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

GapMind for Amino acid biosynthesis

Aligments 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 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for Amino acid biosynthesis