GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Methylocapsa aurea KYG

Align acetaldehyde dehydrogenase (EC 1.2.1.3) (characterized)
to candidate WP_036264374.1 DL86_RS17780 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::Burk376:H281DRAFT_01117
         (795 letters)



>NCBI__GCF_000746085.1:WP_036264374.1
          Length = 1033

 Score =  143 bits (360), Expect = 5e-38
 Identities = 155/507 (30%), Positives = 221/507 (43%), Gaps = 52/507 (10%)

Query: 14   PAPEDDQPARQWLAQHEARFGHFIGGAWHAPASGAQFVSHAP-ASGERLADIAQGDAADI 72
            P PED  P R+     E      IG    A A  A     AP  SG      A+  A+ I
Sbjct: 504  PLPEDLHPGRKTAKGVEFGDRQEIGALMAAIAREAGAFEAAPIVSGAAREGAARAIASPI 563

Query: 73   D-AALAAARAAQPGWL------ALGGKG---------RARHLYALARMVQRHSRLFAVLE 116
            D +++   R A PG L      A GG           RA  L   A+ ++  +  +  L 
Sbjct: 564  DGSSIGLVREAAPGLLQEAMREARGGFKIWSRTPVGLRAACLDRAAQELEAQAPRWLHLL 623

Query: 117  ALDNGKPIRETRDLDVPLVARHFLHHAGWAQLQDSEFADHAPL---------------GV 161
             ++ GK + +   +     A  F  +  +AQ     FA  AP+               GV
Sbjct: 624  QIEAGKTLEDA--IGEWREAIDFCRY--YAQEARRRFASPAPMPGPTGEDNRLFCHGRGV 679

Query: 162  IGQIVPWNFPLLMLAWKIAPAIATGNCVVLKPAEYTPLTALLFAELAHQAGLPAGVLNVV 221
               I PWNFPL +   +IA A+A GN V+ KPAE TPL A     L ++AG+PA VL+++
Sbjct: 680  FVCISPWNFPLSIFLGQIAAALAAGNSVLAKPAEQTPLIAAQAVSLLYRAGVPASVLHLL 739

Query: 222  TGDGSTGAALVEHPQVDKIAFTGSTEVG-KLIRSVTAGSG--KSLTLELGGKSPFIVFDD 278
             GDG  GAALV    V  +A TGS +   K+ RS+ A SG    L  E GG +  I    
Sbjct: 740  PGDGDVGAALVALDGVAGVAITGSMDTATKINRSLAAKSGPIAQLIAETGGVNAMIADAT 799

Query: 279  ADLDGAVEGVVDAIWFNQGQVCCAGSRLLVQEGIEARFIAKLKRRMETLRVGPSLDKSID 338
            A  +   + VV + + + GQ C A   L +QE +  R IA +K     L VG      + 
Sbjct: 800  ALPEQVCDDVVASAFRSAGQRCSALRLLCLQEDVADRMIAMIKGAARELLVGDPRALGVH 859

Query: 339  MGAIVDPVQLERIHSLVETGRREGCAIWQ---AADTPLPANGCFYPPTLVTNVAPASTLA 395
            +G ++D      + + +E  R   CAI      A +  P  G FY    +  ++  S L 
Sbjct: 860  VGPVIDLAAKRSLEAHIEDMR--ACAIVHYAGRAPSTAPPRG-FYLAPHIFELSSVSDL- 915

Query: 396  QEEIFGPVLVTMSFRTPDEAIAL--ANNSRYGLAASVWSETIGRALDVAPRLAAGVVWVN 453
            + E FGP+L    ++  +    L     + +GL   V S       ++  R  AG  +VN
Sbjct: 916  RREAFGPILHVARYKASELGGLLDSIEAAGFGLTLGVHSRIDAVIDEIVERRLAGNCYVN 975

Query: 454  ATNLFDAAVG---FGGYRESGYGREGG 477
              N+  A VG   FGG+  SG G + G
Sbjct: 976  -RNMIGAVVGTQPFGGFGLSGTGPKAG 1001



 Score = 59.3 bits (142), Expect = 1e-12
 Identities = 61/210 (29%), Positives = 87/210 (41%), Gaps = 4/210 (1%)

Query: 544 DGTRVGEVGEGNRKDIRNAVQAARAAQK-WSQASTHNRAQVLFYLAENLAVRADEFAHQL 602
           DG+ +G V E     ++ A++ AR   K WS+     RA  L   A+ L  +A  + H L
Sbjct: 564 DGSSIGLVREAAPGLLQEAMREARGGFKIWSRTPVGLRAACLDRAAQELEAQAPRWLHLL 623

Query: 603 TVRNGATDAAAHAEVEASVTRLFTYAAWADK-FDGAVHTPPLRGVALAMH-EPLGVIGIA 660
            +  G T   A  E   ++     YA  A + F      P   G    +     GV    
Sbjct: 624 QIEAGKTLEDAIGEWREAIDFCRYYAQEARRRFASPAPMPGPTGEDNRLFCHGRGVFVCI 683

Query: 661 CPDEAPLLAFVSLAAPALAMGNRVVVLPGEACPLAVTDFYQVVETSDVPGGVVNIVTGKR 720
            P   PL  F+   A ALA GN V+  P E  PL       ++  + VP  V++++ G  
Sbjct: 684 SPWNFPLSIFLGQIAAALAAGNSVLAKPAEQTPLIAAQAVSLLYRAGVPASVLHLLPGDG 743

Query: 721 EALLPALARHDDVDAVWCFGSAADATLIER 750
           + +  AL   D V  V   GS   AT I R
Sbjct: 744 D-VGAALVALDGVAGVAITGSMDTATKINR 772


Lambda     K      H
   0.320    0.135    0.411 

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: 1706
Number of extensions: 98
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 795
Length of database: 1033
Length adjustment: 43
Effective length of query: 752
Effective length of database: 990
Effective search space:   744480
Effective search space used:   744480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 24 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