Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate CCNA_00647 CCNA_00647 nitrate transport ATP-binding protein nrtD
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >FitnessBrowser__Caulo:CCNA_00647 Length = 261 Score = 155 bits (392), Expect = 1e-42 Identities = 86/227 (37%), Positives = 137/227 (60%), Gaps = 10/227 (4%) Query: 2 AHLKIKNL----QKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTA 57 A+L I+N+ KG ++ G+DL+++ EFV +G SGCGKSTLL ++AGL VT Sbjct: 4 AYLSIENVGVTFAKGSVRSEVLTGVDLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVPVTT 63 Query: 58 GTIELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALD--LAGVNKAEVEKK-V 114 G + LD +++ P D A+VFQ ++L P +SVR+N+S A+D GV A K+ V Sbjct: 64 GAVILDRQEVNAPGP---DRAVVFQNHSLLPWLSVRENVSLAVDKVFGGVKSAAERKEWV 120 Query: 115 NEAARILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRL 174 ++++ L+++P ++SGG +QRV I RA+ PK+ L DEP LDA R ++ Sbjct: 121 LHNLELVKMTHALDKRPAEISGGMKQRVGIARALSMEPKVLLLDEPFGALDALTRAHLQD 180 Query: 175 ELARLHKELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLEL 221 + +H L+ T++ +THD EA L+D++V++ G VG L++ Sbjct: 181 SVMEIHSALKNTVLMITHDVDEATLLSDRIVMMTNGPRACVGQVLDV 227 Lambda K H 0.321 0.137 0.390 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: 193 Number of extensions: 12 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: 367 Length of database: 261 Length adjustment: 27 Effective length of query: 340 Effective length of database: 234 Effective search space: 79560 Effective search space used: 79560 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