Align spermidine/putrescine ABC transporter, permease protein PotC (characterized)
to candidate WP_011841150.1 RSPH17029_RS08330 ABC transporter permease
Query= CharProtDB::CH_088340 (264 letters) >NCBI__GCF_000015985.1:WP_011841150.1 Length = 268 Score = 150 bits (380), Expect = 2e-41 Identities = 84/251 (33%), Positives = 146/251 (58%), Gaps = 6/251 (2%) Query: 8 GGFMTAIYAYL---YIPIIILIVNSFNSSR-FGINWQGFTTKWYSLLMNNDSLLQAAQHS 63 GGF AYL Y PII+L + +FN GF+TKW+ + +L QA ++S Sbjct: 4 GGFRIYALAYLLFLYAPIILLPLFAFNEGTVIAFPLTGFSTKWFVQAAHQPTLWQAVKNS 63 Query: 64 LTMAVFSATFATLIGSLTAVALYRYRFRGKPFVSGMLFVVMMSPDIVMAISLLVLFMLLG 123 L +A ++ +T++G A A RY F GK + G++ + ++ P+I++A+SLLV+ + LG Sbjct: 64 LIIAGSASVLSTVLGIFAARASTRYHFPGKAGLMGLIMLPLVLPEIIVAVSLLVVLLGLG 123 Query: 124 IQLGFWSLLFSHITFCLPFVVVTVYSRLKGFDVRMLEAAKDLGASEFTILRKIILPLAMP 183 I L ++++ H+ C PF + + S + D + EAA DLG + + R IILPL MP Sbjct: 124 INLTIFTVILGHVLICTPFTIAILTSAFQSLDRSLEEAAYDLGETAISTFRLIILPLVMP 183 Query: 184 AVAAGWVLSFTLSMDDVVVSSFVTGPSYEILPLKIYSMVKVGVS-PEVNALATILLVLSL 242 + + ++SFT+S+D+ +++ F+ G + LP+ I+S + + P + AL T+L+ S+ Sbjct: 184 GIISSLLISFTISLDEFIIAFFLAG-TEPTLPIYIFSQFRFPQAVPVIMALGTVLVACSI 242 Query: 243 VMVIASQLIAR 253 V++ ++ R Sbjct: 243 VLLATAEYFRR 253 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: 195 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: 264 Length of database: 268 Length adjustment: 25 Effective length of query: 239 Effective length of database: 243 Effective search space: 58077 Effective search space used: 58077 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 Apr 10 2024. 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