Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039 (367 letters) >NCBI__GCF_000009985.1:WP_011383734.1 Length = 452 Score = 148 bits (373), Expect = 3e-40 Identities = 81/195 (41%), Positives = 127/195 (65%), Gaps = 6/195 (3%) Query: 17 SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDITEVSPAKRD 76 ++++G+D ++ + E V +G SG GKSTLLR++AGL + +GG ++ G +T PAK Sbjct: 29 TVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKANGGEVKYRGHLMT--GPAK-G 85 Query: 77 LAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILELGPMLERKPKQLSG 136 ++MVFQ++AL+P ++V +N+ L+ AGVAKAE E++ +EA ++ LG PK+LSG Sbjct: 86 ISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERANEAIDLIGLGGYESAYPKELSG 145 Query: 137 GQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKELQAT---MIYVTHD 193 G RQRV RA+V P + L DEP S LD +R +LL L E + ++ V+H+ Sbjct: 146 GMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLREDLLELWDERKIPTKGILLVSHN 205 Query: 194 QVEAMTMADKVVVLN 208 EA++MAD+V+V + Sbjct: 206 IEEAVSMADRVLVFS 220 Lambda K H 0.320 0.137 0.389 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: 356 Number of extensions: 17 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 367 Length of database: 452 Length adjustment: 31 Effective length of query: 336 Effective length of database: 421 Effective search space: 141456 Effective search space used: 141456 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: 50 (23.9 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