Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate WP_028582871.1 G494_RS0100140 C4-dicarboxylate ABC transporter permease
Query= reanno::PV4:5208943 (465 letters) >NCBI__GCF_000429965.1:WP_028582871.1 Length = 466 Score = 702 bits (1813), Expect = 0.0 Identities = 357/465 (76%), Positives = 405/465 (87%) Query: 1 MTIATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAI 60 MT A LFI LF CML+GMPIA+ALG SS+ TIL FS DSLAS+ALKL+E+ SEHYTLLAI Sbjct: 1 MTTAALFILLFGCMLIGMPIALALGLSSITTILFFSSDSLASIALKLFEALSEHYTLLAI 60 Query: 61 PFFILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIG 120 PFFILSSAFLSTGGVA+RII FA+ VGHIRGGLAMASVMACM+FAAVSGSSPATVAAIG Sbjct: 61 PFFILSSAFLSTGGVAKRIIRFALSLVGHIRGGLAMASVMACMIFAAVSGSSPATVAAIG 120 Query: 121 SIVIVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGL 180 SIVIVGMVRAGYPE FAAGVIT +GTLGILIPPSIVMLVYAAATEVSAARMFMAG IPGL Sbjct: 121 SIVIVGMVRAGYPESFAAGVITNAGTLGILIPPSIVMLVYAAATEVSAARMFMAGFIPGL 180 Query: 181 MMGLLLMLAIYIVARIKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTE 240 MMG +LMLAIYI ARIKKLP+ P+ GF + + + A GGL LI+IVLGSIYGG+ASPTE Sbjct: 181 MMGGILMLAIYIAARIKKLPAMPWMGFGEVLAAGSSAFGGLMLIIIVLGSIYGGVASPTE 240 Query: 241 AAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIR 300 AAAV+ VYA+ +++FGYRD+GPLK V+WR+ GE + A+LRN + A+ + D ++R Sbjct: 241 AAAVSAVYAFLVSIFGYRDVGPLKEVAWRNQGEGVASAVLRNCARSIQAIPRCLNDPDVR 300 Query: 301 HVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLA 360 ++ D +KVSIMLLFIIANAMLFAHVLTTERIPH +AE I+G GL W FLI+VNLLLL Sbjct: 301 KIILDASKVSIMLLFIIANAMLFAHVLTTERIPHHLAELIIGWGLSPWMFLIVVNLLLLM 360 Query: 361 AGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420 AGNFMEPSAILLIMAPILFPIA +LGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT Sbjct: 361 AGNFMEPSAILLIMAPILFPIAVKLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGIT 420 Query: 421 GRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYIDKLNGY 465 G S+GWVI +C+PWL LLL FL +ITYIPQ+SLFLPE++DKL+GY Sbjct: 421 GNSIGWVIRACLPWLMLLLIFLIIITYIPQVSLFLPEFLDKLHGY 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: 779 Number of extensions: 24 Number of successful extensions: 2 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: 466 Length adjustment: 33 Effective length of query: 432 Effective length of database: 433 Effective search space: 187056 Effective search space used: 187056 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 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