Align proline porter II (characterized)
to candidate WP_057508837.1 ABB28_RS11900 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >NCBI__GCF_001431535.1:WP_057508837.1 Length = 408 Score = 214 bits (546), Expect = 3e-60 Identities = 137/420 (32%), Positives = 218/420 (51%), Gaps = 17/420 (4%) Query: 30 ASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGGLFFGML 89 A+L +EW+DF +Y + A L +VFF G + + ++A LA F+V +L+RPLG L FG L Sbjct: 4 AALSTVVEWYDFTLYLYFATVLSRVFFGGGETA--LLATLAGFAVSYLMRPLGALCFGHL 61 Query: 90 GDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGGEYTGAS 149 GD+ GR+ +L ++ +M+ + L+P+Y IG A +LLL + FSVGGEYTG Sbjct: 62 GDRLGRRWMLLASMALMAAAMLATALLPTYAQIGASAGVLLLALRCVMAFSVGGEYTGVV 121 Query: 150 IFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIPFFIALP 209 ++ E +P R+RG + S S G +L + L ++ WGWRIPFF+ Sbjct: 122 AYLLESAPPRRRGLVTSLASAASEVGALLAVALSALTVALLPAPALDTWGWRIPFFVGAG 181 Query: 210 LGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLTCIGLVI 269 L ++ L R + E+P F E+ REG P ++I + ++ + Sbjct: 182 LALLILLARSGMHESPEF-------ERQQREG--SVPSAPIRQILRSHPGAVARTFAISA 232 Query: 270 ATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRFGRRPFVL 329 ++TYY+ +TY+P++L H E + + + ++ P+ GLLSDRFGRRP +L Sbjct: 233 LGSITYYVGITYVPAFL-HANGRGEGEALWLSTIAAVAVILATPLFGLLSDRFGRRPLLL 291 Query: 330 LGSVALFVLAIPAF-ILINSNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPTHIRYSA 388 ++ +L + F + ++ +G+I A ++LA + + V AS FP R S Sbjct: 292 GLTLLSALLPLSMFGWMAQASTMGVIGAA-VVLACVAGGISAVAASATAEQFPGEGRLSG 350 Query: 389 LAAAFNISVLV-AGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVTMKETANRPLK 447 LA ++ + G TP LA W VE S P + +VAV L+ V + RPL+ Sbjct: 351 LALGVTMATAIFGGATPWLAQWWVERSGWNAAPGAMIAIVAV--LVLPVLWRLPETRPLR 408 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: 534 Number of extensions: 26 Number of successful extensions: 6 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: 408 Length adjustment: 33 Effective length of query: 467 Effective length of database: 375 Effective search space: 175125 Effective search space used: 175125 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