Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate 199508 SO0313 putrescine-ornithine antiporter (NCBI ptt file)
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__MR1:199508 Length = 439 Score = 655 bits (1689), Expect = 0.0 Identities = 318/432 (73%), Positives = 378/432 (87%), Gaps = 3/432 (0%) Query: 7 NKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFAKCGMFS 66 NK+GVVQLTI+T+VNMMGSGIIMLPT+LA+VGTIS++SWLVTA GS ALA+AFAKCGMFS Sbjct: 6 NKIGVVQLTIITIVNMMGSGIIMLPTQLAQVGTISVLSWLVTAAGSTALAFAFAKCGMFS 65 Query: 67 RKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLGASLSPVQIGL 126 +KSGGMGGYAEYAFG+SGNFMANYTY VSLLIANVAIAISAVGY LL +LSP+ I L Sbjct: 66 KKSGGMGGYAEYAFGRSGNFMANYTYAVSLLIANVAIAISAVGYAAVLLEVNLSPMAICL 125 Query: 127 ATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVDSWNPHHA 186 ATIGVLW+ TVANFGGARITG++SS+TVWG+I+PV+G+ +IGWFWF LY +WNPH Sbjct: 126 ATIGVLWLATVANFGGARITGRVSSVTVWGIILPVIGVSLIGWFWFDIDLYKGAWNPHDM 185 Query: 187 PFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYIVSTNVIA 246 PFF A+G SIAMTLWAFLGLESACAN++ V+NPE+NVPIAV+GGTLGAA+IYIVSTNVIA Sbjct: 186 PFFKALGGSIAMTLWAFLGLESACANSEAVDNPEKNVPIAVMGGTLGAALIYIVSTNVIA 245 Query: 247 GIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQVFKSSSDE 306 GIVPN ELA+S APFGLAFAQMF P VGK++MA ++SC GSLLGWQFTIAQVFK+S+DE Sbjct: 246 GIVPNAELASSNAPFGLAFAQMFNPVVGKIVMACAIISCTGSLLGWQFTIAQVFKASADE 305 Query: 307 GYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVTNIIPYIL 366 G+FPK+F++V+K DAP+ GM IV IQ+ L+LMTISPSL+ QF LVNLAVVTNI+PYIL Sbjct: 306 GFFPKVFAKVSKADAPIWGMTIIVSIQTLLSLMTISPSLSKQFEALVNLAVVTNIVPYIL 365 Query: 367 SMAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTFLGWTLYG 426 SMAAL ++QK VP +KA+VAN +A +GA+YSFYALYSSGE A++ G+I TF GWT+YG Sbjct: 366 SMAALGVMQKQLKVPANKARVANVIAVIGALYSFYALYSSGETAVMLGAIATFFGWTIYG 425 Query: 427 LVS---PRFELK 435 ++S P E+K Sbjct: 426 VISNKTPSVEIK 437 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: 824 Number of extensions: 33 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: 439 Length adjustment: 32 Effective length of query: 407 Effective length of database: 407 Effective search space: 165649 Effective search space used: 165649 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