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_017597377.1 D471_RS0103690 tripartite tricarboxylate transporter substrate binding protein

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



>NCBI__GCF_000341125.1:WP_017597377.1
          Length = 324

 Score =  197 bits (501), Expect = 3e-55
 Identities = 115/325 (35%), Positives = 167/325 (51%), Gaps = 16/325 (4%)

Query: 12  AAAAALAMT---------GGAHAEGE-QMLESIHFLIPGGAGGGWDGTARGTGEALTKAG 61
           AAAA L +          G  +A+G  +    I    P G GGGWD  AR +   L   G
Sbjct: 2   AAAAVLPLALSACGGEDGGNTNADGTWEPNGPIEITAPAGTGGGWDTLARTSARLLESEG 61

Query: 62  LVG-SASYENMSGGGGGKAIAYLIENANSSHGTLMVNSTPIVIRSLTGEISQSFRDLTLV 120
           LV  S    N  G GG    AY+  N       L V S PI++  + G+      D T +
Sbjct: 62  LVDQSIQVVNKPGAGGAIGWAYIAGNEGDPQ-KLFVTSPPILLVPMAGDSEYDHEDFTPI 120

Query: 121 AGTIGDYAAIVVGKDSPINSMADLIAAYD-ADPNATAVGGGSVPGGMDHLVAAMVMEAAG 179
           A    DY   +V  DS + +  DL+   D  D N   +GGGS PG MDH+  A  ++AAG
Sbjct: 121 ARLATDYIVYLVPADSELETFDDLVETVDEGDAN---IGGGSAPGSMDHVALAGAIDAAG 177

Query: 180 KDALGVKYIPYDAGGKAMAALLSGEIAALSTGFSEAIDLAEAGEVKIIGVTAPERVAAYD 239
            +A    Y+P+D GG+AM ALL G + A   G SEA  + EAGE++ + V++PE V A  
Sbjct: 178 GNAAAASYVPFDGGGEAMTALLGGHVDAAVVGVSEAAGMLEAGELRALAVSSPEPVEAIA 237

Query: 240 SAPTMVEQGIDTTFVNWRGFFAAPGLPEEQLAAYQATLEKMYDTPEWEEVRARNGWVNIH 299
             PT+++Q +D TF  WRG  A  GL E Q+  Y+     + +T  W+E  A  GW + +
Sbjct: 238 DVPTLLDQDVDFTFDIWRGVMAPSGLDEAQVTYYEDLFADLLETQAWQEESASLGWTDAY 297

Query: 300 NSGADFQSFLEAQEAQIGDLMKKLG 324
            + ADF +FL+ + ++  +++ ++G
Sbjct: 298 QNSADFGAFLDEKRSEFTEILTEVG 322


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: 346
Number of extensions: 17
Number of successful extensions: 4
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: 324
Length adjustment: 28
Effective length of query: 298
Effective length of database: 296
Effective search space:    88208
Effective search space used:    88208
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 Apr 09 2024. 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