Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_051305669.1 G494_RS0112690 amino acid ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_000429965.1:WP_051305669.1 Length = 247 Score = 154 bits (390), Expect = 2e-42 Identities = 93/237 (39%), Positives = 137/237 (57%), Gaps = 6/237 (2%) Query: 35 LEKT--GLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDI 92 LEKT G + D ++ ++ GE+ V++G SGSGKST +R LN L E G + +DG+ + Sbjct: 13 LEKTYPGNLKALDDFTVRVKRGEVVVVVGPSGSGKSTFLRCLNGLEEIDSGSITVDGIPL 72 Query: 93 AKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQ-ERREKALDALRQ 151 + L E+RR+ + MVFQ+F L PHMTVL+N +L ++ E E +L L + Sbjct: 73 DDREEHRL-EIRRE-VGMVFQAFNLFPHMTVLENVNLAQQLVRRRSRSEATEFSLALLDK 130 Query: 152 VGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQ 211 VG+ A YPD LSGG +QRV +ARALA+ P ++L DEA SALDP + E+ D + L Sbjct: 131 VGVSEKARVYPDALSGGQQQRVAIARALALMPKVMLFDEATSALDPEMIGEVLDVMRSL- 189 Query: 212 AKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268 A T+V ++H++ A + DR+ M+ G +V+ PA R F R + Sbjct: 190 AGEGMTMVVVTHEMGFAREVSDRVVFMEQGRIVEEAATATFFTAPARKRTRDFLRQI 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: 248 Number of extensions: 15 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: 247 Length adjustment: 27 Effective length of query: 373 Effective length of database: 220 Effective search space: 82060 Effective search space used: 82060 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: 48 (23.1 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