Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_086511770.1 BZY95_RS20650 ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_002151265.1:WP_086511770.1 Length = 422 Score = 162 bits (410), Expect = 1e-44 Identities = 85/232 (36%), Positives = 138/232 (59%), Gaps = 6/232 (2%) Query: 33 ILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNIL 92 + R G T ++ + + G+ +++G SG GKST +R I L + T+G + G ++ Sbjct: 36 VSKRWGDTAAVDAIGFDVAPGEFVILLGPSGCGKSTTLRMIAGLEQATAGRIEIGGRDVT 95 Query: 93 DLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVG 152 L R +SMVFQS+AL PH +V N+V+G R R V K + RE + V Sbjct: 96 HLPPGD------RGISMVFQSYALFPHLSVADNIVFGLRSRKVPKAERRERLARVAQLVD 149 Query: 153 LSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRN 212 L Y + P QLSGG +QRV LARA+ ++ + LMDE S LD +RG+M+ ++ LQ+ Sbjct: 150 LEAYLERKPAQLSGGQRQRVALARAIISEHPICLMDEPLSNLDARLRGEMRREIKALQQR 209 Query: 213 LAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 L T++++THD EA+ +G + +++DG++VQ TP+++ + PA+ + A F+ Sbjct: 210 LGMTVIYVTHDQVEAMSMGDRVILMQDGRIVQDATPSELYERPASAFAAGFI 261 Lambda K H 0.323 0.139 0.397 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: 319 Number of extensions: 15 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: 275 Length of database: 422 Length adjustment: 28 Effective length of query: 247 Effective length of database: 394 Effective search space: 97318 Effective search space used: 97318 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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