GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Marinobacter adhaerens HP15

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate GFF2 HP15_2 acyl-CoA dehydrogenase domain protein

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



>FitnessBrowser__Marino:GFF2
          Length = 389

 Score =  204 bits (520), Expect = 3e-57
 Identities = 128/378 (33%), Positives = 196/378 (51%), Gaps = 18/378 (4%)

Query: 19  LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGL 78
           L E   M+R+    FA  ++APR  E  R+ +    ++R+MG++GLLG T+ E+YGGS +
Sbjct: 12  LGETLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGITVSEEYGGSDM 71

Query: 79  NYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFG 138
            Y+ + +   E+ R  +         S+L +  I+  GTE QKQKYLPKL SGE IG   
Sbjct: 72  GYLAHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPKLVSGEHIGALA 131

Query: 139 LTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG----DIRGF 194
           ++EPN GSD  SM   A+     Y L G+KMWITN P A+ +V++AK D       +  F
Sbjct: 132 MSEPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTDTSAGSRGVTAF 191

Query: 195 VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDV-RGLKGPFTCLNSARY 253
           ++E+   G S      K+G+R S T E+V  +  VP+EN+   V  G K   + L+  R 
Sbjct: 192 IVERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAKVLMSGLDYERL 251

Query: 254 GISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGR 313
            +S G LG  +A       Y  +R+QFG+ +   +L+Q K+ADM T +  A      +  
Sbjct: 252 VLSGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMNTAKSYVYMVAM 311

Query: 314 MKDEGTAAVEITSIMKRNSCGKALDIARMAR-------DMLGGNGISDEFGVARHLVNLE 366
             D G          ++++ G  L  A MA         +LGGNG  +E+   R L + +
Sbjct: 312 SADRGAETT------RKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRLLRDAK 365

Query: 367 VVNTYEGTHDVHALILGR 384
           +     GT ++  +++GR
Sbjct: 366 LYEIGAGTSEIRRMLIGR 383


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: 354
Number of extensions: 12
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