Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_085770056.1 B1812_RS01695 nitrate/sulfonate/bicarbonate ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_002117405.1:WP_085770056.1 Length = 436 Score = 140 bits (354), Expect = 4e-38 Identities = 82/201 (40%), Positives = 123/201 (61%), Gaps = 12/201 (5%) Query: 40 TVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKAL 99 T L+ VSL + G+I ++G SG GKSTL+R ++ L + GEV + G+ + Sbjct: 28 TTVLDHVSLTLKEGEIVGLLGRSGCGKSTLLRIVSGLNRASGGEVRYRGEKV-------- 79 Query: 100 RAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAK 159 A + V+MVFQSFAL P TVL NV G R +G +++AR+ ++ ID +GL G++ Sbjct: 80 -AGPVDGVAMVFQSFALFPWLTVLANVELGLRAKGAPREEARKRALQAIDIIGLDGFENA 138 Query: 160 FPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQL---QRNLAKT 216 +P ++SGGM+QRVG ARAL ++LMDE FSALD L ++ LL L R K+ Sbjct: 139 YPKEISGGMRQRVGFARALVVAPSLLLMDEPFSALDVLTAETLRTDLLDLWVEGRMPIKS 198 Query: 217 IVFITHDLDEALRIGSEIAIL 237 I+ +TH+++EA+ + I +L Sbjct: 199 ILMVTHNIEEAVLMCDRIVVL 219 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: 307 Number of extensions: 17 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: 275 Length of database: 436 Length adjustment: 29 Effective length of query: 246 Effective length of database: 407 Effective search space: 100122 Effective search space used: 100122 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 Apr 09 2024. 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