GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Sphingomonas koreensis DSMZ 15582

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Ga0059261_2666 Ga0059261_2666 Predicted acyl-CoA transferases/carnitine dehydratase

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



>FitnessBrowser__Korea:Ga0059261_2666
          Length = 397

 Score =  220 bits (560), Expect = 7e-62
 Identities = 144/410 (35%), Positives = 216/410 (52%), Gaps = 28/410 (6%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           LS +RVLD S  +AGP+A Q + D+GADV+KVE P +G+  R         A G N  + 
Sbjct: 5   LSGIRVLDCSIAMAGPFAAQRMGDMGADVVKVE-PTSGEWQRH------ASAGGANGNKI 57

Query: 64  -AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAIN 122
              +LS NRNK+S+ +D   PEG+ L+ EL   +D+ ++N++ G     G+DY +L AIN
Sbjct: 58  NVSFLSLNRNKRSLAVDLKAPEGKALLLELVKDADVFLQNYRPGVAERLGVDYATLSAIN 117

Query: 123 PQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILT 182
           P L+Y S++G+G+ GPY    G D ++QG+ G M  TG     EGA P   G  L D +T
Sbjct: 118 PSLVYVSMSGYGEDGPYRNYPGQDLLLQGMSGAMMSTGA----EGAPPSAAGQYLVDAVT 173

Query: 183 GLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLG---NAH 239
              +    LAAL HR+  G GQ + + +LD  +  +  Q ++  T G  P+      +AH
Sbjct: 174 AYSAFEGALAALFHRERTGEGQLVQVNMLDA-ITTIQMQELSVFTVGEKPQARSAEPHAH 232

Query: 240 PNI-VPYQDFPTADGDFILTVGNDGQFRKFAEVAGQP--QWADDPRFATNKVRVANRAVL 296
             I  PY  F TADG   + + +    +K  E+      +  DD R +      A R  +
Sbjct: 233 SYIRAPYGVFATADGYITVAMAS---LKKLGELFEDSFFEGLDDERDSW-----ALRDQI 284

Query: 297 IPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVP 356
              +R+    +T+A+W+  +    +  GP+   A +  DPQ++  G  +E  H   G+V 
Sbjct: 285 FAKVREHLPARTSAQWLEAMRARDIWAGPVYGYADLVEDPQIKHNGTFVEYDHPTEGRVK 344

Query: 357 QVASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
               PIR S+TP       PL+GEH+ E+L R  GLD  A+ A  E+GV+
Sbjct: 345 APGFPIRFSKTPSTVARGAPLVGEHSRELL-REAGLDGKAIEALIESGVV 393


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: 451
Number of extensions: 24
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: 397
Length adjustment: 31
Effective length of query: 375
Effective length of database: 366
Effective search space:   137250
Effective search space used:   137250
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