Alignments for a candidate for gatA in Phaeobacter inhibens BS107

GapMind for Amino acid biosynthesis

Alignments for a candidate for gatA in Phaeobacter inhibens BS107

Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF1174 PGA1_c11890 putative indoleacetamide hydrolase

Query= curated2:Q67KJ2
         (488 letters)



>FitnessBrowser__Phaeo:GFF1174
          Length = 480

 Score =  180 bits (457), Expect = 8e-50
 Identities = 144/468 (30%), Positives = 213/468 (45%), Gaps = 43/468 (9%)

Query: 2   LSAARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAG 61
           LSA  L+R   AG+L+A     ++L+R+  V P + A +   +   + RA++LD  R +G
Sbjct: 9   LSATELSRRTTAGDLTAEAAVAASLTRMTAVNPDLNAVVEDLSSEALGRAQQLDKARASG 68

Query: 62  DTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANM 121
               GPL GVP+ +K N+  +G  T+     LK  ++  DA VV+ L+ AGA++IG+ N 
Sbjct: 69  -APCGPLHGVPVTIKINVDQAGHATSNGVSALKDLIAADDAPVVKNLQDAGAVVIGRTNT 127

Query: 122 DEFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAA 181
            EF+  +  ++   G T NPW     PGGSS G+ AAV AG   LA G D GGS+R PAA
Sbjct: 128 PEFSFRADTDNPLHGRTHNPWGRHISPGGSSGGAGAAVMAGIGALAHGNDIGGSLRFPAA 187

Query: 182 FTGIVGLKPTYGYVSRYGVV------AFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDA 235
             G V +KP  G V  +           A ++   G + R  +D+      +  PD RD 
Sbjct: 188 ANGAVTVKPGLGRVPAWNPSQSAERGILAQNMSVQGLLTRTAQDLHLSMPSLIAPDPRDP 247

Query: 236 TNAGRTPPALKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECS 295
            +     P    G  P    +R+   KE  G  + P V A +E+A A L + G  VEE  
Sbjct: 248 FHV----PLPWHGASPD-GPIRVAFSKETYGYDLHPEVDAALEDARAALSDAGYLVEETV 302

Query: 296 LPSTEYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRG--EGFGTEVK 353
           LP                       FD  R GYRA     + E+Y+  +G  +  G++  
Sbjct: 303 LPDV---------------------FDAGRTGYRAL----MGEVYALMKGDVDAAGSQTV 337

Query: 354 RRIMLGTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVD 413
           R I    +            +    RT   RD+    +RY  ++TP  P   ++     +
Sbjct: 338 RDIFAVYFEEFPPFAGVELLQMMAKRTQYARDWSLFMQRYPLVLTPFLPQPFFRPDRDTE 397

Query: 414 DPVSMY--LG-DICTIPVNLAGLPAVSVPCGFVDGLPVGMQLIGKPFA 458
               ++  LG  + +  +N  GLPA SVP    + LP G Q I    A
Sbjct: 398 GAAGVHEVLGCAVYSYAMNFLGLPAASVPSRLAE-LPSGPQPINVQIA 444


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: 524
Number of extensions: 32
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: 488
Length of database: 480
Length adjustment: 34
Effective length of query: 454
Effective length of database: 446
Effective search space:   202484
Effective search space used:   202484
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 Apr 09 2024. The underlying query database was built on Apr 09 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:

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
the source code
instructions for running GapMind on your computer
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