GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Magnetospirillum magneticum AMB-1

Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_011383786.1 AMB_RS06965 PLP-dependent aminotransferase family protein

Query= reanno::acidovorax_3H11:Ac3H11_1358
         (401 letters)



>NCBI__GCF_000009985.1:WP_011383786.1
          Length = 547

 Score =  133 bits (334), Expect = 1e-35
 Identities = 98/286 (34%), Positives = 140/286 (48%), Gaps = 10/286 (3%)

Query: 79  GYAPLRQAIADFLPWD----VDADQILITTGSQQALDLIAKVLIDENSRVLVETPTYLGA 134
           G+APLR AIA+ L        D  Q++I  GSQQALDL+A+VL++    VLVE P Y G 
Sbjct: 227 GHAPLRHAIAEHLGRSRAVRCDPAQVMIMGGSQQALDLVARVLLEPGEAVLVEDPCYGGL 286

Query: 135 LQAFTPMEPSVVAVASDDEGVLIDDLKAKVGTGADKARFLYVLPNFQNPTGRTMTEARRA 194
                     V AVA D +G   D   A+       AR  +V P+ Q PTG TM  +RR 
Sbjct: 287 TGVLRAAGAQVQAVAVDGQG--FDPELAE--RQCPSARLTFVTPSHQFPTGATMPLSRRL 342

Query: 195 ALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEG-CIYMGSFSKVLAPGLRLGFV 253
           AL+  A  +   ++ED+   D      P A L   +  G  +Y+G+FSK + PGLRLG++
Sbjct: 343 ALIHWAERVGGWVIEDDYDSDFHHAGSPTASLQGLDRGGRTLYLGTFSKSMFPGLRLGWL 402

Query: 254 VAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVPTIRALYKQQCEAMLAAL 313
           V P  + P  + A++ AD+   G  Q  +A  M       H+  +R LY Q+  A+L A 
Sbjct: 403 VVPPPLLPAFVAARRIADMAPAGLTQAAMAAFMTEGHFGAHLRRMRTLYGQRRRALLDA- 461

Query: 314 TQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVAFVP 359
              + G  +     + G+   + LP G    +    A  R +A  P
Sbjct: 462 APRILGPNLPVTAGEAGLHAILWLPAGCDDFQAAEAARARGLAPSP 507


Lambda     K      H
   0.318    0.134    0.392 

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: 543
Number of extensions: 33
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: 401
Length of database: 547
Length adjustment: 33
Effective length of query: 368
Effective length of database: 514
Effective search space:   189152
Effective search space used:   189152
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: 51 (24.3 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