Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate GFF17 Psest_0017 ectoine/hydroxyectoine ABC transporter, permease protein EhuD
Query= uniprot:Q31RN9 (396 letters) >FitnessBrowser__psRCH2:GFF17 Length = 219 Score = 111 bits (277), Expect = 2e-29 Identities = 64/201 (31%), Positives = 110/201 (54%), Gaps = 6/201 (2%) Query: 192 LLTLATALISMVCSLPLGILLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVMVP 251 L T+ AL ++ LG+ LA+GR+S L + W IE R PL+ ++F + P Sbjct: 21 LTTIGIALAGFAIAVVLGLFLAIGRRSRLRWLSWPITGLIEFIRSTPLLIQVYFLFYVFP 80 Query: 252 LMLDSEWRIDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFI 311 + + + I+G+ + + Y AE R GL A+P+ Q+EA AL + + YR + Sbjct: 81 ---NYGLNLSAMQAGIIGIALHYACYTAEVYRAGLDAVPRSQWEAVTALNMKPWTAYRDV 137 Query: 312 VLPQALRISIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILANPAYLGRYAEVYLFLG 371 +LPQALR +PA+ +++L+DT +LS + ++E++ +++I + RY E +G Sbjct: 138 ILPQALRPVLPALGNYLISILKDTPVLSAITVVEIMQRAKNIGSESF---RYLEPITMVG 194 Query: 372 VLYWLCCYGLAQLSRRLEQRL 392 + + + GLA RRLE R+ Sbjct: 195 IFFLILSLGLAWCVRRLENRM 215 Lambda K H 0.329 0.142 0.471 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: 231 Number of extensions: 10 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: 396 Length of database: 219 Length adjustment: 26 Effective length of query: 370 Effective length of database: 193 Effective search space: 71410 Effective search space used: 71410 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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