Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_090275879.1 BLU11_RS18455 methionine ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_900105005.1:WP_090275879.1 Length = 334 Score = 169 bits (429), Expect = 8e-47 Identities = 91/225 (40%), Positives = 142/225 (63%), Gaps = 2/225 (0%) Query: 49 LAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKI 108 L IE G+++ I+G SG+GKST++RL+NRL EP+ G++++ G D ++ LR R++ + Sbjct: 26 LTIEAGQVYGIIGHSGAGKSTLLRLINRLEEPSNGRIMVAGEDTTALNAEGLRRFRQR-V 84 Query: 109 AMVFQSFALMPHMTVLDNTAFGMELAGIA-AQERREKALDALRQVGLENYAHAYPDELSG 167 M+FQ F L+ TV DN A + LAG A Q+ + L +VGL ++A YP +LSG Sbjct: 85 GMIFQHFNLLSSATVADNVALPLRLAGSANRQQIAARVASLLDRVGLSDHASKYPAQLSG 144 Query: 168 GMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDE 227 G +QRVG+ARALA P ILL DEA SALDP ++ L ++ + TIV I+H++D Sbjct: 145 GQKQRVGIARALATEPSILLCDEATSALDPHTTGQVLQLLSEINRELNLTIVLITHEMDV 204 Query: 228 AMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQ 272 R+ D++A+M G +V+ GT ++ +P + R+F G + ++ Sbjct: 205 IRRVCDQVAVMDGGRIVEQGTVADVFLHPQHPTTRSFVFGSESAE 249 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: 282 Number of extensions: 16 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: 334 Length adjustment: 30 Effective length of query: 370 Effective length of database: 304 Effective search space: 112480 Effective search space used: 112480 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