GapMind for catabolism of small carbon sources

 

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

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein

Query= BRENDA::B0EVL5
         (395 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0492
          Length = 386

 Score =  214 bits (545), Expect = 3e-60
 Identities = 130/385 (33%), Positives = 206/385 (53%), Gaps = 10/385 (2%)

Query: 16  LDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYG 75
           +D   T+ +  ++  AR ++Q+R++P   E     +       EMG+LGL+G  +P +YG
Sbjct: 1   MDFSFTEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYG 60

Query: 76  GSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWV 135
           G+GM+ + Y L   E+   D+   ++MSV +SL    I + G+EE KQKY+  +A GE +
Sbjct: 61  GAGMDPIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAI 120

Query: 136 GCFGLTEPNHGSDPGSMVTRARK-VDGGYSLSGAKMWITNSPIADVFVVWAKDDAG---- 190
           G + LTEP  GSD  +M TRA K  DG + ++G K WIT+ P+A   V++A    G    
Sbjct: 121 GAYALTEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGAR 180

Query: 191 DIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCL 249
            +  F+++    G +A     K+G+RAS T EI   +  CP+EN      +G       L
Sbjct: 181 GVSAFIIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVL 240

Query: 250 NSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEI----TLG 305
           ++ R GIA  ++G A A YE   Q++ DRK FG+ + + Q+ Q K+ADM  ++     L 
Sbjct: 241 DAGRIGIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLT 300

Query: 306 LQGCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVN 365
           L+     G+ +  G       S+ K  +   ++ IA  A  + GG G S E  + R+  +
Sbjct: 301 LRAAWTKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRD 360

Query: 366 LEVVNTYEGTHDIHALILGRAITGL 390
            ++   YEGT +I  L++ RA TGL
Sbjct: 361 AKITEIYEGTSEIQRLVIARAETGL 385


Lambda     K      H
   0.319    0.136    0.409 

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: 352
Number of extensions: 17
Number of successful extensions: 5
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: 395
Length of database: 386
Length adjustment: 31
Effective length of query: 364
Effective length of database: 355
Effective search space:   129220
Effective search space used:   129220
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: 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