Align tonoplast dicarboxylate transporter (characterized)
to candidate WP_084609424.1 Q385_RS0108670 anion transporter
Query= CharProtDB::CH_091173 (540 letters) >NCBI__GCF_000619805.1:WP_084609424.1 Length = 460 Score = 215 bits (547), Expect = 3e-60 Identities = 139/456 (30%), Positives = 239/456 (52%), Gaps = 29/456 (6%) Query: 75 MLGVLVWMFAWWLTEAVPMPITSMTPLFLFPLFGISAADDVANSYMDDVISLVLGSFILA 134 +LG+L+ WWL E VP+ IT + L L +GI D V + + VI L++GSF++A Sbjct: 18 VLGILLLCIFWWLFEVVPVGITGLFGLILAVFYGIVDVDKVFIGFSNPVILLMIGSFLIA 77 Query: 135 LAVEHYNIHRRLALNITL--VFCVEPLNAPLLLLGICATTAFVSMWMHNVAAAVMMMPVA 192 +V Y + +R++LNI F P+ +++G T +SMW+ N A MM+P+ Sbjct: 78 HSVNKYGLDKRISLNILSKDFFIKSPIR---VIIGFSLITFLLSMWLSNTATTAMMLPIV 134 Query: 193 TGILQRLPSSSSTTEVVHPAVGKFSRAVVLGVIYSAAVGGMSTLTGTGVNLILVGMWKSY 252 G++ L E F+ ++L + YSA++GG+ T+ G+ NL+ +G K Sbjct: 135 LGVIYLL------KEEKIQGYKNFASFMLLSIAYSASIGGIGTIVGSPTNLVGLGFLKE- 187 Query: 253 FPEADPISFSQWFFFGFPLALCIFVVLWCVLCVMYCPKGAGQALSPYLHKSHLRRELDLL 312 E I F QW P+AL ++V++ +L + + + +P K+ L++E + L Sbjct: 188 --EGISIDFFQWILLMLPIALSMYVIM--ILYIRFFLRKV--KFNPQEIKTILQKEKEKL 241 Query: 313 GPMNFAEKMVLAVFGGLVVLWMTRNITDDI--PGWGRIFAGRAGDGTVSVMMATLLFIIP 370 M+ EK++ VF V LW+ + I G+ + + + V+V+ A LLF+IP Sbjct: 242 PKMSKEEKIIAGVFLLAVFLWIFPSFIGIIGFEELGKQISKKIPESIVAVLSAGLLFLIP 301 Query: 371 SNIKKGEKLMDWNKCKKLPWNIVLLLGAGFAIADGVRTSGLAEVLSKGLV-FLETAPYWA 429 ++K + ++ K++ WN V+L +G +I + +SGL E+++K L ++ P Sbjct: 302 KDLKNYQTILTVEDLKEVDWNTVILFASGISIGKLISSSGLGEIIAKSLSGYITYVPLLL 361 Query: 430 IAPTVCLIAATITEFTSNNATTTLLVPLLIEIAKNMGI---HPLLLMVPGAIGAQFAFLL 486 V +I +TE SN AT P++I + KN I +P L ++ + + FAF+ Sbjct: 362 FILIVVII--LLTEINSNTATVITFAPIIIALLKNNQIDFVYPTLAII---VASSFAFMF 416 Query: 487 PTGTPSNVVGFTTGHIEIKDMIKTGLPLKIAGTIFL 522 P TP N + ++TG I+++DM K GL L G+I + Sbjct: 417 PIATPPNAIVYSTGFIKLQDMAKFGLFLNAVGSIVI 452 Lambda K H 0.326 0.140 0.441 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: 640 Number of extensions: 33 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: 540 Length of database: 460 Length adjustment: 34 Effective length of query: 506 Effective length of database: 426 Effective search space: 215556 Effective search space used: 215556 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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