GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aruG in Shewanella loihica PV-4

Align arginine N-succinyltransferase (EC 2.3.1.109) (characterized)
to candidate 5208067 Shew_0579 arginine N-succinyltransferase (RefSeq)

Query= BRENDA::P80358
         (340 letters)



>FitnessBrowser__PV4:5208067
          Length = 339

 Score =  280 bits (715), Expect = 5e-80
 Identities = 147/338 (43%), Positives = 220/338 (65%), Gaps = 4/338 (1%)

Query: 1   MIVRPVTSADLPALIELARSTGTGLTTLPANEQRLQHRVSWAEKAFRGEAERG-DADYLF 59
           +I+RP+ S+D  AL ++A  +G G T+LP NE+ L+++++  E +F  E E+  D  YL 
Sbjct: 2   LIIRPIRSSDFDALYQIAIESGHGFTSLPVNEELLRNKIARVEASFVKEIEKPFDEGYLM 61

Query: 60  VLED-DAGKVVGISAIAGAVGLREPWYNYRVGLTVSASQELNIHREIPTLFLANDLTGNS 118
           VLED + G+VVG   +  AVG+ + +Y+YR+G  V  S+++++  E+ TL L +D TG +
Sbjct: 62  VLEDTETGEVVGTCGLEAAVGMVDAFYHYRLGTEVYYSEQIDVRNEVETLTLCHDYTGAA 121

Query: 119 ELCSLFLHADHRSGLNGKLLSRARFLFIAEFRHLFGDKLIAEMRGMSDEEGRSPFWESLG 178
           ELC+LFL   +R   NG++LSR+RFLF+A+    FGD +IAEMRG SD EG SPF+  L 
Sbjct: 122 ELCTLFLRDTYRKNNNGRMLSRSRFLFLAQHAERFGDTVIAEMRGESDAEGNSPFYGWLQ 181

Query: 179 RHFFKMEFSQADYLTGVGNKAFIAELMPKFPLYTCFLSEEARGVIGRVHPNTEPALAMLK 238
           ++F  ++F QADYL+G+G KAF+AE+MPK  +Y C L EEA+ VIG VH NT PAL +L+
Sbjct: 182 KNFLGIDFVQADYLSGLGQKAFMAEMMPKNSVYVCLLPEEAQKVIGEVHTNTRPALNLLQ 241

Query: 239 AEGFSYQGYVDIFDAGPAIEAETDKIRAIAESQNLVLAVGTPGDDAEPYLIHNRKREDCR 298
           AEGF  +GYVDIFD GP +E   + IR++ ES+ L + VG     +  ++I N      R
Sbjct: 242 AEGFRCRGYVDIFDGGPTVECNLNDIRSVRESRLLTVKVGEMPVSSSSFIISNTLLAGYR 301

Query: 299 ITAAPARAAAGT--LVVDPLTAKRLRLSAGASVRAVPL 334
            T+A    +  T  +++ P  A  L ++ G  +R + +
Sbjct: 302 ATSANLMVSDETDEVILSPELAGALLVAEGEQIRVLAM 339


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: 288
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: 339
Length adjustment: 28
Effective length of query: 312
Effective length of database: 311
Effective search space:    97032
Effective search space used:    97032
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 17 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