Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate 8500827 DvMF_1568 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= uniprot:B2TBJ8 (250 letters) >FitnessBrowser__Miya:8500827 Length = 224 Score = 137 bits (345), Expect = 2e-37 Identities = 81/221 (36%), Positives = 122/221 (55%), Gaps = 10/221 (4%) Query: 3 FDFDFLFDTI-KQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILV 61 FD DFL D + L A + ++ L S + G L ++I +RV R A AY + Sbjct: 2 FDVDFLVDRVFPSLNAGLWMSVKLIVPSAVFGLLFGVIIGIVRVFGKPWMQRIANAYTAL 61 Query: 62 FRGSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLM 121 FRG PLL+Q+F++Y+G+ G+ E PY +VL LC+A Y +E +RG L+ Sbjct: 62 FRGVPLLVQLFILYFGLPNIGIYLE---------PYAASVLGFILCSAAYNSEYVRGALL 112 Query: 122 AVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVT 181 ++ GQ+ A ++G S L ++ P A+R+ LP E V L+K ++LA ++T E+T Sbjct: 113 SIRQGQLRAAQALGFSTMQTLVSIVVPQAVRRALPGCGNEIVYLIKYSSLAYVITCIELT 172 Query: 182 GVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLETR 222 G A+ + +T+R TEVF+ YLFL V LL LE R Sbjct: 173 GEAKVLASRTFRFTEVFLVVGAYYLFLVTVASWLLHKLEER 213 Lambda K H 0.331 0.143 0.431 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: 152 Number of extensions: 8 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: 250 Length of database: 224 Length adjustment: 23 Effective length of query: 227 Effective length of database: 201 Effective search space: 45627 Effective search space used: 45627 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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