Align Solute-binding protein Bamb_6123 (characterized)
to candidate H281DRAFT_03359 H281DRAFT_03359 tripartite ATP-independent transporter solute receptor, DctP family
Query= SwissProt::Q0B2F6 (328 letters) >FitnessBrowser__Burk376:H281DRAFT_03359 Length = 342 Score = 125 bits (315), Expect = 1e-33 Identities = 76/223 (34%), Positives = 116/223 (52%), Gaps = 2/223 (0%) Query: 38 SFPTNMAVKFMGDELSKLTGGKDSIKVFGNSALGSEKDTVDQVRIGAIDMARVNGASFNE 97 S P N+ K D + K TGG+ +++F N +G++ D + QVR GAID G + Sbjct: 48 SHPLNVRAKEAADAIRKETGGRVDLQIFPNGQMGTDTDMLSQVRSGAIDFLTQGGVVLST 107 Query: 98 IVPESLIPSFPFLFRDVDHFRKAMYGPAGQKILDAFAAKGMIALTF-YESGARSIYAK-R 155 +VP S I F F+D + AM G G I A + G+IA+ +++G R + + + Sbjct: 108 LVPVSAINGIGFAFKDYNQVWAAMDGDLGSYIRRAVSKVGLIAMEKPWDNGFRHLTSSVK 167 Query: 156 PVRTPADMKGLKVRVQPSDLMVDEIRAMGGTPTPMPFAEVYTGLKTGLVDAAENNLPSYE 215 PV +P D+KGLK+RV S L +A+ +PT + F+E Y+ L+T +VDA EN L E Sbjct: 168 PVLSPTDLKGLKIRVPVSPLWTSMFKALDASPTSINFSEAYSALQTKVVDAEENPLALIE 227 Query: 216 ETKHFEVAPDYSETQHAMTPEVLVFSKKIWDTLSPQEQAAIRK 258 + +EV S T H + + + W L P Q + K Sbjct: 228 TGRFYEVQKYCSLTGHIWDGFWFLANARSWGNLPPDLQTIVAK 270 Lambda K H 0.318 0.131 0.375 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: 254 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: 328 Length of database: 342 Length adjustment: 28 Effective length of query: 300 Effective length of database: 314 Effective search space: 94200 Effective search space used: 94200 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: 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