GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Pseudomonas fluorescens FW300-N2C3

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate AO356_08965 AO356_08965 dihydrolipoamide acetyltransferase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_08965
          Length = 546

 Score =  251 bits (641), Expect = 4e-71
 Identities = 155/428 (36%), Positives = 222/428 (51%), Gaps = 28/428 (6%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           I +PD+G    +A+++E  VK GD V  D  L  + +DKA++EIPSP  G V  +  ++ 
Sbjct: 122 IHVPDIGSS-GKAKIIEVLVKVGDTVEADQSLITLESDKASMEIPSPAAGVVESVEIKLE 180

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V     +++++ AG +  AAP       A+       A +   +A+A P P   AP P
Sbjct: 181 DEVGTGDLILKLKVAGASAPAAPAPAAAPAAKAEAAPAPAAAPAAKAEAAPAPVAAAPAP 240

Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR------ 179
           +          AK  A PAVR  ARE G++L  V  +GP GR+  ED+  ++        
Sbjct: 241 S---------GAKVHAGPAVRQLAREFGVELSAVGPSGPHGRVLKEDVQAYVKAMMQKAK 291

Query: 180 -----------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYVEEV 228
                      G  P+PA     R    EEV M  L +  A  +  S   IPH+T  ++ 
Sbjct: 292 NAPAEGATGGAGIPPIPA-VDFSRFGETEEVAMTRLMQIGASSLHRSWLNIPHVTQFDQA 350

Query: 229 DMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRHAAV 288
           D+T LE  R       +    KLT+LP L++A    + E P  N++       + R   V
Sbjct: 351 DITELEAFRVAQKAVAEKAGVKLTVLPLLLKACAHLLKELPDFNSSLAPSGKAVIRKKYV 410

Query: 289 HIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITISSLG 348
           HIG A  TP GL VPV+R+ + + +   A E   LA+ AR    T D++ G+  TISSLG
Sbjct: 411 HIGFAVDTPEGLLVPVIRNVDQKSLLQLAGEAAALAEKARNKKLTADDMQGACFTISSLG 470

Query: 349 AIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDAAVF 408
            IGG   TP++N PEVAI+GV+K  ++PVWDG  F P+ ++ LS S+DHRVI+G  AA F
Sbjct: 471 HIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAAARF 530

Query: 409 VQRLKTLL 416
            +RL  LL
Sbjct: 531 TKRLSDLL 538



 Score = 72.8 bits (177), Expect = 2e-17
 Identities = 44/138 (31%), Positives = 70/138 (50%), Gaps = 12/138 (8%)

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

Query: 65  GDTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPK 124
           GD +     L+ +E  G A  AAP++   A A    ++P A        AP     PAP 
Sbjct: 62  GDRLKEGDELLELEVEGAA--AAPEAAAPAAAPAAAEKPAA--------APAAEAAPAPA 111

Query: 125 PAPAPREAPDLSAKPLAS 142
            APA     D+    + S
Sbjct: 112 AAPAAATVQDIHVPDIGS 129


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: 589
Number of extensions: 26
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 426
Length of database: 546
Length adjustment: 34
Effective length of query: 392
Effective length of database: 512
Effective search space:   200704
Effective search space used:   200704
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