GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Shewanella sp. ANA-3

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 7023012 Shewana3_0250 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::C6KEM4
         (506 letters)



>lcl|FitnessBrowser__ANA3:7023012 Shewana3_0250 aldehyde
           dehydrogenase (RefSeq)
          Length = 506

 Score =  328 bits (840), Expect = 4e-94
 Identities = 189/497 (38%), Positives = 282/497 (56%), Gaps = 21/497 (4%)

Query: 13  FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72
           FIGG W  P  G      +P        IP     D+E+A+ AA  A  +D    W +  
Sbjct: 22  FIGGKWVAPVNGDYFENRSPVNGQNFCKIPRSDYRDIELALDAAHAA--KDA---WGKTS 76

Query: 73  GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEA-SGDMDDVAACFEYYADLAEALD 131
              RAN L  IA +++     LA+ ET ++GK + E  + D+      F Y+A    A +
Sbjct: 77  VTERANLLLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQE 136

Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191
           G           N  SY   EP+GVVG I PWN+PLLMA WK+APALAAG   +LKP+E 
Sbjct: 137 GSAADIDG----NTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQ 192

Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251
             VS L L  +  ++ LPPG+LN++ G G EAG  L++   + K+AFTGSTE G  I+  
Sbjct: 193 TPVSILVLLELIEDL-LPPGILNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGYHILKC 251

Query: 252 AAQMVKPVSLELGGKSPLIVFDDIGD-----IDKAVEWTMFGIFANAGQVCSATSRLLLH 306
           AA+ + P ++ELGGKSP + F D+ D     +DKAVE  +   F N G+VC+  SR+L+ 
Sbjct: 252 AAESLIPSTVELGGKSPNLYFADVMDHEDEYLDKAVEGMLLAFF-NQGEVCTCPSRVLIQ 310

Query: 307 EKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYGG 366
           E I  +F+++++A A+ IK  +PL+   ++G+  S+ Q++KI  +++  + EGA +L GG
Sbjct: 311 ESIYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGG 370

Query: 367 GRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYG 423
              Q      +G+++ PTI+      M+I+QEE+FGPVI V  F+ ++EA+ +ANDT YG
Sbjct: 371 SLCQLEGDQSKGYYISPTIMKG-HNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYG 429

Query: 424 LAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYL 483
           L   V + D  R +R+ + + +G +WINC       A +GG K+SG GRE  +  L++Y 
Sbjct: 430 LGAGVWTRDMNRAQRLGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQ 489

Query: 484 TVKQVTKYCSDEPWGWY 500
             K +       P G++
Sbjct: 490 NTKNLLVSYDINPLGFF 506


Lambda     K      H
   0.318    0.136    0.418 

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: 649
Number of extensions: 30
Number of successful extensions: 6
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: 506
Length of database: 506
Length adjustment: 34
Effective length of query: 472
Effective length of database: 472
Effective search space:   222784
Effective search space used:   222784
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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