Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate SMa0678 SMa0678 putrescine transporter
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__Smeli:SMa0678 Length = 452 Score = 497 bits (1280), Expect = e-145 Identities = 244/433 (56%), Positives = 326/433 (75%), Gaps = 1/433 (0%) Query: 1 MSQAKSNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFA 60 M A KM +VQLT + VNMMGSGIIMLP +A+VG IS++SWLVTAVGSMA+A+ FA Sbjct: 10 MEAASKKKMNLVQLTFIVAVNMMGSGIIMLPANMAQVGAISLLSWLVTAVGSMAIAYGFA 69 Query: 61 KCGMFSRKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLG-ASL 119 + G+F+++ GGM YAE A+GK G F+ Y +SL + NVAI ISAVGY + Sbjct: 70 QAGLFNQRPGGMSAYAEDAYGKPGYFLVFLLYFLSLAVGNVAIGISAVGYLAGFFPWLTS 129 Query: 120 SPVQIGLATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVD 179 +P+ ++ I +LW+ TVANFGG R+TG+I SITVWGVI+PV LCIIGW WFS ++ Sbjct: 130 TPIATCVSLIILLWLTTVANFGGPRVTGRIGSITVWGVILPVGLLCIIGWAWFSSEVFAA 189 Query: 180 SWNPHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYI 239 +WNP+ +GSSI++TLWAFLG+ESA N+D VENP+R+VP+A L GTLGAA+IYI Sbjct: 190 AWNPNGLTLVQGMGSSISLTLWAFLGMESAAQNSDAVENPKRDVPLACLFGTLGAAIIYI 249 Query: 240 VSTNVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQV 299 +ST VI GIVPN ELA ST PF LAFA MF P +G V+MAL V++C GSLLGWQFTIAQ Sbjct: 250 LSTTVIQGIVPNAELAASTGPFALAFATMFNPAIGSVVMALAVLACVGSLLGWQFTIAQT 309 Query: 300 FKSSSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVT 359 ++++DE FP +FSRV ++ APV GM+ + ++QS LALMTISP+LN QF LVNLAVVT Sbjct: 310 ARAAADERMFPSLFSRVNEMGAPVTGMIVMGVVQSLLALMTISPTLNEQFAALVNLAVVT 369 Query: 360 NIIPYILSMAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTF 419 N++PYI+S++AL ++ + A V SK ++ + +A VG +YS +A+Y+SG++A+L G +VT Sbjct: 370 NVLPYIISLSALFVMMRAAGVSESKFRLNSSIAIVGMLYSVFAIYASGKDAVLGGMLVTG 429 Query: 420 LGWTLYGLVSPRF 432 + + +YGL++PRF Sbjct: 430 IAFIIYGLIAPRF 442 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: 714 Number of extensions: 37 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: 452 Length adjustment: 32 Effective length of query: 407 Effective length of database: 420 Effective search space: 170940 Effective search space used: 170940 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