GapMind for catabolism of small carbon sources

 

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

Align acyl-CoA dehydrogenase subunit (EC 1.3.8.4; EC 1.3.8.5) (characterized)
to candidate H281DRAFT_02091 H281DRAFT_02091 hypothetical protein

Query= metacyc::MONOMER-11693
         (386 letters)



>FitnessBrowser__Burk376:H281DRAFT_02091
          Length = 378

 Score =  280 bits (717), Expect = 4e-80
 Identities = 154/372 (41%), Positives = 224/372 (60%), Gaps = 3/372 (0%)

Query: 12  LRRTVEEFAHDVVAPKIGDFYERHEFPYEIVREMGRMGLFGLPFPEEYGGMGGDYLALGI 71
           +R  +  F  + V P    +     FP ++ R++  +G +G+  PE YGG G D LAL +
Sbjct: 10  VRDALRTFVREAVTPYAATWDRERTFPKDVHRQLAELGAYGVLVPETYGGAGMDALALAL 69

Query: 72  ALEELARVDSSVAITLEAGVSLGAMPIHLFGTDAQKAEWLPRLCSGEILGAFGLTEPDGG 131
            LEE+A  D   +  +          +  +G DAQK EWL  L  GE+LGAF LTEP  G
Sbjct: 70  ILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKREWLTPLARGEMLGAFCLTEPQAG 129

Query: 132 SDAGATRTTARLDESTNEWVINGTKCFITNSGTDITGLVTVTAVTGRKPDGKPLISSIIV 191
           SDA A RTTA  D+  + +V+NG K FIT+      G V +      K  GK  IS+ IV
Sbjct: 130 SDASALRTTATRDKDGDAYVLNGVKQFITSGKN---GDVAIVMAVTDKAAGKRGISAFIV 186

Query: 192 PSGTPGFTVAAPYSKVGWNASDTRELSFADVRVPAANLLGEQGRGYAQFLRILDEGRIAI 251
           P+ + G+ VA    K+G ++SDT ++ F D RVPAANL+G +G GY   L  L+ GRI I
Sbjct: 187 PTDSKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLIGAEGEGYRIALSGLEGGRIGI 246

Query: 252 SALATGLAQGCVDESVKYAGERHAFGRNIGAYQAIQFKIADMEMKAHMARVGWRDAASRL 311
           +A + G+A+   + ++ YA ER +FG+ + ++QA+QF++ADM  +   AR     AAS  
Sbjct: 247 AAQSVGMARAAYEAALTYAKERESFGQPLFSHQAVQFRLADMATQLEAARQLIWHAASLK 306

Query: 312 VAGEPFKKEAAIAKLYSSTVAVDNAREATQIHGGYGFMNEYPVARMWRDSKILEIGEGTS 371
            AG+P   EAA+AKL++S  A      A QIHGGYG+++++PV R++RD ++ +I EGTS
Sbjct: 307 DAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQIYEGTS 366

Query: 372 EVQRMLIARELG 383
           ++Q++LIAR LG
Sbjct: 367 DIQKILIARGLG 378


Lambda     K      H
   0.318    0.136    0.402 

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: 410
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: 386
Length of database: 378
Length adjustment: 30
Effective length of query: 356
Effective length of database: 348
Effective search space:   123888
Effective search space used:   123888
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