GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Phaeobacter inhibens BS107

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate GFF109 PGA1_c01110 acyl-CoA dehydrogenase

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



>FitnessBrowser__Phaeo:GFF109
          Length = 561

 Score =  166 bits (419), Expect = 2e-45
 Identities = 126/384 (32%), Positives = 188/384 (48%), Gaps = 20/384 (5%)

Query: 19  LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPA-IFREMGEVGLLGATIPEQYGGSG 77
           L EE  M+RD   ++A +K+ P   +    ++  P  I  E+ E+G+ G TIPE+YGG G
Sbjct: 176 LDEELEMIRDQFRRYALEKVEPNAHDWHLKDELIPMEIIEELAEMGVFGLTIPEEYGGFG 235

Query: 78  LNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCF 137
           L+     +++ E+ R   G  S+   +S +    I   GTE QK  +LPK+AS E +   
Sbjct: 236 LSKASMCVVSEELSRGYIGVGSL-GTRSEIAAELIIAGGTEEQKASWLPKIASAEILPTA 294

Query: 138 GLTEPNHGSDPGSMITRARKVDGG-YRLTGSKMWITNSPIADVFVVWAK--DDAGDIRG- 193
             TEPN GSD GS+ TRA K D G Y++TG+K WIT++    V  + A+   D  D RG 
Sbjct: 295 VFTEPNTGSDLGSLRTRAVKDDNGDYQITGNKTWITHAARTHVMTLLARTDPDTTDHRGL 354

Query: 194 --FVLEK---------GWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF--PDVRG 240
             F+ EK           +G++   I   +G R     E+  D   V  EN+    + +G
Sbjct: 355 SMFLAEKTPGTDENPFPTEGMTGGEIE-VLGYRGMKEYELGFDGFHVKRENLLGGDEGKG 413

Query: 241 LKGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTE 300
            K       SAR   +  A+G A++    A QY  DR+QFG+PL A   +  KLA M  E
Sbjct: 414 FKQLMETFESARIQTAARAIGVAQSALDIAMQYAQDRKQFGKPLIAFPRVASKLAMMAVE 473

Query: 301 ITLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVAR 360
           I +A Q        KD G        + K      A   A     + GGNG + E+ ++R
Sbjct: 474 IMIARQLTYFSAWEKDNGHRCDLEAGMAKLLGARVAWAAADNGLQIHGGNGFALEYKISR 533

Query: 361 HLVNLEVVNTYEGTHDVHALILGR 384
            L +  ++N +EG  ++ A ++ R
Sbjct: 534 VLCDARILNIFEGAAEIQAQVIAR 557


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: 550
Number of extensions: 33
Number of successful extensions: 5
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: 561
Length adjustment: 33
Effective length of query: 360
Effective length of database: 528
Effective search space:   190080
Effective search space used:   190080
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: 51 (24.3 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