GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Nocardioides daejeonensis MJ31

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_110206897.1 DNK54_RS10510 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>NCBI__GCF_003194585.1:WP_110206897.1
          Length = 394

 Score =  194 bits (494), Expect = 3e-54
 Identities = 123/323 (38%), Positives = 176/323 (54%), Gaps = 5/323 (1%)

Query: 37  LSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIAERHRRRSGQAVDAE-QV 95
           L  G PD D PA +V+AA+ +L  G   YA   G R LR+ IA    R  G  +D + +V
Sbjct: 31  LGQGFPDADGPASVVEAAVSALRNGRNQYAPGIGVRELREAIARHQHRHYGLDLDPDTEV 90

Query: 96  VVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGARVVPVPVRSENGFRVQA 155
           VV  GA   + A +  L++PGDEV+V EP Y +Y A+    G    PV +R+ + +R+  
Sbjct: 91  VVTTGATEGIAAALLGLVDPGDEVVVLEPYYDSYLAMIAFAGGVRRPVTLRAPD-YRLDV 149

Query: 156 EEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDLWMISDEVYSELLFDG- 214
             + A +T RTR + LNSPHNP+G  L     +A+A+L + HDL +++DEVY  L+FDG 
Sbjct: 150 AALQAAVTDRTRVILLNSPHNPTGTVLRPEELQAIADLAIEHDLVVVTDEVYEHLVFDGH 209

Query: 215 EHVSPASLPGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCAHLENLALCMLYGSPEFI 274
            HV   +LPGM +RT TL+S  KS + TGW+VGW  GPA L   +      + + S   +
Sbjct: 210 RHVPLCTLPGMFERTVTLSSAGKSFSFTGWKVGWATGPADLVGAVLAAKQWLSFTSGSPL 269

Query: 275 QDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLRPDGGMFVMVDIRPTGL- 333
           Q A   AL+      E +    + RRDL+   LA +  L    P+G  F + D+R  G  
Sbjct: 270 QPAIAHALDHEWRAYEELAADLQLRRDLLCSGLA-ALDLDVRIPEGTYFALTDVRALGWP 328

Query: 334 SAQAFADRLLDRHGVSVLAGEAF 356
             +AF   L +R GV  +  + F
Sbjct: 329 DGRAFCLALPERAGVVAIPTQGF 351


Lambda     K      H
   0.322    0.136    0.411 

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: 426
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: 393
Length of database: 394
Length adjustment: 31
Effective length of query: 362
Effective length of database: 363
Effective search space:   131406
Effective search space used:   131406
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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