GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Paraburkholderia bryophila 376MFSha3.1

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; EC 1.1.1.401 (characterized)
to candidate H281DRAFT_04147 H281DRAFT_04147 L-iditol 2-dehydrogenase

Query= SwissProt::P0DOW0
         (331 letters)



>FitnessBrowser__Burk376:H281DRAFT_04147
          Length = 365

 Score =  124 bits (310), Expect = 5e-33
 Identities = 92/296 (31%), Positives = 144/296 (48%), Gaps = 31/296 (10%)

Query: 27  IALRVAGVGICGSELSGYLGHNELR-------KPPLVMGHEFSGVVEEVGHGVTN---VK 76
           + +R+A  GIC S+   + G            K P++ GHEF G V+E+G G      VK
Sbjct: 39  LVIRIAACGICASDCKCHSGAKMFWGGPSPWVKAPVIPGHEFFGFVQELGDGAAEHFGVK 98

Query: 77  IGDLVTANPLVTCGRCIHCLRGERQRCESRRIIGID---FPGAYAERVLVPSNQC-YAVK 132
           +GD V A  +V C +C +C  G+   CE   I G       G  AE + +P     + + 
Sbjct: 99  VGDRVIAEQIVPCAKCRYCKSGQYWMCEVHNIFGFQREVADGGMAEYMRIPPTAIVHKIP 158

Query: 133 DAI---DGALVEPLACAVRAVGLARIKVGDTAVVIGAGIIGLMTVRLLGLSGAKRIAVVD 189
           D I   D A++EPLACA+  V    +++ D  V+ GAG +GLM  ++  L   K++ V+D
Sbjct: 159 DGISLEDAAIIEPLACAIHTVNRGELQLDDVVVIAGAGPLGLMMTQVAHLKTPKKLVVID 218

Query: 190 PNDERLKISQLWGA-------TEMAPNLGALLTDNHPQSFDCVIDAVGLSTTRRDSLNAL 242
             +ERL +++ +GA       T+ A  +   LTD +    D  I+  G        ++ +
Sbjct: 219 LVEERLALAREYGADVTINPKTDDALAIIHSLTDGY--GCDVYIETTGAPIGVNQGMDLI 276

Query: 243 IRGGRAVWIGLHEALTHLDGNQI-VRDELEVRGS----FCYTDDEFIRAVSLINSQ 293
            + GR V   +  A T LD + I  R EL+VRG+    +CY     + A  L+ S+
Sbjct: 277 RKLGRFVEFSVFGADTTLDWSVIGDRKELDVRGAHLGPYCYPIAIDLLARGLVTSK 332


Lambda     K      H
   0.322    0.139    0.424 

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: 328
Number of extensions: 20
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: 331
Length of database: 365
Length adjustment: 29
Effective length of query: 302
Effective length of database: 336
Effective search space:   101472
Effective search space used:   101472
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 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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