GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Shewanella oneidensis MR-1

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)

Query= BRENDA::P77674
         (474 letters)



>lcl|FitnessBrowser__MR1:203555 SO4480 aldehyde dehydrogenase (NCBI
           ptt file)
          Length = 506

 Score =  314 bits (804), Expect = 5e-90
 Identities = 174/464 (37%), Positives = 268/464 (57%), Gaps = 17/464 (3%)

Query: 23  NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82
           +P  G    +I  + A+ ++ A+ AA AA   WG+T+   R+  LL++AD +E+N +  A
Sbjct: 40  SPVNGQNFCKIPRSDAQDIELALDAAHAAKDAWGKTSVTERSNILLRIADRVEQNLEYLA 99

Query: 83  ELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHT-SMIRRDPLGV 141
             E+   GK +    N ++P  VD FR+FAG  R   G AA   ++G+T S    +PLGV
Sbjct: 100 VAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGSAAD--IDGNTVSYHFPEPLGV 157

Query: 142 VASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILF 201
           V  I PWN+PL+MAAWK+APALAAGNCVVLKP+E TP++ L L EL +D+ P GV+N++ 
Sbjct: 158 VGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPVSILVLLELIEDLLPPGVLNVVN 217

Query: 202 GRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPVIVF----- 256
           G G   G  L    ++  ++ TGS   G HI+   A S+  + +ELGGK+P + F     
Sbjct: 218 GFGAEAGQALATSKRIAKLAFTGSTEVGFHILKCAAESLIPSTVELGGKSPNLYFADVMD 277

Query: 257 -DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATLKSGAPDDE 315
            +D  ++  VEG+    ++N G+ CT   R+  Q+ IYD  +EK+ A   T+K G P D 
Sbjct: 278 QEDEYLDKAVEGM-LLAFFNQGEVCTCPSRVLIQESIYDRFIEKVLARAQTIKQGNPLDT 336

Query: 316 STELGPLSSLAHLERVGKAVEEAKATGHIKVITGG-----EKRKGNGYYYAPTLLAGALQ 370
           +T++G  +S    +++   +   K  G  +V+ GG     E  +  GYY +PT++ G   
Sbjct: 337 ATQVGAQASQEQFDKILSYLAIGKDEG-AQVLLGGSLCQLEGEQSKGYYISPTIMKGH-N 394

Query: 371 DDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVSARLQYGCT 430
              I Q+E+FGPV+SVT F +E + +  AND++YGL + VWT+D+ RA R+   +Q G  
Sbjct: 395 KMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGVWTRDMNRAQRMGRGIQAGRV 454

Query: 431 WVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           W+N +    +    GG K SG G++     L  Y   ++++V +
Sbjct: 455 WINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQNTKNLLVSY 498


Lambda     K      H
   0.317    0.134    0.397 

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: 571
Number of extensions: 23
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: 474
Length of database: 506
Length adjustment: 34
Effective length of query: 440
Effective length of database: 472
Effective search space:   207680
Effective search space used:   207680
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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