GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ltaE in Dyella japonica UNC79MFTsu3.2

Align low-specificity L-threonine aldolase (EC 4.1.2.48) (characterized)
to candidate N515DRAFT_4398 N515DRAFT_4398 L-threonine aldolase

Query= BRENDA::P75823
         (333 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_4398 N515DRAFT_4398
           L-threonine aldolase
          Length = 340

 Score =  357 bits (917), Expect = e-103
 Identities = 188/332 (56%), Positives = 238/332 (71%), Gaps = 3/332 (0%)

Query: 2   IDLRSDTVTRPSRAMLEAMMAAPVGDDVYGDDPTVNALQDYAAELSGKEAAIFLPTGTQA 61
           +DLRSDTVT+P+RAM EAM+ A VGDDVYG+DPTVNALQ   A+  G EA +F+PTGTQ+
Sbjct: 4   VDLRSDTVTKPTRAMREAMLLAVVGDDVYGEDPTVNALQAKLADELGFEAGLFVPTGTQS 63

Query: 62  NLVALLSHCERGEEYIVGQAAHNYLFEAGGAAVLGSIQPQPIDAAADGTLPLDKVAMKIK 121
           NL+AL++HCERG+EY+VG  AH Y FE GGAAVLGSIQPQPI   ADGTLPLDK+A  IK
Sbjct: 64  NLLALMAHCERGDEYLVGADAHTYKFEGGGAAVLGSIQPQPIPHDADGTLPLDKLAAAIK 123

Query: 122 PDDIHFARTKLLSLENTHNGKVLPREYLKEAWEFTRERNLALHVDGARIFNAVVAYGCEL 181
           P D HFART+LL+LENT +G+ LP +YL  A +F RER L  H+DGAR+FNA VA G   
Sbjct: 124 PVDPHFARTRLLALENTWHGRALPLDYLHAAQKFARERGLGFHLDGARLFNAAVASGVHA 183

Query: 182 KEITQYCDSFTICLSKGLGTPVGSLLVGNRDYIKRAIRWRKMTGGGMRQSGILAAAGIYA 241
           +EI    D+ ++CLSKGLG PVGS+L+G    +++A RWRK+ GGG RQ+G+LAAA I+A
Sbjct: 184 REIAGLFDTVSVCLSKGLGAPVGSVLLGPGALVEKARRWRKVAGGGWRQAGMLAAAAIHA 243

Query: 242 LKNNVARLQEDHDNAAWMAEQLRE-AGADVMRQDTNMLFVRVGEENAAALGEYMKARNVL 300
           L ++VARL EDH  AA +A +L    G  ++   TNM+FV V       L  +++   V 
Sbjct: 244 LDHHVARLAEDHARAATLATRLGHLPGVKLLGHHTNMVFVDVPAARLRELDAHLREAQVR 303

Query: 301 INAS--PIVRLVTHLDVSREQLAEVAAHWRAF 330
           I+    P +RLVTHLDV  + L  V   + AF
Sbjct: 304 ISIGYLPTLRLVTHLDVDDDGLERVVDAFEAF 335


Lambda     K      H
   0.319    0.134    0.391 

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: 376
Number of extensions: 12
Number of successful extensions: 2
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: 333
Length of database: 340
Length adjustment: 28
Effective length of query: 305
Effective length of database: 312
Effective search space:    95160
Effective search space used:    95160
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: 49 (23.5 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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