Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate 7024207 Shewana3_1414 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__ANA3:7024207 Length = 465 Score = 809 bits (2089), Expect = 0.0 Identities = 413/465 (88%), Positives = 439/465 (94%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60 M IATLF +L +CM LGMPIAIALGFSSMLTIL FS+DSLASVALKLYES+SEHYTLLAI Sbjct: 1 MAIATLFTALLVCMFLGMPIAIALGFSSMLTILFFSNDSLASVALKLYESSSEHYTLLAI 60 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFFILSSAFLSTGGVARRIIDFAMDS+GHIRGGLAMASVMACMLFAAVSGSSPATVAAIG Sbjct: 61 PFFILSSAFLSTGGVARRIIDFAMDSIGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180 SIVIVGMV+AGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL Sbjct: 121 SIVIVGMVKAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180 Query: 181 MMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTE 240 MMG LLM+ IYIVAR K LPSRPFPGF+ L ISSAKA+GGLALI+IVLGSIYGG+ASPTE Sbjct: 181 MMGFLLMIVIYIVARFKNLPSRPFPGFKQLGISSAKALGGLALIIIVLGSIYGGVASPTE 240 Query: 241 AAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIR 300 A+AVAC+YAYFIAVFGYRDIGPLKNV+WR+ EP+ AI+RNLG M L + KTP DKEIR Sbjct: 241 ASAVACMYAYFIAVFGYRDIGPLKNVAWRNPNEPIPSAIVRNLGHMALGLIKTPIDKEIR 300 Query: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLA 360 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPH+IAE IVGMGLP WGFLIIVNLLLLA Sbjct: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHIIAEHIVGMGLPAWGFLIIVNLLLLA 360 Query: 361 AGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420 AGNFMEPSAI+LIMAPILFPIAT LGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT Sbjct: 361 AGNFMEPSAIVLIMAPILFPIATHLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420 Query: 421 GRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYIDKLNGY 465 GRS+GWVI S +PWLAL+L FLALITY+PQISLFLPE++DKLNGY Sbjct: 421 GRSIGWVIQSVLPWLALMLAFLALITYVPQISLFLPEFLDKLNGY 465 Lambda K H 0.330 0.144 0.424 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: 808 Number of extensions: 15 Number of successful extensions: 1 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: 465 Length of database: 465 Length adjustment: 33 Effective length of query: 432 Effective length of database: 432 Effective search space: 186624 Effective search space used: 186624 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 (21.8 bits) S2: 51 (24.3 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