GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7023012
          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:

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