Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate CCNA_00647 CCNA_00647 nitrate transport ATP-binding protein nrtD
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Caulo:CCNA_00647 Length = 261 Score = 142 bits (358), Expect = 1e-38 Identities = 86/216 (39%), Positives = 135/216 (62%), Gaps = 14/216 (6%) Query: 4 VSVRDLSLNF--GAVT--VLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59 +S+ ++ + F G+V VL ++L ID GEF+ ++G SGCGKSTLLN +AGL+ V+ G Sbjct: 6 LSIENVGVTFAKGSVRSEVLTGVDLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVPVTTGA 65 Query: 60 IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKI-----PPAEIEKRV 114 + + + V P DR + VFQ+++L P ++V +N+S L V K+ AE ++ V Sbjct: 66 VILDRQEVNAPGP-DRAV--VFQNHSLLPWLSVRENVS--LAVDKVFGGVKSAAERKEWV 120 Query: 115 KRASEILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRV 174 E++++ L ++P+E+SGG +QRV I RAL + V L DEP LDA R+ L+ Sbjct: 121 LHNLELVKMTHALDKRPAEISGGMKQRVGIARALSMEPKVLLLDEPFGALDALTRAHLQD 180 Query: 175 EIKRLHQSLKNTMIYVTHDQIEALTLADRIAVMKSG 210 + +H +LKNT++ +THD EA L+DRI +M +G Sbjct: 181 SVMEIHSALKNTVLMITHDVDEATLLSDRIVMMTNG 216 Lambda K H 0.320 0.137 0.392 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: 210 Number of extensions: 10 Number of successful extensions: 3 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: 361 Length of database: 261 Length adjustment: 27 Effective length of query: 334 Effective length of database: 234 Effective search space: 78156 Effective search space used: 78156 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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