Align glycine betaine-binding periplasmic protein (characterized)
to candidate WP_072908816.1 BUB13_RS11060 proline/glycine betaine ABC transporter substrate-binding protein ProX
Query= CharProtDB::CH_024698 (330 letters) >NCBI__GCF_900142125.1:WP_072908816.1 Length = 339 Score = 241 bits (614), Expect = 2e-68 Identities = 129/317 (40%), Positives = 174/317 (54%), Gaps = 12/317 (3%) Query: 25 PGKGITVNPVQSTITEETFQTLLVSRALEKLGYTVNKPSEVDYNVGYTSLASGDATFTAV 84 PGKG+ V P ++T FQ LV L++LGY V P E+ + Y S+A GD + Sbjct: 24 PGKGVEVKPGRATWNTGYFQEALVRTGLKELGYEVEDPKELQNPLFYQSVALGDLDYWTN 83 Query: 85 NWTPLHDNMYEAAGGDKKFYREGVFVN-GAAQGYLIDKKTADQYKITNIAQLKDPKIAKL 143 W P+H +K+ G G QGYL+ KK +QY I ++ K P++ K Sbjct: 84 GWFPIHYAQMPK-NHEKRMELVGYVAKAGGLQGYLVSKKEVEQYNIKSLDDFKRPEVKKA 142 Query: 144 FDTNGDGKADLTGCNPGWGCEGAINHQLAAYELTNTVTHNQGNYAAMMADTISRYKEGKP 203 FD NGDGKADLT C PGWGCE I + AY L + + + Y+A MAD + RY+ GKP Sbjct: 143 FDANGDGKADLTACPPGWGCEKTIGFHMEAYGLEDHINLIKAGYSASMADALGRYQSGKP 202 Query: 204 VFYYTWTPYWVSNELKPGKDVVWLQVP-FSALPGDK-NADTKLPNG--------ANYGFP 253 VF+YTW P W +LKPG+DV+W+ VP K AD +G GF Sbjct: 203 VFFYTWAPNWTIFKLKPGEDVLWMNVPEIKPTEAQKAQADRLTASGVVGAVTDPVKLGFI 262 Query: 254 VSTMHIVANKAWAEKNPAAAKLFAIMQLPVADINAQNAIMHDGKASEGDIQGHVDGWIKA 313 + + IVANK + E NPAA K F + LP+ADI+ QN M +G+ S+ DI HV WI Sbjct: 263 AADIRIVANKRFLENNPAAKKFFEVFTLPLADISEQNTRMENGEKSKEDIDRHVKEWIAK 322 Query: 314 HQQQFDGWVNEALAAQK 330 +Q+ ++GW+ A A K Sbjct: 323 NQETWNGWLEAARKAAK 339 Lambda K H 0.315 0.131 0.400 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: 392 Number of extensions: 21 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: 330 Length of database: 339 Length adjustment: 28 Effective length of query: 302 Effective length of database: 311 Effective search space: 93922 Effective search space used: 93922 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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