GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Pontibacter ramchanderi LP43

Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_101443608.1 BD749_RS04195 amidohydrolase

Query= predicted:W3Y6L2
         (394 letters)



>NCBI__GCF_002846395.1:WP_101443608.1
          Length = 371

 Score =  251 bits (642), Expect = 2e-71
 Identities = 151/376 (40%), Positives = 211/376 (56%), Gaps = 7/376 (1%)

Query: 20  VAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIPFKADVYKYAVIGEIKGAFDGPVVGLR 79
           + WRRHIH HPE+S EE++TS +++ VL+ L         K ++IG +KGA  G  V  R
Sbjct: 1   MTWRRHIHQHPEVSFEEEQTSKYVEEVLSKLPNVEVIKPAKTSLIGVLKGAKPGRTVAFR 60

Query: 80  ADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAAAILQSVKDQLHGTVKLVIQP 139
           ADMDALPI E TGLP+ S+   V HACGHD+H A+LL  AA L  ++ +L GTV  + Q 
Sbjct: 61  ADMDALPIQEETGLPYASKEKNVSHACGHDAHTAMLLATAATLSKMQQELKGTVYFIFQH 120

Query: 140 AEEEALIKGAQGIVDSGVLDDVDEIYGLHVWPQLPVGTVG-LKKGNLMAASDRFLVHIKG 198
           AEE+    GA  IV+SG L  V+  +G+HV P  P G VG L  G    A D F ++I G
Sbjct: 121 AEEQP-PGGAIDIVESGELKGVEAFFGMHVLPNFPAGHVGILPDGAASTAQDIFNLNIIG 179

Query: 199 KATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNLVCTIGVFNSGDRYNVGSGDAY 258
           K +HG+ PH GID IV  A  +  ++++V+R   P +  V TIG F SGD +NV +  A 
Sbjct: 180 KGSHGSMPHLGIDPIVVGAAIVSALQTVVSRNVEPGEMTVVTIGKFQSGDAFNVIADRAE 239

Query: 259 LEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEYRRGHGATINDADAIDYVTHIV 318
           L  + RT     R  +E+R+ E ++++   +G T  L+Y   + A  ND      V    
Sbjct: 240 LAASIRTTSDKTRKQVEQRVKEIIESITKAYGATYELDYINTYPAIQNDKALNAQVRKSA 299

Query: 319 KTYLGKDAVVHPEFPSM-AAEDFSAYLNKIKGAFLWLGTGFEGNPALHNAAFTIDESILE 377
              LGK+ V   + P M A+EDF+ Y      +F+ LG G    PA HN  F +DES L+
Sbjct: 300 AAILGKEQVF--DAPMMTASEDFAYYRKIAPVSFMTLGIG--DGPANHNPGFKVDESALQ 355

Query: 378 PGITMMAGIAAELLQE 393
            G+     +  + L +
Sbjct: 356 NGVKAQVQLILDYLNK 371


Lambda     K      H
   0.318    0.136    0.401 

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: 392
Number of extensions: 17
Number of successful extensions: 5
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: 394
Length of database: 371
Length adjustment: 30
Effective length of query: 364
Effective length of database: 341
Effective search space:   124124
Effective search space used:   124124
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: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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