Aligments for a candidate for ptransferase in Dinoroseobacter shibae DFL-12

GapMind for Amino acid biosynthesis

Aligments for a candidate for ptransferase in Dinoroseobacter shibae DFL-12

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 3607347 Dshi_0762 aminotransferase class I and II (RefSeq)

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__Dino:3607347
          Length = 400

 Score =  554 bits (1428), Expect = e-162
 Identities = 273/397 (68%), Positives = 307/397 (77%)

Query: 1   MAFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRG 60
           M+FL+ +L+RVKPS TIAV+  A ELKA GRDVIGLGAGEPDFDTP NIK A   AID G
Sbjct: 1   MSFLSTSLARVKPSPTIAVTNMANELKAAGRDVIGLGAGEPDFDTPQNIKDAGKAAIDAG 60

Query: 61  ETKYTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVI 120
           +TKYT V GIPEL++AI  KFKR+N LDY   Q  V  GGKQIL NA MAT+NPGDEV+I
Sbjct: 61  KTKYTAVDGIPELKKAIVAKFKRDNGLDYDTTQVTVANGGKQILINALMATMNPGDEVII 120

Query: 121 PAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAA 180
           PAPYWVSYP+MV L GG PV      +  FKL A+ L+ AITP+TKWF+FNSPSNP+GA 
Sbjct: 121 PAPYWVSYPDMVLLAGGEPVIAEASIQTGFKLTADQLEAAITPRTKWFIFNSPSNPTGAG 180

Query: 181 YSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKA 240
           Y+  ELK LTDVL++HPHVWV+TDDMYEHL Y DF FATP +VEP LY RTLT NGVSKA
Sbjct: 181 YTAAELKELTDVLLRHPHVWVMTDDMYEHLVYDDFEFATPAQVEPKLYNRTLTCNGVSKA 240

Query: 241 YAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQG 300
           YAMTGWRIGYAAGP  LI AM  IQ Q TS   SI+QWAAVEAL+G QD+I  N + F+ 
Sbjct: 241 YAMTGWRIGYAAGPKELIGAMRKIQSQSTSNPCSISQWAAVEALDGTQDYIPENNKTFKR 300

Query: 301 RRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGV 360
           RRDLVV MLN A+GISCP PEGAFYVYPS AG IGKT+  G  I  DE F   LLE +GV
Sbjct: 301 RRDLVVGMLNDAQGISCPKPEGAFYVYPSIAGCIGKTSAGGTKITDDEAFAKALLEEKGV 360

Query: 361 AVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFCA 397
           AVV G+AFGL PNFR+SYATS+  L EAC RIQ FCA
Sbjct: 361 AVVFGAAFGLSPNFRVSYATSDDALTEACTRIQDFCA 397


Lambda     K      H
   0.318    0.134    0.402 

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: 555
Number of extensions: 17
Number of successful extensions: 1
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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: 50 (23.9 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