Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate 18160 b4132 predicted lysine/cadaverine transporter (NCBI)
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__Keio:18160 Length = 444 Score = 221 bits (564), Expect = 3e-62 Identities = 137/434 (31%), Positives = 223/434 (51%), Gaps = 30/434 (6%) Query: 1 MSQAKSNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFA 60 MS AK K+G+ T + NMMGSGI +LP LA +G I+I W+++ +G+M+LA+ +A Sbjct: 1 MSSAK--KIGLFACTGVVAGNMMGSGIALLPANLASIGGIAIWGWIISIIGAMSLAYVYA 58 Query: 61 KCGMFSRKSGGMGGYA---EYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLGA 117 + + + GG YA AFG F Y + I N+AI I+AV Y + Sbjct: 59 RLATKNPQQGGPIAYAGEISPAFG----FQTGVLYYHANWIGNLAIGITAVSYLSTFFPV 114 Query: 118 SLSPVQIGLATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLY 177 PV G+A I ++W+ T N G ++++I + V+IPVV I+GW WF Y Sbjct: 115 LNDPVPAGIACIAIVWVFTFVNMLGGTWVSRLTTIGLVLVLIPVVMTAIVGWHWFDAATY 174 Query: 178 VDSWNPHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVI 237 +WN A+ SI + LWAF+G+ESA +T +V+NP+R VP+A + GT A ++ Sbjct: 175 AANWNTADTTDGHAIIKSILLCLWAFVGVESAAVSTGMVKNPKRTVPLATMLGTGLAGIV 234 Query: 238 YIVSTNVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIA 297 YI +T V++G+ P+ +A S APF ++ + + ++ A +C SL W + Sbjct: 235 YIAATQVLSGMYPSSVMAASGAPFAISASTILGNWAAPLVSAFTAFACLTSLGSWMMLVG 294 Query: 298 QVFKSSSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQ-------FN 350 Q ++++G FPK++ V P +G+L + + ALM + +NS F Sbjct: 295 QAGVRAANDGNFPKVYGEVDSNGIPKKGLLLAAVKMT--ALMILITLMNSAGGKASDLFG 352 Query: 351 VLVNLAVVTNIIPYILSMAALVIIQKVANVPPSKAKVANFVAFV----GAMYSFYALYSS 406 L +AV+ ++PY S L+ + V + NFV+ + G ++ F AL + Sbjct: 353 ELTGIAVLLTMLPYFYSCVDLIRFEGV--------NIRNFVSLICSVLGCVFCFIALMGA 404 Query: 407 GEEAMLYGSIVTFL 420 + IV+ + Sbjct: 405 SSFELAGTFIVSLI 418 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: 580 Number of extensions: 27 Number of successful extensions: 3 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: 444 Length adjustment: 32 Effective length of query: 407 Effective length of database: 412 Effective search space: 167684 Effective search space used: 167684 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