Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate 8501224 DvMF_1958 spermidine/putrescine ABC transporter membrane protein (RefSeq)
Query= CharProtDB::CH_088340 (264 letters) >FitnessBrowser__Miya:8501224 Length = 266 Score = 296 bits (758), Expect = 3e-85 Identities = 135/254 (53%), Positives = 198/254 (77%) Query: 4 RLLRGGFMTAIYAYLYIPIIILIVNSFNSSRFGINWQGFTTKWYSLLMNNDSLLQAAQHS 63 R LR G + +YA+LY+PI+++IV SFN +R+ W+GFT KWYS L N L+ AA +S Sbjct: 13 RTLRTGLVWLVYAFLYVPILVVIVYSFNDARYTTEWKGFTLKWYSALAANGPLVDAALNS 72 Query: 64 LTMAVFSATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLLG 123 L++A +AT AT++G+L A+ + RYRF G+ + G ++V+ +SPDIVM ISLL+ F+ +G Sbjct: 73 LSVATLAATIATVLGTLAAICIRRYRFPGRKVLHGCIYVLTVSPDIVMGISLLIFFIAMG 132 Query: 124 IQLGFWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPLAMP 183 +QLGFW+LL +H+T LPFV VTV +RL FD +++EAA+DLGASE+ R ++LPLA P Sbjct: 133 VQLGFWTLLAAHVTLALPFVTVTVLARLAEFDEQLIEAARDLGASEWRAFRHVLLPLAAP 192 Query: 184 AVAAGWVLSFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVLSLV 243 AVAAGW+LSFTLSMDDV+VS FVTGP++E+LPL++YSMV++GV P++NAL+ ++ +++V Sbjct: 193 AVAAGWLLSFTLSMDDVLVSFFVTGPTFEVLPLRVYSMVRLGVKPDINALSAVMFTVTIV 252 Query: 244 MVIASQLIARDKTK 257 +V+ +Q + R + K Sbjct: 253 LVLLAQTLTRTRRK 266 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: 216 Number of extensions: 6 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: 266 Length adjustment: 25 Effective length of query: 239 Effective length of database: 241 Effective search space: 57599 Effective search space used: 57599 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