GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tctC in Cupriavidus basilensis 4G11

Align TctC aka STM2786, component of The tricarboxylate transporter, TctABC (characterized)
to candidate RR42_RS03285 RR42_RS03285 tricarboxylic transport membrane protein

Query= TCDB::Q9FA46
         (325 letters)



>FitnessBrowser__Cup4G11:RR42_RS03285
          Length = 318

 Score =  389 bits (1000), Expect = e-113
 Identities = 187/315 (59%), Positives = 237/315 (75%)

Query: 11  ASILLMSTSVLAQEAPSRTECIAPAKPGGGFDLTCKLIQVSLLETGAIEKPMRVTYMPGG 70
           A   L   +  A+ A +  ECI PAKPGGGFDLTCKL Q +LLE G  E+P+R+ YMPGG
Sbjct: 4   ACAALALAAACARPAAAAPECIVPAKPGGGFDLTCKLAQRALLEAGFTEQPVRLAYMPGG 63

Query: 71  VGAVAYNAIVAQRPGEPGTVVAFSGGSLLNLSQGKFGRYGVDDVRWLASVGTDYGMIAVR 130
           +GAVAYN+IVAQRP EP T+VAFS GSLL L+QGKFG+YG  DVRW+ ++GTDYG+IAVR
Sbjct: 64  IGAVAYNSIVAQRPAEPDTIVAFSDGSLLALAQGKFGKYGAADVRWVGALGTDYGVIAVR 123

Query: 131 ADSPWKTLKDLMTAMEKDPNSVVIGAGASIGSQDWMKSALLAQKANVDPHKMRYVAFEGG 190
           ADSP+KTLKDL+ A+  DP+ V+ GAG +IG+QDWMK+A++A++A V   +MR+V FEGG
Sbjct: 124 ADSPFKTLKDLVAALRSDPDQVLFGAGGTIGNQDWMKAAMVARQAGVGYKRMRFVGFEGG 183

Query: 191 GEPVTALMGNHVQVVSGDLSEMVPYLGGDKIRVLAVFSENRLPGQLANIPTAKEQGYDLV 250
           GE  TAL G HVQ VSGD SE    LG   IR+LAV +  RLPG+LA +PTA+EQG+D+V
Sbjct: 184 GEAFTALQGGHVQAVSGDASEAAMQLGAGGIRILAVLAAQRLPGRLAGVPTAREQGFDIV 243

Query: 251 WPIIRGFYVGPKVSDADYQWWVDTFKKLQQTDEFKKQRDLRGLFEFDMTGQQLDDYVKKQ 310
           WPI+RGFY+GPKV+ ADYQ W + F++LQ +  F + R  +GLF  D+ G  LD YV++ 
Sbjct: 244 WPILRGFYMGPKVAQADYQRWAERFERLQASPAFARLRAEQGLFPADLGGADLDTYVQRT 303

Query: 311 VTDYREQAKAFGLAK 325
           V  YR  AK FGL +
Sbjct: 304 VQRYRTLAKEFGLTR 318


Lambda     K      H
   0.318    0.135    0.401 

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: 418
Number of extensions: 12
Number of successful extensions: 1
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: 325
Length of database: 318
Length adjustment: 28
Effective length of query: 297
Effective length of database: 290
Effective search space:    86130
Effective search space used:    86130
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: 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