GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Flavobacterium sp. LM5

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_024981780.1 BXU11_RS13235 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q8NK50
         (266 letters)



>NCBI__GCF_002017945.1:WP_024981780.1
          Length = 248

 Score =  149 bits (377), Expect = 4e-41
 Identities = 93/250 (37%), Positives = 143/250 (57%), Gaps = 6/250 (2%)

Query: 17  LKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVKVKV 76
           L+GKV ++TGAS  RG+G   A   A+ GA++A TYSS  E A     EL    G+K K 
Sbjct: 4   LEGKVAIITGAS--RGIGKGIAEVFAKHGANIAFTYSSSVESALALENELNT-MGIKAKG 60

Query: 77  YKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVVDGSASDWDHVIQVDLSGTA 136
           Y+ N +D+N+ + FV+ V++DFG +D  I NAG T ++ ++  S +D+D VI V+L    
Sbjct: 61  YQSNAADFNEAQTFVDAVLADFGSVDILINNAGITKDNLMMRMSEADFDQVIDVNLKSVF 120

Query: 137 YCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIHLARSLANEWRD-F 195
              KA+   F KQ  GS++  +S+ G   N    QT+Y  +KAG I  ++S+A E     
Sbjct: 121 NMTKAIQKTFLKQRAGSIINMSSVVGVKGN--AGQTNYAASKAGVIGFSKSVALELGSRN 178

Query: 196 ARVNSISPGYIDTGLSDFIDEKTQELWRSMIPMGRNGDAKELKGAYVYLVSDASSYTTGA 255
            R N I+PG+I+T ++  + +   + WR  IP+ R G   ++  A ++  SD S+Y TG 
Sbjct: 179 IRCNVIAPGFIETEMTAKLSDDVVKGWREGIPLKRGGSTDDVANACLFFASDMSAYVTGQ 238

Query: 256 DIVIDGGYTT 265
            + + GG  T
Sbjct: 239 VLNVCGGMLT 248


Lambda     K      H
   0.314    0.131    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: 142
Number of extensions: 8
Number of successful extensions: 5
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: 266
Length of database: 248
Length adjustment: 24
Effective length of query: 242
Effective length of database: 224
Effective search space:    54208
Effective search space used:    54208
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: 42 (22.0 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