GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolM in Rhodococcus qingshengii djl-6-2

Align scyllo-inosose 3-dehydrogenase; 2-keto-myo-inositol dehydrogenase; EC 1.1.1.- (characterized)
to candidate WP_076949143.1 C1M55_RS05845 glutathione-dependent formaldehyde dehydrogenase

Query= SwissProt::Q9WYP3
         (395 letters)



>NCBI__GCF_002893965.1:WP_076949143.1
          Length = 395

 Score =  101 bits (251), Expect = 4e-26
 Identities = 88/278 (31%), Positives = 124/278 (44%), Gaps = 38/278 (13%)

Query: 27  LTWLGSKVWRYPEVRVEEVPEPRIEKPTEIIIKVKACGICGSDVHMAQTDEEGYILYPGL 86
           +TW G +     +V V+ VP+P+I +PT+ IIKV    ICGSD+H+ +T   G  +  G 
Sbjct: 4   VTWQGKR-----KVSVDTVPDPKIVEPTDAIIKVTTTNICGSDLHLYET--LGAFMNAG- 55

Query: 87  TGFPVTLGHEFSGVVVEAGPEAINRRTNKRFEIGEPVCAEEMLWCGHCRPCAEGFPNHCE 146
                 LGHE  G+V E G E  N        IG+ V     + CG+C  C       CE
Sbjct: 56  ----DILGHEPMGIVEEVGSEVTN------LGIGDRVVIPFQISCGNCFMCDSSLYTQCE 105

Query: 147 --------------NLNELGFNVDGAFAEYVKVDAKYAWSLRELEGVYEGDRLFLAGSLV 192
                           +EL  +V G  AEY++V   +   ++  EG    D  F+  S V
Sbjct: 106 TTQVRDQGTGAALFGFSELYGSVPGGQAEYLRVPQAHFTHIKVPEG--PADSRFVYLSDV 163

Query: 193 EPTSVAYNAVIVRGGGIRPGDNVVILGGGPIGLAAVAILKHAGASKVILSEPSEVRRNLA 252
            PT  A+ +  V    I PG +V ILG GPIG  A  I  H G   + +    E    LA
Sbjct: 164 LPT--AWQS--VEYADIPPGGSVTILGLGPIGDMAARIAHHKGFRVIGVDRVPERLARLA 219

Query: 253 KELGADHVIDPTKENFVEAVLDYTNGLGAKLFLEATGV 290
           +       +D       +A+ D TNG G    ++A G+
Sbjct: 220 ERGIETLNLDDYGSKIGDAIRDATNGRGTDSVIDAVGM 257


Lambda     K      H
   0.319    0.138    0.418 

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: 360
Number of extensions: 25
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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