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_110207253.1 DNK54_RS12200 CoA transferase

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



>NCBI__GCF_003194585.1:WP_110207253.1
          Length = 385

 Score =  339 bits (869), Expect = 9e-98
 Identities = 183/389 (47%), Positives = 245/389 (62%), Gaps = 19/389 (4%)

Query: 1   MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60
           M +L  + V D SRVL+GP     LADLGADVIKVERPG GDDTR+WGPPFL    GE+T
Sbjct: 1   MKSLGDILVADFSRVLSGPTVTMFLADLGADVIKVERPGVGDDTRSWGPPFLG---GEST 57

Query: 61  TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
               Y+LS NRNK+SV +D T  EG    REL A++D+L+ENF+ G +   GL Y+    
Sbjct: 58  ----YFLSVNRNKRSVALDLTSAEGIAAARELVARADVLVENFRPGTMEKLGLGYEETHR 113

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
           +NP L+YCSI+GFG +G  A R GYDF++Q +GGLMS+TG PEG     P+KVGVAL DI
Sbjct: 114 LNPALVYCSISGFG-SGEGADRPGYDFVVQAVGGLMSITGEPEGS----PMKVGVALVDI 168

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
           L GL++   +LA+L  R   G G+H+++ LL   ++ LANQ   Y   G  P+RLGN HP
Sbjct: 169 LAGLHAAIGVLASLRERQSTGRGRHVEVNLLSSLLSSLANQGSAYALAGVIPQRLGNVHP 228

Query: 241 NIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
           +I PY+ F T D    +  G D QF     V G  + ++DPRF++N+ RV NR+ L+ ++
Sbjct: 229 SITPYELFQTRDKQVAIACGTDRQFEGLCRVLGCGELSEDPRFSSNRDRVGNRSALLEVL 288

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLA---GKVPQ 357
           + A     T E +  L+ AGVP G +ND+A+ FA     A  L +E    +A   G +PQ
Sbjct: 289 KPAFAAVGTEELLRALDDAGVPAGAVNDIAEAFA----FAERLGLEPLQRVATVEGDLPQ 344

Query: 358 VASPIRLSETPVEYRNAPPLLGEHTLEVL 386
           V+SP+R         +APP LG+HT E+L
Sbjct: 345 VSSPLRFDGVTPRVNSAPPTLGQHTEEIL 373


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: 456
Number of extensions: 15
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: 385
Length adjustment: 31
Effective length of query: 375
Effective length of database: 354
Effective search space:   132750
Effective search space used:   132750
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