Align ABC-type sugar transport system, periplasmic component protein (characterized, see rationale)
to candidate H281DRAFT_02705 H281DRAFT_02705 monosaccharide ABC transporter substrate-binding protein, CUT2 family
Query= uniprot:D8IZC6 (316 letters) >FitnessBrowser__Burk376:H281DRAFT_02705 Length = 365 Score = 121 bits (304), Expect = 2e-32 Identities = 94/276 (34%), Positives = 133/276 (48%), Gaps = 19/276 (6%) Query: 16 AAAAQPAMAADKPLKSVGVTVGDLANPFFVAIAKGAESGAHKINPDAKVTVVSSKYDLNT 75 A A+ P A VG +V L N FFV + G E GA + D T ++ D Sbjct: 50 APASAPVANASGGKTKVGFSVSTLNNAFFVGLKAGVEKGAKEQGFDLVQT--NANGDAQQ 107 Query: 76 QVGQIENFIANKVDLIVLNAADSKGVGPAVKKAQKAGIVVVAVDVAAAGADVT--VMSDN 133 QV N ++ V +VLN DSK + PAV+KA I V +D + G VT V SDN Sbjct: 108 QVNDAINLLSQGVTALVLNPIDSKAIIPAVEKANSMNIPVFMLDRGSDGGKVTSFVASDN 167 Query: 134 TMAGAESCKFLAEKL-----QGKGNVV-IVNGPPVSAVMDRVTGCKAEFKKSPGIKILSD 187 G + K++A++L KGNVV ++ +A DR G E K P IK+++ Sbjct: 168 VALGQTAAKWIADQLTKRYGSAKGNVVDLIGLVGTTAATDREKGFSDEIAKYPDIKVVA- 226 Query: 188 NQNAGGSRDGGMTTMSNLLAAQPKIDAVFAINDPTAIGAELAIRQAKR------SDIKWI 241 Q ++ + M+N+L P+IDAVF ND +GAE AI A R + Sbjct: 227 RQEGAFDQEKSLNAMTNILQKYPQIDAVFGANDDNTVGAEKAIDNAGRYKPLGDKQHILV 286 Query: 242 SGVDGAPDAERALKDSKSLFAASPAQDPYGMAAESV 277 G DG A A++ K A+ +Q+P MAA+S+ Sbjct: 287 IGADGTAQALSAIRAGKQ--DATISQNPIQMAAKSL 320 Lambda K H 0.314 0.129 0.360 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: 242 Number of extensions: 7 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 316 Length of database: 365 Length adjustment: 28 Effective length of query: 288 Effective length of database: 337 Effective search space: 97056 Effective search space used: 97056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 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