GapMind for catabolism of small carbon sources

 

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

Align 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase; AONS/AKB ligase; 7-keto-8-amino-pelargonic acid synthase; 7-KAP synthase; KAPA synthase; 8-amino-7-ketopelargonate synthase; Alpha-oxoamine synthase; Glycine acetyltransferase; EC 2.3.1.29; EC 2.3.1.47 (characterized)
to candidate Echvi_3961 Echvi_3961 7-keto-8-aminopelargonate synthetase and related enzymes

Query= SwissProt::Q5SHZ8
         (395 letters)



>FitnessBrowser__Cola:Echvi_3961
          Length = 416

 Score =  206 bits (525), Expect = 8e-58
 Identities = 135/381 (35%), Positives = 202/381 (53%), Gaps = 10/381 (2%)

Query: 19  EGLYISPKVLEAPQEPVTRVEGREVVNLASNNYLGFANHPYLKEKARQYLEKWGAGSG-A 77
           EG ++ PK LE    P  + +G EV+  + NNYLG ANHP +++   +  ++WGA     
Sbjct: 22  EGYFMFPK-LEGEIAPRMKFKGEEVLTWSLNNYLGLANHPEIRKADAEAAKRWGAAYPMG 80

Query: 78  VRTIAGTFTYHVELEEALARFKGTESALVLQSGFTANQGVLGALLKEGDVVFSDELNHAS 137
            R ++G    H +LE  LA F G E A +L  G+     V+ +L+   DV+  D   HAS
Sbjct: 81  ARMMSGNTDMHEQLENELAAFVGKEKAYLLNYGYQGIMSVIDSLVDRKDVIVYDSECHAS 140

Query: 138 IIDGLRLTKATRLVFRHADVAHLE-ELLKA----HDTDGLKLIVTDGVFSMDGDIAPLDK 192
           IIDGLR+    R V+ H D+   E +L++A    ++T G  L++T+GVF M G++  L  
Sbjct: 141 IIDGLRMHMGKRFVYPHNDMESFEKQLIRAEKLTNETGGGILVITEGVFGMTGNMGDLKG 200

Query: 193 IVPLAKKYKAVVYVDDAHGSGVLGEKGKGTVHHFGFHQDPDVVQVATLSKAWAGIGGYAA 252
           IV   +KY+  + VDDAHG G +G  G G     G  QD   +  +T +K+ AGIG + A
Sbjct: 201 IVKYKEKYQFRLVVDDAHGFGTMGPTGAGAGEAQGV-QDQVDLYFSTFAKSMAGIGAFVA 259

Query: 253 GARELKDLLINKARPFLFSTSHPPAVVGALLGALELIEKEPERVERLWENTRYFKRELAR 312
           G  ++   L    R  +F+ + P   V   L  LE+I + P+  ERLWE     +  L  
Sbjct: 260 GDTKVVHYLKYNMRSQIFAKALPMIFVEGALKRLEMIRENPKHKERLWEVVNALQNGLKE 319

Query: 313 LGYDTLGSQTPITP-VLFGEAPLAFEASRLLLEE-GVFAVGIGFPTVPRGKARIRNIVTA 370
            G+    + TP+TP VL G    A   S+ L E   +F   + +P VP+G   +R I TA
Sbjct: 320 KGFSIGTTTTPVTPVVLNGTVGEAATLSKDLRENYNIFCSVVIYPVVPKGMIILRLIPTA 379

Query: 371 AHTKEMLDKALEAYEKVGKRL 391
           AHT E + + + A+E +  +L
Sbjct: 380 AHTLEDVSETIIAFEAIKDKL 400


Lambda     K      H
   0.319    0.137    0.394 

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: 367
Number of extensions: 18
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: 395
Length of database: 416
Length adjustment: 31
Effective length of query: 364
Effective length of database: 385
Effective search space:   140140
Effective search space used:   140140
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 (21.7 bits)
S2: 50 (23.9 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