Align Putrescine transport system permease protein PotI (characterized)
to candidate BPHYT_RS34085 BPHYT_RS34085 polyamine ABC transporter permease
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__BFirm:BPHYT_RS34085 Length = 279 Score = 147 bits (372), Expect = 2e-40 Identities = 87/248 (35%), Positives = 137/248 (55%), Gaps = 11/248 (4%) Query: 7 VRSPWRIVILLLG-FTFLYA--PMLMLVIYSFNSSK-LVTVWAGWSTRWYGELLRDDAMM 62 V W + L FT LY P+L +V SF+SS LV GWS RWY L+ D Sbjct: 15 VERVWYFALRALAVFTLLYLILPVLAIVPLSFSSSTFLVYPIPGWSLRWYQNLIASDEWR 74 Query: 63 SAVGLSLTIAACAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLL 122 A S +A A A +LGT+AA+ L + FRG ++ +P+++P V+ G+ + Sbjct: 75 MAAKNSFIVAPSATVVATVLGTLAAIGLTK-ANFRGKGLLMAILISPMIVPVVVVGVGMY 133 Query: 123 LLFVALAHAIGWPADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPL 182 L F L A + + + LAH + +V +++ L+ + ++ A++ LGA P+ Sbjct: 134 LFFAPLGLANTY------IGLILAHASLGVPFVVTTVAATLQGFNYNLVRASLSLGANPV 187 Query: 183 KVFFVITLPMIMPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEI 242 + FF ITLP+I P +ISG L AF S D++V+ F++G TTLP +F+ +R ++P I Sbjct: 188 RTFFRITLPVIAPGVISGALFAFATSFDEVVVTLFLAGADQTTLPRQMFTGIRENISPTI 247 Query: 243 NALATLIL 250 ALAT+++ Sbjct: 248 AALATILI 255 Lambda K H 0.330 0.140 0.430 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: 208 Number of extensions: 11 Number of successful extensions: 4 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: 281 Length of database: 279 Length adjustment: 26 Effective length of query: 255 Effective length of database: 253 Effective search space: 64515 Effective search space used: 64515 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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