Align Putrescine transporter PotE; Putrescine-proton symporter / putrescine-ornithine antiporter (characterized)
to candidate N515DRAFT_1063 N515DRAFT_1063 amino acid/polyamine/organocation transporter, APC superfamily (TC 2.A.3)
Query= SwissProt::P0AAF1 (439 letters) >FitnessBrowser__Dyella79:N515DRAFT_1063 Length = 434 Score = 213 bits (542), Expect = 1e-59 Identities = 134/418 (32%), Positives = 208/418 (49%), Gaps = 8/418 (1%) Query: 9 MGVVQLTILTMVNMMGSGIIMLPTKLAEVGTISIISWLVTAVGSMALAWAFAKCGMFSRK 68 +G LT L + NM+GSG+ +LP LA G S++ W T G++ LA A Sbjct: 8 LGPWMLTALVVGNMIGSGVFVLPAALAPYGAASLLGWAFTMGGALLLALVHAWLAQLVAN 67 Query: 69 SGGMGGYAEYAFGKSGNFMANYTYGVSLLIANVAIAISAVG-YGTELLGASLSPVQIGLA 127 GG YA AFG + F+A ++Y + AN AIA++ G G A+ +P + A Sbjct: 68 HGGAYAYARQAFGDTAGFVAAWSYWTCVWTANAAIAVAFAGSLGAIWPAANATPWRGTAA 127 Query: 128 TIGVLWICTVANFGGARITGQISSITVWGVIIPVVGLCIIGWFWFSPTLYVDSWNPHHAP 187 + VLW+CT N G R G++ +T +IP++ + G Y +NP Sbjct: 128 ALAVLWLCTAINAAGVREAGRMQLVTTALKVIPLLVFGVCGLALVHGAAY-QPFNPSGQS 186 Query: 188 FFSAVGSSIAMTLWAFLGLESACANTDVVENPERNVPIAVLGGTLGAAVIYIVSTNVIAG 247 S ++ A+TLWAFLGLE+A T VV +P+R VP A + G L A V +++ + G Sbjct: 187 LPSVTTATAALTLWAFLGLEAATVPTGVVRDPQRTVPRATVAGMLVAGVATMLACTAVIG 246 Query: 248 IVPNMELANSTAPFGLAFAQMFTPEVGKVIMALMVMSCCGSLLGWQFTIAQVFKSSSDEG 307 ++P+ S AP A AQ + P G + + +SC G+L GW Q +++ +G Sbjct: 247 LLPHGAAQGSAAPMAAAAAQTWGPAAGWAMGLVATVSCLGALNGWVLLQGQTPYAAAQDG 306 Query: 308 YFPKIFSRVTKVDAPVQGMLTIVIIQSGLALMTISPSLNSQFNVLVNLAVVTNIIPYILS 367 FP F+R P G+L ++ S L S SL + F + + L+ ++PY+LS Sbjct: 307 LFPAPFARTDARGTPWFGLLLSSVLASVLIAANGSKSLVALFTLSILLSTAATLLPYVLS 366 Query: 368 MAALVIIQKVANVPPSKAKVANFVAFVGAMYSFYALYSSGEEAMLYGSIVTFLGWTLY 425 + A I + A V A A + YS +AL +G EA+L+G ++ LG ++ Sbjct: 367 VLAWWRIDRGAGVARRTA------AALALAYSLWALIGTGAEALLWGGVLLLLGLPVF 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: 589 Number of extensions: 34 Number of successful extensions: 5 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: 434 Length adjustment: 32 Effective length of query: 407 Effective length of database: 402 Effective search space: 163614 Effective search space used: 163614 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