GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Paraburkholderia bryophila 376MFSha3.1

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate H281DRAFT_06133 H281DRAFT_06133 hypothetical protein

Query= BRENDA::Q60759
         (438 letters)



>FitnessBrowser__Burk376:H281DRAFT_06133
          Length = 377

 Score =  167 bits (423), Expect = 5e-46
 Identities = 122/382 (31%), Positives = 184/382 (48%), Gaps = 22/382 (5%)

Query: 60  LTADEKLIRDTFRNYCQERLMSRILLANRNEVFHRDIVYEMGELGVLGPTIKG-YGCAGV 118
           LT + ++IR++ R +  ERL       ++N  F    + E+GELG LG  ++  +G AG+
Sbjct: 3   LTQEHEMIRESIRTFAAERLAPHASDWDKNHTFPAAALKELGELGALGMVVEEKWGGAGL 62

Query: 119 SSVAYGLLTRELERVDSGYRSMMSVQSSLVMHPIYTYGSEEQRQKYLPGLAKGELLGCFG 178
             ++  L   E+   D    +++SVQ+SL       YGSE+Q++++L  LA+G+ LGCF 
Sbjct: 63  DYMSLVLALEEIAAGDGATSTIVSVQNSLACGITSKYGSEKQKEQWLRPLAQGQKLGCFC 122

Query: 179 LTEPNHGSDPGGMETRARHNPSNQSYTLSGTKTWITNSPVADLFIVWARCEDNC----IR 234
           LTEP+ GSD   + T AR +     + L+G K +IT    AD+ IV+A  + +     I 
Sbjct: 123 LTEPHTGSDASALRTTARRD--GDEWVLNGVKQFITTGKYADVAIVFAVTDKSADKKGIS 180

Query: 235 GFILEKGMRGLSAPRIEGKFSLRASATGMIIMDSVEVPEENVLPNVSSLAGPFGC----- 289
            F++     G    R+E K    AS T  II +   V       ++S++ G  G      
Sbjct: 181 CFLIPTATPGYVVARLEEKMGQHASDTAQIIFEDCRV-------HLSAMMGQEGDGYRIA 233

Query: 290 ---LNTARYGITWGVLGAAEFCLHTARQYALDRIQFGVPLARNQLVQKKLADMLTEITLG 346
              L   R GI    +G A      A +YA +R  FG  L  +Q V  +LADM T+I   
Sbjct: 234 LSNLEAGRIGIAAQAVGMARAAFEAAVKYAKERETFGKLLIEHQAVTFRLADMATQIEAA 293

Query: 347 LHACLQLGRLKDQDKATPEMVSMLKRNNCGKALDIARQARDILGGNGISDEYHVIRHAMN 406
                +   LKD  KA     SM K      A  +   A  I GG G   ++ V R   +
Sbjct: 294 RMMVWRAATLKDAGKACLTEASMAKMFASEMAEKVCSDAIQIHGGCGYVSDFPVERIYRD 353

Query: 407 LEAVNTYEGTHDIHALILGRAI 428
           +     YEG +DI  +++GRAI
Sbjct: 354 VRVCQIYEGANDIQRMVIGRAI 375


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: 320
Number of extensions: 9
Number of successful extensions: 4
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: 377
Length adjustment: 31
Effective length of query: 407
Effective length of database: 346
Effective search space:   140822
Effective search space used:   140822
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