GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mmsA in Shewanella loihica PV-4

Align Malonate-semialdehyde dehydrogenase 1; MSA dehydrogenase 1; EC 1.2.1.-; Methylmalonate-semialdehyde dehydrogenase 1; MMSA dehydrogenase 1; MSDH 1; EC 1.2.1.27 (uncharacterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)

Query= curated2:Q81QR5
         (486 letters)



>lcl|FitnessBrowser__PV4:5211158 Shew_3574 aldehyde dehydrogenase
           (RefSeq)
          Length = 506

 Score =  213 bits (541), Expect = 2e-59
 Identities = 144/469 (30%), Positives = 231/469 (49%), Gaps = 23/469 (4%)

Query: 8   RVKNHINGEWVESTGTEVEAVPNPATGKIIAYVPLSPKEDVEKAVEAAKAAYETWSKVPV 67
           R  N I G+WV   G E     +P  G++   V  S + D+E A++AA AA + W K  V
Sbjct: 18  RYDNFIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAAKDAWGKTSV 77

Query: 68  PNRSRQLYKYLQLLQENKEELAKIITLENGKTLTDA-TGEVQRGIEAVELATSAPNLMMG 126
             RS  L K    +++N E LA   T ENGK + +    ++   ++             G
Sbjct: 78  TERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEG 137

Query: 127 QALPNIASGIDGSIWRY----PIGVVAGITPFNFPMMIPLWMFPLAIACGNTFVLKTSER 182
                 A+ ID +   Y    P+GVV  I P+NFP+++  W    A+A GN  VLK +E+
Sbjct: 138 S-----AADIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQ 192

Query: 183 TPLLAERLVELFYEAGFPKGVLNLVQG-GKDVVNSILENKDIQAVSFVGSEPVARYVYET 241
           TP+    +VEL  +   P GVLN+V G G +   ++  +K I  ++F GS  +  ++ + 
Sbjct: 193 TPVSILVMVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHILKC 251

Query: 242 GTKHGKRVQALAGAKNHAIVMPDC------NLEKTVQGVIGSAFASSGERCMACSVVAVV 295
             +         G K+  I   D        L+K V+G++  AF + GE C   S V + 
Sbjct: 252 AAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGML-LAFFNQGEVCTCPSRVLIA 310

Query: 296 DEIADEFIDVLVAETKKLKVGDGFHEDNYVGPLIRESHKERVLGYINSGVADGATLLVDG 355
           + I D+FID ++A  K +K G+    D  VG    +   +++L Y+  G  +GA +L+ G
Sbjct: 311 ESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGG 370

Query: 356 R--KIKEEVGEGYFVGATIFDGVNQEMKIWQDEIFAPVLSIVRVKDLEEGIKLTNQSKFA 413
              ++  +   G+++  TI  G N +M+++Q+EIF PV+S+   KD  E + + N +++ 
Sbjct: 371 TSCQLSGDQSSGFYIEPTILKGHN-KMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYG 429

Query: 414 NGAVIYTSNGKHAQTFRDNIDAGMIGVNVNVPAPMAFFAFAGNKASFFG 462
            GA ++T +   AQ     I AG + +N     P A  AF G K S  G
Sbjct: 430 LGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYP-AHAAFGGYKKSGIG 477


Lambda     K      H
   0.317    0.135    0.392 

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: 597
Number of extensions: 31
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: 486
Length of database: 506
Length adjustment: 34
Effective length of query: 452
Effective length of database: 472
Effective search space:   213344
Effective search space used:   213344
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 (21.6 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