GapMind for catabolism of small carbon sources

 

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

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__Cola:Echvi_0535
          Length = 514

 Score =  172 bits (437), Expect = 2e-47
 Identities = 136/465 (29%), Positives = 214/465 (46%), Gaps = 24/465 (5%)

Query: 22  SSSPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFD 81
           S SP++   + KV    R   +  +  A+ A K AW ++   QR EV+  +  GI  R  
Sbjct: 39  SYSPVDGKELGKVQMTTRESYEKVLDQAEKAFK-AWRKVPAPQRGEVVRQI--GIELRNK 95

Query: 82  DFLAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVK---NVPTEFFEMPT-PDGVGAIN 137
             L       GK +S         G    +   D+      +  + + +    +      
Sbjct: 96  KSLL------GKLVSYEMGKSYQEGLGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRM 149

Query: 138 YAVRRPVGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAA----LLGEVM 193
           Y    P+G+VGVI  +N P+ + +W    A  CG+  V KPSE+TP T+     +  +V 
Sbjct: 150 YEQWHPLGIVGVISAFNFPVAVWSWNTMIAWVCGDVCVWKPSEKTPLTSVACQLIAADVF 209

Query: 194 NTAGVPPGVYNVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLE 253
           N  G P G+ +++ G G N  G FLT  P V  I+ TG T  G+++ +        V LE
Sbjct: 210 NRNGFPEGITSLLIG-GAN-VGAFLTQDPRVALISATGSTQMGKSVGETVGGRLGKVLLE 267

Query: 254 LGGKNAAIVFADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEG 313
           LGG NA I+    DLD AI G L       GQ C  T R+ +   +F+    R+      
Sbjct: 268 LGGNNAIIITEHADLDIAIRGALFGAVGTAGQRCTSTRRLIIHESVFEEVKERMVAAYSK 327

Query: 314 MQLGRPEDLATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQP 373
           + +G P D    +GPLI ++  +  L+  ++    G   V  GG+ E  E +  G +V+P
Sbjct: 328 LTIGNPLDEDNIVGPLIDKDAVQNYLTAIERVKAEGGKEVVAGGLLEGEEYV-SGCYVRP 386

Query: 374 TIWTGLGDDSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVA 433
           +++       +V ++E FGP   +M +   +E I   N+   GL+  I TTN+  A R  
Sbjct: 387 SVFEAENHFQIV-QKETFGPILYLMKYSEFDEAIAMQNNVPQGLSSAIMTTNMREAERYL 445

Query: 434 GA--IEVGIAWVN-SWFLRDLRTAFGGSKQSGIGREGGVHSLEFY 475
            +   + GI+ VN      ++  AFGG K++G GRE G  + + Y
Sbjct: 446 SSEGSDCGISNVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAY 490


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: 608
Number of extensions: 27
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: 485
Length of database: 514
Length adjustment: 34
Effective length of query: 451
Effective length of database: 480
Effective search space:   216480
Effective search space used:   216480
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 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