GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctC in Nocardiopsis lucentensis DSM 44048

Align Tricarboxylate transport protein TctC (characterized)
to candidate WP_017597374.1 D471_RS0103675 tripartite tricarboxylate transporter substrate-binding protein

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



>NCBI__GCF_000341125.1:WP_017597374.1
          Length = 330

 Score =  185 bits (470), Expect = 1e-51
 Identities = 110/326 (33%), Positives = 169/326 (51%), Gaps = 11/326 (3%)

Query: 6   TRRTLIAA------AAALAMTGGAHAEGEQMLESIHFLIPGGAGGGWDGTARGTGEALTK 59
           +RR ++AA      AA L +TG     G   L     ++P   GGG+D TAR     L +
Sbjct: 5   SRRAVLAAGFVLPLAAFLPLTGCLPVRGPAELR---IMVPTPPGGGYDHTARTIKAVLEE 61

Query: 60  AGLVGSASYENMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTL 119
            G V   +  N+ G  G  A+A L+    +  G ++     ++  S     S S  + T 
Sbjct: 62  TGTVSEVTVFNLPGVSGTAALARLVYERGTP-GLILQMGLGVLANSHIESASHSATEATP 120

Query: 120 VAGTIGDYAAIVVGKDSPINSMADLIAAYDADPNATAVGGGSVPGGMDHLVAAMVMEAAG 179
           +A  I +  A++V  DSP +++ D+  A+ ADP++  +GGGS PGG DH+V  ++ E  G
Sbjct: 121 LARLIEEPEALLVPPDSPFDTIDDMARAWRADPSSVVIGGGSTPGGPDHMVTMLLAEELG 180

Query: 180 KDALGVKYIPYDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYD 239
            D   V Y  YD GG   AALLS E++  + G SE     ++G+++++ VT  +     D
Sbjct: 181 IDPAEVDYRTYDGGGPMQAALLSHEVSVAAAGPSEQRAAIDSGQLRVLAVTGADPDPGTD 240

Query: 240 SAPTMVEQGIDTTFVNWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIH 299
            APT+ E GI   F+NWRG  A PGL         A +  ++D+PEW     RN W + +
Sbjct: 241 -APTLAEAGIPLHFLNWRGLLAPPGLSAADREELLAVVATLHDSPEWRAELERNRWTDAY 299

Query: 300 NSGADFQSFLEAQEAQIGDLMKKLGF 325
             GA+F +FL  +E ++G  + +LGF
Sbjct: 300 LEGAEFAAFLAEEEERVGTALNRLGF 325


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: 328
Number of extensions: 19
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: 326
Length of database: 330
Length adjustment: 28
Effective length of query: 298
Effective length of database: 302
Effective search space:    89996
Effective search space used:    89996
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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