GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaB in Ruegeria conchae TW15

Align 3-carboxy-cis,cis-muconate cycloisomerase; EC 5.5.1.2; 3-carboxymuconate lactonizing enzyme; CMLE (uncharacterized)
to candidate WP_010442059.1 G7G_RS0114000 adenylosuccinate lyase

Query= curated2:O31385
         (451 letters)



>NCBI__GCF_000192475.1:WP_010442059.1
          Length = 434

 Score =  157 bits (396), Expect = 8e-43
 Identities = 124/423 (29%), Positives = 187/423 (44%), Gaps = 9/423 (2%)

Query: 9   LAPMLSSAAMRAACDDRSTLQNMLDFEAALARAEAATGVIPAAAVGPIETACKAATFDIA 68
           + P  S   M A     S  +   + EA    A A  GVIP      +  A K   FD+A
Sbjct: 1   MIPRYSRPEMVAIWSPESKFRIWYEIEAHACDAMADLGVIPRENAEAVWKA-KDVEFDVA 59

Query: 69  ALAEAATRSGNLAIPLVKALTANVAKADAEAARYVHWGATSQDVIDTATMLTLRAAIDAL 128
            + E    + +  I  +  L  +V    +E AR+VH G TS DV+DT   + L  A D L
Sbjct: 60  RIDEIEAVTKHDVIAFLTHLAEHVG---SEEARFVHQGMTSSDVLDTCLNVQLTRAADIL 116

Query: 129 DADLSRAIKGFAALARNHRNTAMVARTWLQHALPMPFGLKAAEYAASLARARCRLRRLSR 188
            +DL   +      A  H+NT  + R+   HA P   GL  A + A + R   R+R    
Sbjct: 117 ISDLEGLLAALKRRAIEHKNTIRIGRSHGIHAEPTTMGLTFARFYAEMDRNLSRMRDARA 176

Query: 189 DGLALQFGGAAGTLAALGDKGLVVAERLAQELNL-PLPEAPWHTHRDRIAEAASALAILA 247
           +       GA GT A +  +   V E +  +L L P P +     RDR A   + L ++A
Sbjct: 177 EIATGAISGAVGTFANVDPQ---VEEHVCDKLGLVPEPISTQVIPRDRHAAFFATLGVIA 233

Query: 248 GSCGKIARDVSLMMQTDVAEAFEPAGEGRGGSSTMPHKRNPVAAASALGCATMAPQLAAT 307
            S   IA ++  M +T+V E  E    G+ GSS MPHK+NPV   +  G A M       
Sbjct: 234 SSIENIAIEIRHMQRTEVLEGAEFFSMGQKGSSAMPHKKNPVLTENLTGLARMVRAAVIP 293

Query: 308 IFAAQVQDHERSAGPWHAEWPTLPQLMLVTSGALAAIVDIAEGLDVDAARMRSNLDATHG 367
                   HER       E    P   +    A A +  + + + +    M  N++   G
Sbjct: 294 AMENVALWHERDISHSSVERMIGPDATITLDFAFARLTGVIDKMLIFPENMLENMNKFPG 353

Query: 368 LIMAEAVTFALAER-IGKSDAHHLIEAASKRAVAEKKHLREVLAADSQVTAHLSPEKIAA 426
           L+M++ V  AL +  + + DA+ +++  + +    +   +E L AD+ VTA LSPE+I  
Sbjct: 354 LVMSQRVLLALTQAGVSREDAYSMVQRNALKVWEHRTDFKEELLADADVTAALSPEEIEE 413

Query: 427 LFE 429
            F+
Sbjct: 414 KFD 416


Lambda     K      H
   0.318    0.128    0.362 

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: 301
Number of extensions: 8
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: 451
Length of database: 434
Length adjustment: 32
Effective length of query: 419
Effective length of database: 402
Effective search space:   168438
Effective search space used:   168438
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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