GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Nocardioides daejeonensis MJ31

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_110207232.1 DNK54_RS12090 acyl-CoA dehydrogenase

Query= BRENDA::Q60759
         (438 letters)



>NCBI__GCF_003194585.1:WP_110207232.1
          Length = 384

 Score =  379 bits (973), Expect = e-110
 Identities = 195/382 (51%), Positives = 261/382 (68%), Gaps = 3/382 (0%)

Query: 54  LILEEQLTADEKLIRDTFRNYCQERLMSRILLANRNEVFHRDIVYEMGELGVLGPTIKGY 113
           L L+  LT DE  +RDT R   +++L+  +       +   +I   +G  G+ G  ++GY
Sbjct: 6   LDLDLLLTPDELAVRDTVRALGRDKLLPDVATWFEEGILPSEIPPLLGSHGLFGMHLQGY 65

Query: 114 GCAGVSSVAYGLLTRELERVDSGYRSMMSVQSSLVMHPIYTYGSEEQRQKYLPGLAKGEL 173
           GCAG+S+V YG+   ELE +DSG RS++SVQ SL M  I+ +GSEEQ+Q++LPG+A GE+
Sbjct: 66  GCAGMSAVDYGIACLELEAIDSGLRSLVSVQGSLAMTAIHKFGSEEQKQEWLPGMATGEI 125

Query: 174 LGCFGLTEPNHGSDPGGMETRARHNPSNQSYTLSGTKTWITNSPVADLFIVWARCEDNCI 233
           +GCFGLTEP+HGSDPG M T AR + ++  + L+GTK WITN  +A + +VWA+ ++  +
Sbjct: 126 VGCFGLTEPDHGSDPGSMRTHARRDGAD--WVLNGTKMWITNGGIAGVAVVWAQTDEG-V 182

Query: 234 RGFILEKGMRGLSAPRIEGKFSLRASATGMIIMDSVEVPEENVLPNVSSLAGPFGCLNTA 293
           RGFI+  G  G     I+ K SLRAS T  +I+D   +P + VLP V  L GP  CLN A
Sbjct: 183 RGFIVPAGTPGFRTQNIKHKMSLRASITSELILDDCRLPADAVLPEVKGLRGPLSCLNEA 242

Query: 294 RYGITWGVLGAAEFCLHTARQYALDRIQFGVPLARNQLVQKKLADMLTEITLGLHACLQL 353
           RYGI WG +GAA  C   A++YA  RIQFG P+A  QL QKKLADM  E+  G    LQ+
Sbjct: 243 RYGIVWGAMGAARACFEAAQEYAGSRIQFGRPIAGFQLTQKKLADMYLELAKGTLLALQI 302

Query: 354 GRLKDQDKATPEMVSMLKRNNCGKALDIARQARDILGGNGISDEYHVIRHAMNLEAVNTY 413
           GRLKD+ KATP+ VS+ K NN  +AL IA +AR ILG NGI+ EY VIRHA NLE+V TY
Sbjct: 303 GRLKDEGKATPQQVSLGKLNNVREALHIAHEARGILGANGITLEYPVIRHANNLESVYTY 362

Query: 414 EGTHDIHALILGRAITGIQAFT 435
           EGT++IH LI+G+A+TGI A++
Sbjct: 363 EGTNEIHTLIVGQALTGIAAYS 384


Lambda     K      H
   0.320    0.136    0.408 

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: 471
Number of extensions: 17
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: 438
Length of database: 384
Length adjustment: 31
Effective length of query: 407
Effective length of database: 353
Effective search space:   143671
Effective search space used:   143671
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 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