GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Sinorhizobium meliloti 1021

Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate SM_b21121 SM_b21121 isovaleryl-CoA dehydrogenase

Query= reanno::pseudo3_N2E3:AO353_25680
         (375 letters)



>FitnessBrowser__Smeli:SM_b21121
          Length = 387

 Score =  274 bits (701), Expect = 3e-78
 Identities = 148/363 (40%), Positives = 217/363 (59%)

Query: 13  AARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAMALE 72
           + R+FA ER+ P A + DR + FP     EM ELG  G+   E  GG   GYLA+ +A+E
Sbjct: 20  SVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHGGAGLGYLAHCVAME 79

Query: 73  EIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAGSDA 132
           EI+    +       H+++    I + G   QK R+L  L SG  +GA A++EP AGSD 
Sbjct: 80  EISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVGALAMSEPGAGSDV 139

Query: 133 SSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSPGYK 192
            S+K +A   GD YVLNG K +IT+G +A V++V+A TDP+AG RGI+AF+V    PG+ 
Sbjct: 140 VSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPRGITAFLVEKAFPGFS 199

Query: 193 VARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSVGMA 252
             +  DKLG   S+T +++F D +VP  N LG  GEG K+ ++ L+  RV +++  +G+ 
Sbjct: 200 AGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMSGLDYERVVLSAGPLGIM 259

Query: 253 RAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKPALV 312
            A  +    Y  ER+ FG+PI E Q +  +LADM   +  AR  V+  AA  D G+ A  
Sbjct: 260 AACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYAVAAACDRGETARK 319

Query: 313 EASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRMVIS 372
           +A+   L+A+E A  +   A+Q LGG GY +D+P  R+ RD ++ +I  GTS+I+RM+I 
Sbjct: 320 DAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYEIGAGTSEIRRMLIG 379

Query: 373 RNL 375
           R L
Sbjct: 380 REL 382


Lambda     K      H
   0.319    0.134    0.389 

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: 338
Number of extensions: 15
Number of successful extensions: 1
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: 375
Length of database: 387
Length adjustment: 30
Effective length of query: 345
Effective length of database: 357
Effective search space:   123165
Effective search space used:   123165
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