Align Putrescine transport system permease protein PotI (characterized)
to candidate SMa1751 SMa1751 ABC transporter permease
Query= SwissProt::P0AFL1 (281 letters) >FitnessBrowser__Smeli:SMa1751 Length = 260 Score = 137 bits (345), Expect = 2e-37 Identities = 88/254 (34%), Positives = 137/254 (53%), Gaps = 13/254 (5%) Query: 18 LGFTFLYAPMLMLVIYSFNSSKLVTV-WAGWSTRWYGELLRDDAMMSAVGLSLTIAACAA 76 L FL AP++ ++ +F SS ++T WS RW+ EL DA A+ SL I Sbjct: 13 LTILFLVAPLIAILPLAFTSSVILTYPIPSWSLRWFEELFTADAWRRAIFNSLIIGTGTT 72 Query: 77 TAAAILGTIAAVVLV-RFGRFRGSNGFAFMITAPLVMPDVITGLSLLLLFVALAHAIGWP 135 A ILGT A++ L R FRGS F++ P+V+P V+ G+ + +L G+ Sbjct: 73 LLATILGTAASLGLRNRLIFFRGSMRTLFLL--PMVVPAVVLGVGMQVLLA------GFG 124 Query: 136 ADRGMLTIWLAHVTFCTAYVAVVISSRLRELDRSIEEAAMDLGATPLKVFFVITLPMIMP 195 + +AH +V V + L +D +E AA LGA+P VF +TLP+ +P Sbjct: 125 LTNSYAGVIIAHTVVAVPFVVVSVIGALDGIDERVELAAQSLGASPATVFHRVTLPLALP 184 Query: 196 AIISGWLLAFTLSLDDLVIASFVSGPGATTLPMLVFSSVRMGVNPEINALATLILGAV-- 253 ++SG +LAF SLD++V+ FV+GP TL +FSS+R ++P I A A L + A Sbjct: 185 GVLSGAVLAFATSLDEVVLTLFVAGPNQRTLARQMFSSIRENISPAIAAAAFLFIAATIF 244 Query: 254 -GIVGFIAWYLMAR 266 G+V ++ +++A+ Sbjct: 245 FGLVVVLSRFMLAK 258 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: 189 Number of extensions: 12 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: 260 Length adjustment: 25 Effective length of query: 256 Effective length of database: 235 Effective search space: 60160 Effective search space used: 60160 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