GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Pseudomonas fluorescens FW300-N2E3

Align Dihydrolipoyllysine-residue acyltransferase component of branched-chain alpha-ketoacid dehydrogenase complex; Branched-chain alpha-ketoacid dehydrogenase complex component E2; BCKADH E2; Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase; EC 2.3.1.168 (characterized)
to candidate AO353_15585 AO353_15585 branched-chain alpha-keto acid dehydrogenase subunit E2

Query= SwissProt::O06159
         (393 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_15585 AO353_15585
           branched-chain alpha-keto acid dehydrogenase subunit E2
          Length = 369

 Score =  202 bits (513), Expect = 2e-56
 Identities = 138/395 (34%), Positives = 203/395 (51%), Gaps = 39/395 (9%)

Query: 7   IRSFPVPDLGEGLQEVTVTCWSVAVGDDVEINQTLCSVETAKAEVEIPSPYAGRIVELGG 66
           ++ F +PDLGEGLQE  +  W V VGD V+ +Q L SVETAKA V+IP+PY G + +  G
Sbjct: 1   MKYFKLPDLGEGLQEAEIVEWHVKVGDTVKADQLLVSVETAKALVDIPAPYDGVVAKTFG 60

Query: 67  AEGDVLKVGAELV----RIDTGPTAVAQPNGEGAVPT---LVGYGADTAIETSRRTSRPL 119
            EGD+L VG  L+      D G T V +  G G+       VG     A  ++R    P 
Sbjct: 61  GEGDILHVGEPLLGYEGEADAG-TVVGRLEGGGSHQDDQFFVG-----AAPSTREHMSPR 114

Query: 120 AAPVVRKLAKELAVDLAALQRGSGAGGVITRADVLAAAR------GGVGAGPDVRPVHGV 173
           A P VR+LA++L V+L  L  GSG  G+ITR+DV +A++      GG         + GV
Sbjct: 115 ATPAVRQLARQLGVELTGLS-GSGPDGLITRSDVESASQTERDKFGG-------EKLRGV 166

Query: 174 HARMAEKMTLSHKEIPTAKASVEVICAELLRLRDRFVSAAPEITPFALTLRLLVIALKHN 233
              MA+ MT SH E+       +       R RD  +  A          + +  A    
Sbjct: 167 RRSMAQNMTRSHAEVVPVTIYADADLHRWGRARDPLIRLA----------KAMAAACAVE 216

Query: 234 VILNSTWVDSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELASRVAELITG 293
            +LNS +   G+   +  H  ++LG    T  GL VPV+ D  ++++ +L   +  L   
Sbjct: 217 PMLNSGF--DGKSLSIKHHDALNLGIAVDTPDGLFVPVLRDVGNRSSDDLKEGITRLRAD 274

Query: 294 AREGTLTPAELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGEVVAR 353
            +  ++   E+ G+T T+SNFG +      PV+  P+ AIL  GAI+  PV + G+VV  
Sbjct: 275 VQARSIPAKEMMGATLTLSNFGTMFGRYANPVVVPPQVAILAAGAIRDEPVAMAGKVVVH 334

Query: 354 PTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPET 388
           P + L+  FDHRVV G + A+F   L + +E P++
Sbjct: 335 PILPLSLTFDHRVVTGGEAARFFKVLVEALEQPDS 369


Lambda     K      H
   0.317    0.135    0.388 

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: 428
Number of extensions: 26
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: 393
Length of database: 369
Length adjustment: 30
Effective length of query: 363
Effective length of database: 339
Effective search space:   123057
Effective search space used:   123057
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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