GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Desulfovibrio vulgaris Miyazaki F

Align TRAP dicarboxylate transporter, DctP subunit (characterized, see rationale)
to candidate 8501405 DvMF_2135 TRAP dicarboxylate transporter, DctP subunit (RefSeq)

Query= uniprot:Q88NN8
         (323 letters)



>FitnessBrowser__Miya:8501405
          Length = 365

 Score =  139 bits (350), Expect = 1e-37
 Identities = 88/284 (30%), Positives = 151/284 (53%), Gaps = 6/284 (2%)

Query: 8   LLAVLPFAFSVAMPASALDIKFAEIHPAGYPTVVAEQNMGKKLEDASNGEITFKMFAGGV 67
           L A+LP     A  ++A ++  A +   G    V  +   + LE+ S+G     +   G 
Sbjct: 44  LAAILPGWPRTA--SAATELTLAVVTTPGSAQHVCAERFRQLLEERSHGAYRVVVHHSGT 101

Query: 68  LGSEKEVIEQAQIGAVQMTRVSLGIVGPVVPDVNVFNMPFVFRDHDHMRKIIDGEIGQEI 127
           LG+E E+++Q Q+G VQ+  ++LG++ P VP+V V + PF+FRD     +++DG  G+ +
Sbjct: 102 LGTETEILQQLQLGGVQLAIITLGVLDPFVPEVKVLDYPFLFRDAAEADRVLDGATGRAL 161

Query: 128 LDKITNSDFNLVALAWMDGGSRSIYTK-KPVRSLEDLKGMKIRVQGNPLFIDMMNAMGGN 186
           LD +      L  L + + G R +    +PVRS++D++G+KIRV  + L  ++  A+G N
Sbjct: 162 LDALER--VGLKGLHFSENGFRHLTNNVRPVRSVDDVRGLKIRVLESTLHRELWRALGAN 219

Query: 187 GIAMDTGEIFSALQTGVIDGAENNPPTLLEHNHFQSAKYYTLTGHLILPEPVVMSKTTWN 246
              M    I++ LQ G IDG EN    + E+   +  KY +LTGH+      + +   +N
Sbjct: 220 PTPMG-WPIYAELQQGTIDGQENPLWVMAEYRMPEVQKYLSLTGHVYSAHADLANLAWFN 278

Query: 247 KLSPEQQALVKKVAREAQMEERALWDAKSAASEEKLKAAGVEFI 290
            L P ++ LV +   +A   +RA    K A    +L+ AG++ +
Sbjct: 279 GLPPAERTLVMQCMADAAAYQRAYNRQKDADYLRRLREAGMQVV 322


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: 205
Number of extensions: 7
Number of successful extensions: 3
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: 365
Length adjustment: 29
Effective length of query: 294
Effective length of database: 336
Effective search space:    98784
Effective search space used:    98784
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: 49 (23.5 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