GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdH in Shewanella amazonensis SB2B

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 6937588 Sama_1743 acyl-CoA dehydrogenase family protein (RefSeq)

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



>lcl|FitnessBrowser__SB2B:6937588 Sama_1743 acyl-CoA dehydrogenase
           family protein (RefSeq)
          Length = 578

 Score =  112 bits (281), Expect = 2e-29
 Identities = 109/376 (28%), Positives = 168/376 (44%), Gaps = 54/376 (14%)

Query: 56  FREMGEVGLLGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEF 115
           F E G VGL G     +YGG G+  +  G++  E+        ++    ++   + IN  
Sbjct: 87  FVEGGWVGLSG---DPEYGGMGMPKML-GVLVDEMGYSACNAFNLYGSLTAGAALAINAH 142

Query: 116 GTEAQKQKYLPKLASGEWIGCFGLTEPNHGSDPGSMITRAR-KVDGGYRLTGSKMWIT-- 172
           GTE  K  YLPKL SGEW G   +TEP  GSD   + TRA  + DG Y +TGSK++IT  
Sbjct: 143 GTEELKSTYLPKLYSGEWAGAMDMTEPQAGSDLRHIRTRAEPQEDGSYLITGSKIFITGG 202

Query: 173 NSPIAD--VFVVWAKDDAG-------------DIRGFVLEKGWQGLSAPAIHGKVGLRAS 217
           +  + +  + +V AK                 D +G + E    G+S  +I  K+GL+ S
Sbjct: 203 DQDLTENVIHLVLAKISGSNTLSLFLVPKIGVDDQGNLTEP--NGVSVGSIEHKMGLKGS 260

Query: 218 ITGEIVMDNV---FVPEENIFPDVRGLKGPFTCLNSARYGISWGALGAAEACWHTARQYT 274
            T  +  D+     +  EN     +GL   FT +N  R  I    LG+A+A    A  Y 
Sbjct: 261 ATCVMNFDSARGWLIGREN-----KGLACMFTMMNYERLAIGIQGLGSAQAAVQMASDYA 315

Query: 275 LDRQQ---FGRPLAANQLI-----------QKKLADMQTEITLALQGCLRLGRMKDEGTA 320
            +R Q    G   AA+ ++            + L D    + +     L L +  D+   
Sbjct: 316 RERLQGNAVGSTAAADPILVHGDVRRMLLTTRTLTDAGRALAVHTGKQLDLAKFADDDAV 375

Query: 321 AVE-------ITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEG 373
             +       +T + K     + LDI  MA+ + GG+G   E G+ + + +  +   YEG
Sbjct: 376 KTKAGRYVGLLTPVAKAFLTDRGLDITIMAQQVFGGHGYIRETGIEQLVRDTRIAQIYEG 435

Query: 374 THDVHAL-ILGRAQTG 388
           T+ + A+  LGR  TG
Sbjct: 436 TNGIQAIDFLGRKVTG 451


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: 537
Number of extensions: 31
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: 578
Length adjustment: 33
Effective length of query: 360
Effective length of database: 545
Effective search space:   196200
Effective search space used:   196200
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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