GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Burkholderia phytofirmans PsJN

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate BPHYT_RS31850 BPHYT_RS31850 CoA-transferase

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



>FitnessBrowser__BFirm:BPHYT_RS31850
          Length = 394

 Score =  463 bits (1191), Expect = e-135
 Identities = 220/388 (56%), Positives = 279/388 (71%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G LS +RVLDLSR+LAGPW+ Q+LADLGADV+KVERPG GDDTRAWGPPF     G  + 
Sbjct: 3   GTLSGIRVLDLSRILAGPWSTQLLADLGADVVKVERPGGGDDTRAWGPPFAPGGDGTPSA 62

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
           E+AY+L+ANR K+S+ +DF+  EGQ +VRELA  +D++IEN K G +  YGLDY+SL+ +
Sbjct: 63  ESAYFLAANRGKRSIAVDFSVAEGQDIVRELAKTADVVIENLKCGDMQRYGLDYESLRCL 122

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           NP+LIYCSITGFGQTGPY+KRAGYDF+IQ +GGLMS+TG  +G  G GP K GV ++D++
Sbjct: 123 NPKLIYCSITGFGQTGPYSKRAGYDFVIQAMGGLMSITGESDGRPGGGPQKCGVPISDMM 182

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
           TG+Y+T  IL+AL  R   G GQ+IDM+LLD QV  LAN  +NYL +G+  +R GNAHPN
Sbjct: 183 TGMYATVGILSALHERQTSGEGQYIDMSLLDTQVGWLANHGLNYLVSGSPARRWGNAHPN 242

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
           + PYQ FP  DG  I+ VGND QF+    V      A D RF+TN  R+ANR  L+ LI 
Sbjct: 243 LCPYQAFPAIDGYLIIAVGNDRQFQSLCRVLSMSTVASDSRFSTNSGRLANRDSLVELIE 302

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361
           Q        EW+  LEQAGVP GPIN +A+  ADPQV +RG+   + H +   VPQ+A+P
Sbjct: 303 QRLRTGNRDEWLEMLEQAGVPAGPINTVAEALADPQVISRGMVFSMKHTMGASVPQIANP 362

Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRV 389
           I+ S T +EY   PP+LGEHT EVL  +
Sbjct: 363 IKFSRTAIEYHRPPPMLGEHTAEVLASI 390


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: 565
Number of extensions: 18
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: 394
Length adjustment: 31
Effective length of query: 375
Effective length of database: 363
Effective search space:   136125
Effective search space used:   136125
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