GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Caulobacter crescentus NA1000

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate CCNA_03838 CCNA_03838 gluconate 2-dehydrogenase/glyoxylate reductase/hydroxypyruvate reductase

Query= BRENDA::Q9I530
         (329 letters)



>FitnessBrowser__Caulo:CCNA_03838
          Length = 328

 Score =  138 bits (347), Expect = 2e-37
 Identities = 101/312 (32%), Positives = 158/312 (50%), Gaps = 27/312 (8%)

Query: 26  ELHFQQAHLQADTAVLAQG-FEVVCAFVNDDLSRPVLERLAAGGTRLVALRSAGYNHVDL 84
           EL+     + AD  V A    +V+   + D +   +L R +    +L+A   AG +++D+
Sbjct: 29  ELNVSDKPMTADELVDAMSRADVLVPTITDRIDSRLLSR-SGDRLKLIANFGAGVDNIDV 87

Query: 85  AAAEALGLPVVHVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGDFSLHG-----LTG 139
           A A A G+ V + P       A+  + LI+  +RR+       + G F  HG     + G
Sbjct: 88  ATANARGIIVTNTPGVLTEDTADLTMTLIMAASRRIVEGAEVVKAGGF--HGWSPTWMMG 145

Query: 140 FDLHGKRVGVIGTGQIGETFARIMAGFGCELLAYDPYP-NPRI-QALGGRYL-ALDALLA 196
             L GKR+G+IG G+IG+  AR    FG ++  ++  P +PRI + LG  Y  +LD +LA
Sbjct: 146 RRLWGKRLGIIGMGRIGQAVARRAKAFGMQVHYHNRKPVSPRIAEELGCTYWESLDQMLA 205

Query: 197 ESDIVSLHCPLTADTRHLIDAQRLATMKPGAMLINTGRGALVNAAALIEALKSGQLGYLG 256
             D VS++CP T  T HL+ A+RL  ++P A+++NT RG +++  AL   L  G++   G
Sbjct: 206 RMDFVSVNCPHTPATYHLLSARRLKLLRPHAVVVNTARGEVIDEGALANMLAKGEIAGAG 265

Query: 257 LDVYEEEADIFFEDRSDQPLQDDVLARLLSFPNVVVTAHQAFLTREALAAIADTTLDNIA 316
           LDVYE E  I                +LL  PNVV+  H    T E    + +  + N+ 
Sbjct: 266 LDVYEHEPAI--------------NPKLLKLPNVVLLPHMGSATVEGRIDMGEKVIVNVK 311

Query: 317 AWQDG-TPRNRV 327
            + DG  P +RV
Sbjct: 312 TFMDGHRPPDRV 323


Lambda     K      H
   0.323    0.137    0.402 

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: 232
Number of extensions: 11
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: 329
Length of database: 328
Length adjustment: 28
Effective length of query: 301
Effective length of database: 300
Effective search space:    90300
Effective search space used:    90300
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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