GapMind for catabolism of small carbon sources

 

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

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate Pf1N1B4_1477 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1477 Dihydrolipoamide
           acetyltransferase component of pyruvate dehydrogenase
           complex (EC 2.3.1.12)
          Length = 655

 Score =  244 bits (623), Expect = 6e-69
 Identities = 160/430 (37%), Positives = 222/430 (51%), Gaps = 34/430 (7%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           I +PD+G    +A+++E  VK GD V  D  L  + +DKA++EIPSP  G V  +  ++ 
Sbjct: 233 IHVPDIGSA-GKAKIIEVLVKAGDTVVADQSLITLESDKASMEIPSPAAGVVESVSIKLD 291

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V     +++++  G A  AAP   P A A      P A +    A AP  P   AP  
Sbjct: 292 DEVGTGDLILKLKVKGAAPAAAP--APAAAA------PSAPAPAPAAAAPAAPAPAAPVA 343

Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR------ 179
           APA        AK  A PAVR  ARE G++L  V  +GP GRI  ED+ +++        
Sbjct: 344 APAKP-----GAKVHAGPAVRQLAREFGVELSAVGASGPHGRILKEDVQVYVKAMMQKAK 398

Query: 180 -------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVE 226
                        G  P+P      R   +EEV M  L +  A  +  S   IPH+T  +
Sbjct: 399 EAPTAAAGATGGAGIPPIPV-VDFSRFGEIEEVPMTRLMQIGASSLHRSWLNIPHVTQFD 457

Query: 227 EVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHA 286
             D+T LE  R       +    KLTILP L+++    + E P  N++       I R  
Sbjct: 458 SADITELEAFRIAQKAVAEKAGVKLTILPLLLKSCAHLLKELPDFNSSLAPSGKAIIRKK 517

Query: 287 AVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISS 346
            V+IG A  TP GL VPV+++ + + +   AAE   LA  AR    T D++ G+  TISS
Sbjct: 518 YVNIGFAVDTPEGLLVPVIKNVDQKSLLQLAAEAAALAAKARDKKLTADDMQGACFTISS 577

Query: 347 LGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAA 406
           LG IGG   TP++N PEVAI+GV+K  ++PVWDG  F P+ ++ LS S+DHRVI+G  AA
Sbjct: 578 LGHIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAAA 637

Query: 407 VFVQRLKTLL 416
            F +RL  LL
Sbjct: 638 RFTKRLSDLL 647



 Score = 62.8 bits (151), Expect = 3e-14
 Identities = 41/128 (32%), Positives = 64/128 (50%), Gaps = 15/128 (11%)

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  GDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPK 124
           GD +     L+ +E  G A  A     P A A        A +   +A+A P   K    
Sbjct: 62  GDRLKEGDELLELEVEGAAAPA-----PAAAA--------AAAPAAKAEAAPAAAKAPAA 108

Query: 125 PAPAPREA 132
           PA AP  A
Sbjct: 109 PAAAPAAA 116



 Score = 58.9 bits (141), Expect = 4e-13
 Identities = 37/113 (32%), Positives = 55/113 (48%), Gaps = 8/113 (7%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           + +PD+G    +A+++E  VK GD V  D  L  + +DKA++EIPSP  G V  +  ++ 
Sbjct: 121 VHVPDIGSS-GKAQIIEIQVKVGDTVEADQSLITLESDKASMEIPSPAAGVVKAISVKLN 179

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQP 118
           D V     ++ +E AG A        P A A      P A +    A AP  P
Sbjct: 180 DEVGTGDLILDLEVAGAAA-------PAAAAPAQAAAPAAAAPAPAAAAPAAP 225


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: 731
Number of extensions: 33
Number of successful extensions: 6
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: 655
Length adjustment: 35
Effective length of query: 391
Effective length of database: 620
Effective search space:   242420
Effective search space used:   242420
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.

Links

Downloads

Related tools

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, 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