GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Phyllobacterium endophyticum PEPV15

Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate WP_106716146.1 CU100_RS08350 glutamate--tRNA ligase

Query= metacyc::MONOMER-13959
         (483 letters)



>NCBI__GCF_003010935.1:WP_106716146.1
          Length = 457

 Score =  225 bits (573), Expect = 3e-63
 Identities = 162/486 (33%), Positives = 246/486 (50%), Gaps = 44/486 (9%)

Query: 5   VRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLK 64
           + VR+APSPTG++HIGN R ALFN+LFA    G+FI+R +DTD  R+      + +  L 
Sbjct: 3   ITVRFAPSPTGYIHIGNTRIALFNWLFALKNNGQFILRFDDTDTVRSKTEYADATIADLD 62

Query: 65  WLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIA 124
           WLGI+         EY    QS+R  +Y    E L   G+ Y CY T EELE++R+ ++A
Sbjct: 63  WLGIE-----PARIEY----QSKRIPVYDAAAERLKAAGVLYPCYETSEELERKRKLRLA 113

Query: 125 RGEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGK---------VIAFNDIVKGEI 175
           R   P Y      LT  ++EK  AEGR+P  RF +P  K          + +ND+V+   
Sbjct: 114 RRLPPIYGRDALKLTAADREKLEAEGRQPHWRFLLPNFKDDPFAIERTEVHWNDLVRDRE 173

Query: 176 SFESDGIGDFVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWD 235
           + +   + D V+V++DGT  Y F   +DD  M+++H++RG DHI+N+  QI I +A G  
Sbjct: 174 TVDLASLSDPVLVREDGTYLYTFTSVVDDIDMEISHIIRGNDHITNSGVQIAIIEALGAK 233

Query: 236 IPQFGHMTLIVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELF 295
           +P  GH+ L+   S + +SKR  ++   I   +  GY P A+ +   L+G S      + 
Sbjct: 234 VPDLGHINLLTTASGEGISKRTGAL--SIGSLRRDGYEPMAVASLAVLIGTSE-NVTAVP 290

Query: 296 TKEQFIEIFDVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKAGKVGTEL 355
                 +IFD    SKS + FD  +L  +N   +  +   Q  +       +   +G E 
Sbjct: 291 DMATLADIFDPAATSKSASKFDPAELDALNRALIHAMPYAQAKD-------RLAALGIEG 343

Query: 356 SAEEQEW--VRKLISLYHEQLSYGAEIVELTDLFFTDEIEYNQEAKAVLEEEQVPEVLST 413
              E+ W  VR  +S   +   +   I    D   TDE          L +E    V + 
Sbjct: 344 ERAEEFWLAVRGNLSRISDAAGWWKII---KDGPATDE---------QLADEDRDFVRTA 391

Query: 414 FAAKLEELEEFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIGK 473
           F   L   E ++ +  K    AV+ ++G KGK LFMP+R+A+TG + GPEL   + L+G+
Sbjct: 392 F--DLLPREPWSRETWKLWTDAVKIQSGRKGKPLFMPLRIALTGLSSGPELADLLPLLGR 449

Query: 474 ETAIQR 479
           E  + R
Sbjct: 450 EGTLAR 455


Lambda     K      H
   0.316    0.137    0.394 

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: 466
Number of extensions: 25
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: 483
Length of database: 457
Length adjustment: 33
Effective length of query: 450
Effective length of database: 424
Effective search space:   190800
Effective search space used:   190800
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 (21.6 bits)
S2: 51 (24.3 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