GapMind for catabolism of small carbon sources

 

Alignments for a candidate for patD in Shewanella loihica PV-4

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P77674
         (474 letters)



>FitnessBrowser__PV4:5211158
          Length = 506

 Score =  310 bits (795), Expect = 6e-89
 Identities = 171/464 (36%), Positives = 266/464 (57%), Gaps = 17/464 (3%)

Query: 23  NPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVIEENGQVFA 82
           +P  G V  ++A +    ++ A+ AA AA   WG+T+   R+  LLK+AD +E+N +  A
Sbjct: 40  SPVDGQVFCQVARSDERDIELALDAAHAAKDAWGKTSVTERSNLLLKIADRVEQNLEFLA 99

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

Query: 142 VASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFPAGVINILF 201
           V  I PWN+PL+MAAWK+APALAAGNC+VLKP+E TP++ L + EL +D+ PAGV+NI+ 
Sbjct: 158 VGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQTPVSILVMVELIQDLLPAGVLNIVN 217

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

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

Query: 316 STELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEK-----RKGNGYYYAPTLLAGALQ 370
            T++G  +S    +++   +E  +  G  +V+ GG        + +G+Y  PT+L G   
Sbjct: 337 DTQVGAQASQEQFDKILSYLEIGRNEG-AEVLIGGTSCQLSGDQSSGFYIEPTILKGH-N 394

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

Query: 431 WVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474
           W+N +    +    GG K SG G++     L  Y   ++++V +
Sbjct: 455 WINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQNTKNLLVSY 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: 580
Number of extensions: 24
Number of successful extensions: 4
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 (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