Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate WP_043917613.1 jaqu_RS03895 TRAP transporter large permease
Query= reanno::PV4:5208943 (465 letters) >NCBI__GCF_000877395.1:WP_043917613.1 Length = 438 Score = 247 bits (630), Expect = 6e-70 Identities = 153/461 (33%), Positives = 254/461 (55%), Gaps = 40/461 (8%) Query: 4 ATLFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAIPFF 63 A + I+ + + G+ +A+ L S +L+F + ++ +++ LL+IP F Sbjct: 8 AIVAIATIVVLFSGVSVALGLLIVSGGFLLIFDGARSLELMPEIMFGKLDNFALLSIPMF 67 Query: 64 ILSSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIV 123 I+ A +++ + + + + GGL ++++ AC LF+A+SGSSPAT AAIG + Sbjct: 68 IIMGASIASTRAGADLYEALERWLTRVPGGLVVSNLGACALFSAMSGSSPATCAAIGKMG 127 Query: 124 IVGMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLMM- 182 I M + GYP++ AAG I GTLGILIPPS+ M+VY ATE S R+F+AG+ PGLM+ Sbjct: 128 IPEMRKRGYPDEVAAGSIAAGGTLGILIPPSVTMIVYGIATETSIGRLFLAGVFPGLMLV 187 Query: 183 GLLLMLAIYIVAR---IKKLPSRPFPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPT 239 GL + +++ R + L R + + L + + + + +I+ VL ++YGGIA+P+ Sbjct: 188 GLFMAWSLFSTWRSGNAQVLAPRSYTMAQRLEV-LPRVLPFILIILGVLYAMYGGIATPS 246 Query: 240 EAAAVACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEI 299 E AAV + IA+ YR P+K + Sbjct: 247 ETAAVGALLCILIAMVIYRLWSPMK----------------------------------L 272 Query: 300 RHVVRDGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLL 359 V+RD + S+M+LFII A +F+++L++ I IAE I + + W + VNL LL Sbjct: 273 WEVLRDSTRESVMILFIIGAAGVFSYMLSSLFITQSIAEWIGTLDVNRWVLMGAVNLFLL 332 Query: 360 AAGNFMEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGI 419 AG F+ P A++L+ APIL PI T G DPI +++ +NMEIG+++PPVGLNL+V GI Sbjct: 333 VAGFFLPPVAVILMAAPILLPIITTAGFDPIWFAVVLTINMEIGLISPPVGLNLYVINGI 392 Query: 420 T-GRSMGWVIHSCIPWLALLLFFLALITYIPQISLFLPEYI 459 + ++ +P++ ++ + ++ P I+ +LP+ + Sbjct: 393 APDIKLKTILTGSLPFVGCMVIAIVILCLFPGIATWLPDAV 433 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: 620 Number of extensions: 41 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 465 Length of database: 438 Length adjustment: 33 Effective length of query: 432 Effective length of database: 405 Effective search space: 174960 Effective search space used: 174960 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