Align proline porter II (characterized)
to candidate WP_057507757.1 ABB28_RS05925 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >NCBI__GCF_001431535.1:WP_057507757.1 Length = 430 Score = 213 bits (542), Expect = 1e-59 Identities = 125/412 (30%), Positives = 217/412 (52%), Gaps = 18/412 (4%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYAL-GKVFFPGADPSVQMVAALATFSVPFLIRPLG 82 ++ + A+ +G +E+FDF +Y A + +FFP + M+ +LATF+V F+ RP+G Sbjct: 19 QRVLLASLIGTTIEFFDFYIYATAAVLVFPHLFFPESSDKAAMLQSLATFAVAFIARPVG 78 Query: 83 GLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVG 142 FG GD+ GR+ L ++ M +ST IGL+P++ IG+WAP LL +C+ QG +G Sbjct: 79 SAVFGHFGDRIGRKATLVAALLTMGLSTVLIGLLPTHAQIGLWAPALLALCRFGQGLGLG 138 Query: 143 GEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRI 202 GE+ GA + E +P KR + G + G+ GF+L AG+ +++ ++ +FL WGWRI Sbjct: 139 GEWGGAVLLATENAPPGKRAWYGMFPQLGAPLGFLLSAGIFLILGRLLSADDFLQWGWRI 198 Query: 203 PFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLL 262 PF + L +GL++R + ETPAFQ+ +D + K+ + + +L Sbjct: 199 PFVASALLVGLGLWVRLNIHETPAFQKALDAHAR---------VKLPMLTVLRDHAMPML 249 Query: 263 TCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQ---PVMGLLS 319 AT V +Y++ + + + L YS + +L+ M+G+LF P+ Sbjct: 250 LGTLGAFATFVLFYLMTVFALGHGTAVLGYSREQFLLL---QMVGILFFAAGIPISARYG 306 Query: 320 DRFGRRPFVLLGSVALFVLAIPAFILINSNVIGLIFAGLLMLAVILNCFTGVMASTLPAM 379 DR+G R +++ S + V + + + ++ A L + ++ G + L + Sbjct: 307 DRWGTRRTMIIASGLIVVFGVLLAPMFQAGSPWMVLAFLSLGLFLMGLTYGPCGTFLAEI 366 Query: 380 FPTHIRYSALAAAFNIS-VLVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVV 430 +P +RY+ + +FN++ +L A P LA WL E L+ YYL + A+V Sbjct: 367 YPVEVRYTGASLSFNLAGILGAAPAPYLATWLAERF-GLVAVGYYLCIAALV 417 Lambda K H 0.327 0.142 0.429 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: 626 Number of extensions: 46 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: 500 Length of database: 430 Length adjustment: 33 Effective length of query: 467 Effective length of database: 397 Effective search space: 185399 Effective search space used: 185399 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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