Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate CCNA_00647 CCNA_00647 nitrate transport ATP-binding protein nrtD
Query= TCDB::P96483 (377 letters) >FitnessBrowser__Caulo:CCNA_00647 Length = 261 Score = 132 bits (333), Expect = 8e-36 Identities = 75/192 (39%), Positives = 118/192 (61%), Gaps = 6/192 (3%) Query: 24 LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83 +D+ I+ GEF+ ++G SGCGKST L ++AGL V GA+ I DR + P DR A+VF Sbjct: 28 VDLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVPVTTGAV-ILDRQEVNAPGPDR--AVVF 84 Query: 84 QNYALYPHMTVADNMGFAL-KIAGVPK--AEIRQKVEEAAKILDLTQYLDRKPKALSGGQ 140 QN++L P ++V +N+ A+ K+ G K AE ++ V +++ +T LD++P +SGG Sbjct: 85 QNHSLLPWLSVRENVSLAVDKVFGGVKSAAERKEWVLHNLELVKMTHALDKRPAEISGGM 144 Query: 141 RQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAM 200 +QRV + RA+ EP+V L+DEP LDA R + + + L T + +THD EA Sbjct: 145 KQRVGIARALSMEPKVLLLDEPFGALDALTRAHLQDSVMEIHSALKNTVLMITHDVDEAT 204 Query: 201 TMGDRVAVLKDG 212 + DR+ ++ +G Sbjct: 205 LLSDRIVMMTNG 216 Lambda K H 0.317 0.135 0.379 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: 243 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: 377 Length of database: 261 Length adjustment: 27 Effective length of query: 350 Effective length of database: 234 Effective search space: 81900 Effective search space used: 81900 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 (21.6 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