GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Sinorhizobium meliloti 1021

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate SMa1400 SMa1400 acyl-CoA dehydrogenase

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__Smeli:SMa1400
          Length = 380

 Score =  152 bits (385), Expect = 1e-41
 Identities = 113/373 (30%), Positives = 177/373 (47%), Gaps = 8/373 (2%)

Query: 18  LADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGL 77
           L + +  VRD A A+A   + P      R E   A ++ EM ++GL G  +PE  GGPG 
Sbjct: 3   LTEIQGQVRDMARAFADEVIRPMAESLDREERFPAELYGEMAKLGLFGIGVPEHLGGPGF 62

Query: 78  DYVSYGLIAREVERVDSGYRSMMSVQS--SLVMVPIFEFGSDAQKEKYLPKLATGEWIGC 135
           D ++Y ++  E+ R   GY S+        L+   +   G++ Q ++ LP +        
Sbjct: 63  DTLTYAVVMEELSR---GYASVADQCGLVELISTLLVRHGTEGQ-QRMLPDVLNMSAKVA 118

Query: 136 FGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEIR 194
           + +TEP  G+D   + T A +   G+ L+G K+WI N+P+ADV  V A+ D E G   + 
Sbjct: 119 YCITEPEAGTDVSGIRTTAERDGDGWMLNGGKIWIHNAPVADVGFVLARTDKEAGNRGMS 178

Query: 195 GFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNSA 253
            FI++    G+       K+G RAS  G +   +  +P   +L    +G     + L+  
Sbjct: 179 IFIVDLNSAGVERGPKEHKMGQRASQVGALTFTDVRLPGGALLGQEGRGFHMMMSVLDKG 238

Query: 254 RYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRL 313
           R GIA  A+G A++    A  Y   RKQFG+ ++  Q +Q  LADM  +I      V   
Sbjct: 239 RVGIAALAVGIAQAGLEAAVDYAGTRKQFGKAISDFQGVQWLLADMAKDIEAARLLVHSA 298

Query: 314 GRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTY 373
               D G  A +  SI K  +   A+     A  + GG+G    F V R   + ++   Y
Sbjct: 299 ASKIDRGLDATKACSIAKCFAGDMAVQRTADAVQVFGGSGYIRGFEVERLYRDAKITQIY 358

Query: 374 EGTHDIHALILGR 386
           EGT+ I  +I+ R
Sbjct: 359 EGTNQIQRMIIAR 371


Lambda     K      H
   0.320    0.138    0.414 

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: 362
Number of extensions: 18
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: 395
Length of database: 380
Length adjustment: 30
Effective length of query: 365
Effective length of database: 350
Effective search space:   127750
Effective search space used:   127750
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: 50 (23.9 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