Align The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized)
to candidate BWI76_RS24055 BWI76_RS24055 MFS transporter
Query= TCDB::A2R3H2 (518 letters) >FitnessBrowser__Koxy:BWI76_RS24055 Length = 464 Score = 200 bits (509), Expect = 8e-56 Identities = 146/468 (31%), Positives = 241/468 (51%), Gaps = 38/468 (8%) Query: 10 YLLTAVAYSGSLLFGYDTGVMGSVLSLTSFKEDFGIPTGSSGFASSKSSEISSNVVSLLT 69 + + +A LLFG D GV+ L + +F I S+ VVS + Sbjct: 16 FFVCFLAALAGLLFGLDIGVIAGALPFIA--NEFQI-----------SAHTQEWVVSSMM 62 Query: 70 AGCFFGAIFAAPLNERIGRRYALMIFTVIFLIGAAVQVASKHHIGQIYGGRVIAGLGIGG 129 G GA+ + L+ ++GR+ +LMI ++F+ G+ A+ + + + RV+ GL +G Sbjct: 63 FGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPN-VEVLLISRVLLGLAVGV 121 Query: 130 MSSITPVFVSENCPPSIRGRVAGMFQEFLVIGSTFAYWLDYGVSLHIPSSTKQWRVPVAV 189 S P+++SE P IRG + M+Q + IG AY D S + WR + V Sbjct: 122 ASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSY-----SGAWRWMLGV 176 Query: 190 QLIPGGLMLLGLFFLKESPRWLAGKGRHEEALQSLAYIRNESPDSEEIQKEFAEIRAAID 249 +IP L+L+G+ FL +SPRW A K R +A + L +R+ S E ++E EIR ++ Sbjct: 177 IIIPAVLLLIGVVFLPDSPRWFAAKRRFVDAERVLLRLRD---TSAEAKRELDEIRESLK 233 Query: 250 EEVAATEGLTYKEFIQPSNLKRFGF-AFTLMLSQQFTGTNSIGYYAPEIFQTIGLSATNS 308 + + + F + SN +R F L + QQFTG N I YYAP+IF+ G + T Sbjct: 234 VKQSG-----WSLFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYANTTE 288 Query: 309 SLFATGVYGTVKVVATAIFLFVG-IDRWGRKLSLVGGSIWMASMMFIIGAVLATHPPDTS 367 ++ T + G V+AT F+ +G +DRWGRK +L+ G I MA M I+G+++ H S Sbjct: 289 QMWGTVIVGLTNVLAT--FIAIGLVDRWGRKPTLILGFIVMALGMGILGSMM--HIGIHS 344 Query: 368 ASGVSQASIAMVVMIYLYVIGYSASWGPTPWVYVSEIFPTRLRSYGVGLAATSQWLWSFV 427 A+ A V+M+ ++++G++ S GP WV SEI P + R +G+ + + W+ + + Sbjct: 345 AT----AQYFAVLMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMI 400 Query: 428 VTEITPKAVHNIG-WRTFLMFGIFCVAMCVFVIVFAKETKGRSLEDMD 474 V ++++G TF ++G + + ETK SLE ++ Sbjct: 401 VGATFLTMLNSLGSANTFWVYGGLNILFIFLTLWLIPETKNVSLEHIE 448 Lambda K H 0.323 0.137 0.411 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: 613 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: 518 Length of database: 464 Length adjustment: 34 Effective length of query: 484 Effective length of database: 430 Effective search space: 208120 Effective search space used: 208120 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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