GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Acidovorax sp. GW101-3H11

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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