GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1018 Dihydrolipoamide acyltransferase component of branched-chain alpha-keto acid dehydrogenase complex (EC 2.3.1.168)

Query= SwissProt::O06159
         (393 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1018 Dihydrolipoamide
           acyltransferase component of branched-chain alpha-keto
           acid dehydrogenase complex (EC 2.3.1.168)
          Length = 369

 Score =  192 bits (487), Expect = 2e-53
 Identities = 138/398 (34%), Positives = 191/398 (47%), Gaps = 47/398 (11%)

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

Query: 67  AEGDVLKVGAELVRIDTGPTAVAQPNGEGAVPTLVGYGADT-----------AIETSRRT 115
            EGD+L VG  L+  +          GE    T+VG   D            A  ++R  
Sbjct: 61  GEGDILHVGEPLLGYE----------GEADAGTVVGRLEDGGTNQEDAFFIGAAPSTREH 110

Query: 116 SRPLAAPVVRKLAKELAVDLAALQRGSGAGGVITRADVLAAAR------GGVGAGPDVRP 169
               A P VR+LA++L V+L+ L  GSG  G ITR+DV  AA+      GG         
Sbjct: 111 LANRATPAVRQLARQLGVELSGLT-GSGQDGQITRSDVENAAQTERERFGG-------EK 162

Query: 170 VHGVHARMAEKMTLSHKEIPTAKASVEVICAELLRLRDRFVSAAPEITPFALTLRLLVIA 229
           + GV   MA  M  SH E+       +       + R+  +  A          + +  A
Sbjct: 163 LRGVRRSMALNMARSHAEVVPVTIFGDADLHRWGQAREPLIRLA----------KAMAAA 212

Query: 230 LKHNVILNSTWVDSGEGPQVHVHRGVHLGFGAATERGLLVPVVTDAQDKNTRELASRVAE 289
                +LNS +   G+   +  H  + LG    T  GL VPV+ D   +   +L   V  
Sbjct: 213 CAVEPVLNSAF--DGKTQALKQHERLDLGIAVDTPDGLFVPVLRDVGQRTAADLKEGVMR 270

Query: 290 LITGAREGTLTPAELRGSTFTVSNFGALGVDDGVPVINHPEAAILGLGAIKPRPVVVGGE 349
           L    +  ++ P E+ G+T T+SNFG L      PV+  P+ AIL  GAI+  PV V G 
Sbjct: 271 LRADVQARSIPPQEMMGATLTLSNFGTLFGRYANPVVVPPQVAILAAGAIREEPVAVEGA 330

Query: 350 VVARPTMTLTCVFDHRVVDGAQVAQFMCELRDLIESPE 387
           VV  P + L+  FDHRVV G + A+F   L + +E PE
Sbjct: 331 VVVHPILPLSLTFDHRVVTGGEAARFFKALVEALEQPE 368


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: 434
Number of extensions: 22
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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