Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 200225 SO1042 amino acid ABC transporter, ATP-binding protein (NCBI ptt file)
Query= uniprot:P0DTT6 (251 letters) >FitnessBrowser__MR1:200225 Length = 241 Score = 119 bits (297), Expect = 7e-32 Identities = 73/227 (32%), Positives = 124/227 (54%), Gaps = 8/227 (3%) Query: 4 LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63 ++ I ++HKS+G L G++ I +GEVV+++G +G+GKST ++ I+ P +GD+ Sbjct: 1 MINITNLHKSYGDNAVLKGINEHIRQGEVVSVIGPSGSGKSTFLRCINLLENPTQGDIEI 60 Query: 64 EGKKVIFNSPN-DARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESK 122 EG+ + D + ++Q+ L P + NI LA + L E Sbjct: 61 EGQSITAKDACVDKLRQKVGMVFQNFNLFPHKTVLQNITLA-----PVSLKLMTQAEADN 115 Query: 123 KLLDSL-QIRIPD-INMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180 K L L Q+ + D N +LSGGQ+Q VA+ARA+ ++L DEPT+AL V Sbjct: 116 KALALLTQVGLQDKANAYPSSLSGGQKQRVAIARALAMEPDLMLFDEPTSALDPEMVGDV 175 Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEE 227 L++ ++L +KG+ ++I+TH + +V+DR+ +D G ++ EE Sbjct: 176 LDVMKDLAQKGMTMVIVTHEMGFARDVSDRVIFMDGGYVVESNIPEE 222 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: 130 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: 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