GapMind for Amino acid biosynthesis

 

Aligments for a candidate for ptransferase in Paraburkholderia bryophila 376MFSha3.1

Align aspartate transaminase (EC 2.6.1.1); aspartate-prephenate aminotransferase (EC 2.6.1.78); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate H281DRAFT_04024 H281DRAFT_04024 Aspartate/methionine/tyrosine aminotransferase

Query= BRENDA::Q9SIE1
         (475 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_04024 H281DRAFT_04024
           Aspartate/methionine/tyrosine aminotransferase
          Length = 399

 Score =  203 bits (516), Expect = 1e-56
 Identities = 139/403 (34%), Positives = 210/403 (52%), Gaps = 26/403 (6%)

Query: 70  MSLSPRVQSLKPSKTMVITDLAATLVQSGVPVIRLAAGEPDFDTPKVVAEAGINAIREGF 129
           M L+ RV S++P   M +   AA L + G  +I +  GEPDF  P+ V EA  NA+R G 
Sbjct: 9   MRLAARVDSIQPFYVMELAKEAALLERDGRDIIHMGIGEPDFTAPEPVIEAAANALRRGV 68

Query: 130 TRYTLNAGITELREAICRKLKEENGLSYAPDQILVSNGAKQSLLQAVLAVCSPGDEVIIP 189
           T+YT   G+  LREAI     E  G++  P +I+V+ GA  +LL A  A+    DEV++P
Sbjct: 69  TQYTSALGLHALREAISAHYAEVYGVNVDPARIVVTAGASAALLLACAALVDRDDEVLMP 128

Query: 190 APYWVSYTEQARLADATPVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSNPTGSVY 249
            P +         A+  PV++P+  +  F L   D+E    E++R ++L SPSNPTG+  
Sbjct: 129 DPCYPCNRHFVIAAEGKPVMVPSGPAERFQLTAADVERLWNERTRGVLLASPSNPTGTSI 188

Query: 250 PKSLLEEIARIIAKHPRLLVLSDEIYEHIIY--APATHTSFASLPDMYERTLTVNGFSKA 307
             + LE I + +       ++ DEIY+ + Y   P +  S+       +  +TVN FSK 
Sbjct: 189 EPAELERIVKAVRARGGFTIV-DEIYQGLSYDAKPVSALSYG------DDVITVNSFSKY 241

Query: 308 FAMTGWRLGYLAGPKHIVAACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAEMVK- 366
           F MTGWRLG+L  P  +V+A  KL   +   AS++AQ A +A         +T+A     
Sbjct: 242 FNMTGWRLGWLVVPPGMVSAFEKLAQNLFICASALAQHAALACF-----EPQTIATYEAR 296

Query: 367 --AYRERRDFLVKSLGDIKGVKISEPQGAFYLFIDFSAYYGSEAEGFGLINDSSSLALYF 424
              ++ RRDF+  +L  +       P GAFY++ D  +     A       DSS+L    
Sbjct: 297 RLEFKRRRDFIAPALESLGFTVPVMPDGAFYVYADCRSVAHPAA------GDSSALTKAM 350

Query: 425 LDKFQVAMVPGDAFGDDS---CIRISYATSLDVLQAAVEKIRK 464
           L +  V +VPG  FG  +    IR+SYAT+ + L+ AVE++ +
Sbjct: 351 LHEAGVVLVPGMDFGSHAPKQYIRLSYATAYEKLEEAVERLAR 393


Lambda     K      H
   0.317    0.132    0.370 

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: 393
Number of extensions: 14
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: 475
Length of database: 399
Length adjustment: 32
Effective length of query: 443
Effective length of database: 367
Effective search space:   162581
Effective search space used:   162581
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 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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