Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate PfGW456L13_3775 Putrescine/proton symporter, putrescine/ornithine antiporter PotE
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3775 Length = 461 Score = 587 bits (1513), Expect = e-172 Identities = 288/431 (66%), Positives = 350/431 (81%), Gaps = 2/431 (0%) Query: 1 MSQAKSNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFA 60 MS AK KM V QLT+LT VNM+GSGI++LPTKLAEVG ISI+SWL+TA GS+ALA+AFA Sbjct: 1 MSVAK--KMSVGQLTMLTAVNMLGSGIVLLPTKLAEVGAISILSWLITATGSLALAYAFA 58 Query: 61 KCGMFSRKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLGASLS 120 +CGM SRK+GGMGGYAEY FGK+GN++ NYTYG+SLLIANVAI+I+AVGY L G L Sbjct: 59 RCGMLSRKTGGMGGYAEYTFGKAGNYITNYTYGLSLLIANVAISITAVGYIQVLFGIELD 118 Query: 121 PVQIGLATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVDS 180 +Q+GLATI +LWI T ANFGGA ITG+I ++TVWGVI PVV + +GWFWF ++Y Sbjct: 119 SLQVGLATIALLWITTFANFGGASITGRIGAVTVWGVIAPVVLVSTVGWFWFDSSVYAAG 178 Query: 181 WNPHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYIV 240 WNPH +F A G+S+A+TLWAFLGLESACANTD VENPERNVPIAVLGGTLGAAVIYIV Sbjct: 179 WNPHDKGWFEAAGASVAITLWAFLGLESACANTDAVENPERNVPIAVLGGTLGAAVIYIV 238 Query: 241 STNVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQVF 300 STNVI GIV N ELA STAPFGL FA+MFTP VG ++MA MV++C GSLLGWQFTIAQV+ Sbjct: 239 STNVIFGIVGNEELAASTAPFGLVFAKMFTPMVGDIVMAAMVLACIGSLLGWQFTIAQVY 298 Query: 301 KSSSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVTN 360 KSS+D GYF IF++ K P+ GML ++ Q+ LAL+TISP L+ QF+ LVNLAVVTN Sbjct: 299 KSSADTGYFLPIFAKGNKAGTPIVGMLVLLAAQTALALLTISPDLSKQFDTLVNLAVVTN 358 Query: 361 IIPYILSMAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTFL 420 ++PYILSMAAL+ +QKV+NVP KA N +A + A YS+ ALYSSGE+A++ G + T + Sbjct: 359 LVPYILSMAALMTMQKVSNVPEGKALATNVIALIAAAYSYLALYSSGEQALMLGGVATIV 418 Query: 421 GWTLYGLVSPR 431 G+TL+G V+ R Sbjct: 419 GYTLFGFVNNR 429 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: 726 Number of extensions: 27 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: 439 Length of database: 461 Length adjustment: 33 Effective length of query: 406 Effective length of database: 428 Effective search space: 173768 Effective search space used: 173768 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