Align The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)
Query= TCDB::A2R3H2 (518 letters) >FitnessBrowser__Keio:17022 Length = 464 Score = 202 bits (515), Expect = 2e-56 Identities = 144/470 (30%), Positives = 238/470 (50%), Gaps = 42/470 (8%) Query: 10 YLLTAVAYSGSLLFGYDTGVMGSVLSLTSFKEDFGIPTGSSGFASSKSSEISSNVVSLLT 69 + + +A LLFG D GV+ L + ++F I +S VVS + Sbjct: 16 FFVCFLAALAGLLFGLDIGVIAGALPFIA--DEFQI-----------TSHTQEWVVSSMM 62 Query: 70 AGCFFGAIFAAPLNERIGRRYALMIFTVIFLIGAAVQVASKHHIGQIYGGRVIAGLGIGG 129 G GA+ + L+ ++GR+ +LMI ++F+ G+ A+ + + + RV+ GL +G Sbjct: 63 FGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSLFSAAAPN-VEVLILSRVLLGLAVGV 121 Query: 130 MSSITPVFVSENCPPSIRGRVAGMFQEFLVIGSTFAYWLDYGVSLHIPSSTKQWRVPVAV 189 S P+++SE P IRG + M+Q + IG AY D S T WR + V Sbjct: 122 ASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAFSY-----TGAWRWMLGV 176 Query: 190 QLIPGGLMLLGLFFLKESPRWLAGKGRHEEALQSLAYIRNESPDSEEIQKEFAEIRAAID 249 +IP L+L+G+FFL +SPRW A K R +A + L +R+ S E ++E EIR ++ Sbjct: 177 IIIPAILLLIGVFFLPDSPRWFAAKRRFVDAERVLLRLRD---TSAEAKRELDEIRESLQ 233 Query: 250 EEVAATEGLTYKEFIQPSNLKRFGF-AFTLMLSQQFTGTNSIGYYAPEIFQTIGLSATNS 308 + + + F + SN +R F L + QQFTG N I YYAP+IF+ G + T Sbjct: 234 VKQSG-----WALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNTTE 288 Query: 309 SLFATGVYGTVKVVATAIFLFVG-IDRWGRKLSLVGGSIWMASMMFIIGAV--LATHPPD 365 ++ T + G V+AT F+ +G +DRWGRK +L G + MA+ M ++G + + H P Sbjct: 289 QMWGTVIVGLTNVLAT--FIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGIHSP- 345 Query: 366 TSASGVSQASIAMVVMIYLYVIGYSASWGPTPWVYVSEIFPTRLRSYGVGLAATSQWLWS 425 A + M+ ++++G++ S GP WV SEI P + R +G+ + + W+ + Sbjct: 346 -------SAQYFAIAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIAN 398 Query: 426 FVVTEITPKAVHNIG-WRTFLMFGIFCVAMCVFVIVFAKETKGRSLEDMD 474 +V ++ +G TF ++ V + + ETK SLE ++ Sbjct: 399 MIVGATFLTMLNTLGNANTFWVYAALNVLFILLTLWLVPETKHVSLEHIE 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: 609 Number of extensions: 39 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 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