Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 176 bits (445), Expect = 8e-49 Identities = 95/263 (36%), Positives = 150/263 (57%), Gaps = 26/263 (9%) Query: 2 ADIEIRNVYKIFGHDAKKALTMVEDGLDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGL 61 A I RN+ K +G D+ AL + +S ++ G + I+G Sbjct: 6 AGIVFRNITKRYGTDSSAALAV--------------------KGISFEVPRGTLTTILGP 45 Query: 62 SGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRMRRVSMVFQSFALMPHRT 121 SG GK+T +R I L PTSGE+ G ++ LG R VSM+FQS+AL PH Sbjct: 46 SGCGKTTTLRMIAGLESPTSGEIFIGGKDVTTLGPA------QRNVSMMFQSYALFPHMN 99 Query: 122 VLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQLSGGMKQRVGLARALAAD 181 V++NV+YG R+ G K+ AR ++ + VGL G+D + P +LSGG +QRV LARAL + Sbjct: 100 VVENVMYGLRMSGQPKEQARAKAVEALRGVGLVGFDDRLPSELSGGQQQRVALARALVLE 159 Query: 182 TDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQ 241 +V+L DE S LD +R +M++++ LQ+ L+ T+ ++THD EA+ + +I ++ G Sbjct: 160 PEVLLFDEPLSNLDARLRREMREEIRALQQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGL 219 Query: 242 VVQVGTPNDILDNPANDYVARFV 264 + Q G+P + + P +++VA F+ Sbjct: 220 IAQKGSPRALYETPHSEFVAGFM 242 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: 254 Number of extensions: 10 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: 360 Length adjustment: 27 Effective length of query: 248 Effective length of database: 333 Effective search space: 82584 Effective search space used: 82584 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: 48 (23.1 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