GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dctP in Caulobacter crescentus NA1000

Align C4-dicarboxylate-binding periplasmic protein DctP (characterized, see rationale)
to candidate CCNA_01513 CCNA_01513 C4-dicarboxylate-binding protein

Query= uniprot:I7END8
         (333 letters)



>FitnessBrowser__Caulo:CCNA_01513
          Length = 327

 Score =  129 bits (325), Expect = 8e-35
 Identities = 92/310 (29%), Positives = 151/310 (48%), Gaps = 16/310 (5%)

Query: 13  LTMSAGTAMAAC--DDGEIVVKFSHVTNTDKHPKGI----AASLLEKRINEEMNGTMCLE 66
           +T +    +AAC  + GE  ++       D HP G     A +     I++  NG + L+
Sbjct: 9   ITTALAAPLAACVQEIGERPLR-----GADSHPAGYPTVEAVNHFGALISQRTNGRLRLQ 63

Query: 67  VYPNSTLYNDNKVLEAMLQGDVQLAAPSLSKFEKFTKQFRLFDLPFMFKNIDAVDAFQGS 126
            Y    L  +   LE  + G + +   +L+          +  LPF+F++ D +      
Sbjct: 64  NYAGGQLGEEKDTLEITVFGGLDINRVNLAPLNPIEPLTLVPSLPFLFQSTDHMRRSLDG 123

Query: 127 ENGQAMLDSMQRRGLQGLSYWHNGMKQM-SANKPLINPSDANGLKFRVQSSDVLVAQMEA 185
             G+ +L+S++R GL GL+++ +G +   +   P+  P+D  GLK RVQ+S++ +A ++A
Sbjct: 124 APGRTILNSLERHGLIGLAFYDSGERSFYNTRGPIRTPADMRGLKLRVQTSNLPIAMVQA 183

Query: 186 IGGSPQKMAFSEVYGALQQGVVDGQENTWSNIYGKKFFEVQDGVTETNHGALDYLVVTSV 245
           +G SP  M++ EV+ AL QGV+DG EN W +    + FEV    + T H     ++V S 
Sbjct: 184 LGASPIPMSYGEVFQALVQGVIDGAENNWPSYQDSRHFEVARFYSVTRHVMAPEVLVASA 243

Query: 246 DWLDSLDPAVREQFLTILGEVTATRNSESTKVNAEARQSIIDAG-GVVRELTPEQRAAWV 304
                L  + RE       E               ARQ++IDAG  VV +L    R+A+ 
Sbjct: 244 RTWAKLSSSDREIIRDAATESVPFMRRLWEARETSARQAMIDAGVEVVEDL---DRSAFQ 300

Query: 305 EAMKPVWEQF 314
            AM PVW++F
Sbjct: 301 AAMAPVWDRF 310


Lambda     K      H
   0.316    0.130    0.371 

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: 239
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 333
Length of database: 327
Length adjustment: 28
Effective length of query: 305
Effective length of database: 299
Effective search space:    91195
Effective search space used:    91195
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 (21.6 bits)
S2: 49 (23.5 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