GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Magnetospirillum magneticum AMB-1

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_011383120.1 AMB_RS03480 isovaleryl-CoA dehydrogenase

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>NCBI__GCF_000009985.1:WP_011383120.1
          Length = 389

 Score =  223 bits (568), Expect = 7e-63
 Identities = 139/375 (37%), Positives = 201/375 (53%), Gaps = 5/375 (1%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74
           L+  L E   M+RDS   FA  ++APR  E  R  +    ++  +G +GLLG T+ E+YG
Sbjct: 8   LNFDLGETADMMRDSVAAFAATEIAPRAAEIDRSNEFPNELWPRLGAMGLLGITVDEKYG 67

Query: 75  GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134
           G+G+ Y+ + +   E+ R  +         S+L +  I   GTEAQK KYLPKL SGE+I
Sbjct: 68  GAGMGYLEHVVAMEEISRASASVGLSYGAHSNLCVNQIKRNGTEAQKMKYLPKLISGEYI 127

Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD--AG--D 190
           G   ++EPN GSD  SM  +A K    Y L G+KMWITN P ADV VV+AK D  AG   
Sbjct: 128 GALAMSEPNAGSDVVSMKLKAEKKGDRYVLNGTKMWITNGPDADVIVVYAKTDVTAGPRG 187

Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDV-RGLKGPFTCLN 249
           I  F++EK ++G S      K+G+R S TGE+V  +  VPEEN+   V +G+    + L+
Sbjct: 188 ITAFLVEKTFKGFSVAQKLDKLGMRGSNTGELVFQDCEVPEENVLGAVGKGVNVLMSGLD 247

Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309
             R  ++ G LG   AC      Y  +R QFG+P+   QL+Q KLADM T          
Sbjct: 248 YERVVLTGGPLGIMAACMDVVVPYVHERTQFGQPIGTFQLMQGKLADMYTTFNACRAYTY 307

Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369
            + +  D G  + +  + +      KA  +A  A   LGGNG  +E+   R L + ++  
Sbjct: 308 AVAKACDRGETSRKDAAGVILYGAEKATWMALEAIQTLGGNGYINEYATGRLLRDAKLYE 367

Query: 370 TYEGTHDVHALILGR 384
              GT ++  +++GR
Sbjct: 368 IGAGTSEIRRMLIGR 382


Lambda     K      H
   0.320    0.137    0.413 

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: 356
Number of extensions: 14
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: 393
Length of database: 389
Length adjustment: 31
Effective length of query: 362
Effective length of database: 358
Effective search space:   129596
Effective search space used:   129596
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 (21.8 bits)
S2: 50 (23.9 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