GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpC in Marinobacter algicola DG893

Align 2-methylcitrate synthase (EC 2.3.3.5) (characterized)
to candidate WP_007152345.1 MDG893_RS03515 citrate (Si)-synthase

Query= BRENDA::Q9I5E3
         (375 letters)



>NCBI__GCF_000170835.1:WP_007152345.1
          Length = 424

 Score =  194 bits (494), Expect = 3e-54
 Identities = 121/360 (33%), Positives = 197/360 (54%), Gaps = 26/360 (7%)

Query: 32  LTYRGYDVRDLAAAAIFEEVAYLLLYGELPNKQQLDAYLKKLQGQRDLPQALKEVLERIP 91
           L +RGY + +LA  + + EV YLLL GELP  ++   +   ++    L   ++   +   
Sbjct: 66  LLHRGYPIEELAENSDYLEVCYLLLNGELPTAEENKRFHDTIKNHTMLHDQMRNFFQGFR 125

Query: 92  KDAHPMDVMRTGASVLGTL------EPELSFDQQRDV-ADRLLAAFPAIMTYWYRFTHEG 144
           +DAHPM +M     V+G L      + +++  +QR++ A RL+A  P I  + Y+++  G
Sbjct: 126 RDAHPMAIM---CGVVGALSAFYHDQMDVTNIEQREITAHRLVAKMPTIAAWCYKYSI-G 181

Query: 145 QRIDCNSDEPTIGGHFLALLHGK-----KPSELHVKVMNVSLILYAEHEFNASTFTARVC 199
           Q      ++ T   +FL ++ G      KP+ +  K M+   IL+A+HE NAST T R+ 
Sbjct: 182 QPFMYPRNDLTYSENFLQMMFGVPCEEYKPNPILAKAMDKIFILHADHEQNASTSTVRLA 241

Query: 200 ASTLSDLYSCVTGAIGSLRGPLHGGANEAAMELIERFSSPQEATAELLKMLERKD--KIM 257
            ST ++ Y+C+   I +L GP HGGANEA ++++            + K  ++ D  ++M
Sbjct: 242 GSTGANPYACIASGIAALWGPAHGGANEAVLDMLAEIGDESNIEKFIAKAKDKDDPFRLM 301

Query: 258 GFGHAIYKDSDPRNEVIKGWSKQLADEVG--DKVLFAVSEAIDKTMWE-----QKKLFPN 310
           GFGH +YK+ DPR +V+   + ++  E+G  +  L  +++ ++K   E     Q+KL+PN
Sbjct: 302 GFGHRVYKNFDPRAKVMAETAHEVLTELGLENDPLLKIAQRLEKIALEDEYFVQRKLYPN 361

Query: 311 ADFYHASAYHFMGIPTKLFTPIFVCSRTSGWTAHVFEQRANN-RIIRPSAEYTGVEQRAF 369
            DFY       +GIPT +FT IF  SRT GW +H  E  + + RI RP   YTG E R++
Sbjct: 362 VDFYSGLILKAIGIPTSMFTVIFALSRTIGWFSHWNEMVSGDYRIGRPRQLYTGSEARSY 421


Lambda     K      H
   0.319    0.134    0.396 

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: 368
Number of extensions: 23
Number of successful extensions: 6
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: 375
Length of database: 424
Length adjustment: 31
Effective length of query: 344
Effective length of database: 393
Effective search space:   135192
Effective search space used:   135192
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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