GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argE in Marivita geojedonensis DPG-138

Align Predicted argE by GapMind curators (no experimental data)
to candidate WP_085635731.1 MGEO_RS05575 amidohydrolase

Query= predicted:W3Y6L2
         (394 letters)



>NCBI__GCF_002115805.1:WP_085635731.1
          Length = 387

 Score =  222 bits (566), Expect = 1e-62
 Identities = 128/385 (33%), Positives = 207/385 (53%), Gaps = 14/385 (3%)

Query: 8   IKQYASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIP-FKADVYKYAVIGE 66
           +K   ++ ++++ AWRR  H +PE+  E   TSA +   L + G       + +  V+G 
Sbjct: 3   VKNRFAELQDEITAWRRDFHENPEILFETHRTSALVAERLKEFGCDEIVTGIGRTGVVGV 62

Query: 67  IKGAFD--GPVVGLRADMDALPITEVTGLPFTSENPGVMHACGHDSHMAILLGAAAILQS 124
           IKG  D  G V+GLRADMDALPI E TGL + S+  G MHACGHD H A+LLGAA  L  
Sbjct: 63  IKGKSDTSGKVIGLRADMDALPIHEQTGLEYKSKTDGAMHACGHDGHTAMLLGAAKYLSE 122

Query: 125 VKDQLHGTVKLVIQPAEEEALIKGAQGIVDSGVLD--DVDEIYGLHVWPQLPVGTVGLKK 182
            ++   GTV ++ QPAEE     G + + + G+++   + E+YG+H WP  PVG+  ++ 
Sbjct: 123 TRN-FDGTVVVIFQPAEEGG--GGGREMCEDGMMERWGIQEVYGMHNWPGKPVGSFAIRP 179

Query: 183 GNLMAASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETNPMDNLVCTIG 242
           G   AA+D+F +  +G+  H A+P   +D  V AA  ++ ++++ +R  +P+D +V ++ 
Sbjct: 180 GAFFAATDQFDITFEGRGGHAAKPQETVDTTVMAAQAVLALQTIASRNADPIDQVVVSVT 239

Query: 243 VFNSGDR-YNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLEYRRGH 301
            F +  + +NV      L+GT RT     RD  E R+ +    +   FG T  + Y RG+
Sbjct: 240 SFETSSKAFNVIPQRVQLKGTVRTMSKDMRDLAETRIKDICAGIAATFGGTVDVTYHRGY 299

Query: 302 GATINDADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGTGFEGN 361
              +N  +  D+   + K   G D    P    M  EDF+  L +  GA++ +G G   +
Sbjct: 300 PVMVNHEEQTDFAAEVAKAVSG-DCEEAPLV--MGGEDFAFMLEERPGAYILVGNG--DS 354

Query: 362 PALHNAAFTIDESILEPGITMMAGI 386
            A+H+  +  ++  +  G +  A I
Sbjct: 355 AAVHHPEYNFNDEAIPAGCSWWAEI 379


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: 383
Number of extensions: 15
Number of successful extensions: 6
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: 387
Length adjustment: 31
Effective length of query: 363
Effective length of database: 356
Effective search space:   129228
Effective search space used:   129228
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