Align ABC transporter (characterized, see rationale)
to candidate CCNA_00647 CCNA_00647 nitrate transport ATP-binding protein nrtD
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__Caulo:CCNA_00647 Length = 261 Score = 143 bits (361), Expect = 5e-39 Identities = 87/233 (37%), Positives = 136/233 (58%), Gaps = 11/233 (4%) Query: 4 LKLDNVNKQL--GGMR--ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59 L ++NV G +R +L V L+I GEFV +G SGCGKSTLL ++AGL + G Sbjct: 6 LSIENVGVTFAKGSVRSEVLTGVDLKIDKGEFVSIIGHSGCGKSTLLNVVAGLVPVTTGA 65 Query: 60 LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRER---VLK 116 +++D + VN P +R V VFQ+++L P +SV +N+S + S ER VL Sbjct: 66 VILDRQEVNAPGP-DRAV--VFQNHSLLPWLSVRENVSLAVDKVFGGVKSAAERKEWVLH 122 Query: 117 TAQILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEI 176 +++++ L ++P E+SGG +QRV + RA++ EP +LL DEP LDA R +++ + Sbjct: 123 NLELVKMTHALDKRPAEISGGMKQRVGIARALSMEPKVLLLDEPFGALDALTRAHLQDSV 182 Query: 177 ARLHDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPREL-YERPASR 228 +H L +T++ +THD EA L+D+IV++ G VG ++ RP R Sbjct: 183 MEIHSALKNTVLMITHDVDEATLLSDRIVMMTNGPRACVGQVLDVPLARPRDR 235 Lambda K H 0.320 0.137 0.394 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: 209 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: 381 Length of database: 261 Length adjustment: 27 Effective length of query: 354 Effective length of database: 234 Effective search space: 82836 Effective search space used: 82836 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