GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Acidovorax sp. GW101-3H11

Align 2-aminoadipate:2-oxoglutarate aminotransferase (EC 2.6.1.39) (characterized)
to candidate Ac3H11_1602 Aspartate aminotransferase (EC 2.6.1.1)

Query= reanno::Smeli:SMc04386
         (410 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1602
          Length = 408

 Score =  547 bits (1409), Expect = e-160
 Identities = 263/407 (64%), Positives = 320/407 (78%)

Query: 3   INATVKEAGFQPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQA 62
           +NA +    F+ A R+ +IGVSEI+++   A  +KR+G+PVI+LG GEPDFDTP H+ +A
Sbjct: 1   MNAPIPATAFRAADRLGAIGVSEIVRLTQEANQLKRQGQPVIVLGLGEPDFDTPAHILEA 60

Query: 63  ASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASL 122
           A  A+ RGET YT LDGT ELK AI+ KF+  NGL ++L+EIT   GAKQIL+NA+MAS+
Sbjct: 61  AQQAMARGETHYTVLDGTAELKAAIQHKFKHYNGLDFQLNEITAGAGAKQILYNALMASV 120

Query: 123 DPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNS 182
           +PGDEVI+P PYWTSY+D+V I  G PV++ C  ++GFR+T E+LEAAITPRTRWV +NS
Sbjct: 121 NPGDEVILPAPYWTSYADMVLIAGGVPVVVPCTEANGFRITPEQLEAAITPRTRWVFINS 180

Query: 183 PSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTL 242
           PSNPSGAAYSA   RP+LEV+ RHP VWLL DD+YEHI+YDG  F TPA + P L++RTL
Sbjct: 181 PSNPSGAAYSAEQLRPVLEVVERHPQVWLLADDIYEHILYDGRAFATPAAVLPSLRDRTL 240

Query: 243 TVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLK 302
           TVNGVSKAYAMTGWR+GY  GP+ LI AMAVVQSQATSCPSSISQAA+VAAL GPQD ++
Sbjct: 241 TVNGVSKAYAMTGWRLGYGAGPKALIAAMAVVQSQATSCPSSISQAAAVAALTGPQDVVR 300

Query: 303 ERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCA 362
           ER ++FQ RRDLVV  LN   GL CRVPEGAFYTF+ C G LG+ TP G  ++TD DFCA
Sbjct: 301 ERCQAFQDRRDLVVAALNVSPGLRCRVPEGAFYTFASCEGALGRTTPGGLLLRTDADFCA 360

Query: 363 YLLEDAHVAVVPGSAFGLSPFFRISYATSEAELKEALERIAAACDRL 409
           YLL + HVAVVPG   GL+P+FRISYA S A+L+EA  RI  AC  L
Sbjct: 361 YLLREHHVAVVPGGVLGLAPYFRISYAASTADLQEACARIQRACQAL 407


Lambda     K      H
   0.318    0.134    0.393 

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: 599
Number of extensions: 22
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: 410
Length of database: 408
Length adjustment: 31
Effective length of query: 379
Effective length of database: 377
Effective search space:   142883
Effective search space used:   142883
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:

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