Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate BWI76_RS07190 BWI76_RS07190 lysine/cadaverine antiporter
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__Koxy:BWI76_RS07190 Length = 445 Score = 228 bits (580), Expect = 4e-64 Identities = 143/438 (32%), Positives = 227/438 (51%), Gaps = 26/438 (5%) Query: 1 MSQAKSNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFA 60 MS AK K+G+ T + NMMGSGI +LP LA +G+I+I W+++ +G+M+LA+ +A Sbjct: 1 MSSAK--KIGLFACTGVVAGNMMGSGIALLPANLASIGSIAIWGWVISIIGAMSLAYVYA 58 Query: 61 KCGMFSRKSGGMGGYA---EYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLGA 117 + + + GG YA AFG F Y + I N+AI I+AV Y + Sbjct: 59 RLATKNPQQGGPIAYAGEISPAFG----FQTGVLYYHANWIGNLAIGITAVSYLSTFFPI 114 Query: 118 SLSPVQIGLATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLY 177 +PV G+A I ++WI T N G ++++I + V+IPVV ++GW WF Y Sbjct: 115 LNNPVPAGIACIAIVWIFTFVNMLGGTWVSRLTTIGLVLVLIPVVMTAVVGWHWFDVATY 174 Query: 178 VDSWNPHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVI 237 +WN AV SI + LWAF+G+ESA +T +V+NP+R VP+A + GT A ++ Sbjct: 175 QANWNTSATTDSHAVVKSILLCLWAFVGVESAAVSTGMVKNPKRTVPLATMLGTALAGIV 234 Query: 238 YIVSTNVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIA 297 YI +T VIAG+ P E+A S APF ++ + + ++ A +C SL W + Sbjct: 235 YIAATQVIAGMYPASEMAASGAPFAISASTILGGWAAPMVSAFTAFACLTSLGSWMMLVG 294 Query: 298 QVFKSSSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGL-ALMTISPSLNSQ----FNVL 352 Q ++++G FPKI+ + K P +G+L + + L L+T+ S + F L Sbjct: 295 QAGVRAANDGNFPKIYGELDKNGNPKKGLLLAAVKMTVLMVLITLMNSTGGKASDLFGEL 354 Query: 353 VNLAVVTNIIPYILSMAALVIIQKVANVPPSKAKVANFVAFV----GAMYSFYALYSSGE 408 +AV+ ++PY S L+ + + V NFV+ + G + F AL + Sbjct: 355 TGIAVLLTMLPYFYSCVDLIRFEGI--------NVRNFVSLICSVLGCGFCFIALMGASS 406 Query: 409 EAMLYGSIVTFLGWTLYG 426 + IV+ + YG Sbjct: 407 FELAGTFIVSLIILMFYG 424 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: 602 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: 445 Length adjustment: 32 Effective length of query: 407 Effective length of database: 413 Effective search space: 168091 Effective search space used: 168091 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