Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate WP_046010385.1 OLEAN_RS18015 choline ABC transporter ATP-binding protein
Query= CharProtDB::CH_001555 (400 letters) >NCBI__GCF_000967895.1:WP_046010385.1 Length = 402 Score = 279 bits (713), Expect = 1e-79 Identities = 145/281 (51%), Positives = 196/281 (69%), Gaps = 4/281 (1%) Query: 5 LEIKNLYKIFGEHPQRAFKYIEQGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMGLSG 64 + IKNL IFG+ P+RA ++QG +E+I TGL +GV +A+L I +GEI V+MGLSG Sbjct: 2 INIKNLDVIFGDQPERALALLDQGQEREEISNSTGLVVGVNNANLQISKGEICVLMGLSG 61 Query: 65 SGKSTMVRLLNRLIEPTRGQVLIDG----VDIAKISDAELREVRRKKIAMVFQSFALMPH 120 SGKS+++R +N L + TRG + ID +D+ LR +R K+++MVFQ FALMP Sbjct: 62 SGKSSLLRCINGLNDTTRGSIEIDHEGEVIDLVSADADMLRAIRTKRMSMVFQKFALMPW 121 Query: 121 MTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPDELSGGMRQRVGLARALA 180 +TV N A +EL G++ +E +++ L VGLE +A P ELSGGM+QRVGLARAL Sbjct: 122 LTVAQNVAMPLELQGLDKKEIKQRVDAQLELVGLEQWAKHKPSELSGGMQQRVGLARALV 181 Query: 181 INPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQN 240 DILLMDE FSALDPLIRT++QDEL++LQ K +TI+F+SHDLDEA+++G IAIM++ Sbjct: 182 TESDILLMDEPFSALDPLIRTQLQDELIQLQEKLNKTIIFVSHDLDEALKLGTNIAIMKD 241 Query: 241 GEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIAR 281 GE+VQ G P+ I+ NP NDYV+ F + V AK I R Sbjct: 242 GEIVQQGKPESIVLNPVNDYVKQFVAHTNPIHVLKAKSIMR 282 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: 409 Number of extensions: 15 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: 400 Length of database: 402 Length adjustment: 31 Effective length of query: 369 Effective length of database: 371 Effective search space: 136899 Effective search space used: 136899 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