Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate SM_b20282 SM_b20282 spermidine/putrescine ABC transporter permease
Query= CharProtDB::CH_088340 (264 letters) >FitnessBrowser__Smeli:SM_b20282 Length = 263 Score = 130 bits (326), Expect = 4e-35 Identities = 69/238 (28%), Positives = 132/238 (55%), Gaps = 2/238 (0%) Query: 17 YLYIPIIILIVNSFNSSRF-GINWQGFTTKWYSLLMNNDSLLQAAQHSLTMAVFSATFAT 75 YL +P+ ++ SF + F +T WY+ ++N+ ++A+ +S+ +A+ + AT Sbjct: 23 YLLLPLALMTAMSFKDASFVAFPITDWTLNWYAQVLNDKQFIEASLYSIGIALATTAAAT 82 Query: 76 LIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLLGIQLGFWSLLFSH 135 +IG A+ + GK + + + + P ++ AIS+ + + I G +++ SH Sbjct: 83 VIGVWIALLVSTEGIWGKAIIFALACLPAVVPGLINAISMRIFIRTVDIPTGTAAIILSH 142 Query: 136 ITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPLAMPAVAAGWVLSFTL 195 +PFVV+ V +RL+ +++AA+DLGA F ++ +P MPA+ G + Sbjct: 143 AVHAVPFVVIMVLTRLRSMPANLVDAARDLGADRFVAFLRVTIPYLMPALLGGMIFCVLT 202 Query: 196 SMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVLSLVMVIASQLIAR 253 S+DD V +F G LP+ I++ V+ G+SPE+NA+ATI+LV++ + + ++ + R Sbjct: 203 SIDD-FVRTFFLGGYKPTLPMLIFAKVQGGMSPEINAMATIVLVVTAAVGVYAEHLTR 259 Lambda K H 0.329 0.141 0.412 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: 155 Number of extensions: 7 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: 264 Length of database: 263 Length adjustment: 25 Effective length of query: 239 Effective length of database: 238 Effective search space: 56882 Effective search space used: 56882 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: 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