GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Nocardioides daejeonensis MJ31

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_110207576.1 DNK54_RS13740 CoA transferase

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



>NCBI__GCF_003194585.1:WP_110207576.1
          Length = 398

 Score =  190 bits (483), Expect = 6e-53
 Identities = 127/407 (31%), Positives = 195/407 (47%), Gaps = 17/407 (4%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G L+ LRV++   + A P AG++L D GADVIK+E P  GD  R W P     A G    
Sbjct: 5   GPLAGLRVIEAGSMYAAPTAGRMLRDFGADVIKIEDPAQGDFARQWQPAHEGTAIG---- 60

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
               +   N  K+SV ID   PEG+ L++ L A +D+LIENF+ G +  +G+ Y  L A 
Sbjct: 61  ----FARLNSGKRSVGIDMRAPEGRDLLKRLVADADVLIENFRPGRMEKWGMSYAELAAD 116

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           +P L+   ++GFGQTGPY +R G+  + +   G   L G P     A P        D +
Sbjct: 117 HPGLVMARVSGFGQTGPYRERPGFGTVAETASGYAFLNGWPHTPPTAPP----FGFADSI 172

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
            G+ +   +  AL  R   G G+ +D+AL +  +  L +  +NY  +G   +R GNA   
Sbjct: 173 AGISAAYGVAMALFERGRTGAGREVDVALYEPLMFILGDAVLNYTASGTIMQRHGNASGA 232

Query: 242 IVPYQDFPTADGDFILTVG-NDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
             P   +  ADG ++   G N     +  +   +P    D R+ATN  R+AN   L  ++
Sbjct: 233 ASPRGIYEAADGGWLSIAGSNQAIAMRLFDAMERPDLKADERYATNVARMANNESLQAIV 292

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
                 +   E +  L++  V    +ND + + ADP  + R L   L +   G+      
Sbjct: 293 IDWVKQRPRDEVLNILDEYEVVAAAVNDSSDIVADPHFRERTLT-SLTNSALGEALVPGP 351

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRV-LGLDEAAVMAFREAGVL 406
            + ++       +  P +GEHT E+L    +  DE A +A   AGV+
Sbjct: 352 ILHVNGYDGPRYDGVPAVGEHTTEILTAAGVSTDELARLA--TAGVI 396


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: 414
Number of extensions: 19
Number of successful extensions: 5
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: 398
Length adjustment: 31
Effective length of query: 375
Effective length of database: 367
Effective search space:   137625
Effective search space used:   137625
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