GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Burkholderia phytofirmans PsJN

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate BPHYT_RS15070 BPHYT_RS15070 amidase

Query= curated2:A7NKM0
         (490 letters)



>FitnessBrowser__BFirm:BPHYT_RS15070
          Length = 459

 Score =  216 bits (550), Expect = 1e-60
 Identities = 170/485 (35%), Positives = 235/485 (48%), Gaps = 60/485 (12%)

Query: 9   VAQAREMLARGEISSLELTDALLTRIAAVEPKVRA-FLVVDAAGARAQARAADARRAAGD 67
           +AQ    LA G  +S  L +  L RIA    +  A F+ VDA  AR+ A A D  RAAG 
Sbjct: 11  LAQLAADLAAGRTTSRALVETALERIADPAGQGAAVFMHVDADSARSAADAHDRLRAAGT 70

Query: 68  A-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVY-DATAVARLKAAGAVILGKLNCD 125
             SPL GIP+ +KD+   +G  T   S +L +      DA AVARLK AGAV++G+ N  
Sbjct: 71  VLSPLAGIPVSVKDLFDIEGQPTRAGSTVLADAPAAKADAVAVARLKRAGAVLVGRTNMS 130

Query: 126 EFAMGSSTENSAFQQTRNPWNL-----ERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIR 180
           EFA      N  +    +P+       ER+ GGSS G+AA+VA G A  ALGTDTGGSIR
Sbjct: 131 EFAFSGLGLNPHYGNPLSPYQRGVKGDERISGGSSSGAAASVADGMAAIALGTDTGGSIR 190

Query: 181 QPAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATC 240
            PAALCG+TG KPT  R+ + G V  +S+LD  GP+  +V  CA+V R++AG +P     
Sbjct: 191 IPAALCGLTGFKPTADRIPKQGGVPLSSTLDSFGPIGVSVACCALVDRMLAGLEP----- 245

Query: 241 TDYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLP 300
                          + G+R+GV   +   G++P V AA+ TA++ L   GA V E+   
Sbjct: 246 --------RIPAARPLEGVRLGVLTNFVTDGVEPAVAAAIDTALKHLEAAGAIVSEVR-- 295

Query: 301 HTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYF---DELERTRGAGFGPEVRRR 357
                       AP +    + RF         P E+Y      LE+ R   + P V  R
Sbjct: 296 -----------FAPLDRLPEINRFG------FSPIEAYAWHRPLLEKHRDQ-YDPRVLVR 337

Query: 358 IMLGTYALSAGYYDAYYKR----AQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAH 413
           I+ G  A +A Y D   +R    A+  RTL        +++ D + APT P V  ++   
Sbjct: 338 ILKGQPASAADYLDLLAEREAMLAEAARTL--------WQRFDAVVAPTVPVVPPRVADL 389

Query: 414 TDDPLAMYLEDVCTL----PLNLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLRVGD 469
            DD  A    +   L      N      L +PC      P+GL L G    +++LL +G 
Sbjct: 390 VDDDEAFGRTNALILRNPSVFNFLDTCALSLPCHLRGDAPVGLMLAGAPHADDALLAIGR 449

Query: 470 AYQRV 474
             + V
Sbjct: 450 GAEAV 454


Lambda     K      H
   0.320    0.136    0.398 

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: 542
Number of extensions: 39
Number of successful extensions: 7
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: 490
Length of database: 459
Length adjustment: 33
Effective length of query: 457
Effective length of database: 426
Effective search space:   194682
Effective search space used:   194682
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 (21.8 bits)
S2: 51 (24.3 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