Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_046007888.1 OLEAN_RS02305 ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_000967895.1:WP_046007888.1 Length = 270 Score = 146 bits (368), Expect = 8e-40 Identities = 80/220 (36%), Positives = 127/220 (57%), Gaps = 2/220 (0%) Query: 49 LAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKI 108 L I G++ IMG SG+GK+T++RL+ + P G +L+DG D+ + A+L E+R+K + Sbjct: 28 LDIPRGKVTAIMGPSGTGKTTLLRLIGGQLLPDSGSILVDGHDVPTLKRAQLFELRKKSM 87 Query: 109 AMVFQSFALMPHMTVLDNTAFGMEL-AGIAAQERREKALDALRQVGLENYAHAYPDELSG 167 M+FQS AL ++V DN AF + + + R+ L L VGL P ELSG Sbjct: 88 GMLFQSGALFTDLSVFDNVAFPIRVHTDLPESMIRDLVLMKLEAVGLRGARDLMPAELSG 147 Query: 168 GMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDE 227 GM +RV LAR +A++P+++L DE F+ LDP+ + T V ++HD+DE Sbjct: 148 GMARRVALARTIALDPEMMLYDEPFTGLDPISLGVTVKLIKSFNDALGLTSVLVTHDIDE 207 Query: 228 AMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRG 267 A I D + ++ G+V+ TP+ ++ N ++ VR F +G Sbjct: 208 ACSIADYVCLLSEGKVIGFDTPENLIKN-GSEQVRQFMQG 246 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: 232 Number of extensions: 10 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: 400 Length of database: 270 Length adjustment: 28 Effective length of query: 372 Effective length of database: 242 Effective search space: 90024 Effective search space used: 90024 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 (21.8 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