GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Cupriavidus basilensis 4G11

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate RR42_RS28435 RR42_RS28435 amidase

Query= curated2:B8HY89
         (482 letters)



>FitnessBrowser__Cup4G11:RR42_RS28435
          Length = 508

 Score =  211 bits (537), Expect = 5e-59
 Identities = 148/478 (30%), Positives = 236/478 (49%), Gaps = 43/478 (8%)

Query: 7   LHQQLVSKERSAKEITQDALEKIQQLEPKVHAFLTLTAEQALAQAERVDQQIATGTEIGL 66
           L + + SKE S  E+ +  + +I+ + P ++A      E+A  +A   ++ +  G  +GL
Sbjct: 15  LRRLIGSKEISPVELLEACIARIEAVNPFINAITATCYERAREEARAAERAVLDGAPLGL 74

Query: 67  LAGIPIAIKDNLCTKGIPTTCGSKILQGFIPPYESTVTSRLAAAGAVMVGKTNLDEFAMG 126
           L G+P+ +KD   T G+ TT GS + +  +P  ++ + +RL AAGA++ GKTN+ E   G
Sbjct: 75  LHGLPLGVKDLEATAGLLTTYGSPLYRDNVPSADNVLVARLRAAGAIVTGKTNIPEMGAG 134

Query: 127 SSTENSAYQLTANPWDLQRVPGGSSGGSAAAVAAGETLIALGSDTGGSIRQPASFCGVVG 186
           +++ N+ +  T NP++     GGSSGGSAAA+A     +  GSDTGGS+R PA+ CGVVG
Sbjct: 135 ANSRNAVWGATGNPFNPNLNAGGSSGGSAAALATDMLPVCTGSDTGGSLRIPAAKCGVVG 194

Query: 187 LKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDPQDSTSLNVPIPDYTQ 246
            +P+ G+V     +   + +  +GP    V DA L L A AG    D  +  +   D   
Sbjct: 195 FRPSPGVVPSSRKLLGWTPISVVGPMGRTVADACLQLAASAGVSASDPLTYAL---DPMS 251

Query: 247 FLIP---DLKGKKIGIIQETYGEGLDPQVEQVTHKAIQQLEELGAEVREISCPRFRYGLP 303
           FL+P   DL   ++G  ++     +D Q+ QV    I  +  L     EI          
Sbjct: 252 FLLPANVDLGSLRVGWTEDFGVCAVDNQIRQVFRDKIAAMRHLFRSCDEIQ--------- 302

Query: 304 TYYIIAPSEASANLARYDGVKYGFRSP---DPENLLSMYTRTRAEGFGPEVKRRIMIGTY 360
             + +  +    ++ R +    G R     DP++L            GP  +    +G  
Sbjct: 303 --FDLGDAHRCFDVLRAESFVAGTREAYQRDPQSL------------GPNTRANYEMGA- 347

Query: 361 ALSAGYYDAYYLKAQKVRTLIKQDFEAAFEQVDVLVCPTAPTTAFAAGAKTADPL----- 415
           A+S    D+ + +A++ R L +  F+AAFE  DV++ PT P + F      A+ +     
Sbjct: 348 AMSLS--DSAWAQAEQTRILGR--FQAAFEDYDVILSPTTPVSPFPWTNLYAETINGEKQ 403

Query: 416 -SMYLSDLMTIPVNLAGLPGLSLPCGFDQQGLPIGLQLIGNVLREDLVFQVAYAYEQA 472
            + Y     T  V L   P +SLPCG D  G+P GLQ++G    +     VA+A EQA
Sbjct: 404 ENYYRWLAPTYVVTLTTHPAISLPCGLDHAGMPFGLQVVGRFRADHHTLGVAHAMEQA 461


Lambda     K      H
   0.317    0.134    0.388 

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: 552
Number of extensions: 20
Number of successful extensions: 4
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: 482
Length of database: 508
Length adjustment: 34
Effective length of query: 448
Effective length of database: 474
Effective search space:   212352
Effective search space used:   212352
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