GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__PV4:5211158
          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 (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