GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG 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= BRENDA::P80358
         (340 letters)



>NCBI__GCF_001294205.1:WP_053935843.1
          Length = 338

 Score =  341 bits (875), Expect = 1e-98
 Identities = 178/338 (52%), Positives = 231/338 (68%), Gaps = 2/338 (0%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERGDADYLFV 60
           M +R +  +DL  L+ LA++ G G+TTL A+ QRL  R++ + ++  G  +  DA Y FV
Sbjct: 1   MRIRFLQDSDLDGLLALAQAAGVGVTTLSADPQRLAARIAASTQSVEGSPDLADASYFFV 60

Query: 61  LEDDA-GKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNSE 119
           LED+  G +VG S I  A+G+ + WYNYRVGL V AS+EL I++++ TLFL +DLTG SE
Sbjct: 61  LEDETTGTLVGTSGIEAAIGMHDTWYNYRVGLAVHASRELEIYKQLTTLFLNSDLTGASE 120

Query: 120 LCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLGR 179
           LCSLFL  D R   NG LLSR RFLF+AEF   F +++IAEMRG+SDE GRSPFWESLGR
Sbjct: 121 LCSLFLLPDWRKDGNGSLLSRCRFLFMAEFPERFSERVIAEMRGVSDENGRSPFWESLGR 180

Query: 180 HFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLKA 239
           HFFKM+F++AD+L+ VG+K+FIAELMP +P+YTC LSEEA+  IG VHP T PA  +L+ 
Sbjct: 181 HFFKMDFARADFLSYVGDKSFIAELMPSYPIYTCLLSEEAQAAIGEVHPGTRPARKLLEG 240

Query: 240 EGFSYQGYVDIFDAGPAIEAETDKIRAIAESQ-NLVLAVGTPGDDAEPYLIHNRKREDCR 298
           EGF Y GYVDIFDAGP++E+    IRAI +S+    LAV        P+L+ NRK    +
Sbjct: 241 EGFRYSGYVDIFDAGPSLESPLKDIRAIRDSRLYQALAVNAEPKGGVPWLVSNRKLGSFK 300

Query: 299 ITAAPARAAAGTLVVDPLTAKRLRLSAGASVRAVPLSA 336
              A  R    +L +      RL +  G  VRAVPLSA
Sbjct: 301 CALAQTRPLEDSLPLTAAVLARLDIEDGDVVRAVPLSA 338


Lambda     K      H
   0.320    0.136    0.398 

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: 339
Number of extensions: 12
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: 340
Length of database: 338
Length adjustment: 28
Effective length of query: 312
Effective length of database: 310
Effective search space:    96720
Effective search space used:    96720
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