Align glycine betaine-binding periplasmic protein (characterized)
to candidate WP_012967377.1 KVAR_RS05310 proline/glycine betaine ABC transporter substrate-binding protein ProX
Query= CharProtDB::CH_024698 (330 letters) >NCBI__GCF_000025465.1:WP_012967377.1 Length = 332 Score = 556 bits (1434), Expect = e-163 Identities = 266/332 (80%), Positives = 293/332 (88%), Gaps = 2/332 (0%) Query: 1 MRHSVLFAT-AFATLISTQTFAADLPGKGITVNPVQSTITEETFQTLLVSRALEKLGYTV 59 MRH + AT AFATLI+T TFAADLPGKGITV P QSTI+EETFQTLLVSRALEKLGYTV Sbjct: 1 MRHRTMMATTAFATLIATSTFAADLPGKGITVKPAQSTISEETFQTLLVSRALEKLGYTV 60 Query: 60 NKPSEVDYNVGYTSLASGDATFTAVNWTPLHDNMYEAAGGDKKFYREGVFVNGAAQGYLI 119 KPSEVDYNV YTS+A+GD TF A NW PLHD+MY AAGGD KFYR+GV+V+GAAQGYLI Sbjct: 61 EKPSEVDYNVAYTSIAAGDTTFIATNWQPLHDDMYAAAGGDNKFYRKGVYVSGAAQGYLI 120 Query: 120 DKKTADQYKITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEGAINHQLAAYELTNT 179 DKKTA+QY IT+I QLKDP+IAKLFDTN DGKADLTGC PGWGCE INHQ+ AY L+ T Sbjct: 121 DKKTAEQYHITSIDQLKDPQIAKLFDTNNDGKADLTGCTPGWGCEAVINHQIDAYGLSKT 180 Query: 180 VTHNQGNYAAMMADTISRYKEGKPVFYYTWTPYWVSNELKPGKDVVWLQVPFSALPGD-K 238 VTHNQGNYAAMMADTI+RYKEGKPV YYTWTPYWVS+ LKPGKDVVWLQVPFS+LPG+ K Sbjct: 181 VTHNQGNYAAMMADTIARYKEGKPVLYYTWTPYWVSDVLKPGKDVVWLQVPFSSLPGEQK 240 Query: 239 NADTKLPNGANYGFPVSTMHIVANKAWAEKNPAAAKLFAIMQLPVADINAQNAIMHDGKA 298 N DTKL NGANYGFPV+TMHIVANK WAEKNPAAA LF++M+LP+ADINA+NA+MH+G A Sbjct: 241 NIDTKLANGANYGFPVNTMHIVANKTWAEKNPAAATLFSVMKLPIADINAENAMMHEGHA 300 Query: 299 SEGDIQGHVDGWIKAHQQQFDGWVNEALAAQK 330 SE DI GHVDGWIKAHQ FD WV ALAAQ+ Sbjct: 301 SEADINGHVDGWIKAHQPLFDSWVKAALAAQQ 332 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: 530 Number of extensions: 16 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: 330 Length of database: 332 Length adjustment: 28 Effective length of query: 302 Effective length of database: 304 Effective search space: 91808 Effective search space used: 91808 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