Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate CCNA_03226 CCNA_03226 basic amino acid/polyamine antiporter (APA) family transporter
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__Caulo:CCNA_03226 Length = 438 Score = 202 bits (515), Expect = 1e-56 Identities = 129/432 (29%), Positives = 219/432 (50%), Gaps = 8/432 (1%) Query: 1 MSQAKSNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFA 60 M+ +S +GV L + NM+GSG+ MLP LA G ++I+W++T GS+ LA+ FA Sbjct: 6 MTAVRSKPLGVWMCAALVVGNMIGSGVFMLPASLAPYGWNAVIAWILTIGGSLCLAYVFA 65 Query: 61 KCGMFSRKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLGA-SL 119 K ++GG Y E AFG++ F+ ++Y +S+ +AN AIAI+A+ Y + L + Sbjct: 66 KLAGAFPRAGGPFAYTEEAFGRAPGFLVAWSYWISVWVANAAIAIAAISYLSVFLPVIAK 125 Query: 120 SPVQIGLATIGVLWICTVANFGGARITGQISSITVWGVIIP---VVGLCIIGWFWFSPTL 176 P L T+ V+W T N GAR G +T ++P V GL + P Sbjct: 126 VPALPALLTVAVVWTATAINCAGARSAGWTQVVTTVLKLVPLIAVAGLAVSVLLRKGPAA 185 Query: 177 YVDSWNPHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAV 236 + + P A +++ ++ A+TLWA LG+E+A D V++P R +P A L GT A + Sbjct: 186 -ITPFEP-SALSGASITAAAALTLWALLGVETATIPADKVKDPARTIPRATLAGTAFAGL 243 Query: 237 IYIVSTNVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTI 296 +Y+V ++ + + P L S APF + + + A +S G+L GW Sbjct: 244 VYLVVSSGVLLLTPTAVLQGSNAPFVDFVSYHGGGDFRLALAAFATISALGALNGWSLIQ 303 Query: 297 AQVFKSSSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLA 356 ++ + + EG FP F++ + PV+ L ++ + L LM + S+ F + L+ Sbjct: 304 GELPAAMAREGVFPAWFAKTSANGTPVRAHLVSSVLVTILVLMNYAKSMADAFTFMALLS 363 Query: 357 VVTNIIPYILSMAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSI 416 + + Y+ A++ +Q + SKA VA +GA+YS + +G L+G + Sbjct: 364 TTSTLFAYLFCSLAVLRLQGQGRMDRSKA--LTLVAALGALYSVWTFSGAGWSVTLWGLV 421 Query: 417 VTFLGWTLYGLV 428 + +G +Y L+ Sbjct: 422 LLAVGAPIYWLM 433 Lambda K H 0.323 0.136 0.411 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: 583 Number of extensions: 28 Number of successful extensions: 7 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: 439 Length of database: 438 Length adjustment: 32 Effective length of query: 407 Effective length of database: 406 Effective search space: 165242 Effective search space used: 165242 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 51 (24.3 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