GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mt2d in Methylocystis bryophila S285

Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase

Query= SwissProt::Q8NK50
         (266 letters)



>NCBI__GCF_002117405.1:WP_085770280.1
          Length = 246

 Score =  123 bits (308), Expect = 4e-33
 Identities = 79/250 (31%), Positives = 132/250 (52%), Gaps = 10/250 (4%)

Query: 14  LFSLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVK 73
           +F L GK  +VTGAS   G+G+  AR   + GA + ++  +R+E  E  A EL +    +
Sbjct: 1   MFDLTGKTALVTGASS--GLGLAIARTLHQAGATVGLS-GTRREALETLAGELKE----R 53

Query: 74  VKVYKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVVDGSASDWDHVIQVDLS 133
             +   N SD  + ++ +       G +D  + NAG T +   +     DWD V+ V+L+
Sbjct: 54  AHILPCNLSDRAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLT 113

Query: 134 GTAYCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIHLARSLANEWR 193
                ++AV     ++ HG ++   S++G V N    Q +Y+ AKAG   + +SLANE  
Sbjct: 114 AAFRLSRAVLRGMMRKRHGRIINITSVAGAVGN--PGQANYSAAKAGLTGMTKSLANEVA 171

Query: 194 DFA-RVNSISPGYIDTGLSDFIDEKTQELWRSMIPMGRNGDAKELKGAYVYLVSDASSYT 252
                VN ++PG I++ ++  ++E  +E    +IPM R G A E+  A +YL SD +++ 
Sbjct: 172 SRGVTVNCVAPGVIESPMTQVLNEAQRERLLKLIPMERFGSADEIGAAVLYLASDEAAFI 231

Query: 253 TGADIVIDGG 262
           TG  + I+GG
Sbjct: 232 TGQTLHINGG 241


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: 135
Number of extensions: 8
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: 266
Length of database: 246
Length adjustment: 24
Effective length of query: 242
Effective length of database: 222
Effective search space:    53724
Effective search space used:    53724
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 Apr 09 2024. 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