GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsB in Marinobacter adhaerens HP15

Align 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) (characterized)
to candidate GFF1376 HP15_1343 2-hydroxy-3-oxopropionate reductase

Query= reanno::pseudo3_N2E3:AO353_05985
         (294 letters)



>FitnessBrowser__Marino:GFF1376
          Length = 290

 Score =  165 bits (418), Expect = 1e-45
 Identities = 103/287 (35%), Positives = 159/287 (55%), Gaps = 10/287 (3%)

Query: 3   IAFIGLGNMGAPMARNLIKAGHSLNLVDLNKAVLAE--LAQLGGTISATAREAAQGAELV 60
           +AFIGLG MG+ MA NL+  G  +NL+  N++  AE  L   G  ++ +A +A + A++V
Sbjct: 5   LAFIGLGIMGSRMAANLLDKG-DVNLIVFNRSTEAEKSLKDKGAKVADSAADAVRQADVV 63

Query: 61  ITMLPAAVHVRSVWLGEDGVLAGIAKGVPAVDCSTIDPQTARDVAAAAAKQGVAMADAPV 120
            +ML +   V+ + LGEDG ++ +A+    VDCST++P         A  QG+   DAPV
Sbjct: 64  FSMLASPPVVQDMALGEDGFVSAMAENALWVDCSTVNPSFTEYAGEVARAQGIRFMDAPV 123

Query: 121 SGGTGGAAAGTLTFMVGATPELFATLQPVLAQMGRNIVHCGEVGTGQIAKICNNLLLAIS 180
           +G    AA+G LTF+VGA  E F +++P+L  MG+ IVH G+VG G   K+  N +LA S
Sbjct: 124 AGTREPAASGELTFLVGADDEDFQSVEPLLQTMGKKIVHVGQVGRGTAFKMLVNAMLAQS 183

Query: 181 MVGVSEAMALGDALGIDTQVLAGIINSSTGRCWSSEMYNPWPGIVETAPASRGYTGGFGA 240
           M+  +E   LG+ LG     L   +        +  +  P+ G       +  +   F  
Sbjct: 184 MLAFAETTLLGEKLGFSRDFLMDTLP-------NLPVTPPFIGGKAELIRNGDFDAQFPL 236

Query: 241 ELMLKDLGLATEAARQAHQPVMLGAVAQQLYQAMSQRGEGGKDFSAI 287
           ELM KDL L  + A +  QP+ L  +A+++Y + S  G G KDF+++
Sbjct: 237 ELMHKDLHLLEQTAYEVGQPLYLANLAKEVYGSASSSGWGRKDFASV 283


Lambda     K      H
   0.317    0.132    0.382 

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: 181
Number of extensions: 8
Number of successful extensions: 3
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: 294
Length of database: 290
Length adjustment: 26
Effective length of query: 268
Effective length of database: 264
Effective search space:    70752
Effective search space used:    70752
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: 48 (23.1 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