Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000009985.1:WP_011383734.1 Length = 452 Score = 130 bits (328), Expect = 5e-35 Identities = 76/199 (38%), Positives = 116/199 (58%), Gaps = 11/199 (5%) Query: 17 KTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGYIYFDNEAVSSPRR 76 + E ++ V ++ G +LG SG GK+T LR++AGL + G + + ++ P + Sbjct: 25 RRERTVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKANGGEVKYRGHLMTGPAK 84 Query: 77 VMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKVKEVSEELGLSGVL 136 GI+MVFQ++AL+P +TV +N+ L+ A V K + E + E + +GL G Sbjct: 85 --------GISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERANEAIDLIGLGGYE 136 Query: 137 NRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARALVRKIQRERKLTT 196 + YPKELSGG QR ARALV P VLLLDEPFS LD E+ R + ++ ERK+ T Sbjct: 137 SAYPKELSGGMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLREDLLELWDERKIPT 196 Query: 197 ---LIVSHDPADIFAIANK 212 L+VSH+ + ++A++ Sbjct: 197 KGILLVSHNIEEAVSMADR 215 Lambda K H 0.317 0.136 0.374 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: 360 Number of extensions: 18 Number of successful extensions: 2 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: 371 Length of database: 452 Length adjustment: 31 Effective length of query: 340 Effective length of database: 421 Effective search space: 143140 Effective search space used: 143140 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: 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