Align proline porter II (characterized)
to candidate Ac3H11_3022 putative sugar transport protein
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3022 Length = 543 Score = 222 bits (566), Expect = 2e-62 Identities = 120/325 (36%), Positives = 188/325 (57%), Gaps = 16/325 (4%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 RK I A+SLG EW+DF +YG +A + K FF G D + AL F+ F++RP G Sbjct: 6 RKVIFASSLGTVFEWYDFYLYGSLAAIIAKQFFSGLDSGSAFIFALLAFAAGFIVRPFGA 65 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 +FFG LGD GR+ +TI+IM +STF +G++P+Y +IG+ API+L++ ++ QG ++GG Sbjct: 66 IFFGRLGDMIGRKYTFLVTILIMGLSTFIVGILPTYASIGVAAPIILIVLRLLQGLALGG 125 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 EY GA+ +VAE++P +RG +W+ + G L V++ TIVGE F DWGWR+P Sbjct: 126 EYGGAATYVAEHAPHGRRGAYTAWIQTTATLGLFLSLMVILGTRTIVGEEAFADWGWRVP 185 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSL-- 261 F +++ L I +++R A+ E+PAFQ+ + + + + K SF E W++L Sbjct: 186 FIVSIVLLAISVWIRLAMNESPAFQK-----MKAEGKTSKAPLKESFGE-----WKNLKI 235 Query: 262 --LTCIGLVIATNVTYYMLLTYMPSYLSHNLHY-SEDHGVLIIIAIMIGMLFVQPVMGLL 318 L +GL V +Y Y +L+ L +L+ ++++IG F V G L Sbjct: 236 VILALVGLTAGQAVVWYSGQFYALFFLTQALKVDGATANILVAVSLLIGTPFF-IVFGSL 294 Query: 319 SDRFGRRPFVLLGSVALFVLAIPAF 343 SD+ GR+P +L G + + P F Sbjct: 295 SDKIGRKPIILAGCLLAALTYFPVF 319 Score = 45.8 bits (107), Expect = 4e-09 Identities = 28/91 (30%), Positives = 53/91 (58%), Gaps = 2/91 (2%) Query: 353 LIFAGLLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLV 411 ++ A L+ L +++ G +A+ L MFPT IRY++++ ++I + GL PT A +V Sbjct: 444 MVTAILVYLVLLVTMVYGPIAAMLVEMFPTRIRYTSMSLPYHIGNGWFGGLLPTTAFAIV 503 Query: 412 ESSQNLMMPAYY-LMVVAVVGLITGVTMKET 441 + N+ +Y +++ A +I G+ +KET Sbjct: 504 AQTGNMYNGLWYPIIIAAATVVIGGLFIKET 534 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: 693 Number of extensions: 35 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 543 Length adjustment: 35 Effective length of query: 465 Effective length of database: 508 Effective search space: 236220 Effective search space used: 236220 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: 52 (24.6 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