Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 8499753 DvMF_0518 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Miya:8499753 Length = 251 Score = 192 bits (488), Expect = 6e-54 Identities = 92/227 (40%), Positives = 142/227 (62%), Gaps = 3/227 (1%) Query: 24 LQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERGMVF 83 L + F V + +FV I+GP+GCGK+T L ++ L A++G++L+DG P + VF Sbjct: 26 LDDISFSVAEGEFVAIVGPTGCGKTTFLNALSCLLPASNGQILIDGTPADPKRHNISYVF 85 Query: 84 QSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSGGMQQR 143 Q T PW T+ +N+ +G+ +G P + ER + + VGL +P Q+S MQQR Sbjct: 86 QEPTCLPWRTVRENVAYGMEVKGRPRKEIDERLDHILDMVGLTQCASLYPNQISASMQQR 145 Query: 144 TAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDEAIFMA 203 A++RA A DP +LLMDEP+G LD + R +++ L+ +W R TVLF+TH+I+EA++++ Sbjct: 146 IAVSRAFAVDPDLLLMDEPYGQLDVKLRFYLEDELVNLWRKLRSTVLFITHNIEEAVYVS 205 Query: 204 NRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDLKARLTEEIR 250 R+ V S +P RIK E+ VDLP PR + PEF+ ++ +T IR Sbjct: 206 ERILVLSNKPTRIKAEVKVDLPRPRDF---MDPEFVRIREHVTNLIR 249 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: 168 Number of extensions: 6 Number of successful extensions: 1 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: 251 Length adjustment: 24 Effective length of query: 235 Effective length of database: 227 Effective search space: 53345 Effective search space used: 53345 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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