GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Dinoroseobacter shibae DFL-12

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate 3609948 Dshi_3330 Formyl-CoA transferase (RefSeq)

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



>FitnessBrowser__Dino:3609948
          Length = 411

 Score =  300 bits (769), Expect = 4e-86
 Identities = 161/405 (39%), Positives = 246/405 (60%), Gaps = 12/405 (2%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G L  ++V++L+ ++AGP  G +LAD+GADVIKVE+P +GDD+R + PP   D  GE+  
Sbjct: 7   GPLKGMKVIELAHIMAGPVCGMMLADMGADVIKVEKP-DGDDSRRFLPP---DINGES-- 60

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
             A Y+  NR K+ ++++   P+   ++  L   +D++IEN+++G +   GL Y++L+  
Sbjct: 61  --AAYMMMNRGKRGISLNLKDPDAVEVLHALLRDADVVIENYRMGTMEKLGLGYETLRKE 118

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
           NP+LIYC I+GFG+TGPYA R G+D + QG+ GLMS+TG  EG  G  PVK G  ++DI 
Sbjct: 119 NPRLIYCEISGFGRTGPYAHRGGFDLIAQGMSGLMSITG--EGP-GRPPVKPGAPISDIT 175

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
           +G+ +   + AA AH    G GQ +D +L +  +     Q+     TG AP+  G+AHP 
Sbjct: 176 SGIVAAMGVNAAYAHALRTGQGQRVDTSLFEAAITQTYWQSAIAFATGTAPEPEGSAHPI 235

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIR 301
             PYQ F TADG   +   N   + +  EV    +  DDPRFATN+ R  N + L+PL+ 
Sbjct: 236 NAPYQAFHTADGWINIGAANQKNWLRLLEVLEADELRDDPRFATNRDRRVNLSELVPLLE 295

Query: 302 QATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASP 361
                +TT +W+ ++E+AG+P GP+  + ++ ADPQ +AR + +E  H +AG+V  +  P
Sbjct: 296 AHFETRTTQDWLVRMEEAGLPAGPVLTVPEMHADPQARAREMIVETEHPVAGRVQALGLP 355

Query: 362 IRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
           ++ SETP   +   PLLG+H+  VL   LG D  AV     +G +
Sbjct: 356 VKFSETPGAVQRPAPLLGQHSRAVLAD-LGYDADAVARLIASGAV 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: 479
Number of extensions: 20
Number of successful extensions: 3
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: 411
Length adjustment: 31
Effective length of query: 375
Effective length of database: 380
Effective search space:   142500
Effective search space used:   142500
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