Align TreV, component of Trehalose porter (characterized)
to candidate Pf1N1B4_3027 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q97ZC0 (324 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3027 Length = 372 Score = 232 bits (592), Expect = 9e-66 Identities = 121/281 (43%), Positives = 186/281 (66%), Gaps = 7/281 (2%) Query: 1 MTVELIDIVKKYGKNIVINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60 + V+ ++ +++G+ ++ ++ I+ GEFF +LGPSG GK+T L+++AG E+ G I Sbjct: 30 LAVQFTNVSRQFGEVKAVDRVSIDIQDGEFFSMLGPSGSGKTTCLRLIAGFEQPSAGSIR 89 Query: 61 ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120 GA+ PP +R+V VFQ+YAL+P+M+V DN+A+ LK++G+ K E +R E+A ++ Sbjct: 90 IHGAEAAGLPPYQRDVNTVFQDYALFPHMNVLDNVAYGLKVKGVGKTERQKRAEEALDMV 149 Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180 + ++K Q+SGGQ+QRVALARA+V P LLDEPL LD ++R +GELK++Q+ Sbjct: 150 ALGGYGERKPVQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQR 209 Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNF 240 +L TFI+VTHDQ EALS++DR+A+ +KG+ EQV P+ LY P T +VA+FVG N Sbjct: 210 QLGITFIFVTHDQTEALSMSDRVAVFNKGRIEQVDTPRNLYMKPATTFVAEFVG--TSNV 267 Query: 241 LPGELMKE---KAQEIGFRPEWVEVGKGNLSCMVESVEASG 278 + G+L ++ Q RPE V +G L+ +E SG Sbjct: 268 IRGDLAQQLSGNPQPFSIRPEHVRFAEGPLAS--HEIEVSG 306 Lambda K H 0.318 0.137 0.385 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: 297 Number of extensions: 10 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: 324 Length of database: 372 Length adjustment: 29 Effective length of query: 295 Effective length of database: 343 Effective search space: 101185 Effective search space used: 101185 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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