GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Sphingomonas koreensis DSMZ 15582

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Ga0059261_0564 Ga0059261_0564 Predicted acyl-CoA transferases/carnitine dehydratase

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>FitnessBrowser__Korea:Ga0059261_0564
          Length = 390

 Score =  189 bits (480), Expect = 1e-52
 Identities = 132/379 (34%), Positives = 191/379 (50%), Gaps = 18/379 (4%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G LS +RVLDLS  +AGP+   +LAD GADVIKVE PG GD+ R + P  L    GEN  
Sbjct: 17  GPLSGIRVLDLSAYIAGPYGCSLLADQGADVIKVEPPG-GDNLRQY-PSTLA---GENRA 71

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
               +L  NR+KQ V +D  +   + ++ +LA ++D+L+ NF+ G     G+D+ +L A 
Sbjct: 72  ----FLGVNRSKQGVVLDLKQDGERAVLLDLADQADVLVHNFRPGVPERLGIDHAALSAR 127

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           NP+LIYC++TG+G+ GP   +AGYD ++Q + G+  L G P    G   +  G +  D  
Sbjct: 128 NPRLIYCAVTGYGEEGPLRAKAGYDQVLQAMTGMCVLQGPP----GTPEITYG-SPVDYY 182

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
                 A + +AL  R+  G GQ++ ++LL  + A     A      G  P    +    
Sbjct: 183 AAALVAAGVASALYERERSGVGQYVGVSLL--RSALTMQSARLIRAEGEDPGISRDMRSG 240

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
            +     PTA G   L+      +R   E  G     +D RF T K R A+   +IP +R
Sbjct: 241 GITGL-HPTALGHLYLSANTPHFWRALCERTGLADLLEDSRFDTVKGRAAHADEIIPRLR 299

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361
            A + +T AEW   L  A VPC     +  +F D QV A  +  ++PH + G    VA  
Sbjct: 300 AALMERTAAEWEASLGDA-VPCSVARSIDDMFDDAQVAAEAMLSDIPHPVLGSYRGVARA 358

Query: 362 IRLSETPVEYRNAPPLLGE 380
           I+   TP       PLL E
Sbjct: 359 IKFGRTPGPDPFKAPLLDE 377


Lambda     K      H
   0.319    0.137    0.408 

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: 486
Number of extensions: 26
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 406
Length of database: 390
Length adjustment: 31
Effective length of query: 375
Effective length of database: 359
Effective search space:   134625
Effective search space used:   134625
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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