Align The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized)
to candidate Ga0059261_1891 Ga0059261_1891 MFS transporter, sugar porter (SP) family
Query= TCDB::A2R3H2 (518 letters) >FitnessBrowser__Korea:Ga0059261_1891 Length = 466 Score = 204 bits (518), Expect = 7e-57 Identities = 147/479 (30%), Positives = 228/479 (47%), Gaps = 40/479 (8%) Query: 9 VYLLTAVAYSGSLLFGYDTGVMGSVLSLTSFKEDFGIPTGSSGFASSKSSEISSNVVSLL 68 + + AVA G LLFGYD+G + K F + G GF V L Sbjct: 12 IMAIVAVATIGGLLFGYDSGAVNGTQD--GLKSAFALSEGGLGFT-----------VGSL 58 Query: 69 TAGCFFGAIFAAPLNERIGRRYALMIFTVIFLIGAAVQVASKHHIGQIYGGRVIAGLGIG 128 GCF GA A L + IGRR +++ V+FLIGA +Q S H R+ G+ +G Sbjct: 59 LIGCFIGAFLAGRLADLIGRRNVMILTAVLFLIGALIQGFS-HEQWIFVAARIAGGMAVG 117 Query: 129 GMSSITPVFVSENCPPSIRGRVAGMFQEFLVIGSTFAYWLDYGVSLHIPSST-------K 181 S ++P ++SE P +IRGR+ + Q ++ G T A+ ++Y ++ +ST + Sbjct: 118 AASVLSPAYISEVAPANIRGRMTTIQQIMIISGLTAAFVVNYWLAKTAGASTNLFWGGYE 177 Query: 182 QWRVPVAVQLIPGGLMLLGLFFLKESPRWLAGKGRHEEA---LQSLAYIRNESPDSEEIQ 238 WR +Q IP + L+ LFF+ ESPR+L KGR+ EA L SL + EIQ Sbjct: 178 AWRWMYWMQAIPATVFLIALFFIPESPRYLVSKGRNAEATRVLTSLFGAGTATNKLTEIQ 237 Query: 239 KEFAEIRAAIDEEVAATEGLTYKEFIQPSNLKRFGFAFTLM-LSQQFTGTNSIGYYAPEI 297 F++ R + + + +G ++ +A L+ + QQ G N I YY + Sbjct: 238 ASFSDHRPTLRDILDPVKG----------GVRPIVWAGLLLAVFQQLVGINVIFYYGATL 287 Query: 298 FQTIGLSATNSSLFATGVYGTVKVVATAIFLFVGIDRWGRKLSLVGGSIWMASMMFIIGA 357 +Q G + N +L V G V + A + + + +DR GRK L+ GS MA +F + Sbjct: 288 WQLAGFTE-NDALLINIVSGFVSIAACFVTVAL-VDRIGRKPLLLIGSAGMAVALFAMVF 345 Query: 358 VLATHPPDTSASGV--SQASIAMVVMIYLYVIGYSASWGPTPWVYVSEIFPTRLRSYGVG 415 + D V Q I V+ LYV+ ++ SWGP WV + E+FP ++R + Sbjct: 346 AFSRGSLDAQGKLVLSQQLGIIAVIAANLYVVFFNVSWGPVMWVMLGEMFPNQIRGSALA 405 Query: 416 LAATSQWLWSFVVTEITPKAVHNIGWRTFLMFGIFCVAMCVFVI-VFAKETKGRSLEDM 473 + +QW ++++ + P +G F C + F++ F ETKG LEDM Sbjct: 406 VCGFAQWFSNYLIAQSFPIMAAGLGLAVSYSFYAVCAVISFFLVSKFIHETKGVELEDM 464 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: 554 Number of extensions: 30 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: 466 Length adjustment: 34 Effective length of query: 484 Effective length of database: 432 Effective search space: 209088 Effective search space used: 209088 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