Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 136 bits (343), Expect = 4e-37 Identities = 76/211 (36%), Positives = 121/211 (57%), Gaps = 5/211 (2%) Query: 43 LNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFDGDNILDLGAKALRAF 102 L+DVSL I G ++G SG+GK+TL++ INRL+E +G + +G ++ LR Sbjct: 17 LDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVAELR-- 74 Query: 103 RMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKWIDTVGL-SGYDAKFP 161 RR+ VFQ L PH +V +NV R++GV +++ + +D V L + + + P Sbjct: 75 --RRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADFAERRP 132 Query: 162 HQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLLQLQRNLAKTIVFIT 221 QLSGG QRVG ARALAA ++LMDE F ALDP+ R ++ L + T + +T Sbjct: 133 AQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLIVT 192 Query: 222 HDLDEALRIGSEIAILRDGQVVQVGTPNDIL 252 HD+ EAL + + ++ +G+++ P ++ Sbjct: 193 HDMAEALLLADRVIVIGEGRILADQPPRALI 223 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: 160 Number of extensions: 9 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: 252 Length adjustment: 25 Effective length of query: 250 Effective length of database: 227 Effective search space: 56750 Effective search space used: 56750 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 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