Align TRAP-type large permease component (characterized, see rationale)
to candidate 3610328 Dshi_3709 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Dino:3610328 Length = 420 Score = 297 bits (760), Expect = 5e-85 Identities = 154/410 (37%), Positives = 251/410 (61%), Gaps = 12/410 (2%) Query: 17 GVPVAFSLMFCGVVLMWYMGMFNTQIIA---QNMIAGADTFTLLAIPFFILAGELMNAGG 73 GVP+A L ++ +W G N + Q + G + + LLAIP F+L GELMN GG Sbjct: 13 GVPIALVLAITAMIYIWASG--NDVLFLSYPQQLYGGLEKYGLLAIPLFMLVGELMNEGG 70 Query: 74 LSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIPMMAKAGYNV 133 +++R++ FA VG +RGGL + ++A + MA+I GS A A + +++P M K GY+ Sbjct: 71 ITKRLVKFASVFVGSLRGGLAYINLVANMFMAAIIGSTNAQIAVMGHVMVPEMVKRGYDR 130 Query: 134 PRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGIALVATWLLVV 193 +A + AAGG+++P+IPPSM F+++GV A +SI +F+AGI+PGL+MG A + L+VV Sbjct: 131 NFAAAVTAAGGLMSPIIPPSMLFVIYGVLAQISIGDMFIAGIIPGLLMGAAFI---LVVV 187 Query: 194 RKDDIQPLPRTPMKERVGATG---RALWALGMPVIILGGIKAGVVTPTEAAVVAAVYALF 250 P R A RAL +L +PV+I+GGI G+ TPTE+A VA+V A+ Sbjct: 188 VLGFFYTYPTEAKLSRGMAVSHILRALPSLSIPVVIIGGIAGGIATPTESAAVASVAAII 247 Query: 251 VGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFISPLID 310 VG +RE P +PG++++ ++++++FLV A V W+I IP + ++ L + Sbjct: 248 VGWAFHREFDPSHIPGMLVRLLASSSMVLFLVATANVFGWIIVYEKIPQNLAAYLVTLTE 307 Query: 311 RPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPI-IKQAGIDPVYFGVLFIMNTCIGL 369 P + M ++ +++L+VGT +D ++++ P+++PI + GIDP +FGV +N IGL Sbjct: 308 NPIVFMLLLNVMLLLVGTVIDAIAALILVVPIMLPIAMLSYGIDPFHFGVAVCLNLVIGL 367 Query: 370 LTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVIV 419 LTPPVG L V + V ++ + PFL+A +++L L+ ++P + +V Sbjct: 368 LTPPVGTALYVTAQVSNCKPMSIMKPLAPFLLAALVILLLVSVWPALTLV 417 Lambda K H 0.331 0.145 0.430 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: 488 Number of extensions: 27 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: 425 Length of database: 420 Length adjustment: 32 Effective length of query: 393 Effective length of database: 388 Effective search space: 152484 Effective search space used: 152484 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 50 (23.9 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