Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_052717993.1 OLEAN_RS11540 ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_000967895.1:WP_052717993.1 Length = 362 Score = 149 bits (377), Expect = 1e-40 Identities = 87/273 (31%), Positives = 149/273 (54%), Gaps = 18/273 (6%) Query: 26 EKGLSKEQILEKTGLSLGVKDASLAIE-------------EGEIFVIMGLSGSGKSTMVR 72 +K +S E+ +K +L + + LAI+ EGEI ++G SG GK+T ++ Sbjct: 3 DKNISNERYTQKKTTALELFNIQLAIDNHAILQALTFDLTEGEILCLLGPSGCGKTTALK 62 Query: 73 LLNRLIEPTRGQVLIDGVDIAKISDAELREV-RRKKIAMVFQSFALMPHMTVLDNTAFGM 131 + L P +G + + G + SD + + ++ I +FQ +AL PHMTV N A+G Sbjct: 63 TIAGLSIPQQGHISLFGDTV--FSDNIINQPPEQRSIGFIFQDYALFPHMTVSQNIAYG- 119 Query: 132 ELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEA 191 L+ + QER+++ ++L V L + YP ELSGG +QR+ +ARALA P +LLMDE Sbjct: 120 -LSHLGKQERQQRIKESLELVELSDLEQRYPHELSGGQQQRIAVARALAPKPKLLLMDEP 178 Query: 192 FSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDE 251 FS +D ++ M +L +L +H + +F++H +EA D+ A+M NG + Q+ P + Sbjct: 179 FSNIDGQVKRRMMADLRRLLKEHNISCIFVTHAKEEAFAFADKTAVMINGHIEQLDIPAK 238 Query: 252 ILNNPANDYVRTFFRGVDISQVFSAKDIARRSP 284 + N P V F +++ + ++ + + P Sbjct: 239 VFNQPNTFAVAEFMEAGNLATLKHSQQVLDKIP 271 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: 320 Number of extensions: 17 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: 362 Length adjustment: 30 Effective length of query: 370 Effective length of database: 332 Effective search space: 122840 Effective search space used: 122840 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: 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