Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate 3608728 Dshi_2120 ABC transporter related (RefSeq)
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Dino:3608728 Length = 376 Score = 164 bits (415), Expect = 3e-45 Identities = 86/233 (36%), Positives = 135/233 (57%), Gaps = 6/233 (2%) Query: 32 DILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNI 91 +++ R G + +IG G+ IMG SG GK+T +R + L +PT G + DG+ + Sbjct: 19 NVVKRFGSFTAVKKADFEIGRGEFLAIMGSSGCGKTTTLRMLAGLEDPTEGAIYLDGEQV 78 Query: 92 LDLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTV 151 +A R MV+QS AL P TV +NV + ++RG+ K++ R+ KW+D + Sbjct: 79 NG------KATWDRDTPMVWQSLALFPFLTVQENVEFALKMRGIGKEERRQRADKWLDKM 132 Query: 152 GLSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQR 211 ++ + + +QLSGG KQRV LARAL + ++L+DE SALD ++ MQ L LQ+ Sbjct: 133 QITEFADRNINQLSGGQKQRVALARALVTEPKILLLDEPLSALDAHLKVRMQSVLSNLQK 192 Query: 212 NLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 +L T V++TH + EA + + I+ GQ+ Q+GTP +I P N +VA F+ Sbjct: 193 DLGITFVYVTHSMSEAFSMADRVVIMSRGQIEQIGTPEEIYREPHNRFVAEFL 245 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: 223 Number of extensions: 13 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: 376 Length adjustment: 28 Effective length of query: 247 Effective length of database: 348 Effective search space: 85956 Effective search space used: 85956 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