Align dicarboxylate TRAP transporter (succinate, fumarate, L-malate, and alpha-ketoglutarate), large permease component (characterized)
to candidate 8501197 DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= reanno::PV4:5208943 (465 letters) >FitnessBrowser__Miya:8501197 Length = 640 Score = 316 bits (810), Expect = 1e-90 Identities = 176/451 (39%), Positives = 272/451 (60%), Gaps = 36/451 (7%) Query: 6 LFISLFLCMLLGMPIAIALGFSSMLTILLFSDDSLASVALKLYESTSEHYTLLAIPFFIL 65 LF L +L+G+PIA +LG +++ T+L L +A + S + + +LAIPFFI Sbjct: 224 LFGYFVLFLLVGVPIAFSLGLATIATVLGAGTLPLEYLAQIAFVSI-DSFPILAIPFFIA 282 Query: 66 SSAFLSTGGVARRIIDFAMDSVGHIRGGLAMASVMACMLFAAVSGSSPATVAAIGSIVIV 125 + F+ GG++RR++ + VG + GG+A+A+++ CM FAA+SGS PATVAAIGSI I Sbjct: 283 AGVFMGAGGLSRRLLALGDELVGALPGGMALATIVTCMFFAAISGSGPATVAAIGSITIP 342 Query: 126 GMVRAGYPEKFAAGVITTSGTLGILIPPSIVMLVYAAATEVSAARMFMAGLIPGLMMGLL 185 MV GY + FAA V+ ++G +G++IPPS +VY A + S ++F+AG++PG++ GL Sbjct: 343 AMVERGYDKFFAAAVVASAGCIGVMIPPSNPFVVYGVAAQASVGKLFLAGIVPGVLCGLA 402 Query: 186 LMLAIYIVARIKKLPSRP-FPGFRPLAISSAKAMGGLALIVIVLGSIYGGIASPTEAAAV 244 LM Y ++ K FR + + +A L + VIVLG IYGGI +PTEAAAV Sbjct: 403 LMAVAYYISLKKGWRGEARHRDFRSVMQAMWEAKWALLVPVIVLGGIYGGIMTPTEAAAV 462 Query: 245 ACVYAYFIAVFGYRDIGPLKNVSWRDSGEPLIRAILRNLGFMVLAVFKTPADKEIRHVVR 304 + +Y + +F YR+I +WR + ++ Sbjct: 463 SALYGMIVGLFIYREI------TWRRMWDCMV---------------------------- 488 Query: 305 DGAKVSIMLLFIIANAMLFAHVLTTERIPHLIAETIVGMGLPVWGFLIIVNLLLLAAGNF 364 + A+ S +++ ++A A LF +++T E++P IA I+G+ L+++N+ LL G F Sbjct: 489 ESAQTSSVIIVLMAMATLFGNIMTIEQVPDHIAAMILGVTSNKIAILLLINVFLLWVGTF 548 Query: 365 MEPSAILLIMAPILFPIATQLGIDPIHLGIIMVVNMEIGMLTPPVGLNLFVTAGITGRSM 424 ME A ++I+ PIL P+ TQ+G+DPIH G+IMVVN+ IG +TPPVG+NLFV + I+ S+ Sbjct: 549 MEALAAIVIITPILLPLVTQVGVDPIHFGVIMVVNLAIGFITPPVGVNLFVASSISKVSI 608 Query: 425 GWVIHSCIPWLALLLFFLALITYIPQISLFL 455 G V+ + P+L +++ L ITYIP ISL L Sbjct: 609 GDVVRAAWPFLLVMIALLMAITYIPAISLCL 639 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: 817 Number of extensions: 49 Number of successful extensions: 4 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: 640 Length adjustment: 35 Effective length of query: 430 Effective length of database: 605 Effective search space: 260150 Effective search space used: 260150 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: 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