GapMind for catabolism of small carbon sources

 

Alignments 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:

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