GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ilvE in Limnohabitans curvus MWH-C5

Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_108402496.1 B9Z44_RS11585 PLP-dependent aminotransferase family protein

Query= reanno::acidovorax_3H11:Ac3H11_1358
         (401 letters)



>NCBI__GCF_003063475.1:WP_108402496.1
          Length = 396

 Score =  276 bits (706), Expect = 8e-79
 Identities = 159/396 (40%), Positives = 228/396 (57%), Gaps = 17/396 (4%)

Query: 15  ARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAAVLANDGPAALQY 74
           A R   +  S IRE+ K+  KPGIIS AGG P    F V     AS   L  +  AALQY
Sbjct: 4   ADRLNNVETSAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIREASNLALTQEPGAALQY 63

Query: 75  AASEGYAPLRQAIADFLP----WDVDADQILITTGSQQALDLIAKVLIDENSRVLVETPT 130
            A+EGY PLR+ +A F+       + AD +++TTGSQQALDLIAK L++ N   LVE PT
Sbjct: 64  GATEGYQPLREQLAAFMASKGVKGLSADGLIVTTGSQQALDLIAKTLLNPNDVALVEGPT 123

Query: 131 YLGALQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTE 190
           +L  +Q F    P VV V  D  GV +D L+  +     K + +Y++P F NP+G T++ 
Sbjct: 124 FLATIQCFRLYGPQVVGVPIDAHGVQVDKLEEMI--VQHKPKLVYLIPTFGNPSGATLSL 181

Query: 191 ARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNP------EGCIYMGSFSKVL 244
            RR  +++ A +    +VED+PYGDL+F   PP  L A +       E  I+ GS SKVL
Sbjct: 182 ERRLRVLELAVKYKTVVVEDDPYGDLYFGEAPPPSLLALSDQVPGSREWLIHCGSLSKVL 241

Query: 245 APGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQ 304
           +PGLR+G+++AP  +  +    KQ +D HT  + Q   A  +K   +   +  +R++Y +
Sbjct: 242 SPGLRVGWMIAPPELLARATMCKQFSDAHTSTFAQATAAHYLKAGRMPATLAHVRSVYAE 301

Query: 305 QCEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLP----EGMSAIELLPQAVERNVAFVPG 360
           + +AM  AL +E+ G  + + +P GG+F W  L     +     EL  +A+E+ VAFVPG
Sbjct: 302 RAQAMGDALKREL-GDALTFTQPKGGLFFWANLTGVGGKLNDGAELAKRAIEKGVAFVPG 360

Query: 361 AAFYADNADPRTLRLSFVTSTVEQIATGIAALAAAI 396
           A F+A+N D   +RLSF T+ VE+I  GIA L  A+
Sbjct: 361 APFFANNPDTTAIRLSFATADVEKIKEGIARLGQAL 396


Lambda     K      H
   0.318    0.134    0.392 

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: 400
Number of extensions: 24
Number of successful extensions: 6
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: 401
Length of database: 396
Length adjustment: 31
Effective length of query: 370
Effective length of database: 365
Effective search space:   135050
Effective search space used:   135050
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 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