Aligments for a candidate for bkdC in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for bkdC in Pseudomonas fluorescens GW456-L13

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate PfGW456L13_215 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_215
           Dihydrolipoamide acetyltransferase component of pyruvate
           dehydrogenase complex (EC 2.3.1.12)
          Length = 653

 Score =  242 bits (618), Expect = 2e-68
 Identities = 156/430 (36%), Positives = 221/430 (51%), Gaps = 32/430 (7%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           I +PD+G    +A+++E  VK GD V  D  L  + +DKA++EIPSP  G V  +  ++ 
Sbjct: 229 IHVPDIGSA-GKAKIIEVLVKAGDTVVADQSLITLESDKASMEIPSPAAGVVESVSIKLD 287

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V     +++++  G A  A   +   A A        A S+   A A P    PA  P
Sbjct: 288 DEVGTGDLILKLKVKGAAPAAPVAATAPAAA--------APSAPAPAAAAPAAAAPAAAP 339

Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR------ 179
             AP +     AK  A PAVR  ARE G++L  V  +GP GRI  ED+ +++        
Sbjct: 340 VAAPAKP---GAKVHAGPAVRQLAREFGVELSAVGASGPHGRILKEDVQVYVKAMMQKAK 396

Query: 180 -------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVE 226
                        G  P+P      R   +EEV M  L +  A  +  S   +PH+T  +
Sbjct: 397 EAPAAAAGASGGAGIPPIPV-VDFSRFGEIEEVPMTRLMQVGAANLHRSWLNVPHVTQFD 455

Query: 227 EVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHA 286
             D+T LE  R       +    KLTILP L++     + E P  N++       I R  
Sbjct: 456 SADITELEAFRVAQKAVAEKAGVKLTILPLLLKTCAHLLKELPDFNSSLAPSGKAIIRKK 515

Query: 287 AVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISS 346
            V+IG A  TP GL VPV+++ + + +   AAE   LA+ ART   + DE+ G+  TISS
Sbjct: 516 YVNIGFAVDTPDGLLVPVIKNVDQKSLLQLAAEAASLAEKARTKKLSSDEMQGACFTISS 575

Query: 347 LGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAA 406
           LG IGG   TP++N PEVAI+GV+K  ++PVWDG  F P+ ++ LS S+DHRVI+G  AA
Sbjct: 576 LGHIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAAA 635

Query: 407 VFVQRLKTLL 416
            F +RL  LL
Sbjct: 636 RFTKRLSDLL 645



 Score = 63.9 bits (154), Expect = 1e-14
 Identities = 37/112 (33%), Positives = 60/112 (53%), Gaps = 5/112 (4%)

Query: 5   IIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEV 64
           +I++PD+G G  E E++E  VK GD +  D  +  + +DKA++E+P+P  G +  L  ++
Sbjct: 4   LIRVPDIGSG--EGEVIELFVKVGDRIEADQSILTLESDKASMEVPAPKAGIIKSLKVKL 61

Query: 65  GDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPP 116
           GD +     L+ +E  G A  A   + P A AE    +P A  +   A A P
Sbjct: 62  GDRLKEGDELLELEVEGAAAAAPAAAAPAAKAEA---KPAAAPAAAPAPAAP 110



 Score = 62.8 bits (151), Expect = 3e-14
 Identities = 45/148 (30%), Positives = 65/148 (43%), Gaps = 30/148 (20%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           + +PD+G    +A+++E  VK GD V  D  L  + +DKA++EIPSP  G V  +  ++ 
Sbjct: 118 VHVPDIGSS-GKAQIIEIQVKVGDTVAADQSLITLESDKASMEIPSPAAGVVKAISVKLN 176

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V     ++ +E AG A  AA                          AP Q   PAP  
Sbjct: 177 DEVGTGDLILDLEVAGAAAPAA--------------------------APAQAAAPAPAA 210

Query: 126 APAPREAPDLSAKPLASPAVRLRARESG 153
           APA   AP   A P+A     +   + G
Sbjct: 211 APAAAAAP---AAPVADSVQDIHVPDIG 235


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: 726
Number of extensions: 34
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 426
Length of database: 653
Length adjustment: 35
Effective length of query: 391
Effective length of database: 618
Effective search space:   241638
Effective search space used:   241638
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