GapMind for Amino acid biosynthesis

 

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

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_011383786.1 AMB_RS06965 PLP-dependent aminotransferase family protein

Query= BRENDA::Q72LL6
         (397 letters)



>NCBI__GCF_000009985.1:WP_011383786.1
          Length = 547

 Score =  136 bits (343), Expect = 1e-36
 Identities = 117/367 (31%), Positives = 167/367 (45%), Gaps = 17/367 (4%)

Query: 37  FAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRAFVAEWIG----VR-- 90
           FA G+P    FP  E      R+ R      +      G+APLR  +AE +G    VR  
Sbjct: 189 FAPGVPDLAAFPHAEWRRVLGRLWRRPPLELMGGIDPLGHAPLRHAIAEHLGRSRAVRCD 248

Query: 91  PEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPD 150
           P +V+I  GSQQALDLV +V L+ G  VL+E P Y G     R  G +   V    +G D
Sbjct: 249 PAQVMIMGGSQQALDLVARVLLEPGEAVLVEDPCYGGLTGVLRAAGAQVQAVAVDGQGFD 308

Query: 151 LDALEEVLKRERP--RFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLVVVEDDAYREL 208
                E+ +R+ P  R  ++ PS Q PTG   PL  R  L+      G  V+EDD   + 
Sbjct: 309 ----PELAERQCPSARLTFVTPSHQFPTGATMPLSRRLALIHWAERVGGWVIEDDYDSDF 364

Query: 209 YFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADL 268
           +   +   SL  L R       +YLG+FSK + PGLR+ + V  P  L   V A++ AD+
Sbjct: 365 HHAGSPTASLQGLDRGG---RTLYLGTFSKSMFPGLRLGWLVVPPPLLPAFVAARRIADM 421

Query: 269 HTPMLNQMLVHELLKEG-FSERLERVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFV 327
               L Q  +   + EG F   L R+R +Y ++ +A+L A  R +   +  T  + G+  
Sbjct: 422 APAGLTQAAMAAFMTEGHFGAHLRRMRTLYGQRRRALLDAAPRILGPNLPVTAGEAGLHA 481

Query: 328 WMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLG 387
            + LP G         A    +A  P   F     G   L L Y  L    + E ++RL 
Sbjct: 482 ILWLPAGCDDFQAAEAARARGLAPSPLS-FHRVTKGCPGLVLGYGNLAGSSLEEALQRLR 540

Query: 388 RALKGLL 394
            A+  L+
Sbjct: 541 EAIITLI 547


Lambda     K      H
   0.320    0.139    0.403 

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: 524
Number of extensions: 32
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: 397
Length of database: 547
Length adjustment: 33
Effective length of query: 364
Effective length of database: 514
Effective search space:   187096
Effective search space used:   187096
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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