GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Phyllobacterium endophyticum PEPV15

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_106717548.1 CU100_RS15780 amidase

Query= curated2:C6BSE9
         (487 letters)



>NCBI__GCF_003010935.1:WP_106717548.1
          Length = 473

 Score =  147 bits (370), Expect = 1e-39
 Identities = 140/479 (29%), Positives = 217/479 (45%), Gaps = 36/479 (7%)

Query: 10  TEIHAMLMTKEVTATEAVKACLEQIAKSEPETKALLHICNDEALKQAEEMDAAGPDASKP 69
           T +  ++  +EVTA+E + A L  +A  + E  A++    +EA +   +  + GP     
Sbjct: 12  TGLAELVAKQEVTASELLDAALAGVAAVDGELNAVIATFEEEARRFIAQELSDGP----- 66

Query: 70  LWGVPVVIKDALAT-NGIPTTAGSKILEGFTPFYDSTAVAKLKEAGAIIVGKANMDEFAM 128
             GVP ++KD  A   G PT AG        P  DS  V + K++G +I GK ++ E AM
Sbjct: 67  FKGVPFLLKDLTAHYGGQPTGAGWPPRAAVRPAEDSELVRRFKKSGVVIFGKTSVPELAM 126

Query: 129 GSTTENSAYQTTTNPWDASRVPGGSSGGSGATVAAGQCYAALGTDTGGSIRLPASFCGCV 188
             TT + A+  T NPWD +R  G SSGG+ A VAAG      G D GGSIR+P+S CGC 
Sbjct: 127 DWTTRSRAHGVTNNPWDTTRTAGTSSGGTAAAVAAGVVPMGHGNDGGGSIRVPSSACGCF 186

Query: 189 GVKPTYGR--VSRYGMIAYGSSLDQIGPMTRTVEDAARVLNVIGG-HDQRDSTSAEQPME 245
           G+KP+ GR  V+  G    G  ++ +  ++R+V D+A +L+   G H  +   S   P E
Sbjct: 187 GLKPSRGRNPVAPSGSTWQGMLVEHV--LSRSVRDSAGMLDATQGLHVGQFFNS--PPGE 242

Query: 246 DFVAALEERKDLSGLTIGLPEEY-WGEGLSKEVSEACRAAIAKAEELGAKTVPVKLSMTE 304
            F  A E  +D   L IG+  +  +G     +   A    +   E LG       + +  
Sbjct: 243 GF--ASEVGRDPGKLRIGVSTKAPYGAATHPDCVTAIEETMKLLEGLGHICESHDIELPP 300

Query: 305 YAIATYYIIAMAEASSNLSRFDGVRYGHRTEDPKELAELYTKSRTEAFGDEVQRRIIIGT 364
              + +    +AE ++++   + V              L  K   + F   +   I  G 
Sbjct: 301 DGWSAFETFILAEYATDMRLEEDV--------------LGRKLTADDFPPMLWEMIDAGN 346

Query: 365 YVLSAGYYDAYYRKAAQIRRLLREDFNK--AFESCDIIASPACPTTAFPVGELTSDPLQM 422
            + +     A  R  A +   +   FN+   F S   +A P     AFP      +  + 
Sbjct: 347 GISAVDVNVATTRLHA-VASAVTSTFNRYDVFLS-PTLAQPPLAHDAFPQATSMREHYEF 404

Query: 423 YLQDI-FTISLNLVGMPGMSLPVAFGKETNMPVGLQFMAPAFDEKTMLQAAHVLEKNLP 480
           YL  + FT   N+ G P MS+P+ +  E  +P+G+QF A    E  + + A  LE   P
Sbjct: 405 YLSWMPFTHIFNVNGSPAMSVPLVWNAE-GLPIGVQFAAAPAAEGLLFRLASQLEMARP 462


Lambda     K      H
   0.315    0.131    0.374 

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: 497
Number of extensions: 30
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 487
Length of database: 473
Length adjustment: 34
Effective length of query: 453
Effective length of database: 439
Effective search space:   198867
Effective search space used:   198867
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