GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Dechlorosoma suillum PS

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate Dsui_0037 Dsui_0037 putative acyl-CoA transferase/carnitine dehydratase

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



>FitnessBrowser__PS:Dsui_0037
          Length = 403

 Score =  229 bits (585), Expect = 8e-65
 Identities = 146/408 (35%), Positives = 222/408 (54%), Gaps = 21/408 (5%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L+ L+V++L  ++AGP+A ++LA+ GA+V+K+E P  GD  R W   +      E T+  
Sbjct: 12  LAGLKVVELGTLIAGPFASRLLAEFGAEVVKIESPDGGDPLRKWRKLY------EGTS-- 63

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
            ++   +RNKQSVT++   P+G+ +VR+L A++DI++ENF+ G +   GL ++ L A+NP
Sbjct: 64  LWWFVQSRNKQSVTVNLKHPQGRDIVRKLVAEADIVVENFRPGVMEKLGLSWEELSALNP 123

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
            L+   ++GFGQTGPY  + G+  + + +GGL  +TG  +      PV+ G+++ D +  
Sbjct: 124 GLVMLRLSGFGQTGPYKDQPGFGAVGESMGGLRYITGFAD----RPPVRTGISIGDSIAA 179

Query: 184 LYSTAAILAALAHRDHVGG-GQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNI 242
           L+     L AL H++  GG GQ +D+AL +   A + +    +   G   +R GN  P I
Sbjct: 180 LWGVFGTLMALRHKEVQGGKGQVVDVALYEAIFAMMESLVPEFDVFGFVRERTGNIMPGI 239

Query: 243 VPYQDFPTADGDFILTVGNDGQ--FRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLI 300
            P     T DG F+ T+G +G   F++     G+   A DP  A N  R   R  +  LI
Sbjct: 240 TPSNTHKTRDGKFV-TIGANGDAIFQRLMRALGREDLATDPGLADNAGRDGRRDEVYALI 298

Query: 301 RQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGL--AMELPHLLAGKVPQV 358
                    AE + +LE A VP   +  +A +FADPQ  AR +  +  LP     KVP +
Sbjct: 299 DAWVAGLDEAELLAKLEAAEVPASRVYSVADMFADPQFLAREMIQSARLPDGKDFKVPGI 358

Query: 359 ASPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
               +LS TP       P LGEHT  VL R LG D  A+ A REAG +
Sbjct: 359 VP--KLSATPGGTEWLGPGLGEHTEAVLTR-LGYDAEAIAALREAGAI 403


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: 444
Number of extensions: 19
Number of successful extensions: 7
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: 403
Length adjustment: 31
Effective length of query: 375
Effective length of database: 372
Effective search space:   139500
Effective search space used:   139500
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