GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Dechlorosoma suillum PS

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate Dsui_0105 Dsui_0105 NAD-dependent aldehyde dehydrogenase

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__PS:Dsui_0105
          Length = 476

 Score =  279 bits (713), Expect = 2e-79
 Identities = 170/458 (37%), Positives = 243/458 (53%), Gaps = 13/458 (2%)

Query: 24  SPLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           +P    VIA+V E    + D A  AA AA   AW  +S A+R   L  +ADG+  R D+ 
Sbjct: 26  NPATETVIARVPEGTATDADRAARAAAAAFP-AWAALSGAERGAFLQKIADGLKARQDEL 84

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
                 + G P+ LA  V        F   A +      E       + +G  +  ++ P
Sbjct: 85  GRLIASEVGMPVKLATRVQAGNPIFTFAACARIAAEGFAE-------ERIGQ-SLVLKVP 136

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
            G V  I PWN PL  +  KVG ALA G TVV+KPSE  P  A LL EV+  AG+P GV+
Sbjct: 137 TGPVACITPWNFPLHQIAAKVGAALAAGCTVVLKPSEVAPLNAFLLAEVIEAAGLPAGVF 196

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVF 263
           N+V G+GP   GE L +HP + A++FTG T  G+ +   AA   + VSLELGGK+A++V 
Sbjct: 197 NLVTGYGP-VVGEALAAHPALAAVSFTGSTAAGKRVAAVAAATVKRVSLELGGKSASVVL 255

Query: 264 ADCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLA 323
            D DL  A++GT+  CF N GQ C    R+ V +  +    +   + A    LG P    
Sbjct: 256 PDADLAAAVKGTVAGCFLNSGQACSALTRLLVPQERYAEAAALAVQAAAAYTLGDPLAEG 315

Query: 324 TGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDS 383
           + +GPL+S   R++V +  ++AV  GA ++ GG     PE L  G +V+PT++  +  D+
Sbjct: 316 SRLGPLVSGLQRQRVRAMIEQAVADGAELLCGGSA--APEGLPTGYYVRPTVFGRVRPDA 373

Query: 384 VVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWV 443
            +AREE+FGP   ++ +  E E    AN  DYGLA  +W+   +RA   A  +  G   +
Sbjct: 374 ALAREEVFGPVLAILTYRDEAEAEAIANGTDYGLAAAVWSAEEARALAFARRLRAGQVDI 433

Query: 444 NSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNV 481
           N  F  +L   FGG KQSG GRE G H +E + E +++
Sbjct: 434 NGAFF-NLLAPFGGFKQSGYGRELGRHGVEDFLETQSI 470


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: 553
Number of extensions: 37
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: 476
Length adjustment: 34
Effective length of query: 451
Effective length of database: 442
Effective search space:   199342
Effective search space used:   199342
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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