GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bkdC in Limnohabitans curvus MWH-C5

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate WP_108402665.1 B9Z44_RS13465 dihydrolipoyllysine-residue acetyltransferase

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



>NCBI__GCF_003063475.1:WP_108402665.1
          Length = 552

 Score =  231 bits (588), Expect = 5e-65
 Identities = 160/435 (36%), Positives = 232/435 (53%), Gaps = 42/435 (9%)

Query: 2   GEFIIKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLG 61
           G   I +PD+G+   +  ++E  VKPGD ++ +  L  V +DKA++EIPS   G +  L 
Sbjct: 116 GPIEIHVPDIGD-FKDVAVIEVFVKPGDSIKVEQSLITVESDKASMEIPSSHAGVLKELK 174

Query: 62  AEVGDTVAVKAPLVRIE---TAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQP 118
            +VGDTV +   L  +E   +A  A  AA  S   A+A   +  P  V++ + A A    
Sbjct: 175 VKVGDTVNIGDLLAILEGTVSAAAAPVAAAASAVAAVAPAAVAAPTTVAAAVAAVA---- 230

Query: 119 EKPAPKPAPAPREAPDLSAKPLASPAVRLRARESGIDLRQVAGTGPAGRITHEDLDLF-- 176
              AP  AP    AP L   P ASP+VR  ARE G+ L ++ G+G  GRIT +D+  F  
Sbjct: 231 ---APAHAPG---APTLGL-PHASPSVRKFARELGVPLEELKGSGVKGRITQDDVQTFTK 283

Query: 177 -ISRGAEPLPAQT--------------GLV--------RKTAVEEVRMIGLRRRIAEKMS 213
            +  GA    AQ               GL+        +   VE   M  +++     + 
Sbjct: 284 AVMSGATQTKAQAAKGGASAGGDGAGLGLIPWPKVDFAKFGPVERKEMGRIKKISGANLL 343

Query: 214 LSTSRIPHITYVEEVDMTALEDLRATMNRDRKPEQAKLTILPFLMRALVKTVAEQPGVNA 273
            +   IP +T  ++ D+T LE  R + N++ +    K+T+L FL++A V  + + P  N+
Sbjct: 344 RNAVMIPAVTNHDDCDITDLEAFRVSTNKENEKSGVKVTMLAFLIKACVAALKKYPEFNS 403

Query: 274 TFDDHAGVIHRHAAVHIGIATQTPAGLTVPVVRHAEARGIWDCAAELNRLADAARTGTAT 333
           + D  A V   +   HIG A  TP GL VPV+R  + +G+   + E++ LA  AR G   
Sbjct: 404 SLDGDALVYKNYW--HIGFAADTPNGLMVPVIRDCDKKGVLQISQEMSELAKKARDGKLG 461

Query: 334 RDELTGSTITISSLGAIGGIASTPVINHPEVAIVGVNKIAVRPVWDGAQFVPRKIMNLSS 393
             E+TG+T TISSLG IGG   TP+IN PEVAI+GV K  + PVW+G +FVPR ++ LS 
Sbjct: 462 PAEMTGATFTISSLGGIGGKYFTPIINAPEVAILGVCKSTMEPVWNGKEFVPRLMLPLSL 521

Query: 394 SFDHRVIDGWDAAVF 408
           ++DHRVIDG  AA F
Sbjct: 522 TWDHRVIDGAAAARF 536



 Score = 62.8 bits (151), Expect = 3e-14
 Identities = 52/155 (33%), Positives = 76/155 (49%), Gaps = 28/155 (18%)

Query: 6   IKMPDVGEGVAEAELVEWHVKPGDPVREDMVLAAVMTDKATVEIPSPVTGKVLWLGAEVG 65
           +K+PD+G+   E  ++E  VK GD V+ +  L  V +DKA++EIPS   G V  L   +G
Sbjct: 6   VKVPDIGD-FDEVAVIELLVKVGDTVKAEQSLITVESDKASMEIPSSTAGVVKELRVNLG 64

Query: 66  DTVAVKAPLVRIETAGEAGEAAPDSIPEALAEQVLDEPVAVSSRLEAKAPPQPEKPAPKP 125
           D V   + ++ +E AG A  A P + P A A      PVA +             PAP  
Sbjct: 65  DKVKEGSVVLVVEAAGAA--AGPAAAPAAAA------PVAAA-------------PAPVA 103

Query: 126 APAPREAPDLSAKPLASPAVRLRARESGIDLRQVA 160
           A AP     ++A P AS  + +   + G D + VA
Sbjct: 104 AAAP-----VAAAPSASGPIEIHVPDIG-DFKDVA 132


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: 500
Number of extensions: 16
Number of successful extensions: 6
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: 552
Length adjustment: 34
Effective length of query: 392
Effective length of database: 518
Effective search space:   203056
Effective search space used:   203056
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 24 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