Align putrescine transport system permease protein PotH (characterized)
to candidate Ac3H11_1611 ABC transporter, permease protein
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1611 Length = 299 Score = 143 bits (361), Expect = 4e-39 Identities = 87/289 (30%), Positives = 159/289 (55%), Gaps = 18/289 (6%) Query: 34 ALPYIWL----ILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLNLGNFLQL 89 ALP+ WL +LLF + L+ ++ A P T G + L ++ + Sbjct: 21 ALPW-WLSGPALLLFTVLLLVPLGLTAVLSFNAFDPAT-------GVKAGEFTLEHYGHV 72 Query: 90 TDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILPSWTSFLI 149 D Y + ++ +A + T C+LIG P A+ ++ + R+ILLL+V+ P S ++ Sbjct: 73 FADAYYHAIFWRTFWIAGLVTLICVLIGAPEAYVLSRMRNPWRSILLLVVLAPLLVSVVV 132 Query: 150 RVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTALIR 209 R + W +L G++N +G+ P+ +L+T +AV I +V+ +PFMV+P++T+L + Sbjct: 133 RAFGWSMLLGPEGLVNAAFGLVGI--GPVKMLYTEIAVVIALVHVMLPFMVIPVWTSLQK 190 Query: 210 IDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGGPDSIM 269 +D + AAL L A P T +++P GI++GS++VF A F IP LLGG M Sbjct: 191 LDPGVENAALSLQATPFTTLRRIVLPQVLPGILSGSLIVFGLAASSFAIPGLLGGRRLKM 250 Query: 270 IGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHK----HQQKSVG 314 + V++ E+ + +WP+ +A+A+ +L+ +V ++ +++ +KS+G Sbjct: 251 VATVVYDEYLHELNWPLGAAIALTLLVANLVVMLSYNRLVEGRYKKSLG 299 Lambda K H 0.328 0.144 0.457 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: 251 Number of extensions: 16 Number of successful extensions: 2 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: 317 Length of database: 299 Length adjustment: 27 Effective length of query: 290 Effective length of database: 272 Effective search space: 78880 Effective search space used: 78880 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 (21.7 bits) S2: 48 (23.1 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