Align Putrescine transport system permease protein PotI (characterized)
to candidate Ac3H11_1612 ABC transporter, permease protein
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1612 Length = 264 Score = 122 bits (306), Expect = 8e-33 Identities = 75/242 (30%), Positives = 125/242 (51%), Gaps = 8/242 (3%) Query: 10 PWRIVILLLGFTFLYAPMLMLVIYSFNSSKLVTV-WAGWSTRWYGELLRDDAMMSAVGLS 68 P + L TF+ AP+L++ I +F +T+ +S RW+ + + + S Sbjct: 6 PIALAFNALVITFMLAPLLVVCIVAFTPHNTLTLPTTEFSLRWFKAVFEHSDFVQSFWNS 65 Query: 69 LTIAACAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVAL 128 L +A +AT A L A + + R+ F G + +PL++P ++ G++LL LF Sbjct: 66 LWLALASATLATALAVPAGIAITRYD-FPGRGFLNGLFLSPLIIPHLVLGVALLRLFAL- 123 Query: 129 AHAIGWPADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVI 188 IG G L + AH T Y ++ + L DRS E AA+ LGA+ VF I Sbjct: 124 ---IGGTGSFGWLVV--AHALIVTPYTLRLVVAALVGFDRSAEHAALSLGASQATVFTRI 178 Query: 189 TLPMIMPAIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATL 248 TLPMI+P + GW+LAF S D++ ++ FV+ P TLP+ ++ ++P + A++ L Sbjct: 179 TLPMILPGVTGGWMLAFINSFDEVTMSIFVTSPSTVTLPVRMYMYATESIDPLMAAVSAL 238 Query: 249 IL 250 ++ Sbjct: 239 MV 240 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: 214 Number of extensions: 8 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: 281 Length of database: 264 Length adjustment: 25 Effective length of query: 256 Effective length of database: 239 Effective search space: 61184 Effective search space used: 61184 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