Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate 209025 DVU0096 polyamine ABC transporter, permease protein
Query= CharProtDB::CH_088340 (264 letters) >MicrobesOnline__882:209025 Length = 257 Score = 277 bits (708), Expect = 2e-79 Identities = 135/257 (52%), Positives = 192/257 (74%) Query: 1 MIGRLLRGGFMTAIYAYLYIPIIILIVNSFNSSRFGINWQGFTTKWYSLLMNNDSLLQAA 60 M R L ++ +YA+LY+PI+++IV SFN+S++ W GFT WY+ L+ N L+ AA Sbjct: 1 MFMRRLGMAWVWLVYAFLYLPILVVIVYSFNASKYSTAWSGFTLDWYAKLLANTPLVDAA 60 Query: 61 QHSLTMAVFSATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFM 120 +SL++A SAT ATL+GSL A+ L+RYRF G+ + ++V+ +SPDIVM ISLL+ F+ Sbjct: 61 LNSLSVATLSATLATLLGSLAAMCLHRYRFPGRKVLHSSIYVLTVSPDIVMGISLLIFFI 120 Query: 121 LLGIQLGFWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPL 180 L ++LGF +LL +H T LPFV VTV +RL FD ++EAA+DLGASE R IILPL Sbjct: 121 ALRMELGFVTLLIAHTTLGLPFVTVTVLARLAEFDEHLVEAARDLGASEAAAYRHIILPL 180 Query: 181 AMPAVAAGWVLSFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVSPEVNALATILLVL 240 +PAVAAGW+LSFTLSMDDV++S FVTGPS+E+LPLKIYSMV++GV P++NAL+ ++ + Sbjct: 181 TLPAVAAGWLLSFTLSMDDVLISFFVTGPSFEVLPLKIYSMVRLGVKPDINALSAVMFGV 240 Query: 241 SLVMVIASQLIARDKTK 257 ++V+V+ +Q + + K Sbjct: 241 TIVLVLLAQALTNMRRK 257 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: 238 Number of extensions: 13 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: 264 Length of database: 257 Length adjustment: 25 Effective length of query: 239 Effective length of database: 232 Effective search space: 55448 Effective search space used: 55448 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