GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Pseudomonas fluorescens FW300-N2E2

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate Pf6N2E2_3675 Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1.12)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3675
          Length = 545

 Score =  257 bits (656), Expect = 7e-73
 Identities = 163/431 (37%), Positives = 227/431 (52%), Gaps = 34/431 (7%)

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

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V     +++++ AG A  AAP             +  A +++ EA   P    PA K 
Sbjct: 180 DEVGTGDLILKLKVAGAAAPAAPA------------QAAAPAAKTEAAPAPAAAAPAAKA 227

Query: 126 --APAPREAPDLS-AKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLFISR--- 179
             APAP  AP  S AK  A PAVR  ARE G++L  V  +GP GR+  ED+  ++     
Sbjct: 228 EAAPAPAAAPAPSGAKVHAGPAVRQLAREFGVELSAVGPSGPHGRVLKEDVQAYVKAMMQ 287

Query: 180 --------------GAEPLPAQTGLVRKTAVEEVRMIGLRRRIAEKMSLSTSRIPHITYV 225
                         G  P+PA     R    EEV M  L +  A  +  S   IPH+T  
Sbjct: 288 KAKNAPAEGATGGAGIPPIPA-VDFSRFGETEEVAMTRLMQIGASSLHRSWLNIPHVTQF 346

Query: 226 EEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNATFDDHAGVIHRH 285
           ++ D+T LE  R       +    KLT+LP L++A    + E P  NA+       + R 
Sbjct: 347 DQADITELEAFRVAQKAVAEKAGVKLTVLPLLLKACAHLLKELPDFNASLAPSGKAVIRK 406

Query: 286 AAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTATRDELTGSTITIS 345
             VHIG A  TP GL VPV+R+ + + +   AAE   LA+ AR    T D++ G+  TIS
Sbjct: 407 KYVHIGFAVDTPEGLLVPVIRNVDQKSLLQLAAEAAALAEKARNKKLTADDMQGACFTIS 466

Query: 346 SLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSSSFDHRVIDGWDA 405
           SLG IGG   TP++N PEVAI+GV+K  ++PVWDG  F P+ ++ LS S+DHRVI+G  A
Sbjct: 467 SLGHIGGTGFTPIVNAPEVAILGVSKATIQPVWDGKAFQPKLMLPLSLSYDHRVINGAAA 526

Query: 406 AVFVQRLKTLL 416
           A F +RL  LL
Sbjct: 527 ARFTKRLSDLL 537



 Score = 68.6 bits (166), Expect = 5e-16
 Identities = 43/138 (31%), Positives = 69/138 (50%), Gaps = 13/138 (9%)

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 ++   A AP     PAP 
Sbjct: 62  GDRLKEGDELLELEVEGAA--AAPEAAAPA---------AAPAAEKPAAAPAAEAAPAPA 110

Query: 125 PAPAPREAPDLSAKPLAS 142
            APA     D+    + S
Sbjct: 111 AAPAAATVQDIHVPDIGS 128


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: 581
Number of extensions: 27
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 426
Length of database: 545
Length adjustment: 34
Effective length of query: 392
Effective length of database: 511
Effective search space:   200312
Effective search space used:   200312
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