LA + + + E Sbjct: 61 DGQSI--TAPDACIDKLRQKVGMVFQNFNLFPHKTVQQNITLAPVKLG--LMTQAEADSE 116 Query: 121 SKKLLDSLQIRIPD-INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179 + +LLD Q+ + D + +LSGGQ+Q VA+ARA+ +++L DEPT+AL Sbjct: 117 AMRLLD--QVGLSDKASAYPASLSGGQKQRVAIARALAMKPELMLFDEPTSALDPEMVGD 174 Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKII 220 VL++ + L + G+ ++I+TH + +V+DR+ +D G ++ Sbjct: 175 VLDVMKQLAQAGMTMVIVTHEMGFAKDVSDRVIFMDGGYVV 215 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: 122 Number of extensions: 4 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: 241 Length adjustment: 24 Effective length of query: 227 Effective length of database: 217 Effective search space: 49259 Effective search space used: 49259 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: 46 (22.3 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