Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate CCNA_00647 CCNA_00647 nitrate transport ATP-binding protein nrtD
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Caulo:CCNA_00647 Length = 261 Score = 138 bits (348), Expect = 1e-37 Identities = 78/209 (37%), Positives = 124/209 (59%), Gaps = 6/209 (2%) Query: 16 TQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTVEPADR 75 ++ L ++L I+ GEFV +G SGCGKSTLL +AGL V++G + + ++V P Sbjct: 22 SEVLTGVDLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVPVTTGAVILDRQEVNAPGP--- 78 Query: 76 DLAMVFQSYALYPHMTVRENMEFGM-KVNGFEPDL--RKERIAEAARVLQLEDYLDRKPG 132 D A+VFQ+++L P ++VREN+ + KV G RKE + ++++ LD++P Sbjct: 79 DRAVVFQNHSLLPWLSVRENVSLAVDKVFGGVKSAAERKEWVLHNLELVKMTHALDKRPA 138 Query: 133 QLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMIYVTH 192 ++SGG +QRV I RA+ P V L DEP LDA R ++ + +H L T++ +TH Sbjct: 139 EISGGMKQRVGIARALSMEPKVLLLDEPFGALDALTRAHLQDSVMEIHSALKNTVLMITH 198 Query: 193 DQVEAMTMADKIVVLNRGRIEQVGSPMDL 221 D EA ++D+IV++ G VG +D+ Sbjct: 199 DVDEATLLSDRIVMMTNGPRACVGQVLDV 227 Lambda K H 0.320 0.139 0.396 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: 189 Number of extensions: 7 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: 338 Length of database: 261 Length adjustment: 26 Effective length of query: 312 Effective length of database: 235 Effective search space: 73320 Effective search space used: 73320 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