GapMind for Amino acid biosynthesis

 

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

Align Bifunctional aspartate aminotransferase and glutamate/aspartate-prephenate aminotransferase; PhPPA-AT; EC 2.6.1.1; EC 2.6.1.78; EC 2.6.1.79 (characterized)
to candidate Ac3H11_256 Aspartate aminotransferase (EC 2.6.1.1)

Query= SwissProt::E9L7A5
         (479 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_256
          Length = 390

 Score =  149 bits (377), Expect = 1e-40
 Identities = 111/352 (31%), Positives = 168/352 (47%), Gaps = 28/352 (7%)

Query: 105 VIRLAAGEPDFDTPAPIVEAGINAIREGHTRYTPNAGTMELRSAIS---HKLKEENGLSY 161
           V++   GE D  TP  I +A I ++++G T Y  N G  ELR AI+   H L  +     
Sbjct: 26  VLQFWFGESDEVTPDFIRDAAIASLQKGETFYAHNLGLPELRHAIAGYMHGLHPQQHTDA 85

Query: 162 TPDQILVSNGAKQSIIQAVLAVCSPGDEVLIPAPYWVSYPEMARLADATPVILPTSISED 221
             D+I V++G    ++ AV A+   GDEV++  P W +     R+  A    +P     D
Sbjct: 86  WFDRIAVTSGGVNGLMVAVQALVDAGDEVVLVTPVWPNLVAQPRILGAQVRTVPLVADAD 145

Query: 222 --FLLDPKLLESKLTEKSRLLILCSPSNPTGSVYPRKLLEQIAEIVA--RHPRLLVISDE 277
             + LD   L + +T  +RLL++ +P+NPTG    R   E+ A I+A  R     +++DE
Sbjct: 146 GAWQLDMDALLAAITPGTRLLVVNAPNNPTGWTLTR---EEQATILAHCRRTGTWIVADE 202

Query: 278 IYEHIIYAPATHT----SFASLPGMWDRTLTVNGFSKAFAMTGWRLGYIAGPKHFIAACN 333
           +YE + YA  T      SF  +    DR +  + FSK+F MTGWRLG++  P     A  
Sbjct: 203 VYERLYYAGDTANGAAPSFLDVAEPEDRLVVTHSFSKSFLMTGWRLGWLVLPPSMTPAVG 262

Query: 334 KIQSQFTSGASSISQKAAVAALGLGYAGGELVATMVKSFRERRDYLVKSFGEIEGVKISE 393
           K+    TS A    Q+ A  AL       E+   +V   R  RD LV    ++ GV ++ 
Sbjct: 263 KLIEFNTSCAPVFVQRGATVAL---QRTDEVTPALVNHLRNCRDTLVPLLADVPGVSVAT 319

Query: 394 PRGAFYLFIDLSSYYGVEVDGFGSINNSESLCRYLLDKAQVALVPGDAFGDD 445
           PRG  Y F  +  +           +    L + L+ +A + L PG AFG +
Sbjct: 320 PRGGMYAFFHIDGH-----------DECLPLAKRLVREAGLGLAPGSAFGGE 360


Lambda     K      H
   0.317    0.132    0.375 

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: 437
Number of extensions: 19
Number of successful extensions: 8
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: 479
Length of database: 390
Length adjustment: 32
Effective length of query: 447
Effective length of database: 358
Effective search space:   160026
Effective search space used:   160026
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: 51 (24.3 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