GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Dinoroseobacter shibae DFL-12

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate 3609737 Dshi_3120 L-carnitine dehydratase/bile acid-inducible protein F (RefSeq)

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>FitnessBrowser__Dino:3609737
          Length = 396

 Score =  227 bits (578), Expect = 5e-64
 Identities = 142/403 (35%), Positives = 209/403 (51%), Gaps = 17/403 (4%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L+ +RVLDL+ VLAGP+ G  LA +GA+VIKVERPG+GD  R  G    ++A     +  
Sbjct: 11  LTGVRVLDLTNVLAGPYCGYQLALMGAEVIKVERPGSGDLARQLGADPARNAANMGIS-- 68

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
             +L+ N  K+SVT+D   P+G+ L+R L A +D+L+ENF+ G +   GL YD L+  NP
Sbjct: 69  --FLAQNAQKRSVTLDLKHPQGKALLRRLVAGADVLVENFRPGVMDRLGLGYDVLRLDNP 126

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           +L+YC+I+GFGQ GP      YD ++QG+ G+MS+TG PE      P +VG  + D   G
Sbjct: 127 ELVYCAISGFGQDGPRKDDPAYDQIVQGVSGVMSITGAPE----TAPCRVGYPVADTFGG 182

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           + +  AI AAL  R     G  +D+++ +  ++ +     NYL  G AP   GN +    
Sbjct: 183 MTAAFAIAAALNARPR---GAFLDVSMTEALLSSMGWVVSNYLIGGVAPAPHGNENTTSA 239

Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303
           P   F TAD    +    D Q+   A   G       P +AT + R A+R  L   + + 
Sbjct: 240 PSGTFATADQPINIAANRDSQWESLARHLGLEALLRHPDYATREARKAHRDALRAELERV 299

Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIR 363
              +   +WV +L   GVP G +  + +  A+      GL  E+  L   ++P   +P R
Sbjct: 300 LTTRAARDWVAELNALGVPAGQVMTVPEALAEQS----GLIAEVA-LAEERLPLAGAPCR 354

Query: 364 LSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           +          PP LG  T  VL   LG+  A + A R  GV+
Sbjct: 355 VDGRRPVPDAPPPTLGADTERVLAE-LGVPGAEIAALRAEGVI 396


Lambda     K      H
   0.319    0.137    0.408 

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: 459
Number of extensions: 25
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: 406
Length of database: 396
Length adjustment: 31
Effective length of query: 375
Effective length of database: 365
Effective search space:   136875
Effective search space used:   136875
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 (21.7 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