Alignments for a candidate for gatA in Shewanella amazonensis SB2B

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Shewanella amazonensis SB2B

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate 6938403 Sama_2522 amidase (RefSeq)

Query= curated2:Q67KJ2
         (488 letters)



>FitnessBrowser__SB2B:6938403
          Length = 567

 Score =  122 bits (306), Expect = 3e-32
 Identities = 103/340 (30%), Positives = 148/340 (43%), Gaps = 47/340 (13%)

Query: 2   LSAARLNRLFLAGELSAVEIAESALSRI-----AQVEPAVGAFITVAADHVIERAKKLDA 56
           +S A L     +G  +AVE+ ++ L+RI     A  +  + A +    D  ++ A+  DA
Sbjct: 7   VSIAELRGALESGRTTAVELVKAYLARIEAYDGADTDTKLNAVVVHNPD-ALKEAEASDA 65

Query: 57  RRKAGDTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMII 116
           RR  G+T LGPL G+P   KD+    G+     S   K  V+  DA  VERLRA GA+ +
Sbjct: 66  RRARGET-LGPLDGIPYTAKDSYLVKGLTAASGSPAFKDLVAQRDAFTVERLRANGAICL 124

Query: 117 GKANMDEFAMGSSGESSAFGVTRNPWDLERV----PGGSSSGSAAAVAAGEAPLALGTDT 172
           GK NM   A G   +   +G   +P++   +      GSS+G+  A AA      L  +T
Sbjct: 125 GKTNMPPMANGGM-QRGVYGRAESPYNAAYLTAPFASGSSNGAGTATAASFCAFGLAEET 183

Query: 173 GGSIRQPAAFTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDR 232
             S R PA+  G+    P+ G +S  G      ++D V P  R + D+  + +V+   D 
Sbjct: 184 WSSGRGPASNNGLCAYTPSRGVISVRGNWPLTPTMDVVVPYARTMADLLEVLDVVVADDS 243

Query: 233 RDATNAGRTPPALKFG---------------GEPSLSGVRLGVPK------ELLGPGIDP 271
               +  R  P ++                 G  SL G R GVPK      EL G   +P
Sbjct: 244 ETRGDLWRMQPWVQIPKASEVRPESYIALACGADSLKGKRFGVPKMFINKDELAGTSENP 303

Query: 272 G--------------VKARVEEAIAQLEELGATVEECSLP 297
           G              V A  E+A A LE  GA V E   P
Sbjct: 304 GIGGPTGQRIHTRDSVIALWEQARAALEAAGAEVIEVDFP 343



 Score = 37.4 bits (85), Expect = 1e-06
 Identities = 25/86 (29%), Positives = 40/86 (46%), Gaps = 12/86 (13%)

Query: 394 DALVTPTTPFTAWKIGEKVDDPVSMYLGDICTIPVNLAGLPAVSVPCGFVD--GLPVGMQ 451
           DA V P +   AW  G  V +           + +   G+P V+VP G +   G+PVG+ 
Sbjct: 482 DADVNPASADIAWSNGVWVANG---------NLAIRHLGVPTVTVPMGIMADIGMPVGLT 532

Query: 452 LIGKPFADTQILQIAWAYQKV-TKHH 476
             G+ + D  +L +A A++    K H
Sbjct: 533 FAGRAYDDNALLSLASAFESTGNKRH 558


Lambda     K      H
   0.318    0.135    0.391 

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: 660
Number of extensions: 30
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: 488
Length of database: 567
Length adjustment: 35
Effective length of query: 453
Effective length of database: 532
Effective search space:   240996
Effective search space used:   240996
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: 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis