GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Dyella japonica UNC79MFTsu3.2

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate N515DRAFT_0465 N515DRAFT_0465 aldehyde dehydrogenase (NAD+)

Query= BRENDA::P42412
         (487 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0465
          Length = 511

 Score =  197 bits (500), Expect = 9e-55
 Identities = 146/477 (30%), Positives = 218/477 (45%), Gaps = 10/477 (2%)

Query: 13  GEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRARIL 72
           GEW  +        VNPAT EV+  V  S+  D +   + A EAFKTW     PRR   +
Sbjct: 23  GEWSRTSDAGALQPVNPATGEVIGTVHASSAADYETIVKRAQEAFKTWRTTPAPRRGEAV 82

Query: 73  FNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLASIAT 132
               + L +HK+ L  L+ +E GK   E  GEV   I+  +FA G   ++ G ++ S   
Sbjct: 83  RLCGEALRKHKDALGSLVALEMGKIKPEGDGEVQEMIDIADFAVGQSRMLYGYTMHSERP 142

Query: 133 DVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPL---LTEKLV 189
                   +P+G+VG I+ FNFP+ V  W   +A   G+  I KPS +TPL    T K+ 
Sbjct: 143 GHRMYEQYHPLGLVGIISAFNFPVAVWAWNAFLAAICGDICIWKPSPKTPLSAIATMKIC 202

Query: 190 -ELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQ 248
            E  +  G P   F       D+  G ++   I  ISF GS  VG  V ++ +  + R  
Sbjct: 203 NEALKAGGFPDIFFLFNDAGTDLSQGFVDDKRIPLISFTGSTKVGRMVGERVARRMGRSL 262

Query: 249 SLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL--QE 306
              G  N  I+   A+L+  +  IV  A G+AG+RC     + V E I  E   KL    
Sbjct: 263 LELGGNNAIILDASADLKLAIPAIVFGAVGTAGQRCTTTRRLFVHESIVGEVTDKLVAAY 322

Query: 307 KVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGP 366
           K  + KIG+       +GP+  +D  +  L  +EK    G +++  G       G FV P
Sbjct: 323 KQVEGKIGDPTLATTLMGPLNSQDAVQAYLGAVEKAKASGGKVLTGGAALSDRKGNFVLP 382

Query: 367 TIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFR 426
           TI   V     + + E FAP+L ++  K+L EAIE+ N       + +FT +  A   + 
Sbjct: 383 TIVTGVKNSDEVVQTETFAPILYIMPFKSLDEAIELQNDVPQGLSSAIFTRDLKAAEQYL 442

Query: 427 ENI--DAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVTARY 481
            +   D G+  +N+G         F G K +  G    +G D+   Y R++  T+ Y
Sbjct: 443 SSAGSDCGIANVNIGTSGAEIGGAFGGEKET--GGGRESGSDAWKVYMRRQTNTSNY 497


Lambda     K      H
   0.318    0.136    0.396 

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: 518
Number of extensions: 27
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: 487
Length of database: 511
Length adjustment: 34
Effective length of query: 453
Effective length of database: 477
Effective search space:   216081
Effective search space used:   216081
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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