GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-c in Dyella japonica UNC79MFTsu3.2

Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate N515DRAFT_0703 N515DRAFT_0703 Cytochrome c

Query= BRENDA::C9K502
         (472 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0703
          Length = 429

 Score =  278 bits (711), Expect = 3e-79
 Identities = 162/409 (39%), Positives = 224/409 (54%), Gaps = 32/409 (7%)

Query: 30  DEDLIKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTF 89
           D  LI KGEY+  +GDC +CHT   G ++AGG  + TP G I + N+TPD   G+G ++F
Sbjct: 45  DPALIAKGEYLTLVGDCASCHTGQGGARFAGGRVVGTPFGDIPAPNLTPDRETGLGEWSF 104

Query: 90  KEFDEAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGVQPIAQKNHPTDISW 149
           + F +A+  GV + G  LYPA PY S+ ++++DD  A++AY +  + P+ Q      + +
Sbjct: 105 EAFRQALHSGVDRHGQFLYPAFPYTSYTKVSRDDALAIFAY-LQSLPPLKQAAKQPGLGF 163

Query: 150 PMSMRWPLSIWRSVF---APAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHIPR-GFGM 205
           P ++R  L  WR+++        D T +P    E  RG YLV G GHC  CH+ R  FG 
Sbjct: 164 PYNVRNTLKAWRALYFREGEYVADSTKSP----EWNRGAYLVQGLGHCNECHVERDSFGG 219

Query: 206 QEKALDASGGPDFLGGGGVIDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFG 265
                  SGG         + NW AP L      GL  WS+ D+   LK+G++   AAFG
Sbjct: 220 MRSDQSLSGGQI------PVQNWYAPDLSTQANGGLAGWSERDIADLLKTGQSAKGAAFG 273

Query: 266 GMADVVGWSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDAS---TAQMLDSNNFSGNA 322
            MA+VV  STQ+  DADLHA+  Y++SL    PAR   SY+ S   T  MLD        
Sbjct: 274 PMAEVVARSTQHLNDADLHAIATYLQSL----PARPRVSYEPSLLDTKPMLDQ------- 322

Query: 323 GAKTYVEQCAICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSA 382
           GAK Y E+CA CH  DG GVA ++PPL+GN  V      +   +V+ GG  P T   P  
Sbjct: 323 GAKVYAERCADCHGRDGQGVAGVYPPLSGNSSVNEPTGINAIRVVLLGGFAPSTQGNPRP 382

Query: 383 VAMPDYKNILSDQQIADVVNFIRSAWGNRAPANTTAADIQKLRLDHTPL 431
            +MP +   L+D  +A VV +IR +WGN+AP      D+ K R  HTP+
Sbjct: 383 YSMPPFAQQLNDADVAAVVTYIRQSWGNQAPL-VQERDVIKYR--HTPI 428


Lambda     K      H
   0.318    0.135    0.431 

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: 681
Number of extensions: 49
Number of successful extensions: 6
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: 472
Length of database: 429
Length adjustment: 33
Effective length of query: 439
Effective length of database: 396
Effective search space:   173844
Effective search space used:   173844
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 (21.7 bits)
S2: 51 (24.3 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