GapMind for catabolism of small carbon sources

 

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

Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::Q88RC0
         (480 letters)



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

 Score =  268 bits (685), Expect = 3e-76
 Identities = 174/491 (35%), Positives = 252/491 (51%), Gaps = 32/491 (6%)

Query: 10  RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTA 69
           R   +I G+W+    G+     +P  G+V   V +    +   A++AA  A  AW   + 
Sbjct: 18  RYDNFIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAAKDAWGKTSV 77

Query: 70  KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG--------EIAYAASFIEWFAE 121
            ERS  L +  + + +N + LA   T E GK + E              Y A  I     
Sbjct: 78  TERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEG 137

Query: 122 EAKRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181
            A  I  +T+  H P+        P+GV   I PWNFP  M   K  PALAAG  +VLKP
Sbjct: 138 SAADIDNNTVSYHFPE--------PLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKP 189

Query: 182 ASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQL 241
           A QTP S L +VEL     +PAGVL++V G   E G  L  +  + KL+FTGST+IG  +
Sbjct: 190 AEQTPVSILVMVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHI 248

Query: 242 MEECAKDIKKVSLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRI 295
           ++  A+ +   ++ELGG +P I F      +D  LDKAVEG +++ + N G+ C C +R+
Sbjct: 249 LKCAAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLLA-FFNQGEVCTCPSRV 307

Query: 296 YVQDGVYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVL 355
            + + +YD F +K+ A    +K GN L+  T  G     +   K+  ++E   ++GA+VL
Sbjct: 308 LIAESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVL 367

Query: 356 SGGKLIE-------GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDT 408
            GG   +       G + EPTIL    K   V +EE FGP+  +  FKDEAE +A++NDT
Sbjct: 368 IGGTSCQLSGDQSSGFYIEPTILKGHNK-MRVFQEEIFGPVISVTTFKDEAEALAIANDT 426

Query: 409 EFGLASYFYARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIE 468
           E+GL +  + RDM+R  R+   ++ G V IN        A FGG K SG+GRE  K  + 
Sbjct: 427 EYGLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLS 486

Query: 469 DYLEIKYLCIS 479
            Y   K L +S
Sbjct: 487 HYQNTKNLLVS 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: 587
Number of extensions: 27
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 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