Align The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)
Query= TCDB::A2R3H2 (518 letters) >FitnessBrowser__Keio:18059 Length = 491 Score = 198 bits (504), Expect = 3e-55 Identities = 144/502 (28%), Positives = 240/502 (47%), Gaps = 66/502 (13%) Query: 9 VYLLTAVAYSGSLLFGYDTGVM-GSVLSLTSFKEDFGIPTGSSGFASSKSSEISSNVVSL 67 ++ +T VA G LLFGYDT V+ G+V SL + + + S ++ + V+ Sbjct: 10 IFSITLVATLGGLLFGYDTAVISGTVESLNT------VFVAPQNLSESAANSLLGFCVAS 63 Query: 68 LTAGCFFGAIFAAPLNERIGRRYALMIFTVIFLIGAA-----------------VQVASK 110 GC G + R GRR +L I V+F I V V Sbjct: 64 ALIGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLA 123 Query: 111 HHIGQIYGGRVIAGLGIGGMSSITPVFVSENCPPSIRGRVAGMFQEFLVIGSTFAYWLDY 170 ++ + R+I G+G+G S ++P++++E P IRG++ Q ++ G Y ++Y Sbjct: 124 GYVPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNY 183 Query: 171 GVSLHIPSS---TKQWRVPVAVQLIPGGLMLLGLFFLKESPRWLAGKGRHEEALQSLAYI 227 ++ +S T WR A + IP L L+ L+ + ESPRWL +G+ E+A L I Sbjct: 184 FIARSGDASWLNTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKI 243 Query: 228 RNESPDSEEIQKEFAEIRAAIDEEVAATEGLTYKEFIQPSNLKRFG-----FAFTLMLSQ 282 + ++ +Q EI+ ++D T G L FG L + Q Sbjct: 244 MGNTLATQAVQ----EIKHSLDHG-RKTGG----------RLLMFGVGVIVIGVMLSIFQ 288 Query: 283 QFTGTNSIGYYAPEIFQTIGLSATNSSLFATGVYGTVKVVATAIFLFVGIDRWGRKLSLV 342 QF G N + YYAPE+F+T+G S T+ +L T + G + + T + + +D++GRK + Sbjct: 289 QFVGINVVLYYAPEVFKTLGAS-TDIALLQTIIVGVINLTFTVLAIMT-VDKFGRKPLQI 346 Query: 343 GGSIWMASMMFIIGAVLATHPPDTSASGVSQASIAMVVMIYLYVIGYSASWGPTPWVYVS 402 G++ MA MF +G T P +A++ M++ YV ++ SWGP WV +S Sbjct: 347 IGALGMAIGMFSLGTAFYTQAPGI---------VALLSMLF-YVAAFAMSWGPVCWVLLS 396 Query: 403 EIFPTRLRSYGVGLAATSQWLWSFVVTEITPK-------AVHNIGWRTFLMFGIFCVAMC 455 EIFP +R + +A +QWL ++ V+ P H ++ ++G V Sbjct: 397 EIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAA 456 Query: 456 VFVIVFAKETKGRSLEDMDILF 477 +F+ F ETKG++LE+++ L+ Sbjct: 457 LFMWKFVPETKGKTLEELEALW 478 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: 606 Number of extensions: 38 Number of successful extensions: 8 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: 491 Length adjustment: 34 Effective length of query: 484 Effective length of database: 457 Effective search space: 221188 Effective search space used: 221188 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