GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SM_b21632
          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:

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