Align proline porter II (characterized)
to candidate WP_099093415.1 AU252_RS22340 MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >NCBI__GCF_001484605.1:WP_099093415.1 Length = 450 Score = 254 bits (650), Expect = 3e-72 Identities = 139/426 (32%), Positives = 233/426 (54%), Gaps = 11/426 (2%) Query: 18 IDDGKLRKAITAASLGNAMEWFDFGVYGFV-AYALGKVFFPGADPSVQMVAALATFSVPF 76 +D K+RK A+ +G +EW+D V+G A K+FFP DP V + A TF+ + Sbjct: 16 LDLTKMRKIALASVIGTTVEWYDLFVFGTASALVFNKIFFPSFDPLVGTMLAFGTFASAY 75 Query: 77 LIRPLGGLFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMA 136 + R +G + FG GD+ GR+ +L I+++ M +TF IGL+P Y++IGI AP+LLL ++ Sbjct: 76 IARMVGAIIFGHFGDRLGRKSMLLISLLTMGAATFAIGLLPDYNSIGIMAPLLLLFLRVI 135 Query: 137 QGFSVGGEYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFL 196 QG ++GGE+ GA + E++P +RGF GS + G AG ++ +++++ V L Sbjct: 136 QGLALGGEWGGAVLMTVEHAPASQRGFYGSLVQVGVPAGTLIANVAFLIVASTVSTEALL 195 Query: 197 DWGWRIPFFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATK 256 WGWRIPF + L +G+Y+R +EETP+FQ D + K+ F + K Sbjct: 196 SWGWRIPFLASALLVAVGIYIRLHIEETPSFQAVKDAGAKA---------KLPFAALMAK 246 Query: 257 YWRSLLTCIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMG 316 YW+ ++ ++T T+ +L+ SY L +SE + +++A + P G Sbjct: 247 YWKQVILGGVATLSTGSTFTLLVASGVSYGKKELGHSESLMLWVVLASCALCFVLIPFFG 306 Query: 317 LLSDRFGRRPFVLLGSVALFVLAIPAFILINSNVIGLIFAGLLMLAVILNCFTGVMASTL 376 LSD++GR+P + G A LA P F ++++ + L+F L + G +A+ L Sbjct: 307 RLSDKYGRKPIIFAGVAAEAALAFPMFWMMDTKSVALLFIAYLAMMTAFAANYGPIATFL 366 Query: 377 PAMFPTHIRYSALAAAFNIS-VLVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITG 435 +F + +RYS L+ A+ +S +L + TP + WL+ + A+Y+M ++V L Sbjct: 367 AELFGSKVRYSGLSVAYMLSGLLGSAATPFITTWLLGVTHQSSSIAWYIMGASLVSLAAL 426 Query: 436 VTMKET 441 V + ET Sbjct: 427 VILTET 432 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: 589 Number of extensions: 30 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: 450 Length adjustment: 33 Effective length of query: 467 Effective length of database: 417 Effective search space: 194739 Effective search space used: 194739 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