GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bcd in Dyella japonica UNC79MFTsu3.2

Align butyryl-CoA dehydrogenase; EC 1.3.99.2 (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein

Query= CharProtDB::CH_091785
         (379 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0492
          Length = 386

 Score =  343 bits (880), Expect = 5e-99
 Identities = 177/379 (46%), Positives = 256/379 (67%), Gaps = 5/379 (1%)

Query: 1   MDFNLTREQELVRQMVREFAENEVKPIAAEIDETERFPMENVKKMGQYGMMGIPFSKEYG 60
           MDF+ T +Q  ++ + R+FA+  + P+AAE+D    FP+EN+++MGQ G+MGI    EYG
Sbjct: 1   MDFSFTEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYG 60

Query: 61  GAGGDVLSYIIAVEELSKVCGTTGVILSAHTSLCASLINEHGTEEQKQKYLVPLAKGEKI 120
           GAG D ++Y++A+ E++     T  ++S + SL  + I +HG EEQKQKY+  +A+GE I
Sbjct: 61  GAGMDPIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAI 120

Query: 121 GAYGLTEPNAGTDSGAQQTVAVLEGD-HYVINGSKIFITNGGVADTFVIFAMTDRTKGTK 179
           GAY LTEP +G+D+ A  T A    D  +VING K +IT+G VA   V+FA++    G +
Sbjct: 121 GAYALTEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGAR 180

Query: 180 GISAFIIEKGFKGFSIGKVEQKLGIRASSTTELVFEDMIVPVENMIGKEGKGFPIAMKTL 239
           G+SAFII+    GF+ GK E KLGIRAS+T E+ F D + P EN++G+EGKGF IAM  L
Sbjct: 181 GVSAFIIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVL 240

Query: 240 DGGRIGIAAQALGIAEGAFNEARAYMKERKQFGRSLDKFQGLAWMMADMDVAIESARYLV 299
           D GRIGIA+Q++GIA  A+     + ++RK FG+++  FQ     +ADM   +++A  L 
Sbjct: 241 DAGRIGIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLT 300

Query: 300 YKAAYLK----QAGLPYTVDAARAKLHAANVAMDVTTKAVQLFGGYGYTKDYPVERMMRD 355
            +AA+ K    + G  +  +A+ AKL A+  AM +  +AVQ+ GG GY+K+ P+ER  RD
Sbjct: 301 LRAAWTKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRD 360

Query: 356 AKITEIYEGTSEVQKLVIS 374
           AKITEIYEGTSE+Q+LVI+
Sbjct: 361 AKITEIYEGTSEIQRLVIA 379


Lambda     K      H
   0.317    0.135    0.377 

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: 421
Number of extensions: 15
Number of successful extensions: 3
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: 379
Length of database: 386
Length adjustment: 30
Effective length of query: 349
Effective length of database: 356
Effective search space:   124244
Effective search space used:   124244
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: 50 (23.9 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