GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galactonolactonase in Echinicola vietnamensis KMM 6221, DSM 17526

Align D-galactono-lactonase (EC 3.1.1.-) (characterized)
to candidate Echvi_3728 Echvi_3728 3-carboxymuconate cyclase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3314
         (389 letters)



>FitnessBrowser__Cola:Echvi_3728
          Length = 392

 Score =  220 bits (561), Expect = 5e-62
 Identities = 132/353 (37%), Positives = 194/353 (54%), Gaps = 13/353 (3%)

Query: 30  VGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKSANPSWLTLSKDQRHLFVVNENGPGQT 89
           +G+YT+  S G + + +   T   D S L      NPS++  +  +  +F V E G G+ 
Sbjct: 43  LGTYTSKPSDGFHLIQYHPETSTFD-SVLMESDINNPSFVISNLKRDLVFTVQEEG-GEN 100

Query: 90  DPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSLSIDGSHLFVSNYSVAEDPGGTLAV 149
              G V SF  D   ++L  +S   S G+ P + +LS D   +F  NY       G LAV
Sbjct: 101 G--GSVCSFRFDRSANSLKKLSTSASQGSGPCYITLSPDEKFIFAGNYG-----SGDLAV 153

Query: 150 LPVAADGKLKAVVQMSSHPASRVNPERQASAHVHSTIPSPDGRYVFANDLGADKVFAYRF 209
           LP+  DG L   VQ   H  S VN  RQ+S HVHS +  P+G+ +F  DLG DKV  Y +
Sbjct: 154 LPINEDGTLGEAVQTIQHTGSSVNEGRQSSPHVHSLVFHPNGKQLFVADLGTDKVSIYNY 213

Query: 210 DPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGKHAWLTMEMSAQVAVFDYHDGQLEQ 269
           DP      PLT ++PA   +  GSGPRHL F+  G   +L  E++++V ++DY+  + + 
Sbjct: 214 DPDRKE--PLTASSPASFTVKAGSGPRHLAFNQSGDKIYLIHEITSEVGLYDYNLDENKI 271

Query: 270 TQMVDLAAGQP--VSDKAAAALHASADGKFLYVSNRGTANQLLVFAIDPATGHLSELQRR 327
           T +   A        +K AA +  S DG+FLY SNRG +N+++VF+I+  TG L ++Q  
Sbjct: 272 THLDSYALTPQGFEGEKGAAEIKISDDGQFLYASNRGDSNEIIVFSINAQTGTLDKIQAI 331

Query: 328 AVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDARTGLLGKTVQKLPMDAP 380
           +  G  PR F+L P G FL + NQ S+ I+  ER+ R+G++ KT  KLP+  P
Sbjct: 332 SSGGKTPRNFALSPDGTFLFVGNQNSDSILAYERNPRSGIIKKTNAKLPIHRP 384



 Score = 29.6 bits (65), Expect = 2e-04
 Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 7/83 (8%)

Query: 4   LWPLLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKS 63
           L P    G  GA  ++++  +D Q L  S   G S  I   + +++TG +D   +Q I S
Sbjct: 279 LTPQGFEGEKGAAEIKIS--DDGQFLYAS-NRGDSNEIIVFSINAQTGTLDK--IQAISS 333

Query: 64  AN--PSWLTLSKDQRHLFVVNEN 84
               P    LS D   LFV N+N
Sbjct: 334 GGKTPRNFALSPDGTFLFVGNQN 356


Lambda     K      H
   0.316    0.132    0.382 

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: 428
Number of extensions: 30
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 389
Length of database: 392
Length adjustment: 31
Effective length of query: 358
Effective length of database: 361
Effective search space:   129238
Effective search space used:   129238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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