Align proline porter II (characterized)
to candidate BWI76_RS03450 BWI76_RS03450 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Koxy:BWI76_RS03450 Length = 454 Score = 254 bits (648), Expect = 6e-72 Identities = 132/429 (30%), Positives = 245/429 (57%), Gaps = 9/429 (2%) Query: 22 KLRKAITAASLGNAMEWFDFGVYGFVA-YALGKVFFPGADPSVQMVAALATFSVPFLIRP 80 KL + + G +E++DF +YG A +FFP P + ++ + T S+ F+ RP Sbjct: 26 KLLTVLGSGLSGTTIEFYDFFIYGTAAALVFPSLFFPNLSPLMALLVSFLTLSITFVSRP 85 Query: 81 LGGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFS 140 +G + FG GDK GR+K L ++++IM ISTF IGLIPSY+TIG AP++L+ ++ QGF+ Sbjct: 86 IGAIVFGHYGDKIGRKKSLVLSLMIMGISTFFIGLIPSYNTIGNAAPLILIFLRLCQGFA 145 Query: 141 VGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGW 200 +GGE+ GA+ + EY+P +RGF G+++ G++ G + GV L+ ++ E + + WGW Sbjct: 146 IGGEWGGATTLITEYAPRHRRGFFGTFVQLGNVLGLFIATGVFALV-VMLPEEDLMSWGW 204 Query: 201 RIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRS 260 R+PF +++ L +G+++R +EETP FQ++ + + + Q P ++ + + ++ Sbjct: 205 RVPFLLSIALLFVGMFIRSRIEETPVFQENQKQQQNAPKAAEQKFPILT---VLKHHRKA 261 Query: 261 LLTCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVL-IIIAIMIGMLFVQPVMGLLS 319 + +G+ + V ++ + + SY++ L+++ + + +++A +G +F P G LS Sbjct: 262 VFLAMGMRMGEIVLGWLTVAFFMSYVTRELNFTRETALNGLLLASFVG-IFTFPFFGWLS 320 Query: 320 DRFGRRPFVLLGSVALFVLAIPAFILINSNVIGL-IFAGLLMLAVILNCFTGVMASTLPA 378 D+ GRRP L G+ + A P F +I+S + + +FA +V L V + Sbjct: 321 DKIGRRPVYLAGAAITLIFAFPLFWMIDSGSVKMFMFATTFCYSVGLGMMFSVQPAFFSE 380 Query: 379 MFPTHIRYSALAAAFNISVLVAGLTPTLAAWLVESSQNLMMP-AYYLMVVAVVGLITGVT 437 +F T +RY+ ++ F ++ +V GLTP + L+ S P + +L +A++ ++ Sbjct: 381 LFDTSVRYTGVSLGFQLANIVGGLTPMIGTLLLVWSGGASWPISLFLACMALITILCVCV 440 Query: 438 MKETANRPL 446 +E+ N L Sbjct: 441 TRESYNDEL 449 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: 652 Number of extensions: 36 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: 454 Length adjustment: 33 Effective length of query: 467 Effective length of database: 421 Effective search space: 196607 Effective search space used: 196607 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 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