GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Sphingomonas koreensis DSMZ 15582

Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate Ga0059261_3317 Ga0059261_3317 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs

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



>FitnessBrowser__Korea:Ga0059261_3317
          Length = 486

 Score =  156 bits (395), Expect = 1e-42
 Identities = 112/372 (30%), Positives = 180/372 (48%), Gaps = 13/372 (3%)

Query: 30  LKVTEKPGIISLAGGLPSPKTFPVSAFAAA--SAAVLANDGPAALQYAASEGYAPLRQAI 87
           L +   PG+  L  G P  + FP    A A  SAA  A+      QY    G   LR++I
Sbjct: 120 LALPSGPGL-KLDEGAPDGRLFPADLLARAYRSAAHRASR-ENRFQYGNPRGTPALRESI 177

Query: 88  ADFLPWD----VDADQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGALQAFTPMEP 143
           A  L       V A+ I IT GSQ  + L A+VL+     V+VE  TY  A+ AF  +  
Sbjct: 178 ATMLKSQRGLPVTAENICITRGSQNGIFLAAQVLVRPGDTVIVEALTYEPAVAAFRALGA 237

Query: 144 SVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRAALVKAAAEL 203
           ++VAV  D++G+ ID ++      A +A  ++V P+ Q PT  ++   RR  L++ + + 
Sbjct: 238 NIVAVGLDEDGIDIDAVEHACRRNAVRA--VFVTPHHQFPTTVSLRPERRLRLLELSHQF 295

Query: 204 NLPLVEDNPYGDLWFDNPPPAPLTARNPEGCIYMGSFSKVLAPGLRLGFVVAPKAVYPKL 263
              ++ED+   +  F++ P  P+    P   IY+GS SK+L P LR+G+V AP  V   +
Sbjct: 296 GFAIIEDDYDHEFHFESQPLLPMAGYGPGHVIYVGSMSKLLLPALRIGYVAAPPPVIDAI 355

Query: 264 LQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAALTQEMAGLGVE 323
                  D       +   AE+++   L RH   +R +Y ++ E   A + + +  + V+
Sbjct: 356 AHMVSLTDGMGNALTEDAAAELIENGELRRHARKVRQVYAKRRENFAAEIDRTLGDI-VD 414

Query: 324 WNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVPGAAFYADNADPRTLRLSFVTSTVE 383
           +  PDGG+  W+R    + A+E   +A    + F    +F   +  PR LR+ F +    
Sbjct: 415 YKMPDGGLAFWLRFHTDLDAME--ARAAAMGLRFAASRSFMTRDDAPRGLRIGFASLNEH 472

Query: 384 QIATGIAALAAA 395
           +  T +AAL  A
Sbjct: 473 EAKTAVAALREA 484


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: 402
Number of extensions: 23
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: 401
Length of database: 486
Length adjustment: 32
Effective length of query: 369
Effective length of database: 454
Effective search space:   167526
Effective search space used:   167526
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: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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