GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysN in Synechococcus elongatus PCC 7942

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

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



>lcl|FitnessBrowser__SynE:Synpcc7942_0031 Synpcc7942_0031
           aminotransferase
          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 Sep 17 2021. The underlying query database was built on Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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