GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA1 in Methanoculleus horonobensis T10

Align NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized)
to candidate WP_067073002.1 MCUHO_RS02500 glucose 1-dehydrogenase

Query= metacyc::MONOMER-16231
         (254 letters)



>NCBI__GCF_001602375.1:WP_067073002.1
          Length = 270

 Score =  178 bits (451), Expect = 1e-49
 Identities = 98/256 (38%), Positives = 148/256 (57%), Gaps = 7/256 (2%)

Query: 1   MKLLEGKTVLVTGASTGIGRAAAIGAAQHGADVAINYAHSDGPAQSCVAEIEAL------ 54
           MK LEGK VLVTG STGIGR  AI  A  GA+VAINY  S+  A++ + +++        
Sbjct: 1   MKRLEGKNVLVTGGSTGIGRETAIRFADEGANVAINYHSSETEAETTLEDVQDACSIIRE 60

Query: 55  -GQRAIAVKGDVADPQTAQDFVAKAVETFGKVDVMVSNAGICPFHAFLDMPVDVVERTFK 113
            G R + V+GDVA  +  +    + +  +G++DV+++NAGI       +M +D  +R   
Sbjct: 61  RGCREMLVQGDVASEEDVERIFREVLGAWGRLDVLINNAGIQTASPTHEMTLDAYDRVLA 120

Query: 114 VNLHGAYFMVQAAAQQMVRQGHGGSIVAVSSISALVGGEYQTHYTPTKAGVHSLMQSTAI 173
           VNL GA+   + A +  + +G GG I+  +S+   +       Y  +KAG+ +L ++ A+
Sbjct: 121 VNLRGAFLCSREAVRHFLDRGGGGVILNNTSVHETIPKPQYAPYAASKAGIGALTRTLAL 180

Query: 174 ALGKHGIRCNSVLPGTILTEINKDDLADQEKREYMEARTPLGRLGAPEDLAGPIVFLASD 233
                GIR N+V PG I T IN++ + D EK+  +E   P+GR G P ++A    FLASD
Sbjct: 181 EYAGQGIRVNAVAPGAIATPINREWVDDPEKKAAVEGHIPMGRAGEPGEIAAVFAFLASD 240

Query: 234 MAAYVTGAALLVDGGM 249
            AAY+TG  + VDGG+
Sbjct: 241 EAAYITGQTIYVDGGL 256


Lambda     K      H
   0.318    0.133    0.379 

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: 128
Number of extensions: 4
Number of successful extensions: 2
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: 254
Length of database: 270
Length adjustment: 25
Effective length of query: 229
Effective length of database: 245
Effective search space:    56105
Effective search space used:    56105
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