GapMind for Amino acid biosynthesis

 

Aligments for a candidate for tyrB in Magnetospirillum magneticum AMB-1

Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_043743690.1 AMB_RS07030 1-aminocyclopropane-1-carboxylate deaminase

Query= BRENDA::Q8YMS6
         (388 letters)



>lcl|NCBI__GCF_000009985.1:WP_043743690.1 AMB_RS07030
           1-aminocyclopropane-1-carboxylate deaminase
          Length = 384

 Score =  174 bits (440), Expect = 5e-48
 Identities = 120/388 (30%), Positives = 185/388 (47%), Gaps = 14/388 (3%)

Query: 4   AARVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGKTKY 63
           AAR   + P I + +   A A +A G DV     G+P    P  +  AAA+A+      Y
Sbjct: 5   AARRGAIAPFIVMDVMRDAAARQAAGADVIHLEVGQPSGQAPPKVLDAAARAVRTEPLGY 64

Query: 64  GAAAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIPAPY 123
             A G   LRE IAR   +   +   PE V VT G   +     +A  +PGD V + AP 
Sbjct: 65  TLALGRDSLRERIARHYHQAYGVSVVPERVCVTTGSSAAFLLAFLAAFEPGDRVAVAAPG 124

Query: 124 WLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVYTPE 183
           + +Y  ++  +G + V+VP   S+ ++IT E L   +  +    V+ SPSNPTG + +  
Sbjct: 125 YPAYRNILESLGVECVLVPVGPSSRWQITAEVL-AGVEGRLDGVVVASPSNPTGSMLSAH 183

Query: 184 EIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYSMTG 243
           E+  LA       I ++SDEIY  I Y  A   + G          ++ N F+K Y+MTG
Sbjct: 184 EVAELAGWCELHGIRLISDEIYHGITYGRAAATAAGMAAAP---HAVVINSFSKYYAMTG 240

Query: 244 WRLGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALEDSQDCVEEMR---QAFAKRR 300
           WRLG++  P D+ ++   +  +   +  T +Q     A E   DC++E+     A+   R
Sbjct: 241 WRLGWMVLPEDLARSVECLTQNLYISPPTLSQ----VAAESVFDCIDELEARVAAYRANR 296

Query: 301 QVMLDRLNAIPGLSTAKPDGAFYLFPDISKTGLKSLEFCDALIEEHKVAVIPGIAFGADD 360
            +++  L        A  DGAFYL+ D+S+    S EFC  ++ E  VA  PG+ F   +
Sbjct: 297 DILVAELPKAGFDRLAPSDGAFYLYADVSEMTNDSREFCARMLAETGVACTPGVDFDPIE 356

Query: 361 ---NIRLSYATDLATIEKGLDRLEKFVR 385
               +R SYA     + +   RL+ + R
Sbjct: 357 GHRTLRFSYAGSAEHMAEAARRLKAWRR 384


Lambda     K      H
   0.317    0.134    0.381 

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: 334
Number of extensions: 12
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: 388
Length of database: 384
Length adjustment: 30
Effective length of query: 358
Effective length of database: 354
Effective search space:   126732
Effective search space used:   126732
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: 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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