GapMind for catabolism of small carbon sources

 

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

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate AO353_12860 AO353_12860 dihydrolipoamide acetyltransferase

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



>FitnessBrowser__pseudo3_N2E3:AO353_12860
          Length = 544

 Score =  255 bits (651), Expect = 3e-72
 Identities = 159/428 (37%), Positives = 228/428 (53%), Gaps = 28/428 (6%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           I +PD+G    +A+++E  VK GD V  D  L  + +DKA++EIPSP  G V  +  ++ 
Sbjct: 120 IHVPDIGSS-GKAKIIEVLVKVGDTVEADQSLITLESDKASMEIPSPAAGVVESIAVKLE 178

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V     +++++ AG A  AAP   P A A      P A ++   AK   +   PAP  
Sbjct: 179 DEVGTGDFILKLKVAGAAAPAAP--APAAAAPAQAAAPAAAAAAPVAKT--EAAAPAPVS 234

Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR------ 179
           APAP       AK  A PAVR  ARE G++L  V+ +GP GR+  ED+ +++        
Sbjct: 235 APAPS-----GAKVHAGPAVRQLAREFGVELNAVSPSGPHGRVLKEDVQVYVKAMMQKAK 289

Query: 180 -----------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVEEV 228
                      G  P+P      R   +EEV M  L +  A  +  S   +PH+T  +  
Sbjct: 290 EAPAAGATGGAGIPPIPV-VDFSRFGEIEEVPMTRLMQAGAANLHRSWLNVPHVTQFDSA 348

Query: 229 DMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAAV 288
           D+T LE  R       +    KLT+LP L+++    + E P  N++       I R   V
Sbjct: 349 DITELEAFRVAQKAVAEKAGVKLTVLPLLLKSCAHLLKELPDFNSSLAPSGKAIIRKKYV 408

Query: 289 HIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSLG 348
           +IG A  TP GL VPV+++ + + +   AAE   LA+ ART   + DE+ G+  TISSLG
Sbjct: 409 NIGFAVDTPEGLLVPVIKNVDQKSLLQLAAEAASLAEKARTKKLSADEMQGACFTISSLG 468

Query: 349 AIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAVF 408
            IGG   TP++N PEVAI+GV+K  ++PVWDG  F P+ ++ LS S+DHRVI+G  AA F
Sbjct: 469 HIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAAARF 528

Query: 409 VQRLKTLL 416
            +RL  LL
Sbjct: 529 TKRLSDLL 536



 Score = 68.9 bits (167), Expect = 4e-16
 Identities = 46/139 (33%), Positives = 67/139 (48%), Gaps = 16/139 (11%)

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

Query: 65  GDTVAVKAPLVRIETAG-EAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAP 123
           GD +     L+ +E  G  A  AAP + P A A               A AP     PAP
Sbjct: 62  GDRLKEGDELMELEVEGAAAAPAAPAAAPAAAA-------------APAAAPAPQAAPAP 108

Query: 124 KPAPAPREAPDLSAKPLAS 142
             APA     D+    + S
Sbjct: 109 AAAPAAATVQDIHVPDIGS 127


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: 569
Number of extensions: 22
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: 2
Length of query: 426
Length of database: 544
Length adjustment: 34
Effective length of query: 392
Effective length of database: 510
Effective search space:   199920
Effective search space used:   199920
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: 51 (24.3 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