GapMind for catabolism of small carbon sources

 

Alignments for a candidate for yvgN in Caulobacter crescentus NA1000

Align Glyoxal reductase; GR; Methylglyoxal reductase; EC 1.1.1.-; EC 1.1.1.283 (characterized)
to candidate CCNA_03541 CCNA_03541 2,5-diketo-D-gluconic acid reductase

Query= SwissProt::O32210
         (276 letters)



>FitnessBrowser__Caulo:CCNA_03541
          Length = 279

 Score =  199 bits (506), Expect = 6e-56
 Identities = 111/256 (43%), Positives = 156/256 (60%), Gaps = 3/256 (1%)

Query: 15  VEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTAAIYKNEEGVGIGIKESGVAREEL 74
           V MP  G G +++ENG  A   V+ A++ GYR IDTA IY NE  VG  I+ SGV R+E+
Sbjct: 13  VLMPALGFGTWQLENGT-AVPLVEKALEIGYRHIDTAQIYGNERDVGAAIRNSGVKRDEI 71

Query: 75  FITSKVWNEDQGYETTLAAFEKSLERLQLDYLDLYLIHWPGKD-KYKDTWRALEKLYKDG 133
           F+T+KVW +         + EKSLE+L +D +DL L+HWP  +    +T +AL  +   G
Sbjct: 72  FLTTKVWIDQFADGDLQRSAEKSLEKLGVDQVDLLLLHWPKPEVPLAETLKALNAVRAKG 131

Query: 134 KIRAIGVSNFQVHHLEELLKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLM 193
             RAIG+SNF    LEE  K +E     +QVE+HP L+ K L+      G+ + AWSPL 
Sbjct: 132 WTRAIGLSNFPSAQLEEAAKLSEAPIATDQVEYHPYLSLKTLKAKADQLGVSITAWSPLA 191

Query: 194 QGQLLDNEVLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELSQE 253
           QG++  + VL +I   H K+  QV LRW +Q G++ IP++    RI EN DI DFELS++
Sbjct: 192 QGKVAQDPVLIEIGRAHGKTPGQVTLRWIIQQGIIAIPRTSNPKRIEENFDILDFELSEK 251

Query: 254 DMDKIDALNK-DERVG 268
           +M +I  L + D R+G
Sbjct: 252 EMAQIHGLARPDGRIG 267


Lambda     K      H
   0.316    0.135    0.397 

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: 200
Number of extensions: 9
Number of successful extensions: 3
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: 276
Length of database: 279
Length adjustment: 25
Effective length of query: 251
Effective length of database: 254
Effective search space:    63754
Effective search space used:    63754
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: 47 (22.7 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