GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatA in Lentibacillus jeotgali Grbi

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_010529587.1 ON01_RS03315 amidase

Query= curated2:B3DWT4
         (494 letters)



>NCBI__GCF_000224785.1:WP_010529587.1
          Length = 498

 Score =  155 bits (391), Expect = 4e-42
 Identities = 137/509 (26%), Positives = 230/509 (45%), Gaps = 67/509 (13%)

Query: 5   ELSVKELRRLLVQKEVSPLEVVENLLCRIAEVDPKIFAYIYLNHERALEASKKADISLPL 64
           +L   ++  L+  KE++P E +     R+ +V+P + A ++   +R +   +   +    
Sbjct: 8   QLDAVDIAELIRMKEMTPDEFLNLAFQRLEQVNPALNAVVHTRKDRVMAEVESLGVERSF 67

Query: 65  GGVPVAIKDNINVL-GEPCRCASRILEGYLAPYDSTVIEKLKKAGAILLGRTNMDEFAMG 123
            GVP+ +K+    L  EP   +S++++ ++   DS  + KL+ AG + +G TN  EF + 
Sbjct: 68  SGVPMLLKNLSQSLENEPITSSSKLMKDHIGRQDSNYVSKLRAAGFLFMGHTNTPEFGLK 127

Query: 124 SSTENSSVGITRNPWNTERVPGGSSGGSAAAVAAHEAFCALGSDTGGSIRQPAAFCGCVG 183
           + TE    G+TRNPWNT    GGSSGG+AAAVA+     A  SD GGSIR PA+F G  G
Sbjct: 128 NITEPEVHGLTRNPWNTNYASGGSSGGAAAAVASGVVPAAGASDGGGSIRIPASFTGLFG 187

Query: 184 LKPTYGRV---SRYGLTAFASSLDQIGPITKTVEDAALLLEVISGFDPFDNTSEKLPVPR 240
           LKPT GR       G     +S+D    ++++V D+A LL+++    P          P 
Sbjct: 188 LKPTRGRTPVGPGAGRQWQGASID--FALSRSVRDSAALLDILQVVQP----EAAFQTPA 241

Query: 241 FSELLENRPLKDFVLGIPKEYFIEG-----IDGEVRQALSQVIGHYEKLGVKIEEVSLPH 295
           F    +      F   +   Y  E      +  + R+A+ + +   EK G  +EE    H
Sbjct: 242 FPGSYKTDMAVPFKGQLRIAYTTESPVGTPVSDDAREAVVKTVCWLEKSGHIVEEQD--H 299

Query: 296 TPYAV---ATYYILATAEASANLARFDGIRYGKRAKNYNDL-IDYYGKTRDEGFGSEVKR 351
               V     YY++ + E SA  AR +  R  +R     D+ I+ +   +     S  + 
Sbjct: 300 DVDGVRIMQDYYLMNSGEISAVTARLE--RLLERELTPEDVEIETWLLHKAGKSVSAAEF 357

Query: 352 RILLGTYVLSSGYYDAYYLRALKVKEKIKQDFSLAFQKCQALLTPTSPFCAFRIGE--KT 409
              L ++ +++   +A++            DF          +TP + + A  +GE   +
Sbjct: 358 SASLASWDMAAAQMEAFHR---------TYDF---------FITPAAAYTAPEVGELSHS 399

Query: 410 SDPLQMYLADI------------------------FTIAVNLAGICALSIPCGRSTEGLP 445
           S   Q++ + +                        FT   NL G  A+S+P   S EGLP
Sbjct: 400 SGEQQLWRSKMETANKAEQQAIIWDIFLPSLTYTPFTQLANLTGQPAMSVPVHLSKEGLP 459

Query: 446 IGFQLIGPAWKEETILALGYIYQKTTGWV 474
           +G Q++    +E  +L L Y  +++  WV
Sbjct: 460 LGVQVMASKGREYMLLKLAYQLEQSDIWV 488


Lambda     K      H
   0.319    0.139    0.410 

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: 435
Number of extensions: 16
Number of successful extensions: 3
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: 494
Length of database: 498
Length adjustment: 34
Effective length of query: 460
Effective length of database: 464
Effective search space:   213440
Effective search space used:   213440
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 (21.7 bits)
S2: 52 (24.6 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