GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Azospirillum brasilense Sp245

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__azobra:AZOBR_RS24065
          Length = 392

 Score =  216 bits (550), Expect = 9e-61
 Identities = 131/371 (35%), Positives = 191/371 (51%), Gaps = 16/371 (4%)

Query: 27  KAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETKYTPVSGIPELREAIAKKFKRENN 86
           K +G DVI L  G+PDFDTP  ++ AAI A+  G+T YTP+ G PELR A+A+   R   
Sbjct: 28  KGRGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTHYTPIPGRPELRAALARDVARRTG 87

Query: 87  LDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAPYWVSYPEMVALCGGTPVFVPTRQ 146
           L       IV  G +  LFNA +  +  GDEV++P P +++Y   V   G T V V    
Sbjct: 88  LPVEPENVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATLVPV-APD 146

Query: 147 ENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSHEELKALTDVLMKHPHVWVLTDDM 206
               +L    L  A+TP+T+     +P+NP+G   S EEL+A+ D+  +H  +WV+ D++
Sbjct: 147 AATLRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRH-DLWVVADEV 205

Query: 207 YEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAMTGWRIGYAAGPLHLIKAMDMIQG 266
           Y  LT+   R    +   PG+ ERT+T+N +SK++AMTGWR G+   P  L+  M  +  
Sbjct: 206 YASLTFD--RPHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLAL 263

Query: 267 QQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRDLVVSMLNQAKGISCPTPEGAFYV 326
               G     Q AA+ A+    + +   +E ++ RRD+ +  L    G+ C  PE   ++
Sbjct: 264 CMLYGLPGFVQQAALVAVEQGDEAVAAMREGYRRRRDIALEALGSVPGLRCLKPEAGMFM 323

Query: 327 YPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVVHGSAFG--LGPNFRISYATSEAL 384
                G    T           +F   L    GV+V+   AFG       R+S+A SEA 
Sbjct: 324 LVDVRGTGLPTM----------EFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEAE 373

Query: 385 LEEACRRIQRF 395
           L EACRRI  F
Sbjct: 374 LAEACRRIAAF 384


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: 392
Number of extensions: 25
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: 400
Length of database: 392
Length adjustment: 31
Effective length of query: 369
Effective length of database: 361
Effective search space:   133209
Effective search space used:   133209
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