GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argX in Shewanella sp. ANA-3

Align Glutamate--LysW ligase ArgX; EC 6.3.2.- (characterized)
to candidate 7025111 Shewana3_2274 SSU ribosomal protein S6P modification protein (RefSeq)

Query= SwissProt::Q970U6
         (282 letters)



>FitnessBrowser__ANA3:7025111
          Length = 299

 Score = 89.4 bits (220), Expect = 9e-23
 Identities = 74/239 (30%), Positives = 119/239 (49%), Gaps = 12/239 (5%)

Query: 50  AIIRPVSMYRALYSSAVL---EAAGVHTINSSDVINVCGDKILTYSKLYREGIPIPDSII 106
           A+I  +      Y SAVL   E  GV+ +N S  I+   DK+ +   + R GI +P +  
Sbjct: 60  AVIPRIGASITFYGSAVLRQFEMMGVYALNDSVGISRSRDKLRSMQLMSRRGIGLPITGF 119

Query: 107 ALSAEAALKAYEQ-RGFPLIDKPPIGSWGRLVSLIRDVFEGKTIIEHRELMGNSALKAHI 165
           A          +   G PL+ K   G+ G  V L       +++IE    MG   LKA+I
Sbjct: 120 ANKPSDIPDLIDMVGGAPLVIKLLEGTQGIGVVLAETRKAAESVIE--AFMG---LKANI 174

Query: 166 -VQEYI-QYKGRDIRCIAIGEELLGCYARNIPPNEWRANVALGGTPSNIEVDEKLKETVV 223
            VQEYI +  G DIRC  +G++++    R   P E+R+N+  GGT S +++  + +   +
Sbjct: 175 MVQEYIKEANGADIRCFVLGDKVIAAMKRQAMPGEFRSNLHRGGTASLVKLTPEERSVAI 234

Query: 224 KAVSIVHGEFVSIDILEHPNKGYVVNELNDVPEFKGFMVATNINVAQKLVEYIKENYSK 282
           +A   +      +D+L   N G VV E+N  P  +G   AT  +VA  ++E++++N  K
Sbjct: 235 RAAKTMGLNVAGVDLL-RSNHGPVVMEVNSSPGLEGIEGATAKDVAGAIIEFVEKNALK 292


Lambda     K      H
   0.319    0.137    0.392 

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: 194
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: 282
Length of database: 299
Length adjustment: 26
Effective length of query: 256
Effective length of database: 273
Effective search space:    69888
Effective search space used:    69888
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 (21.7 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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