GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6937588
          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:

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