Align proline porter II (characterized)
to candidate 17584 b3523 predicted transporter (NCBI)
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__Keio:17584 Length = 440 Score = 251 bits (640), Expect = 5e-71 Identities = 145/430 (33%), Positives = 244/430 (56%), Gaps = 19/430 (4%) Query: 25 KAITAASLGNAMEWFDFGVYGFVAYAL-GKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 K + A+ +G A+E+FDF +Y A + +FFP DP+ + +LATF++ F+ RP+G Sbjct: 22 KVLVASLIGTAIEFFDFYIYATAAVIVFPHIFFPQGDPTAATLQSLATFAIAFVARPIGS 81 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 FG GD+ GR+ L +++ M IST IGL+P Y TIGI+AP+LL + + QG +GG Sbjct: 82 AVFGHFGDRVGRKATLVASLLTMGISTVVIGLLPGYATIGIFAPLLLALARFGQGLGLGG 141 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 E+ GA++ E +P RKR GS+ G+ GF G +L+S ++ + F+ WGWR+P Sbjct: 142 EWGGAALLATENAPPRKRALYGSFPQLGAPIGFFFANGTFLLLSWLLTDEQFMSWGWRVP 201 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F + L IIGLY+R +L E+P F++ +Q K+ + TK+ R + Sbjct: 202 FIFSAVLVIIGLYVRVSLHESPVFEKVAKAKKQ---------VKIPLGTLLTKHVRVTVL 252 Query: 264 CIGLVIATNVTYYMLLTYMPSYLSH----NLHYSEDHGVLIIIAIMIGMLFVQPVMGLLS 319 +++AT +Y++ Y ++ + L + + +++ +IG + PV GLL+ Sbjct: 253 GTFIMLATYTLFYIMTVYSMTFSTAAAPVGLGLPRNEVLWMLMMAVIGFGVMVPVAGLLA 312 Query: 320 DRFGRRPFVLLGSVALFVLAIPAF--ILINSNVIGLIFAGLLMLAVILNCFTGVMASTLP 377 D FGRR +++ + + + A+ AF +L + N I L+FA LL+ ++ G M + LP Sbjct: 313 DAFGRRKSMVIITTLIILFALFAFNPLLGSGNPI-LVFAFLLLGLSLMGLTFGPMGALLP 371 Query: 378 AMFPTHIRYSALAAAFNI-SVLVAGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLITGV 436 +FPT +RY+ + ++N+ S+L A + P +AAWL +++ L YL +A + LI + Sbjct: 372 ELFPTEVRYTGASFSYNVASILGASVAPYIAAWL-QTNYGLGAVGLYLAAMAGLTLIALL 430 Query: 437 TMKETANRPL 446 ET ++ L Sbjct: 431 LTHETRHQSL 440 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: 631 Number of extensions: 36 Number of successful extensions: 7 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: 440 Length adjustment: 33 Effective length of query: 467 Effective length of database: 407 Effective search space: 190069 Effective search space used: 190069 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