GapMind for catabolism of small carbon sources

 

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

Align branched-chain amino acid aminotransferase subunit (EC 2.6.1.6; EC 2.6.1.42) (characterized)
to candidate Echvi_0009 Echvi_0009 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase

Query= metacyc::MONOMER-11904
         (286 letters)



>FitnessBrowser__Cola:Echvi_0009
          Length = 273

 Score =  111 bits (277), Expect = 2e-29
 Identities = 84/273 (30%), Positives = 143/273 (52%), Gaps = 18/273 (6%)

Query: 10  VEKEQAKISVYDHGLLYGDGVFEGIRVYDGVIFKLKEHIDRLFDSATSLQMDIQTSKDEI 69
           +  E A +   D GL+ G  VF+  R  D     L++++DR   SA    + +    +E+
Sbjct: 12  IPSEDASLHPLDIGLIRGYAVFDFFRTVDYHPLFLEDYLDRFIASAAKAHLVLDQGHEEL 71

Query: 70  SKIVIDTIRINELNNAYIRLVITRGVGDLGLDPRKCPKPTIFCIAEPM-NPLLGEDGIKV 128
             IV++ I+ N+L    IR+V++ G  D    P K     IFC A  M +     +G+ +
Sbjct: 72  KSIVLELIQKNDLKQGGIRMVLSGGNSDNHFSPTK-GSLFIFCEALQMPSDDKYRNGVHL 130

Query: 129 ITSSIRRLPVDVLNPAVKSLNY-LNSILAK-IQANYAGCDEAFLLDSEGYVAEGTGDNIF 186
           +T+   R PV    P +K+ NY L   L+K  +AN A   E  L  ++G ++E +  NIF
Sbjct: 131 LTTEYIR-PV----PEIKTTNYALPVYLSKDWKANNA---EDVLYHADGIISESSRSNIF 182

Query: 187 VIKNGKIKTPPVSSSVLKGITRDAVVDLAKEQGYEIIEEKLTLHDLYVADELFITGTAAE 246
           ++K+G I TP   +++LKGITR  ++ L  +         +TL ++  ADE+F++ T   
Sbjct: 183 IVKDGTISTP--KTNILKGITRKNILALVPDAQI----RDITLEEVMAADEVFMSSTTKR 236

Query: 247 LAHVVEIDGRVINNREMGVITKKLSEEFKKIRK 279
           +  + +ID + I+N  +G  T  L E+FK++ +
Sbjct: 237 ILPITKIDHQPISNGAVGTRTTALMEQFKRMEE 269


Lambda     K      H
   0.319    0.140    0.390 

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: 180
Number of extensions: 11
Number of successful extensions: 3
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: 286
Length of database: 273
Length adjustment: 26
Effective length of query: 260
Effective length of database: 247
Effective search space:    64220
Effective search space used:    64220
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: 47 (22.7 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