GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE 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)



>NCBI__GCF_000009985.1:WP_043743690.1
          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 (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