GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ptransferase in Echinicola vietnamensis KMM 6221, DSM 17526

Align aspartate transaminase (EC 2.6.1.1); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate Echvi_0675 Echvi_0675 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q02635
         (400 letters)



>FitnessBrowser__Cola:Echvi_0675
          Length = 400

 Score =  342 bits (877), Expect = 1e-98
 Identities = 183/398 (45%), Positives = 256/398 (64%), Gaps = 5/398 (1%)

Query: 2   AFLADALSRVKPSATIAVSQKARELKAKGRDVIGLGAGEPDFDTPDNIKKAAIDAIDRGE 61
           + L+D ++ ++ SAT+A+++KARELK +G D+I L  GEPDF TP +I+ AA  AID G+
Sbjct: 3   SILSDRINNMEESATLAMAKKARELKGQGIDIISLSLGEPDFKTPQHIQDAAKAAIDEGK 62

Query: 62  T-KYTPVSGIPELREAIAKKFKRENNLDYTAAQTIV-GTGGKQILFNAFMATLNPGDEVV 119
              Y+PV+G  +LREAIA+K + +N ++   A+ IV  TG K  + N FM  LN GDEVV
Sbjct: 63  YFSYSPVAGYQDLREAIAQKLQTQNKINEAKAENIVLSTGAKHSIANIFMCLLNEGDEVV 122

Query: 120 IPAPYWVSYPEMVALCGGTPVFVPTRQENNFKLKAEDLDRAITPKTKWFVFNSPSNPSGA 179
           I +PYWVSY E++ L GG PV +    ENNFK  A  L+ AIT KTK  +++SP NP+G+
Sbjct: 123 IFSPYWVSYAEIIKLAGGVPVLIEGTLENNFKASAAQLEEAITSKTKAVIYSSPCNPTGS 182

Query: 180 AYSHEELKALTDVLMKHPHVWVLTDDMYEHLTYGDFRFATPVEVEPGLYERTLTMNGVSK 239
            +S EEL+A+ +V+ KH  ++V+ D++YE + Y        +   PG+++RT+T+NG SK
Sbjct: 183 VFSKEELEAIAEVIKKHQDIYVVADEIYELINYTGQH--ASMAALPGMFDRTITVNGFSK 240

Query: 240 AYAMTGWRIGYAAGPLHLIKAMDMIQGQQTSGAASIAQWAAVEALNGPQDFIGRNKEIFQ 299
            YAMTGWR+GY   PL + KA + IQGQ TSG   IAQ AA+ A+ G Q      ++ ++
Sbjct: 241 GYAMTGWRVGYICAPLFIAKACEKIQGQFTSGGTGIAQRAALAAITGDQTPSVEMEKAYK 300

Query: 300 GRRDLVVSMLNQAKGISCPTPEGAFYVYPSCAGLIGKTAPSGKVIETDEDFVSELLETEG 359
            RR+LV+ +L    GI    PEGAFY +P      GK+A   KV   D DF   +L T  
Sbjct: 301 KRRELVLELLRDIPGIKTHVPEGAFYFFPDVTAFFGKSAGEVKVNNAD-DFCLYILNTAH 359

Query: 360 VAVVHGSAFGLGPNFRISYATSEALLEEACRRIQRFCA 397
           V+VV G+AFG     R+SYA SEA L+EA +RI+   A
Sbjct: 360 VSVVTGAAFGAPNCVRLSYAASEAELKEALKRIKEAVA 397


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: 416
Number of extensions: 22
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: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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