Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 122 bits (307), Expect = 1e-32 Identities = 73/240 (30%), Positives = 131/240 (54%), Gaps = 9/240 (3%) Query: 26 RGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGM------PVQKRNVAMVY 79 +G + V++G + +GK++++R++ L PT G + DG D+ M V++ ++MV+ Sbjct: 55 KGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKVRRAKLSMVF 114 Query: 80 QQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLKLTPYLDRTPLNLSGGQQQR 139 Q F P +TV N A + + G D T ++ +A E + L + + P LSGG QQR Sbjct: 115 QSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQVGLEAWAESMPDELSGGMQQR 174 Query: 140 TALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQSGAIFVYATTEPSEALLLG 199 LAR L + ++LMDE + LD +R E+++EL K+ A++ V+ + + EA+ +G Sbjct: 175 VGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFISHDLDEAMRIG 234 Query: 200 GNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTLDVTKSGNVFTRPSGVTIPV 259 A + GRV Q G E+ + P + F ++ ++ +G++ T+ + VTIP+ Sbjct: 235 DRIAIMEGGRVVQVGTPEEILQNPADDYVRAFFRG--VDPTNILTAGDIATQ-TQVTIPI 291 Lambda K H 0.319 0.136 0.392 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: 310 Number of extensions: 9 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: 358 Length of database: 415 Length adjustment: 30 Effective length of query: 328 Effective length of database: 385 Effective search space: 126280 Effective search space used: 126280 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 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