Align putrescine transport system permease protein PotH (characterized)
to candidate WP_041101089.1 SUTH_RS17500 molybdate ABC transporter permease subunit
Query= CharProtDB::CH_088338 (317 letters) >NCBI__GCF_000828635.1:WP_041101089.1 Length = 226 Score = 78.2 bits (191), Expect = 2e-19 Identities = 60/206 (29%), Positives = 101/206 (49%), Gaps = 16/206 (7%) Query: 97 DAYLQSLQVAAISTFCCLLIGYPLAWAVAHSK-----PSTRNILLLLVILPSWTSFLIRV 151 +A L ++++A++ T LLIG P+AW +A ++ P + L +V+ PS F + V Sbjct: 8 EAILLTVKLASVVTALLLLIGTPIAWWLATTRSWLKAPVEAVVALPIVLPPSVLGFYLLV 67 Query: 152 YAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLPIYTALIRID 211 + +G + LG+ P T + + V+ +PF+V PI A I Sbjct: 68 -----AMGPHGPVGQLTQALGLGTLPFTFT----GLVVASVFYSLPFVVQPIQNAFAAIG 118 Query: 212 YSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELLGG--PDSIM 269 L+EAA L A P FFTV +PL + G I ++L F VGEF + ++GG P Sbjct: 119 PGLLEAAATLRATPRDRFFTVALPLARPGFIIAAVLGFAHTVGEFGVVLMVGGNIPGQTR 178 Query: 270 IGRVLWQEFFNNRDWPVASAVAIIML 295 + V ++ ++ A +AI+++ Sbjct: 179 VVSVQIYDYVEALEYGQAHELAIVLM 204 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: 183 Number of extensions: 12 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: 226 Length adjustment: 25 Effective length of query: 292 Effective length of database: 201 Effective search space: 58692 Effective search space used: 58692 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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