Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_072908814.1 BUB13_RS11050 glycine betaine/L-proline ABC transporter ATP-binding protein ProV
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_900142125.1:WP_072908814.1 Length = 415 Score = 152 bits (383), Expect = 1e-41 Identities = 85/214 (39%), Positives = 128/214 (59%), Gaps = 13/214 (6%) Query: 12 VFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAP 71 +FE K + T +Q FE+ + I+G SG GKST++R++ L TSG+VL+DG Sbjct: 36 IFE--KTETTVGVQDASFEIFKGEIFVIMGLSGSGKSTMVRMLNRLIEPTSGQVLIDGED 93 Query: 72 VEGPG---------AERGMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAK 122 + A+ MVFQS+ L P +T+ QN FGL G+ + +++RA + + Sbjct: 94 IVAMNDDQLVKVRRAKLSMVFQSFALMPHMTVLQNAAFGLEMDGVDKQTREQRALQALEQ 153 Query: 123 VGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIW 182 VGL + + P +LSGGMQQR +AR LA DP ILLMDE F ALD R MQ+ LL + Sbjct: 154 VGLEAWAESMPDELSGGMQQRVGLARGLAVDPDILLMDEAFSALDPLIRTEMQDELLKLQ 213 Query: 183 EAERKTVLFVTHDIDEAIFMANRVAVFSARPGRI 216 ++T++F++HD+DEA+ + +R+A+ GR+ Sbjct: 214 AKAKRTIVFISHDLDEAMRIGDRIAIMEG--GRV 245 Lambda K H 0.322 0.136 0.394 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: 258 Number of extensions: 11 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: 259 Length of database: 415 Length adjustment: 28 Effective length of query: 231 Effective length of database: 387 Effective search space: 89397 Effective search space used: 89397 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: 48 (23.1 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