GapMind for catabolism of small carbon sources

 

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

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 7023012 Shewana3_0250 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::Q88RC0
         (480 letters)



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

 Score =  271 bits (693), Expect = 4e-77
 Identities = 171/487 (35%), Positives = 251/487 (51%), Gaps = 32/487 (6%)

Query: 14  YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73
           +I G+W+   NG   +  +P  G+    +P+    +   A++AA  A  AW   +  ER+
Sbjct: 22  FIGGKWVAPVNGDYFENRSPVNGQNFCKIPRSDYRDIELALDAAHAAKDAWGKTSVTERA 81

Query: 74  AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG--------EIAYAASFIEWFAEEAKR 125
             L R  + + +N + LA   T E GK + E              Y A  I      A  
Sbjct: 82  NLLLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGSAAD 141

Query: 126 IYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQT 185
           I G+T+  H P+        P+GV   I PWNFP  M   K  PALAAG  +VLKPA QT
Sbjct: 142 IDGNTVSYHFPE--------PLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQT 193

Query: 186 PYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEEC 245
           P S L L+EL     +P G+L+VV G   E G  L  +  + KL+FTGSTE+G  +++  
Sbjct: 194 PVSILVLLELIEDL-LPPGILNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGYHILKCA 252

Query: 246 AKDIKKVSLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRIYVQD 299
           A+ +   ++ELGG +P + F      +D  LDKAVEG +++ + N G+ C C +R+ +Q+
Sbjct: 253 AESLIPSTVELGGKSPNLYFADVMDHEDEYLDKAVEGMLLA-FFNQGEVCTCPSRVLIQE 311

Query: 300 GVYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGK 359
            +YD F EK+ A    +K GN L+  T  G     +   K+  ++     +GA+VL GG 
Sbjct: 312 SIYDRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGS 371

Query: 360 LIE-------GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGL 412
           L +       G +  PTI+    K   + +EE FGP+  +  FKDEAE +A++NDTE+GL
Sbjct: 372 LCQLEGDQSKGYYISPTIMKGHNK-MRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGL 430

Query: 413 ASYFYARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLE 472
            +  + RDM+R  R+   ++ G V IN        A FGG K SG+GRE  K  +  Y  
Sbjct: 431 GAGVWTRDMNRAQRLGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQN 490

Query: 473 IKYLCIS 479
            K L +S
Sbjct: 491 TKNLLVS 497


Lambda     K      H
   0.317    0.134    0.384 

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: 569
Number of extensions: 23
Number of successful extensions: 7
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: 480
Length of database: 506
Length adjustment: 34
Effective length of query: 446
Effective length of database: 472
Effective search space:   210512
Effective search space used:   210512
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 (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 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