Align proline porter II (characterized)
to candidate WP_004687113.1 BMI_RS14180 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >NCBI__GCF_000022745.1:WP_004687113.1 Length = 632 Score = 204 bits (518), Expect = 1e-56 Identities = 116/328 (35%), Positives = 183/328 (55%), Gaps = 16/328 (4%) Query: 21 GKLRKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRP 80 G+ RK I A+SLG EW+DF +YG +A +G FF + + + L F+ FL+RP Sbjct: 16 GEERKVIFASSLGTVFEWYDFYLYGTLASFIGAAFFNEYPEATRNIFVLLAFAAGFLVRP 75 Query: 81 LGGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFS 140 G L FG +GD GR+ +TIVIM STF +GL+P ++GI+API+L+ +M QG + Sbjct: 76 FGALVFGRIGDLVGRKYTFLVTIVIMGGSTFLVGLLPGSASLGIFAPIILIALRMLQGLA 135 Query: 141 VGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGW 200 +GGEY GA+ +VAE++P+ +RGF SW+ + G L V++ T++ + F WGW Sbjct: 136 LGGEYGGAATYVAEHAPNNRRGFFTSWIQTTATLGLFLSLLVILGAQTLLSKDAFAAWGW 195 Query: 201 RIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWR- 259 RIPF +++ L I +++R + E+PAF++ E+G K E A W+ Sbjct: 196 RIPFLVSVLLLGISVWIRMQMSESPAFKR---MKEEGKTS------KAPLSE-AFGQWKN 245 Query: 260 ---SLLTCIGLVIATNVTYYMLLTYMPSYLSHNLHY-SEDHGVLIIIAIMIGMLFVQPVM 315 +L+ GL V +Y Y +L + L ++ +++ IA++IG F + Sbjct: 246 AKIALIALFGLTAGQAVVWYCGQFYALFFLQNVLKVENQSANIMVAIALLIGTGFF-VIF 304 Query: 316 GLLSDRFGRRPFVLLGSVALFVLAIPAF 343 G LSD+ GR+P ++ G + V P F Sbjct: 305 GWLSDKIGRKPIIMAGLILAAVTYFPLF 332 Score = 37.7 bits (86), Expect = 1e-06 Identities = 26/91 (28%), Positives = 47/91 (51%), Gaps = 2/91 (2%) Query: 353 LIFAGLLMLAVILNCFTGVMASTLPAMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLV 411 L A L +L + + G +A+ L MFPT IRY+ ++ ++I + GL P L Sbjct: 533 LTIAILTILVIYVTMVYGPIAAILVEMFPTRIRYTGMSLPYHIGNGWFGGLLPAGVFALS 592 Query: 412 ESSQNLMMPAYYLMVVAVVGLITGVT-MKET 441 + ++ +Y +++A V + G+ +KET Sbjct: 593 AAKGDIYYGLWYPIIIASVTFVIGMLFVKET 623 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: 758 Number of extensions: 38 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 500 Length of database: 632 Length adjustment: 36 Effective length of query: 464 Effective length of database: 596 Effective search space: 276544 Effective search space used: 276544 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: 53 (25.0 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