Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate Pf1N1B4_4994 Putrescine/proton symporter, putrescine/ornithine antiporter PotE
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4994 Length = 443 Score = 469 bits (1206), Expect = e-136 Identities = 232/430 (53%), Positives = 309/430 (71%), Gaps = 5/430 (1%) Query: 6 SNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFAKCGMF 65 S KM ++ LT L VNMMGSGIIMLPT +A++G +S++SW+VTAVGSMA+A+ F++CG++ Sbjct: 5 SKKMSLMGLTTLVTVNMMGSGIIMLPTSMAQLGAVSLLSWIVTAVGSMAIAYCFSQCGIY 64 Query: 66 SRKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTEL---LGASLSPV 122 SGG+ Y E A KSG F+ +Y Y +SL IANVA+AISAVGY T LG+ P+ Sbjct: 65 CLHSGGLSAYTEEAHAKSGFFLCSYLYFLSLGIANVAVAISAVGYMTSFVPWLGSGAIPL 124 Query: 123 QIGLATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVDSWN 182 IG T+G+LW+ T+ANFGG ITG+I +ITVWGVIIPV GL IIGWFWF P + + +WN Sbjct: 125 FIG--TVGLLWLTTMANFGGPGITGKIGAITVWGVIIPVAGLSIIGWFWFKPDVLIAAWN 182 Query: 183 PHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYIVST 242 P+ P A+ +I +TLWAFLG+ESA +D VE+P+R VP+A L GT+GAAV+Y++ST Sbjct: 183 PNSLPISDAISKAIPLTLWAFLGMESAAQASDAVEDPKRTVPLACLFGTMGAAVVYVLST 242 Query: 243 NVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQVFKS 302 VI GIVPN ELANS+APF L +A MFTP VG ++MAL VM+C GSLLGWQFT+AQ K Sbjct: 243 TVIQGIVPNAELANSSAPFALVYAHMFTPTVGNIVMALAVMACVGSLLGWQFTLAQTAKM 302 Query: 303 SSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVTNII 362 ++D G FPK+FS+V+ +AP+ GML + Q+ +AL TISP+ ++QF LV+LA VTN+I Sbjct: 303 TADRGMFPKLFSKVSTQNAPILGMLVCGVFQTLMALSTISPNASAQFGKLVSLAAVTNLI 362 Query: 363 PYILSMAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTFLGW 422 PY+ + L+++ A V V +G YS YALY+ G++A+ G IV G+ Sbjct: 363 PYVTAATGLLVMMYKAKVSTGIYTRNTMVLLIGVGYSLYALYACGKDAVFGGLIVLAFGY 422 Query: 423 TLYGLVSPRF 432 LYG +S RF Sbjct: 423 LLYGFLSKRF 432 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: 698 Number of extensions: 35 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: 439 Length of database: 443 Length adjustment: 32 Effective length of query: 407 Effective length of database: 411 Effective search space: 167277 Effective search space used: 167277 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