Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_044200027.1 X939_RS0117935 ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_000566685.1:WP_044200027.1 Length = 274 Score = 127 bits (320), Expect = 2e-34 Identities = 78/204 (38%), Positives = 113/204 (55%), Gaps = 5/204 (2%) Query: 45 DVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAFRM 104 D+SL I G I G SG+GK+T++R I L P +G++ + LD + Sbjct: 2 DISLYIPMGSRLAITGPSGAGKTTILRQIAGLSIPQAGKITVGDNCWLDTQNGISIPPQG 61 Query: 105 RRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGLSGYDAKFPHQL 164 R + VFQ +AL PH TV +N+ YG R + D + + M ++ +GL + P QL Sbjct: 62 RNIGFVFQDYALFPHLTVYENLSYGLR----NGQDTKVVDML-LERIGLMELAGRKPDQL 116 Query: 165 SGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFITHDL 224 SGG +QRV LARAL ++L+DEA SALD +R +Q +L+LQR T++ +TH L Sbjct: 117 SGGQQQRVALARALVRKPVLLLLDEALSALDSAMRLSLQGLILELQREQGFTLIMVTHHL 176 Query: 225 DEALRIGSEIAILRDGQVVQVGTP 248 E R+ + L GQVV G+P Sbjct: 177 GEIFRMADRVVQLDHGQVVGQGSP 200 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: 187 Number of extensions: 8 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: 274 Length adjustment: 25 Effective length of query: 250 Effective length of database: 249 Effective search space: 62250 Effective search space used: 62250 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 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