Align proline porter II (characterized)
to candidate GFF1547 Psest_1584 Arabinose efflux permease
Query= CharProtDB::CH_024324 (500 letters) >FitnessBrowser__psRCH2:GFF1547 Length = 452 Score = 255 bits (652), Expect = 2e-72 Identities = 134/413 (32%), Positives = 230/413 (55%), Gaps = 14/413 (3%) Query: 24 RKAITAASLGNAMEWFDFGVYGFVAYALGKVFFPGADPSVQMVAALATFSVPFLIRPLGG 83 + + AA +GNA+EW+DF V+GF+A + ++FFP ++ A ATF V F +RP+GG Sbjct: 10 KNQVLAAVIGNALEWYDFIVFGFLAVVISRLFFPAESEYSALLMATATFGVGFFMRPIGG 69 Query: 84 LFFGMLGDKYGRQKILAITIVIMSISTFCIGLIPSYDTIGIWAPILLLICKMAQGFSVGG 143 + G+ D+ GR+ L + I +M++S I P + IGI AP+L+++ ++ QGF+ GG Sbjct: 70 VLLGIYADRKGRKAALQLIISLMTLSIAMIAFAPPFAAIGIAAPLLIVLARLMQGFATGG 129 Query: 144 EYTGASIFVAEYSPDRKRGFMGSWLDFGSIAGFVLGAGVVVLISTIVGEANFLDWGWRIP 203 E+ A+ F+ E +P +RG GSW FG GAGV L+++ + + WGWRIP Sbjct: 130 EFASATSFLIESAPANRRGLYGSWQMFGQGLAVFCGAGVTALVTSNLSPEDLDSWGWRIP 189 Query: 204 FFIALPLGIIGLYLRHALEETPAFQQHVDKLEQGDREGLQDGPKVSFKEIATKYWRSLLT 263 F I L +G +GL++R L ET AF + Q +E K S + + R ++T Sbjct: 190 FIIGLIIGPVGLWMRRNLSETEAFLE----ARQAPKE------KQSLARMLRSHLRQVVT 239 Query: 264 CIGLVIATNVTYYMLLTYMPSYLSHNLHYS-EDHGVLIIIAIMIGMLFVQPVMGLLSDRF 322 + L + V +Y++L YMP++ + L +D ++A+ + + + PV G LSDR Sbjct: 240 VMALTVCGTVAFYVILVYMPTFANRQLGMQLKDAFTAQVVAVAV-LTLLMPVFGALSDRV 298 Query: 323 GRRPFVLLGSVALFVLAIPAFILIN-SNVIGLIFAGLLMLAVILNCFTGVMASTLPAMFP 381 GR+ +++ ++ L V P F I+ + G + L+L +L F G ++ + FP Sbjct: 299 GRKLLMIVATLGLLVALYPLFSWIHAAPSFGRLLTMQLILCSLLAVFFGPFSAAVAEQFP 358 Query: 382 THIRYSALAAAFNISVLV-AGLTPTLAAWLVESSQNLMMPAYYLMVVAVVGLI 433 +R + LA A+N++V++ G + WL++++ + P +Y++ +GLI Sbjct: 359 AGVRSTGLALAYNLAVMIFGGFAQFIVTWLIQNTGMAIAPVFYVLFAVTLGLI 411 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: 604 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: 452 Length adjustment: 33 Effective length of query: 467 Effective length of database: 419 Effective search space: 195673 Effective search space used: 195673 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