GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_215
          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:

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