GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Synechococcus elongatus PCC 7942

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate Synpcc7942_0031 Synpcc7942_0031 aminotransferase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4013
         (425 letters)



>FitnessBrowser__SynE:Synpcc7942_0031
          Length = 424

 Score =  145 bits (365), Expect = 3e-39
 Identities = 123/416 (29%), Positives = 195/416 (46%), Gaps = 26/416 (6%)

Query: 25  PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84
           P+   S K A +T  +GRE ID      V   GH H +I+ A+ +Q   L H  F   ++
Sbjct: 20  PLKVVSGKGARLTLADGRELIDCISSWWVNLHGHAHLRIVEAIAQQAATLEHVIFAGFSH 79

Query: 85  EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIA-----RAATGRAGVIAFTGAY 139
           EP   L  ++  K+  +   +      GS AVE A+K+A          R+ ++AF GAY
Sbjct: 80  EPAERLAMEL-CKILPEKLTRVFFSDNGSTAVEVALKMALQYWHNLDQPRSRILAFDGAY 138

Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHG-VSIDDSIASIERIFKNDAEP 198
           HG T   + + G+   ++A    +   +    YP    G  +++   A+     +     
Sbjct: 139 HGDTFGAMSV-GERSLFNAPFEKLLFSVEFLPYPETWWGDETVEAKEAAAIAAVEQALAA 197

Query: 199 RDIAAIIIEP-VQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQ 257
            D+AA+IIEP VQG GG  +A  +F+++L A     G LLIADEV TG GRTG +FA ++
Sbjct: 198 GDVAAVIIEPLVQGAGGMRMARPQFLQQLAARVQAAGSLLIADEVMTGFGRTGAWFACQR 257

Query: 258 MGVAADLTTFAKSIAGGF-PLAGVCGKAEYMDAIAPGG------LGGTYAGSPIACAAAL 310
            G+  DL   +K + GGF PL+         D    G        G +Y  +P+ CAAA+
Sbjct: 258 AGIQPDLICLSKGLTGGFLPLSITVATEVIYDTFCSGNPDHTFYHGHSYTANPLGCAAAI 317

Query: 311 AVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVELF-ENGDSHKP 369
           A +E+  +   +   + + +  + GL+ +  ++P +   R  G + A +L  + G    P
Sbjct: 318 ASLELLLDSEAI--VQGLEDAHLPGLELL-AQHPKVTRPRLTGGIAACDLVSDRGGYLDP 374

Query: 370 NAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEECFSEL 425
               V Q    A  +GL+L      GNVL +L P      +L    A + +   E+
Sbjct: 375 IGLRVRQA---AIARGLLL---RPLGNVLYLLPPYCLTPTELQDIYAAIADLLDEI 424


Lambda     K      H
   0.320    0.137    0.395 

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: 464
Number of extensions: 18
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: 425
Length of database: 424
Length adjustment: 32
Effective length of query: 393
Effective length of database: 392
Effective search space:   154056
Effective search space used:   154056
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 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:

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