Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate WP_003940114.1 C1M55_RS25960 ATP-binding cassette domain-containing protein
Query= CharProtDB::CH_001555 (400 letters) >NCBI__GCF_002893965.1:WP_003940114.1 Length = 371 Score = 188 bits (478), Expect = 2e-52 Identities = 96/226 (42%), Positives = 150/226 (66%), Gaps = 6/226 (2%) Query: 41 SLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAEL 100 ++ V L G+I ++G SG GK+T +R++NRLIEPT G + +DG A + A L Sbjct: 15 TIAVDALDLECPTGKITALVGPSGCGKTTSLRMINRLIEPTSGTISLDGESTAGMDPALL 74 Query: 101 REVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLE-NYAH 159 R ++I V Q L PH T++DN A L G + +E R +A++ L VGL N+A Sbjct: 75 R----RRIGYVIQHAGLFPHRTIVDNIATMPRLLGASKKESRTRAMELLETVGLTTNFAD 130 Query: 160 SYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIV 219 YP +LSGG +QRVG+ARALA +P +LMDE FSA+DP++R ++QDE ++LQ + +TI+ Sbjct: 131 RYPWQLSGGQQQRVGVARALAADPSFMLMDEPFSAVDPVVRGQLQDEFLRLQKEIGKTII 190 Query: 220 FISHDLDEAMRIGDRIAIMQNGEVV-QVGTPDEILNNPANDYVRTF 264 ++HD+DEA+++GD++ +++ G ++ Q TP E+L PA+++V F Sbjct: 191 IVTHDIDEALKLGDQVVVLRTGGILAQAATPLELLTQPADEFVADF 236 Lambda K H 0.319 0.137 0.378 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: 344 Number of extensions: 16 Number of successful extensions: 4 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: 400 Length of database: 371 Length adjustment: 30 Effective length of query: 370 Effective length of database: 341 Effective search space: 126170 Effective search space used: 126170 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 (21.7 bits) S2: 50 (23.9 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