GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruH in Desulfoscipio geothermicus DSM 3669

Align arginine-pyruvate transaminase (EC 2.6.1.84) (characterized)
to candidate WP_092483105.1 BM299_RS08755 pyridoxal phosphate-dependent aminotransferase

Query= BRENDA::Q9HUI9
         (393 letters)



>NCBI__GCF_900115975.1:WP_092483105.1
          Length = 397

 Score =  204 bits (520), Expect = 3e-57
 Identities = 131/374 (35%), Positives = 195/374 (52%), Gaps = 13/374 (3%)

Query: 20  IHYRALARVEQGEEILLLSVGDPDFDTPAPIVQAAIDSLLAGNTHYADVRGKRALRQRIA 79
           I  +A   + +G +++    G+PDF TP  I QA + ++    T Y  V G   LR+ I 
Sbjct: 18  IDAQAKKMIAEGIKVINFGAGEPDFGTPENIKQAGVKAIENDMTRYTPVAGIEPLRRAIV 77

Query: 80  ERHRRRSGQAVDAEQVVVLAGAQCALYAVVQCLLNPGDEVIVAEPMYVTYEAVFGACGAR 139
           ++    +G   +  Q+VV AGA+ +LY   Q L   GDEVI+  P +V+Y       GAR
Sbjct: 78  KKLAEDNGLDYEPGQIVVSAGAKHSLYNAFQVLCQEGDEVILPAPYWVSYLEQIKLTGAR 137

Query: 140 VVPVPVRSENGFRVQAEEVAALITPRTRAMALNSPHNPSGASLPRATWEALAELCMAHDL 199
            V V  R EN F++  +E+   ITP TR + LNSP NP+GA        AL E+   + +
Sbjct: 138 PVIVSTRVENNFKLTPDELRRAITPNTRLIVLNSPSNPTGAVYTGDELVALGEILEQNKI 197

Query: 200 WMISDEVYSELLFDG-EHVSPASL-PGMADRTATLNSLSKSHAMTGWRVGWVVGPAALCA 257
            +ISDE+Y +L++DG EHVS A+L PG+ + T  +N +SKS+AMTGWR+G+   PA +  
Sbjct: 198 AVISDEIYEKLIYDGLEHVSIAALSPGLKELTVVINGVSKSYAMTGWRIGYAAAPAPVAK 257

Query: 258 HLENLALCMLYGSPEFIQDAACTALEAPLPELEAMREAYRRRRDLVIECLADSPGLRPLR 317
            + +L            Q A+  ALE     +  M   + +RRD ++E L   PG+   R
Sbjct: 258 AMADLQSHSTSNPTSIAQAASVEALEGTQEPVRQMVAEFVKRRDYMVERLNAMPGVNCNR 317

Query: 318 PDGGMFVMVDIRP------TGL---SAQAFADRLLDRHGVSVLAGEAFGPSAAGHIRLGL 368
           P G  +V  +I+P       G+   SA   A  LL++  V+++ G AFG       RL  
Sbjct: 318 PGGAFYVFPEIKPLLGKSYEGVKIDSASDLAKVLLEKAHVAIVPGIAFGDDTC--FRLSY 375

Query: 369 VLGAEPLREACRRI 382
               + +RE   RI
Sbjct: 376 ATSMDNIREGLDRI 389


Lambda     K      H
   0.322    0.136    0.411 

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: 404
Number of extensions: 17
Number of successful extensions: 2
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: 393
Length of database: 397
Length adjustment: 31
Effective length of query: 362
Effective length of database: 366
Effective search space:   132492
Effective search space used:   132492
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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