GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysN in Synechococcus elongatus PCC 7942

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate Synpcc7942_0031 Synpcc7942_0031 aminotransferase

Query= reanno::Putida:PP_4108
         (416 letters)



>FitnessBrowser__SynE:Synpcc7942_0031
          Length = 424

 Score =  159 bits (403), Expect = 1e-43
 Identities = 135/421 (32%), Positives = 195/421 (46%), Gaps = 36/421 (8%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74
           P+ +  G+ A +   DG+  ID +    V   GH +  +VEAI  QA  L H  F    H
Sbjct: 20  PLKVVSGKGARLTLADGRELIDCISSWWVNLHGHAHLRIVEAIAQQAATLEHVIFAGFSH 79

Query: 75  GPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGA-----TGKRAIIAFDGGF 129
            P   L  +L + +P         +++G+ A E ALK+A          +  I+AFDG +
Sbjct: 80  EPAERLAMELCKILPEKLTRV-FFSDNGSTAVEVALKMALQYWHNLDQPRSRILAFDGAY 138

Query: 130 HGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVE--LA 187
           HG T   +++ G+ + +     +L   V  LPYP    G    +A +A   + +VE  LA
Sbjct: 139 HGDTFGAMSV-GERSLFNAPFEKLLFSVEFLPYPETWWGDETVEAKEAA-AIAAVEQALA 196

Query: 188 VEDVAAFIFEP-VQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246
             DVAA I EP VQG GG     P F Q L       G L+I DE+ +GFGRTG  FA  
Sbjct: 197 AGDVAAVIIEPLVQGAGGMRMARPQFLQQLAARVQAAGSLLIADEVMTGFGRTGAWFACQ 256

Query: 247 RLGIEPDLLLLAKSIAGG-MPLGAVVGRKELMAALPKGG------LGGTYSGNPISCAAA 299
           R GI+PDL+ L+K + GG +PL   V  + +      G        G +Y+ NP+ CAAA
Sbjct: 257 RAGIQPDLICLSKGLTGGFLPLSITVATEVIYDTFCSGNPDHTFYHGHSYTANPLGCAAA 316

Query: 300 LASLAQMTDENLATWGERQEQAIVSRYERWKASGLS-----PYIGRLTGVGAMRGIEFAN 354
           +ASL  + D           +AIV   E     GL      P + R    G +   +  +
Sbjct: 317 IASLELLLD----------SEAIVQGLEDAHLPGLELLAQHPKVTRPRLTGGIAACDLVS 366

Query: 355 ADGSPAPAQLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414
             G        +V +AA ARGLLL P G   +++ LL P  +    L++    +   L E
Sbjct: 367 DRGGYLDPIGLRVRQAAIARGLLLRPLG---NVLYLLPPYCLTPTELQDIYAAIADLLDE 423

Query: 415 L 415
           +
Sbjct: 424 I 424


Lambda     K      H
   0.320    0.137    0.402 

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: 454
Number of extensions: 28
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: 416
Length of database: 424
Length adjustment: 32
Effective length of query: 384
Effective length of database: 392
Effective search space:   150528
Effective search space used:   150528
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: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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