GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoxyribonate-dehyd in Limnohabitans curvus MWH-C5

Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_108358580.1 B9Z44_RS13785 3-oxoacyl-ACP reductase FabG

Query= reanno::Burk376:H281DRAFT_00644
         (263 letters)



>NCBI__GCF_003063475.1:WP_108358580.1
          Length = 255

 Score =  118 bits (296), Expect = 1e-31
 Identities = 81/248 (32%), Positives = 124/248 (50%), Gaps = 17/248 (6%)

Query: 17  VSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAG----IADVSKQAQV 72
           ++  A GIGLA A  F    A V +CDV QAA+DEA  +   L A     + DV+++  V
Sbjct: 19  ITGAAQGIGLATALKFAREGAIVIVCDVKQAAVDEAVKQCQALGAQALGFVVDVTQRDMV 78

Query: 73  DQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFLRKAVPVL 132
           D  +     K G +DVLVNNAGI      ++++   Q++  +  NL   F+   +AV   
Sbjct: 79  DATVKAVLDKFGRIDVLVNNAGIT-QDARLQKMTLEQFDRVIDVNLRGVFH-CAQAVTEA 136

Query: 133 KETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVNAILPGVV 192
                   I+  SSV G  G   +T YA+TK+ ++G  K+ + ELGP  +RVNA+ PG +
Sbjct: 137 MVAQGSGVILNASSVVGIYGNFGQTNYAATKFGVIGFTKTWSRELGPKGIRVNAVAPGFI 196

Query: 193 EGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPAGSNVTGQ 252
           +   +            IP   +  E   ++ L+R+   +DIA +  FLAS   + + G 
Sbjct: 197 QTPILST----------IPEKVI-HEMTDRVPLKRLGQPEDIANVYAFLASDEAAYINGT 245

Query: 253 AISVDGNV 260
            I V G +
Sbjct: 246 VIEVAGGL 253


Lambda     K      H
   0.318    0.134    0.375 

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: 138
Number of extensions: 9
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: 263
Length of database: 255
Length adjustment: 24
Effective length of query: 239
Effective length of database: 231
Effective search space:    55209
Effective search space used:    55209
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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