GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Sinorhizobium meliloti 1021

Align 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized)
to candidate SM_b20752 SM_b20752 3-hydroxyisobutyryl-CoA hydrolase

Query= SwissProt::Q5XIE6
         (385 letters)



>FitnessBrowser__Smeli:SM_b20752
          Length = 356

 Score =  256 bits (654), Expect = 7e-73
 Identities = 145/355 (40%), Positives = 211/355 (59%), Gaps = 8/355 (2%)

Query: 28  MSKHTETAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKG 87
           M   T   EV++ER+G  G + LNRP+ LN+L+  MIR I   L ++ER+P+   +++ G
Sbjct: 1   MEMQTTLPEVIVERQGAIGRLRLNRPRALNSLNRTMIRAIAAALTEFERNPEIAAVLVTG 60

Query: 88  AGGKAFCAGGDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGV 147
            G +  CAGGDI+ + E+ +         +REE+I+N+ I++  KPY+A++DGI MGGGV
Sbjct: 61  EGERGLCAGGDIRMIYESGRERPGEGAQFWREEFIVNSRISAYSKPYIAIMDGIVMGGGV 120

Query: 148 GLSVHGQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVH 207
           G+S HG  RV TER+ FAMPETGIG F DVG  + LPR  G+ G +L LTG  +    V 
Sbjct: 121 GVSSHGSHRVVTERTRFAMPETGIGYFTDVGATWLLPRAPGEFGTYLGLTGRDIGAAAVI 180

Query: 208 RAGIATHFVDSEKLHVLEEELLALK-SPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDK 266
            A +A  FV SE +  L   L +L  S +A+DV+  +     ++   +  +    +H+  
Sbjct: 181 HARLADSFVPSEMIGELLGALSSLSGSATADDVSAAI-----RAVSSEPPASALLDHLSV 235

Query: 267 INSCFSANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEG-STKTLQEVL 325
           I+ CF+ N VE+I   L +D S FA E ++++   S  SLK+TL  L EG S+ TL E L
Sbjct: 236 IDRCFAFNAVEEIFAALEKDESDFARETLELLKTRSAISLKLTLSLLREGRSSATLNECL 295

Query: 326 TMEYRLTQACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFKSLGS 380
             EY  T   +   DF+EGVRA +IDKD+ PKW    L + T E L  + ++ G+
Sbjct: 296 EREYAATLGMLSNPDFYEGVRAAVIDKDRNPKWS-VGLSEATPELLARFGRNDGA 349


Lambda     K      H
   0.320    0.136    0.394 

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: 299
Number of extensions: 9
Number of successful extensions: 3
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: 385
Length of database: 356
Length adjustment: 30
Effective length of query: 355
Effective length of database: 326
Effective search space:   115730
Effective search space used:   115730
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: 49 (23.5 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