Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate Ac3H11_3957 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= uniprot:Q88NN8 (323 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3957 Length = 329 Score = 409 bits (1050), Expect = e-119 Identities = 206/329 (62%), Positives = 249/329 (75%), Gaps = 6/329 (1%) Query: 1 MTFKRKLLLAVLPFAFSVAM-----PASALDIKFAEIHPAGYPTVVAEQNMGKKLEDASN 55 MTF+R LL A ++AM A ++ +K A++HPAGYP VVA +NMGKKL+ A+N Sbjct: 1 MTFRRSLLTACAAAVAAMAMLPVAARAQSMVLKAADVHPAGYPNVVAVENMGKKLDAATN 60 Query: 56 GEITFKMFAGGVLGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHM 115 G + + F GGVLG EKE+IEQ Q GA+ + R SLG VG VVP+VNVFNMPFVFR DHM Sbjct: 61 GRLKIQTFPGGVLGGEKEMIEQTQFGAINILRTSLGPVGTVVPEVNVFNMPFVFRSQDHM 120 Query: 116 RKIIDGEIGQEILDKITNSDFNLVALAWMDGGSRSIYTKKPVRSLEDLKGMKIRVQGNPL 175 R +IDG IG E+L KI+ S LVA+ WMDGGSRS+YTKKPVRS DLKG K+R+ GNPL Sbjct: 121 RAVIDGAIGDELLAKISASPAKLVAIGWMDGGSRSLYTKKPVRSPADLKGQKVRMMGNPL 180 Query: 176 FIDMMNAMGGNGIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQS-AKYYTLTGHLIL 234 F+D MNAMGGNGI+M GE+F+ALQTGV+DGAENN P+ NH+ + AK+YT T HLI+ Sbjct: 181 FVDTMNAMGGNGISMGYGEVFTALQTGVVDGAENNAPSFFTSNHYSTGAKFYTQTNHLII 240 Query: 235 PEPVVMSKTTWNKLSPEQQALVKKVAREAQMEERALWDAKSAASEEKLKAAGVEFITVDK 294 PE +V+SK TW+KLS + QAL+KK REAQ+E+RALWD KLKAAGVEFI VD Sbjct: 241 PELLVVSKVTWDKLSKDDQALLKKFGREAQLEQRALWDKSVEDYTAKLKAAGVEFINVDT 300 Query: 295 KPFYDATASVREKYGAQYADLMKRIDAVQ 323 K FYDATA VR KYGA YADLMKRI+AV+ Sbjct: 301 KAFYDATAPVRAKYGANYADLMKRIEAVK 329 Lambda K H 0.318 0.134 0.381 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: 303 Number of extensions: 12 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: 323 Length of database: 329 Length adjustment: 28 Effective length of query: 295 Effective length of database: 301 Effective search space: 88795 Effective search space used: 88795 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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