GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruF in Amantichitinum ursilacus IGB-41

Align arginine N-succinyltransferase; EC 2.3.1.109 (characterized)
to candidate WP_053935843.1 WG78_RS00585 arginine N-succinyltransferase

Query= CharProtDB::CH_107315
         (338 letters)



>NCBI__GCF_001294205.1:WP_053935843.1
          Length = 338

 Score =  223 bits (569), Expect = 4e-63
 Identities = 136/338 (40%), Positives = 194/338 (57%), Gaps = 11/338 (3%)

Query: 4   MRPAQAADLPQVQRLAADSPVGVTSLPDDAERLRDKILASEASFAAEVSYNGEESYFFVL 63
           +R  Q +DL  +  LA  + VGVT+L  D +RL  +I AS  S         + SYFFVL
Sbjct: 3   IRFLQDSDLDGLLALAQAAGVGVTTLSADPQRLAARIAASTQSVEGSPDL-ADASYFFVL 61

Query: 64  EDSASGELVGCSAIVASAGFSEPFYSFRNETFVHASRSLSIHNKIHVLSLCHDLTGNSLL 123
           ED  +G LVG S I A+ G  + +Y++R    VHASR L I+ ++  L L  DLTG S L
Sbjct: 62  EDETTGTLVGTSGIEAAIGMHDTWYNYRVGLAVHASRELEIYKQLTTLFLNSDLTGASEL 121

Query: 124 TSFYVQRDLVQSVYAELNSRGRLLFMASHPERFADAVVVEIVGYSDEQGESPFWNAVGRN 183
            S ++  D  +     L SR R LFMA  PERF++ V+ E+ G SDE G SPFW ++GR+
Sbjct: 122 CSLFLLPDWRKDGNGSLLSRCRFLFMAEFPERFSERVIAEMRGVSDENGRSPFWESLGRH 181

Query: 184 FFDLNYIEAEKLSGLKSRTFLAELMPHYPIYVPLLPDAAQESMGQVHPRAQITFDILMRE 243
           FF +++  A+ LS +  ++F+AELMP YPIY  LL + AQ ++G+VHP  +    +L  E
Sbjct: 182 FFKMDFARADFLSYVGDKSFIAELMPSYPIYTCLLSEEAQAAIGEVHPGTRPARKLLEGE 241

Query: 244 GFETDNYIDIFDGGPTLHARTSGIRSIAQSRVV-PVKIGEAPKSGRPYLVTNGQLQDFRA 302
           GF    Y+DIFD GP+L +    IR+I  SR+   + +   PK G P+LV+N +L  F+ 
Sbjct: 242 GFRYSGYVDIFDAGPSLESPLKDIRAIRDSRLYQALAVNAEPKGGVPWLVSNRKLGSFKC 301

Query: 303 VVLDLDWAPGKPVALSVEAAEA----LGVGEGASVRLV 336
            +     A  +P+  S+    A    L + +G  VR V
Sbjct: 302 AL-----AQTRPLEDSLPLTAAVLARLDIEDGDVVRAV 334


Lambda     K      H
   0.319    0.135    0.387 

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: 282
Number of extensions: 13
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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 (21.8 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