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_101443903.1 BD749_RS08100 amidohydrolase

Query= predicted:W3Y6L2
         (394 letters)



>NCBI__GCF_002846395.1:WP_101443903.1
          Length = 443

 Score =  226 bits (575), Expect = 1e-63
 Identities = 143/403 (35%), Positives = 214/403 (53%), Gaps = 21/403 (5%)

Query: 12  ASQYKEQVVAWRRHIHSHPELSGEEKETSAFIQSVLTDLGIPFKADVYKYAVIGEIKGAF 71
           A + + +V+ WRR  H +PEL   E +T+  I + L  LG+  +  V    V+G +KG  
Sbjct: 39  ADKLEPKVIEWRRDFHQYPELGNRETKTAEKIAAHLRKLGMEVQTGVAHTGVVGILKGGK 98

Query: 72  DGPVVGLRADMDALPITEVTGLPFTS--------ENPGVMHACGHDSHMAILLGAAAILQ 123
            GPVV LRAD+D LP+TE   LPF S        +  GVMHACGHD+H+A+L+GAA IL 
Sbjct: 99  PGPVVALRADIDGLPVTERVDLPFASKERSTYNGQEVGVMHACGHDTHIAMLMGAAEILA 158

Query: 124 SVKDQLHGTVKLVIQPAEEEALI---KGAQGIVDSGVL---DDVDEIYGLHVWPQLPVGT 177
            +K+ L GTVK + QPAEE + I    GA  +V  GVL      + I+GLH+  Q  VGT
Sbjct: 159 GMKNDLKGTVKFIFQPAEEGSPIGEEGGAALMVKEGVLGKGPKPEVIFGLHINSQTEVGT 218

Query: 178 VGLKKGNLMAASDRFLVHIKGKATHGAEPHNGIDAIVAAANWIVNVESMVARETN-PMDN 236
           +    G  MA++D F + +KGK +HGA P +GID IV +A  I  ++++++R+T  P   
Sbjct: 219 IKYTPGGTMASADIFRIKVKGKQSHGAYPWSGIDPIVVSAQIINGLQTIISRQTQLPEGA 278

Query: 237 LVCTIGVFNSGDRYNVGSGDAYLEGTCRTYDPAKRDYIERRLGESLKALDMMFGTTSTLE 296
            V T+G  + G R N+   +  +EGT R  D   +  +  ++  +   +    G  + + 
Sbjct: 279 AVITVGSIHGGVRNNIIPEEVLMEGTIRALDVEMQKKLHEKINLTATKIAESSGAVAEVV 338

Query: 297 YRRGHGATINDADAIDYVTHIVKTYLGKDAVVHPEFPSMAAEDFSAYLNKIKGAFLWLGT 356
                  T ND    + +   + T  G+D VV  +  +  AEDF+ Y  KI G FL++G 
Sbjct: 339 IIPQTPVTYNDPALTERMLPTLHTVAGRDKVVLAKAVT-GAEDFAFYQEKIPGLFLFVGG 397

Query: 357 GFEGN-----PALHNAAFTIDESILEPGITMMAGIAAELLQEK 394
             +G         H   F IDES L+ G+  +  +    ++ K
Sbjct: 398 MSKGKKPEEVAPHHTPDFFIDESGLKLGVKTLTSLTLNYMEGK 440


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: 442
Number of extensions: 26
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: 443
Length adjustment: 32
Effective length of query: 362
Effective length of database: 411
Effective search space:   148782
Effective search space used:   148782
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