GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Bacteroides thetaiotaomicron VPI-5482

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 353246 BT3720 putative aspartate aminotransferase (NCBI ptt file)

Query= BRENDA::Q9SIE1
         (475 letters)



>FitnessBrowser__Btheta:353246
          Length = 383

 Score =  209 bits (531), Expect = 2e-58
 Identities = 136/397 (34%), Positives = 206/397 (51%), Gaps = 26/397 (6%)

Query: 73  SPRVQSLKPSKTMVITDLAATLVQSGVPVIRLAAGEPDFDTPKVVAEAGINAIREGFTRY 132
           +P+V+ +     M + + A  L + GV VI L  GEPDFD P  VAEA   A     T Y
Sbjct: 5   NPQVEQMTSFIVMDVLERANELQKQGVDVIHLEVGEPDFDVPACVAEAAKAAYDRHLTHY 64

Query: 133 TLNAGITELREAICRKLKEENGLSYAPDQILVSNGAKQSLLQAVLAVCSPGDEVIIPAPY 192
           T + G  ELR  I    + E G++  PD I+V++G+  S+L  ++ +C+   EVI+  P 
Sbjct: 65  THSLGDPELRREIAAFYQREYGVTVDPDCIVVTSGSSPSILLVLMLLCNSDSEVILSNPG 124

Query: 193 WVSYTEQARLADATPVVIPTKISNNFLLDPKDLESKLTEKSRLLILCSPSNPTGSVYPKS 252
           +  Y      A A PV++P    N    D + +   +T  +  + + SP NPTG +  +S
Sbjct: 125 YACYRNFVLAAQAKPVLVPLSEENGLQYDIEAIRKCVTPHTAGIFINSPMNPTGMLLDES 184

Query: 253 LLEEIARIIAKHPRLLVLSDEIYEHIIYAPATHTSFASLPDMYERTLTVNGFSKAFAMTG 312
            L  +A +      + ++SDEIY  ++Y    H    S+ +  ++   +NGFSK FAMTG
Sbjct: 185 FLRSVASL-----GVPIISDEIYHGLVYEGRAH----SILEYTDKAFVLNGFSKRFAMTG 235

Query: 313 WRLGYLAGPKHIVAACSKLQGQVSSGASSIAQKAGVAALGLGKAGGETVAEMVKAYRERR 372
            RLGYL  PK  + +  KLQ  +   ASSIAQ+AG+AAL   +     V  M + Y ERR
Sbjct: 236 LRLGYLIAPKSCMRSLQKLQQNLFICASSIAQQAGIAAL---RQADSDVERMKQIYDERR 292

Query: 373 DFLVKSLGDIKGVKIS-EPQGAFYLFIDFSAYYGSEAEGFGLINDSSSLALYFLDKFQVA 431
            +++  L ++ G +I  EPQGAFY+F D   +            DS   A   L+   V 
Sbjct: 293 RYMISRLREM-GFEIKVEPQGAFYIFADARKF----------TTDSYRFAFDVLENAHVG 341

Query: 432 MVPGDAF--GDDSCIRISYATSLDVLQAAVEKIRKAL 466
           + PG  F  G +  +R SYA SL+ ++  +++I + L
Sbjct: 342 ITPGIDFGTGGEGYVRFSYANSLESIREGLDRISQYL 378


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: 366
Number of extensions: 22
Number of successful extensions: 4
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: 383
Length adjustment: 32
Effective length of query: 443
Effective length of database: 351
Effective search space:   155493
Effective search space used:   155493
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.

Links

Downloads

Related tools

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