Aligments for a candidate for bkdC in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Aligments for a candidate for bkdC in Dyella japonica UNC79MFTsu3.2

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate N515DRAFT_2156 N515DRAFT_2156 pyruvate dehydrogenase E2 component (dihydrolipoamide acetyltransferase)

Query= reanno::Smeli:SMc03203
         (426 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2156
          Length = 562

 Score =  246 bits (627), Expect = 2e-69
 Identities = 160/431 (37%), Positives = 233/431 (54%), Gaps = 25/431 (5%)

Query: 7   KMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVGD 66
           ++PD+G G     ++E  VK GD V +D  L  + +DKAT+E+P+P  G V  L  +VGD
Sbjct: 128 RVPDIG-GHDGVPVIEVLVKVGDTVAKDQSLITLESDKATMEVPAPFGGVVKELKVKVGD 186

Query: 67  TVAVKAPLVRIETAGEAGEAAPDSIP-EALAEQVLDEPVAVSSR--LEAKAPPQPEKPAP 123
            ++  A +  IE+A  A  AAP   P +A   QV ++P  +  R  L   AP     PA 
Sbjct: 187 ELSEGAVIALIESADGAPAAAPAPAPAKAEVPQVEEKPAPIGGRGILPGNAPEGDVAPAA 246

Query: 124 KPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR---- 179
           +P    R      A P ASPA+R  ARE G+D+RQ  G+G  GRI  ED+  ++      
Sbjct: 247 RPPFDSRIVMPGDA-PYASPAIRAFARELGVDIRQAKGSGRGGRIVREDITSYVKHALAS 305

Query: 180 GAEPL----PAQTGL----------VRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYV 225
           GA P     PA  GL           +   +EE  +  +++     ++ + + IPH+T  
Sbjct: 306 GARPSGAAQPAGGGLNLLPWPKVDFAKFGPIEEKPLTRIQKISGANLARNWAMIPHVTQH 365

Query: 226 EEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRH 285
           E+ D+T LE  R  +  + K    K+T L F ++A+V  + + P  NA+ D+    +   
Sbjct: 366 EDADITELEAFRKKLGEENK--DLKITPLVFQIKAVVAALKKFPQFNASLDETGEKLILK 423

Query: 286 AAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITIS 345
              H+GIA  TP GL VPV+R  + +G+ D A EL  ++  AR      ++++G   +IS
Sbjct: 424 KYFHVGIAVDTPDGLVVPVIRDCDKKGLLDLAVELGEISKKARDKKLGPNDMSGGCFSIS 483

Query: 346 SLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDA 405
           SLG IGG A TP++N PEVAI+GV+K   +PVW+G +F PR I+ LS S+DHRVIDG  A
Sbjct: 484 SLGGIGGTAFTPIVNAPEVAILGVSKAQTKPVWNGKEFAPRLILPLSLSYDHRVIDGALA 543

Query: 406 AVFVQRLKTLL 416
           A F   L   L
Sbjct: 544 ARFAAFLANQL 554



 Score = 64.7 bits (156), Expect = 7e-15
 Identities = 50/148 (33%), Positives = 72/148 (48%), Gaps = 26/148 (17%)

Query: 7   KMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVGD 66
           ++PD+G       ++E  VKPGD V ++  L  + +DKAT+E+P+P  G V  +  +VGD
Sbjct: 8   RVPDIGHD--NVPVIEVLVKPGDKVAKEQGLVTLESDKATMEVPAPFAGTVKEVKLKVGD 65

Query: 67  TVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKPA 126
            V+  A +  IE A EA  +AP   P+A                   A P P   AP PA
Sbjct: 66  EVSEGAVIAIIE-ADEA--SAPAPAPQA-------------------AAPAPAPAAPAPA 103

Query: 127 PAPREAPDLSAKPLASPAVRLRARESGI 154
           PA    P  +A P  +PA     RE+ +
Sbjct: 104 PAKAAEPTRAAAP--APAAGGGVREARV 129


Lambda     K      H
   0.317    0.133    0.384 

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: 616
Number of extensions: 31
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 426
Length of database: 562
Length adjustment: 34
Effective length of query: 392
Effective length of database: 528
Effective search space:   206976
Effective search space used:   206976
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 (21.6 bits)
S2: 52 (24.6 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources