GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Nocardioides daejeonensis MJ31

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_110207793.1 DNK54_RS15005 aldehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>NCBI__GCF_003194585.1:WP_110207793.1
          Length = 501

 Score =  324 bits (830), Expect = 5e-93
 Identities = 188/463 (40%), Positives = 260/463 (56%), Gaps = 8/463 (1%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAA-LKGAWGRMSLAQRVEVLYAVADGINRRFDD 82
           SP    ++A V + G AE+DAAVAAA+AA   G W     A+R  ++ AVA  +  R ++
Sbjct: 25  SPATGELVATVAKGGAAEIDAAVAAAKAAHAAGVWRNTPPAERAALINAVAGDLAGRLEE 84

Query: 83  FLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPD--GVGAINYAV 140
             A +  + G  + +   + +    AN +  A          FE   P+   V A     
Sbjct: 85  LAALQSRENGATIRVTGALHVGLSIANMQFIAAQAAEYE---FEKAGPEIGPVPAEGILR 141

Query: 141 RRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPP 200
           R P+GVVG I PWN+PLL + WKV PALA GNTVV+KP E  P  A  L +    AG+P 
Sbjct: 142 REPLGVVGAIVPWNIPLLTIVWKVTPALAAGNTVVLKPDEHAPLLALELAKAFEAAGLPA 201

Query: 201 GVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAA 260
           GV NVV G G +  G  L+ HPDV  I FTG T  G++I+ A+AD  + V+LELGGK   
Sbjct: 202 GVLNVVVGEG-HDAGARLSQHPDVRKIGFTGSTEVGKSILGASADNMKRVTLELGGKGPN 260

Query: 261 IVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPE 320
           I+  D DLD AI+G + +C AN G+ C    R+ V     D  V RL      M++G P 
Sbjct: 261 ILLDDADLDVAIDGAIYACMANNGEACEAGTRLLVPNSRKDEIVERLVARVGTMKIGNPL 320

Query: 321 DLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLG 380
           D AT +GPLI+ + R++VL++  KA   GA V  GG  P   E    G +V+PT+ T + 
Sbjct: 321 DPATDIGPLITADQRDRVLAHIAKAETQGAKVAIGGSAP-AGEEFANGYFVEPTVLTDVT 379

Query: 381 DDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGI 440
               VA EE+FGP   V+ +D+ +E I  AND +YGL+  +W T+ +R   VA  +E G+
Sbjct: 380 PSMTVACEEVFGPVLSVLGYDTVDEAIAIANDTEYGLSAGVWGTDETRVLDVARQLEAGM 439

Query: 441 AWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCI 483
            +VN W +      FGG KQSG+GREGG ++L+ YTE K + +
Sbjct: 440 IYVNDWHVLHPAYPFGGYKQSGLGREGGPNALDAYTEQKYISV 482


Lambda     K      H
   0.318    0.135    0.406 

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: 539
Number of extensions: 20
Number of successful extensions: 5
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: 485
Length of database: 501
Length adjustment: 34
Effective length of query: 451
Effective length of database: 467
Effective search space:   210617
Effective search space used:   210617
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 (21.7 bits)
S2: 52 (24.6 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