GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Pseudomonas fluorescens FW300-N1B4

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate Pf1N1B4_4165 Aspartyl-tRNA(Asn) amidotransferase subunit A (EC 6.3.5.6) @ Glutamyl-tRNA(Gln) amidotransferase subunit A (EC 6.3.5.7)

Query= curated2:Q7UT33
         (499 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4165
          Length = 478

 Score =  176 bits (446), Expect = 2e-48
 Identities = 153/490 (31%), Positives = 216/490 (44%), Gaps = 51/490 (10%)

Query: 14  SGEVTAVEVIAQSLAAIRASQPTINAFTHVAEETAMQAAEAVDADRKAGKTLGPLAGLPV 73
           +GEVT+ E+   ++AA++   P INA   V E  +    E            GPLAG+P 
Sbjct: 20  TGEVTSAELAELAIAAVQQVNPQINA---VIEHWSPTVTEGT----------GPLAGVPF 66

Query: 74  AIKDVLCTS-DMPTTCSSKMLEGFVPPYDATVVARLKSAGAIVVGKTNMDEFAMGASTET 132
            IKD+  TS        S++ +G V   D+ ++ R  +AG   +G+T   E A    TE+
Sbjct: 67  LIKDLAITSAGRRVELGSRLAQGLVAESDSYLMQRFNAAGLATLGRTTTPEMAFSTETES 126

Query: 133 SAMGVTGNPWDTTKTPGGSSGGAAAAVAAGAVPLSLGTDTGGSIRQPAAFCGITGLKPTY 192
              G T NPWDT  + GGSSGG+ AAVAAG VP++  TD  GSIR PA++ G+ GLKPT 
Sbjct: 127 VLQGPTRNPWDTRLSAGGSSGGSGAAVAAGIVPIAHATDAAGSIRVPASYNGLVGLKPTR 186

Query: 193 GRVSRYGLV--AFASSLDQAGPMGWSVDDVAIGLQAMAGYDPRDSTSVNAEVPDFTPAMA 250
           GR S    +   FA    Q G +  +V D A  +  + GY P D     A    F  A  
Sbjct: 187 GRASNGPALDEVFAGFGVQLG-LSRTVRDSAALMDIVQGYAPGDPYYTAAPDEGFL-AQV 244

Query: 251 AEDVRGMRIGVLREGLDQDGISPAVRDALATAESVFREQGAEIVEVELPHSKYWVPTYYV 310
             D   +RIG+L    +   + P + +A           G  +  V  P    W      
Sbjct: 245 GRDPGRLRIGLLDTPWNGAALDPEIAEATLAVARELEALGHRVERVIAPLGTSWDSFVQA 304

Query: 311 IAPCEASSNLSRFDGAHYGYRVADAEIAAADSGPLEAMYSLSRAGGFGSEVKRRIMVGTY 370
            A    ++ +   DG           +AAA S P++ + +L  A            +  Y
Sbjct: 305 NAHIWCATLVRWIDG-----------LAAATSRPID-LSTLEPA-----------TLACY 341

Query: 371 ALSEGYYDAYYNQALKVRRLIRNDYDAAFQQVDLMLGPVTPSPAFALN-----EKTDDPI 425
           A         +  AL+VR LI       F   D++L P  P    AL+      +T D +
Sbjct: 342 AYGLEARAVEFAGALEVRNLIARSVAGWFDDFDVLLTPTLPRLPHALDTYSRGAQTMDGL 401

Query: 426 ----AMYLCDLFTVGANLAGVPAISLPGGFD-AVGLPVGVQLQAPVMEETRLLRAGNVFQ 480
                ++    FT   N+AG PA+SLP       GLP+G+Q  A    E  LLR     +
Sbjct: 402 QWTARVFEHSPFTPVFNVAGTPAMSLPLAMSREQGLPIGLQFAARFGAEEVLLRLAGQLE 461

Query: 481 MASDFHTRRP 490
            A  +H RRP
Sbjct: 462 QALPWHERRP 471


Lambda     K      H
   0.316    0.132    0.381 

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: 567
Number of extensions: 33
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: 499
Length of database: 478
Length adjustment: 34
Effective length of query: 465
Effective length of database: 444
Effective search space:   206460
Effective search space used:   206460
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: 52 (24.6 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