Align The galacturonic acid (galacturonate) uptake porter, GatA, of 518 aas and 12 TMSs (characterized)
to candidate N515DRAFT_1228 N515DRAFT_1228 MFS transporter, SP family, galactose:H+ symporter
Query= TCDB::A2R3H2 (518 letters) >FitnessBrowser__Dyella79:N515DRAFT_1228 Length = 463 Score = 191 bits (484), Expect = 6e-53 Identities = 144/473 (30%), Positives = 229/473 (48%), Gaps = 38/473 (8%) Query: 4 LKNYRVYLLTAVAYSGSLLFGYDTGVMGSVLSLTSFKEDFGIPTGSSGFASSKSSEISSN 63 +K +Y A +G L+FG D GV+ K +F I S Sbjct: 13 VKGTVIYTCVLAALAG-LMFGLDIGVISGASQF--IKAEFAI-----------SDHTIEW 58 Query: 64 VVSLLTAGCFFGAIFAAPLNERIGRRYALMIFTVIFLIGAAVQVASKHHIGQIYGGRVIA 123 +VS + G GA+ A L+ +GR+ +L++ ++F+IG+ + + RVI Sbjct: 59 IVSSMMFGAAVGALGAGWLSSHLGRKRSLILGAILFVIGSLL-CGLAWSPETLIAARVIL 117 Query: 124 GLGIGGMSSITPVFVSENCPPSIRGRVAGMFQEFLVIGSTFAYWLDYGVSLHIPSSTKQW 183 GL IG + P++++E P IRG + +Q + IG A+ D +S H W Sbjct: 118 GLAIGIATFTAPLYLAEVAPEHIRGAMISTYQLMITIGILVAFLSDTALSYH-----GAW 172 Query: 184 RVPVAVQLIPGGLMLLGLFFLKESPRWLAGKGRHEEALQSLAYIRNESPDSEEIQKEFAE 243 R + V IPG L LLG+ L +SPRWL +GR +EA+ L +R D + +E A+ Sbjct: 173 RWMLGVIAIPGALFLLGVLGLPDSPRWLMMRGRRDEAIDVLRRLRG---DEVVVAREAAD 229 Query: 244 IRAAIDEEVAATEGLTYKEFIQPSNLKRFGFAFTLM-LSQQFTGTNSIGYYAPEIFQTIG 302 I EE T + F + N +R F L+ + QQFTG N + YYAP IFQ +G Sbjct: 230 I-----EEQLKTPQRGWDLFAENPNFRRSVFLGALLQIMQQFTGMNVVMYYAPRIFQEMG 284 Query: 303 LSATNSSLFATGVYGTVKVVATAIFLFVGIDRWGRKLSLVGGSIWMASMMFIIGAVLATH 362 T + ++ T + G V+AT I + + IDRWGRK L G MA + ++GA++ Sbjct: 285 YD-TAAQMWFTALVGLTNVLATFIAIAL-IDRWGRKPILYTGFAVMAVGLGVVGALM--- 339 Query: 363 PPDTSASGVSQASIAMVVMIYLYVIGYSASWGPTPWVYVSEIFPTRLRSYGVGLAATSQW 422 + +G ++ V M+ +++G++ S GP W SEI P + R +G+G++ + W Sbjct: 340 --NGGINGQTE-QYTCVAMLLFFIVGFAMSAGPLVWTLCSEIQPLKGRDFGIGVSTFTNW 396 Query: 423 LWSFVVTEITPKAVHNIG-WRTFLMFGIFCVAMCVFVIVFAKETKGRSLEDMD 474 + + VV ++ IG TF ++ V ETKG +LE ++ Sbjct: 397 ITNMVVGFTFLSLLNTIGNASTFWLYAALNAVFIVLTFWLVPETKGVTLEQIE 449 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: 653 Number of extensions: 41 Number of successful extensions: 6 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: 463 Length adjustment: 34 Effective length of query: 484 Effective length of database: 429 Effective search space: 207636 Effective search space used: 207636 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