Align proline porter II (characterized)
to candidate PP_4433 PP_4433 Amino acid MFS transporter
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Putida:PP_4433 Length = 450 Score = 350 bits (899), Expect = e-101 Identities = 179/426 (42%), Positives = 272/426 (63%), Gaps = 8/426 (1%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 RKA+ AA+LGNA EWFD+G+Y + + FPG+ S + LATF++ FLIRPLGG Sbjct: 25 RKAVVAAALGNATEWFDYGIYAYGLTFISAALFPGSQ-SEALYFGLATFAISFLIRPLGG 83 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 +F+G LGD+ GR+++LA+T+++MS++TF IG++P+Y ++G AP+ L+ ++ QGFS GG Sbjct: 84 MFWGPLGDRIGRKRVLAMTVLMMSVATFIIGILPTYQSVGWIAPVALIALRLIQGFSTGG 143 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 EY GA+ F+AEY+PD++RGF GS+L+FGS+AGF LGA V + +S ++G+A +WGWR+P Sbjct: 144 EYGGAATFLAEYAPDKRRGFYGSFLEFGSLAGFSLGALVTLSVSVVIGDAAMYEWGWRVP 203 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F IA PLG+I +YLR +E+TP F + K+ PK S EI KY ++ L+ Sbjct: 204 FLIAAPLGVIAVYLRTRIEDTPVFLELEKKMASEPVR-----PKTSIAEIFGKYKKAALS 258 Query: 264 CIGLVIATNVTYYMLLTYMPSYLSHNLHYSEDHGVLIIIAIMIGMLFVQPVMGLLSDRFG 323 LV A N+TYY+LL YMP+Y+ + SE+ +L + M+ M+ P G +SD G Sbjct: 259 LGVLVAALNITYYILLAYMPTYMHKEVGASENMSLLAPLVGMLAMMMFIPFAGRISDVVG 318 Query: 324 RRPFVLLGSVALFVLAIPAFILINSNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFPTH 383 + + LF+LAIP F L+++ + G + G +L +++ PAMFPT Sbjct: 319 FKKMWFFSLIGLFILAIPMFKLMSTGLTGSMI-GFAVLGAFFVPQLATISAMFPAMFPTQ 377 Query: 384 IRYSALAAAFNISV-LVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGVTMKETA 442 IRY+ALA +NIS + G TP + +++ + PAYY+MV + +G+I + ET Sbjct: 378 IRYAALAIVYNISASIFGGTTPLVCDQIIKFLGSPDAPAYYIMVASALGIIALFFVIETK 437 Query: 443 NRPLKG 448 ++G Sbjct: 438 GCSIRG 443 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: 689 Number of extensions: 44 Number of successful extensions: 5 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 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