GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Halioglobus japonicus S1-36

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_084200120.1 C0029_RS04725 CoA transferase

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



>NCBI__GCF_002869505.1:WP_084200120.1
          Length = 400

 Score =  254 bits (650), Expect = 2e-72
 Identities = 152/406 (37%), Positives = 221/406 (54%), Gaps = 15/406 (3%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTR---AWGPPFLKDARGENT 60
           L+ +RVLDL+ +L+GP+   ILADLGA+ IKVE P  G+ TR   A  P    D  G   
Sbjct: 6   LAGVRVLDLTHMLSGPYGAMILADLGAETIKVE-PLQGEGTRKLLATDPANSLDGMG--- 61

Query: 61  TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
              AY+++ NRNKQSV ID     G+     L  +SDI+I NF  G     G+DY +L  
Sbjct: 62  ---AYFITLNRNKQSVAIDLKSTAGKAEFYRLVEQSDIVISNFGAGVPERLGIDYATLSE 118

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
           INP++I C++TGFG  GP  K   +D + Q  GG MS+T    G +   PV+ G+ + D+
Sbjct: 119 INPRIITCTVTGFGSDGPSCKDPAFDQVAQATGGGMSIT----GVDTDHPVRAGIPIGDL 174

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
             G++    ILAAL  R+  G GQH+D+A+LD Q++ L   A  +  +G  P  +GNAH 
Sbjct: 175 GGGMFGVMGILAALYEREQSGHGQHVDIAMLDCQISLLNYMATMHFLSGEDPYPIGNAHF 234

Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
             VPY  F  ADG  ++ V  D  ++   +V   P + DDP       R A + V+   +
Sbjct: 235 VHVPYNTFRCADGFIVIAVITDNFWQNLKQVVPCPAF-DDPALDEQPGRWAAKDVIEENL 293

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
                 ++   W+ +L+Q  +PC P+N L+Q   DPQV+ R + +EL H          +
Sbjct: 294 NAMLQEQSCDYWLEKLKQQRIPCAPVNQLSQALRDPQVKHRNMVVELHHPDGDSTYGPGN 353

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           PI+LS    +   A PLLG+HT  V   +LG D+A +   ++ GV+
Sbjct: 354 PIKLSRADDDVFTAAPLLGQHTDNVFTELLGYDQAHITRLKQQGVI 399


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: 467
Number of extensions: 28
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: 400
Length adjustment: 31
Effective length of query: 375
Effective length of database: 369
Effective search space:   138375
Effective search space used:   138375
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 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