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_RS00200 BPHYT_RS00200 amidase

Query= curated2:A0L5G0
         (485 letters)



>FitnessBrowser__BFirm:BPHYT_RS00200
          Length = 467

 Score =  212 bits (539), Expect = 3e-59
 Identities = 149/491 (30%), Positives = 233/491 (47%), Gaps = 50/491 (10%)

Query: 7   TLREAADKLATKEISSVELTQACLDQIAKHNPTINAFVTVDAEKALAAAQ-----AADAR 61
           T+ +AA  +   E++ VEL Q CLD I  HNPT++AF  V AE+AL  A+     A + R
Sbjct: 3   TVADAAASIRCGELTPVELVQRCLDSIKTHNPTLHAFGDVYAEEALRYAETLTREAKENR 62

Query: 62  IAAGNGAPLTGIPIAHKDIFNTTDMRTTCSSRMLENFIPPFDATITTHLRQAGAVILGKT 121
              G    L G+P A KD+F T  +RTT  S    N++P  DA +   L++AGA++LGK 
Sbjct: 63  TRGG----LHGVPFAIKDLFATAGLRTTRGSLTAMNWVPQEDAPVIRRLKEAGAILLGKA 118

Query: 122 NLDEFAMGSSTETSYFGASRNPWDTQRTPGGSSGGSSAAIAANMAICATGTDTGGSIRQP 181
              EF    ++ +  FG   NPWD + T GGSS GS+ ++AA M   + G+D GGS+R P
Sbjct: 119 ATTEFGWSGASYSRVFGNGCNPWDARLTSGGSSSGSAISVAARMVPASLGSDGGGSVRIP 178

Query: 182 ASLTNLTGLKPTYGRCSRYGIIAFASSLDQAGPMTRTAEDAAMLLNVMVSYDPKDSTSIQ 241
           ++   +  +K ++GR   +   A    L  AGP+TRT  D+A+L +V+   D +D  ++ 
Sbjct: 179 SAFCGVFAMKGSHGRIPTWPWSA-TEMLSHAGPITRTVRDSALLFDVLAGPDSRDHQALP 237

Query: 242 SPAPDFTQALTGDVKGLKIGIAAEYFGDGLNDEVRAAIETAQQQYQAMGAELVPISL--P 299
           +    +       +K +++      FG  ++ E+   +  A ++     A  +PI L  P
Sbjct: 238 AATGSYLARCEEPLKRVRVAFCPTLFGVDVDPEISRVVGAAVERI----ARALPIDLEMP 293

Query: 300 NSGY--AIPTYYIISPAECSSNLARYDGVKFGYRCEEPKDIRDLYFRSRSEGFGDEVKRR 357
             G+   +PT+  +  A          G+ +G   +   D  D        GF   + R 
Sbjct: 294 VLGWHDPLPTFETLWVAG--------RGIVYGQTLKNCADQLD-------PGFARLIGR- 337

Query: 358 IMLGTYVLSSGYYDAYYRKAQQARRLIADEFKAAFEKVDLILTPTSPTTAF--------K 409
                   +S Y    Y  A Q R   A +  A F+  D +LTPT P   F        +
Sbjct: 338 --------ASDYSLEDYLTAIQRRATFACQVHALFDTYDFLLTPTLPILPFDADLIAPPE 389

Query: 410 FGEKDDPVQMYLSDIYTINVNLAGLPGISVPCGFDSKGLPIGMQLIGRPLDEETLLRSAD 469
               D  +       +T   NL+G P  S+PCG+   GLP+G+Q++G    +  +L+   
Sbjct: 390 LDTHDSALPWACWTPFTYPFNLSGNPAASLPCGWSDTGLPVGLQVVGPRFADADVLQFCS 449

Query: 470 AYQRQTDWHKR 480
           A +    W  R
Sbjct: 450 AIEAIMPWAHR 460


Lambda     K      H
   0.317    0.132    0.383 

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: 34
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: 485
Length of database: 467
Length adjustment: 33
Effective length of query: 452
Effective length of database: 434
Effective search space:   196168
Effective search space used:   196168
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: 51 (24.3 bits)

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

Links

Downloads

Related tools

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