GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctA in Caulobacter crescentus NA1000

Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate CCNA_00264 CCNA_00264 C4-dicarboxylate transport protein

Query= CharProtDB::CH_014038
         (428 letters)



>FitnessBrowser__Caulo:CCNA_00264
          Length = 417

 Score =  274 bits (701), Expect = 3e-78
 Identities = 151/410 (36%), Positives = 245/410 (59%), Gaps = 16/410 (3%)

Query: 7   KSLYFQVLTAIAIGILLG----HFYPEIG-----EQMKPLGDGFVKLIKMIIAPVIFCTV 57
           K   + ++ ++ +G+L+G     F    G     + +  + D F++LIKMIIAP++F T+
Sbjct: 3   KRFAYLIIASMILGVLVGWTCNQFLDPAGAKSAADNLSIITDIFLRLIKMIIAPLVFTTL 62

Query: 58  VTGIAGMESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAV 117
           V G+A ME   AVGR GA  + +F   S ++L++GL++V+++ PGAG+N+    +  K  
Sbjct: 63  VAGVAHMEDAAAVGRIGAKTMTWFIGASAVSLVLGLLMVHLLDPGAGLNMAHVDVAMKTT 122

Query: 118 AVYADQAKDQGIVAFIMDVIPASVIGAFASGNILQVLLFAVLFGFALHRLGSKGQLIFNV 177
           A   D    +G   FI  ++P S+  A A   ILQ+++F++  G A+  L  K   I  +
Sbjct: 123 AT-TDAFTLKG---FITHLVPTSIFDAMAKNEILQIVVFSLFVGTAVAALDDKAPQILEL 178

Query: 178 IESFSQVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITC-ILFVVL 236
           +E  +Q++  +   +M+LAP+  F A+A TI   G+G L   G+ ++ FY    +L+ +L
Sbjct: 179 VEQAAQIMLKVTGFVMKLAPLAIFAALASTIATQGLGMLATYGKFVLGFYSAMGVLWALL 238

Query: 237 VLGSIAKATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPT 296
            +  +    G  +      IR+ +L+   T+SSE+A PR+LD + K+G R+ +V  V+P 
Sbjct: 239 FIAGLL-VLGKRVIPLFGVIRDPVLLAFSTASSEAAYPRILDSLPKVGVRRRIVSFVLPL 297

Query: 297 GYSFNLDGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAA 356
           GYSFNLDG+ +Y T A +FI QA   ++ +  QI +L++L+++SKG AGV  +  +V+ A
Sbjct: 298 GYSFNLDGSMLYCTFATMFIVQAHGVELTVQQQIFMLLLLMVTSKGIAGVPRASLVVIMA 357

Query: 357 TLSAVGHLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELD 406
           TL+  G LP A +AL+LG+D  +   R+ TN+VGN VA  VVAKW  ELD
Sbjct: 358 TLTYFG-LPEAWIALVLGVDHLLDMGRSATNVVGNSVAAAVVAKWEGELD 406


Lambda     K      H
   0.327    0.142    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: 436
Number of extensions: 18
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: 428
Length of database: 417
Length adjustment: 32
Effective length of query: 396
Effective length of database: 385
Effective search space:   152460
Effective search space used:   152460
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 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