GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Sinorhizobium meliloti 1021

Align Peroxisomal bifunctional enzyme; PBE; PBFE; EC 4.2.1.17; EC 5.3.3.8; EC 1.1.1.35 (characterized)
to candidate SM_b21632 SM_b21632 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q08426
         (723 letters)



>lcl|FitnessBrowser__Smeli:SM_b21632 SM_b21632 3-hydroxyacyl-CoA
           dehydrogenase
          Length = 438

 Score =  245 bits (626), Expect = 3e-69
 Identities = 156/441 (35%), Positives = 227/441 (51%), Gaps = 26/441 (5%)

Query: 268 LQYAFFAERKANKWSTPSGASWKTASARPVSSVGVVGLGTMGRGIVISFARARIPVIAVD 327
           L+Y F AER A      +G        RP+ S  V+G GTMG GI  +   A +P++ V+
Sbjct: 20  LRYVFHAERAARHPPALAGIE-----PRPIRSAAVIGGGTMGTGIAAALLHAGLPLVLVE 74

Query: 328 SDKNQLATANKMITSVLEKEASKMQQSGHPWSGPKPRLTSSVK--ELGGVDLVIEAVFEE 385
            D+  +  A   + ++ +    + + S    +     +T S     +   DL+IEAVFE+
Sbjct: 75  RDEAAVERALARLRTIFDGAVKRGRISAGLAAERLAGVTGSTDYTAIAEADLIIEAVFED 134

Query: 386 MSLKKQVFAELSAVCKPEAFLCTNTSALDVDEIASSTDRPHLVIGTHFFSPAHVMKLLEV 445
           + +K+ VF  L+AVC+ +A L TNTS LD + IA+        +G HFFSPA VMKLLE+
Sbjct: 135 LDVKRDVFRRLAAVCRADAILATNTSYLDPERIAADIGSRERFLGLHFFSPAQVMKLLEI 194

Query: 446 IPSQYSSPTTIATVMNLSKKIKKIGVVVGNCFGFVGNRMLNPYYNQAYFLLEEGSKPEEV 505
           +P+Q ++P  +AT   L++ + KI V  G   GF+GNR+L     QA  LL  G+ P  V
Sbjct: 195 VPTQATAPDVLATGFALARMLNKIPVRAGISDGFIGNRILKVTRAQAERLLLSGATPAAV 254

Query: 506 DQVLEEFGFKMGPFRVSDLAGLDVGWKSRKGQGLTGPTLLPGTPARKRGNRRYCPIPDVL 565
           D  +  FG  MGPF   DL GLD+    R+              AR RG   + P+ D L
Sbjct: 255 DAAMRAFGLPMGPFEAQDLGGLDIAAFQRRA-------------ARARGETTFAPVADRL 301

Query: 566 CELGRFGQKTGKGWYQYDKPLGRIHKPDPWLSKFLSRYRKTHHIEPRTISQDEILERCLY 625
             + RFGQK+G GWY Y  P  R  +P   +++ ++   +      R   +  I+   L+
Sbjct: 302 SAIERFGQKSGGGWYDY-APGDRTPRPSATVARIIA--EEARGWPRRDWDEASIVGCILW 358

Query: 626 SLINEAFRILGEGIAASPEHIDVVYLHGYGWPRHKGGPMFYASTVGLPTVLEKLQKYYRQ 685
            ++NEA RIL +G A     ID+V +HGYG+PR +GG M +A   GL  V   L      
Sbjct: 359 PMVNEAARILEDGTALRASDIDLVEIHGYGFPRWRGGLMHHAEAHGLHKVAGALSGLAEA 418

Query: 686 NPDIPQLEPSDYLKKLASQGN 706
               P   P D L + AS+G+
Sbjct: 419 GLADP---PCDPLLRAASRGS 436


Lambda     K      H
   0.319    0.136    0.405 

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: 654
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: 723
Length of database: 438
Length adjustment: 36
Effective length of query: 687
Effective length of database: 402
Effective search space:   276174
Effective search space used:   276174
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: 53 (25.0 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 paper from 2022 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