Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= uniprot:Q88GX0 (260 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 150 bits (380), Expect = 3e-41 Identities = 81/222 (36%), Positives = 131/222 (59%), Gaps = 4/222 (1%) Query: 36 LRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQVDGIDLAATTREAAQV- 94 ++D ++ +GE V+ G SGSGKST++R +NRL G + +DG D+ A + Sbjct: 46 VQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGEDIVAMNDDQLVKV 105 Query: 95 -RSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMYLSKVGIESQAHKYP 153 R+ + MVFQ F L PHM+VL N + G+ ++ E+RA L +VG+E+ A P Sbjct: 106 RRAKLSMVFQSFALMPHMTVLQNAAFG-LEMDGVDKQTREQRALQALEQVGLEAWAESMP 164 Query: 154 SQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLVQL-AGTGMTMLCVT 212 +LSGG QQRV +AR L + P I+L DE SALDP + E+ D L++L A T++ ++ Sbjct: 165 DELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQAKAKRTIVFIS 224 Query: 213 HEMGFARQVAERVLFLEGGQIIEDSPPQVFFNQPRTERAKAF 254 H++ A ++ +R+ +EGG++++ P+ P + +AF Sbjct: 225 HDLDEAMRIGDRIAIMEGGRVVQVGTPEEILQNPADDYVRAF 266 Lambda K H 0.322 0.137 0.395 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: 242 Number of extensions: 13 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: 260 Length of database: 415 Length adjustment: 28 Effective length of query: 232 Effective length of database: 387 Effective search space: 89784 Effective search space used: 89784 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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