GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Desulfovibrio vulgaris Miyazaki F

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__Miya:8501474
          Length = 390

 Score =  329 bits (843), Expect = 1e-94
 Identities = 174/391 (44%), Positives = 242/391 (61%), Gaps = 7/391 (1%)

Query: 4   LADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGETK 63
           ++D L+R+KPSAT+AV+ KA ELKAKG  V+ L  GEPDF TP+++++AA  AID+G T+
Sbjct: 3   ISDRLTRIKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAIDQGFTR 62

Query: 64  YTPVSGIPELREAIAKKFKRENNLDYTAAQTIVGTGGKQILFNAFMATLNPGDEVVIPAP 123
           YT V GIPELR+A+   F R   ++     T+V  GGKQ L+N F   LNPGDEV++PAP
Sbjct: 63  YTQVPGIPELRQAVCGYFARFYGVEAPMEATVVTNGGKQALYNLFQCLLNPGDEVLVPAP 122

Query: 124 YWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGAAYSH 183
           YWVSYP +V L GG PVFV +  E  FK+  E+LDRA+TPKT+  + NSPSNP+GA YS 
Sbjct: 123 YWVSYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSR 182

Query: 184 EELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSKAYAM 243
            E  A+ +  +    ++V++D++Y+ L Y      +  +      E    +NG++K +AM
Sbjct: 183 AETDAIMEWAIAR-DLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTFAM 241

Query: 244 TGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQGRRD 303
           TGWR+GYA     LIKAM  IQGQ TS   S+AQ AA+ AL GP D +   K+ F+ RRD
Sbjct: 242 TGWRVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRRRD 301

Query: 304 LVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEGVAVV 363
           L   +++   G+ CP P+GAFY++     L     P    + T       ++E   VA+V
Sbjct: 302 LAHGIVSSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCT------YIMEQANVALV 355

Query: 364 HGSAFGLGPNFRISYATSEALLEEACRRIQR 394
            G+AFG     R SYA S+  L  A  ++ +
Sbjct: 356 PGAAFGDDACLRFSYAVSDDTLMIALDKVAK 386


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: 456
Number of extensions: 21
Number of successful extensions: 3
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: 390
Length adjustment: 31
Effective length of query: 369
Effective length of database: 359
Effective search space:   132471
Effective search space used:   132471
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