GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdh in Phyllobacterium brassicacearum STM 196

Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate WP_106714048.1 CU102_RS26410 alcohol dehydrogenase AdhP

Query= curated2:Q82MN2
         (342 letters)



>NCBI__GCF_003010955.1:WP_106714048.1
          Length = 341

 Score =  136 bits (342), Expect = 9e-37
 Identities = 103/289 (35%), Positives = 148/289 (51%), Gaps = 15/289 (5%)

Query: 3   ALVKEKAEPGLWLMDVPEPEIGPGDVLIKVLRTGICGTDLHIRSWDGWAQQAVRTPLVLG 62
           ALV+E  +P L + +VP PE GP  +L+++  TG+C TDLH    D   + AV  P + G
Sbjct: 8   ALVRELGKP-LTIEEVPIPEPGPDQILVRIAATGVCHTDLHAVRGDWPVKPAV--PFIPG 64

Query: 63  HEFVGEVVETGRDVVDIKAGDRVSGEG-HLVCGKCRNCQAGRRHLCRATVGLGVGRDGAF 121
           HE VG VV  GR V  +K GDRV     H  CG C +C+ G   LC +    G   +G+F
Sbjct: 65  HEGVGTVVGIGRSVKRVKEGDRVGIPWLHTACGYCSHCRTGWETLCGSQKNSGYSVNGSF 124

Query: 122 AEYVALPAANVWVHRVPVDLD--VAAIFDPFGNAVHTALSFPLV--GEDVLITGAGPIGL 177
           AE+    A   +V R+P  LD   AA     G  V+ AL    V  GE ++I+G G +G 
Sbjct: 125 AEFAV--ADPNYVGRLPDALDWGPAAPILCAGVTVYKALKETEVKPGEWIVISGIGGLGH 182

Query: 178 MAAAVARHAGARNVMITDVSEERLELARKIGVSLALNVADTTIADG-QRALGLREGFDIG 236
           +A   AR  G  +V   D+  ++LELA K G  + +N ++    +  QR +G   G    
Sbjct: 183 VAVQYARAMG-MHVAAVDIYPDKLELAAKFGAEIVINASEVDPGEEVQRRIGGAHG---A 238

Query: 237 LEMSGRPEAMRDMIANMTHGGRIAMLGLPSQEFPVDWARIVTSMITIKG 285
           L  +  P A     A +   G +A++GLPS +F +     V   IT++G
Sbjct: 239 LVTAVSPTAFEQAFAMLRSHGTMALVGLPSGKFAMPIFDTVLKRITVRG 287


Lambda     K      H
   0.322    0.140    0.431 

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: 321
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: 342
Length of database: 341
Length adjustment: 29
Effective length of query: 313
Effective length of database: 312
Effective search space:    97656
Effective search space used:    97656
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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