GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Cupriavidus basilensis 4G11

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate RR42_RS29900 RR42_RS29900 CoA-transferase

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



>FitnessBrowser__Cup4G11:RR42_RS29900
          Length = 407

 Score =  436 bits (1122), Expect = e-127
 Identities = 208/405 (51%), Positives = 273/405 (67%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G L+ ++VLDLSR+LAGPW+ Q+L+DLGADV+KVERPG GDDTRAWGPPFL    G  T 
Sbjct: 3   GPLAGIKVLDLSRILAGPWSTQLLSDLGADVMKVERPGTGDDTRAWGPPFLTREDGTTTE 62

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
           E+AY+L ANR K+S+T+D +   GQ L+ EL    D+ +EN+K G +  YGLD+ +L  I
Sbjct: 63  ESAYFLCANRGKRSITLDVSSKVGQDLLHELVKDCDVFVENYKFGDMQRYGLDFKTLSEI 122

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           NP+L+YCSITGFGQTGPY KRAGYDF++Q +GGLMS+TG  +G  G GP K GV ++D++
Sbjct: 123 NPRLVYCSITGFGQTGPYRKRAGYDFVVQAMGGLMSITGERDGVPGGGPQKCGVPISDLM 182

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
           TG+Y++ AI++AL  R   G GQ+IDM+LLD QVA LANQA NYL  G+ P+R GNAHPN
Sbjct: 183 TGMYASVAIVSALFERVGSGRGQYIDMSLLDTQVAWLANQASNYLVGGSHPRRWGNAHPN 242

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
           + PYQ FP +DG  I+ VGND QFR   E  G     DD R+  N  R+ NR  L+ ++ 
Sbjct: 243 LAPYQSFPASDGSLIVAVGNDRQFRAMCEALGLINLPDDDRYRRNADRLKNRESLVEVLS 302

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361
                +    W+  LE  GVPCGPI  + +   DP ++AR +   LPH      PQVA+P
Sbjct: 303 ARFEEEERDTWLKLLESVGVPCGPIQSIPEALEDPHIRAREMVFSLPHSSGASAPQVANP 362

Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           I+ S + ++Y  APP LGEHT  +L+  LG     + A R  G +
Sbjct: 363 IKFSRSSIDYLRAPPALGEHTETILKNELGKSVEQIEAMRRDGTI 407


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: 537
Number of extensions: 19
Number of successful extensions: 1
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: 407
Length adjustment: 31
Effective length of query: 375
Effective length of database: 376
Effective search space:   141000
Effective search space used:   141000
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.

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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