Align Serine transporter (characterized)
to candidate PP_3589 PP_3589 serine:H+ symport permease, threonine-insensitive
Query= SwissProt::P0AAD6 (429 letters) >FitnessBrowser__Putida:PP_3589 Length = 426 Score = 526 bits (1354), Expect = e-154 Identities = 264/412 (64%), Positives = 326/412 (79%), Gaps = 8/412 (1%) Query: 18 WRKTDTMWMLGLYGTAIGAGVLFLPINAGVGGMIPLIIMAILAFPMTFFAHRGLTRFVLS 77 W + DT WMLGL+GTAIGAG LFLPINAG+GG PL+I+A+LAFPMT+FAHRGLTRFVLS Sbjct: 23 WARHDTTWMLGLFGTAIGAGTLFLPINAGLGGFWPLLILAVLAFPMTYFAHRGLTRFVLS 82 Query: 78 GKNPGEDITEVVEEHFGIGAGKLITLLYFFAIYPILLVYSVAITNTVESFMSHQLGMTPP 137 G++ G DITEVV+EHFGI AG IT+LYFFAI+PILL+YSVA+TNTV SFM HQL M PP Sbjct: 83 GRD-GSDITEVVKEHFGITAGASITVLYFFAIFPILLIYSVALTNTVSSFMEHQLHMQPP 141 Query: 138 PRAILSLILIVGMMTIVRFGEQMIVKAMSILVFPFVGVLMLLALYLIPQWNGAALETLSL 197 PRAILS +LI+G++ IVR GEQ VK MS+LV+PF+ L LL LYL+P W G L++ Sbjct: 142 PRAILSFVLILGLLAIVRCGEQATVKVMSLLVYPFIVALALLGLYLVPHWTGGILDSA-- 199 Query: 198 DTASATGNGLWMTLWLAIPVMVFSFNHSPIISSFAVAKREEYGDMAEQKCSKILAFAHIM 257 T + TLWLAIPVMVFSFNHSPIIS+FAV ++ YG A+++ +IL AH++ Sbjct: 200 -TEVPPASAFLHTLWLAIPVMVFSFNHSPIISAFAVDQKRRYGAHADERSGQILRRAHLL 258 Query: 258 MVLTVMFFVFSCVLSLTPADLAAAKEQNISILSYLANHFNAPVIAWMAPIIAIIAITKSF 317 MV+ V+FFVFSCVL+L+ A LA AK QN+SILSYLANHF+ P IA+ AP+IA +AI KSF Sbjct: 259 MVVMVLFFVFSCVLTLSSAQLAEAKAQNLSILSYLANHFSNPTIAFAAPLIAFVAIAKSF 318 Query: 318 LGHYLGAREGFNGMVIKSLRGKGKSIEINKLNRITALFMLVTTWIVATLNPSILGMIETL 377 LGHY+GA EG G++ K+ G L+R+ A MLV WIVATLNPSILGMIE+L Sbjct: 319 LGHYIGASEGLKGIIAKT----GARPGAKALDRVVAALMLVVCWIVATLNPSILGMIESL 374 Query: 378 GGPIIAMILFLMPMYAIQKVPAMRKYSGHISNVFVVVMGLIAISAIFYSLFS 429 GGPI+A++LFLMPMYAI++VP+MRKYSG SNVFVVV+GL+A++++ Y L S Sbjct: 375 GGPILAVLLFLMPMYAIRRVPSMRKYSGAASNVFVVVVGLVALTSVVYGLVS 426 Lambda K H 0.328 0.140 0.416 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: 632 Number of extensions: 38 Number of successful extensions: 4 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: 429 Length of database: 426 Length adjustment: 32 Effective length of query: 397 Effective length of database: 394 Effective search space: 156418 Effective search space used: 156418 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 (21.8 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