GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctC in Cupriavidus basilensis 4G11

Align Tricarboxylate transport protein TctC (characterized)
to candidate RR42_RS20620 RR42_RS20620 C4-dicarboxylate ABC transporter substrate-binding protein

Query= reanno::Dino:3609740
         (326 letters)



>FitnessBrowser__Cup4G11:RR42_RS20620
          Length = 310

 Score =  189 bits (480), Expect = 8e-53
 Identities = 101/310 (32%), Positives = 166/310 (53%), Gaps = 4/310 (1%)

Query: 15  AALAMTGGAHAEGEQMLESIHFLIPGGAGGGWDGTARGTGEALTKAGLVGSASYENMSGG 74
           A+ A+T    A     L+S+ F+I    GGG+D T R  G AL  AG+  +ASY+N  G 
Sbjct: 2   ASAAITATVAAAPAFALDSVKFMIGANPGGGFDQTGRSLGAALVSAGVAKTASYDNKGGA 61

Query: 75  GGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTLVAGTIGDYAAIVVGK 134
           GG   +   +     +   ++V    +V    T     + ++ T +A    D   I V  
Sbjct: 62  GGTIGLTQFVNTDKGNPNAMIVTGAVMVGAIETNHPPVTLKNATPIARLFADTMVITVPA 121

Query: 135 DSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVMEAAGKDALGVKYIPYDAGG 194
           +SP+ SM DL A   A+P + + GGGS  G +DH++A +V + +G D   + Y+P+  GG
Sbjct: 122 NSPLKSMKDLTAQLRANPGSVSWGGGS-KGSIDHILAGLVAKESGVDPKKINYVPFQGGG 180

Query: 195 KAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYDSAPTMVEQGIDTTFV 254
           +A A++L G +     G SE +   ++G+++ + VT+ +R A     PT+ EQGI+    
Sbjct: 181 EASASILGGHVTVGLAGVSEFLPFIKSGKMRALAVTSKDRTA---DIPTLKEQGINVEIY 237

Query: 255 NWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIHNSGADFQSFLEAQEA 314
           NWRG + APG+  EQ  A    + K  +TP W+E  A+N W     +G +F  F++++ A
Sbjct: 238 NWRGVYGAPGITAEQRKALVDAVVKATETPLWKETLAKNDWTPFLLTGDEFGKFVDSESA 297

Query: 315 QIGDLMKKLG 324
           ++G  +++LG
Sbjct: 298 RLGGSLRELG 307


Lambda     K      H
   0.315    0.132    0.378 

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: 287
Number of extensions: 19
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: 326
Length of database: 310
Length adjustment: 27
Effective length of query: 299
Effective length of database: 283
Effective search space:    84617
Effective search space used:    84617
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: 42 (22.0 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