Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate 18143 b4115 arginine:agmatin (NCBI)
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__Keio:18143 Length = 445 Score = 282 bits (721), Expect = 2e-80 Identities = 141/427 (33%), Positives = 238/427 (55%), Gaps = 4/427 (0%) Query: 2 SQAKSNKMGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFAK 61 S A ++K+G++ +T++ N+MGSG+ +LP LA G I+I WLVT +G++ L+ +AK Sbjct: 3 SDADAHKVGLIPVTLMVSGNIMGSGVFLLPANLASTGGIAIYGWLVTIIGALGLSMVYAK 62 Query: 62 CGMFSRKSGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVGYGTELLGASLSP 121 GG YA FG + N Y ++ I N+A+ + VGY + P Sbjct: 63 MSFLDPSPGGSYAYARRCFGPFLGYQTNVLYWLACWIGNIAMVVIGVGYLSYFFPILKDP 122 Query: 122 VQIGLATIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVDSW 181 + + + + VLWI + N G ++ ++ ++ +IP+VG+ + GWFWF Y+ +W Sbjct: 123 LVLTITCVVVLWIFVLLNIVGPKMITRVQAVATVLALIPIVGIAVFGWFWFRGETYMAAW 182 Query: 182 NPHHAPFFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYIVS 241 N F A+ S++ +TLW+F+G+ESA VV+NP+RNVPIA +GG L AAV Y++S Sbjct: 183 NVSGLGTFGAIQSTLNVTLWSFIGVESASVAAGVVKNPKRNVPIATIGGVLIAAVCYVLS 242 Query: 242 TNVIAGIVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQVFK 301 T I G++PN L S +PFG A G ++ C GSL GW Q K Sbjct: 243 TTAIMGMIPNAALRVSASPFGDAARMALGDTAGAIVSFCAAAGCLGSLGGWTLLAGQTAK 302 Query: 302 SSSDEGYFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVTNI 361 +++D+G FP IF+RV K PV G++ + I+ + L +ISP+ +F ++ +++V+ + Sbjct: 303 AAADDGLFPPIFARVNKAGTPVAGLIIVGILMTIFQLSSISPNATKEFGLVSSVSVIFTL 362 Query: 362 IPYILSMAALVIIQKVANVPPSKAKVANF-VAFVGAMYSFYALYSSGEEAMLYGSIVTFL 420 +PY+ + AAL+++ + KA+ A V + +Y +A+ SG + +++ + + Sbjct: 363 VPYLYTCAALLLL---GHGHFGKARPAYLAVTTIAFLYCIWAVVGSGAKEVMWSFVTLMV 419 Query: 421 GWTLYGL 427 +Y L Sbjct: 420 ITAMYAL 426 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: 656 Number of extensions: 47 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: 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