Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Echvi_1096 Echvi_1096 nitrate transport ATP-binding subunits C and D
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Cola:Echvi_1096 Length = 294 Score = 131 bits (329), Expect = 2e-35 Identities = 89/252 (35%), Positives = 133/252 (52%), Gaps = 39/252 (15%) Query: 1 MADIEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMG 60 MA IE+ NV K FG G + D+LS D++L++ G+ I+G Sbjct: 1 MAIIELNNVSKSFGM-----------GASRVDVLS---------DINLQVAEGEFVAIVG 40 Query: 61 LSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHR 120 SGSGK+TL+ +N L P GEVL G + G ++FQ+++L+P Sbjct: 41 FSGSGKTTLINLLNGLAFPDQGEVLLHGQPVTGPGPDR---------GVIFQNYSLLPWL 91 Query: 121 TVLQNV------VYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGL 174 +V NV V+ Q SK+ A I K+I V L+ K P +LSGGM+QRV + Sbjct: 92 SVYNNVKLAVDEVFPQLS---SKEKASHI-KKYIGMVNLTPAMDKLPKELSGGMRQRVSV 147 Query: 175 ARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEI 234 ARALA + +++LMDE SALD L RG +Q++++++ KT + IT+D+DE + + I Sbjct: 148 ARALAMNPEILLMDEPLSALDALTRGSLQEEIIRIWSQDKKTAILITNDVDEGILMADRI 207 Query: 235 AILRDGQVVQVG 246 L G +G Sbjct: 208 IPLTPGPKATLG 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: 195 Number of extensions: 13 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: 294 Length adjustment: 26 Effective length of query: 249 Effective length of database: 268 Effective search space: 66732 Effective search space used: 66732 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: 47 (22.7 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