GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Acidovorax caeni R-24608

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_054256827.1 BN2503_RS11430 aspartate aminotransferase family protein

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



>NCBI__GCF_001298675.1:WP_054256827.1
          Length = 398

 Score =  175 bits (443), Expect = 2e-48
 Identities = 129/399 (32%), Positives = 191/399 (47%), Gaps = 45/399 (11%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA-FNAAP 73
           PI L  G+   VWD +GK Y+D +GGI V  LGH +  +V A+Q Q  +L H + +   P
Sbjct: 20  PIALERGQGCRVWDVNGKEYLDALGGIAVNTLGHNHAKLVPALQEQIAKLIHTSNYYHVP 79

Query: 74  HGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG-----ATGKRAIIAFDGG 128
               LA     ++ V +S        NSG EA E A+K+AR            I+ ++  
Sbjct: 80  GQERLA-----AKLVELSGMSKVFFCNSGLEANEAAIKIARKFGVDKGIANPEIVVYEKA 134

Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188
           FHGR++AT++  G     +   G L      +P             L  +D +       
Sbjct: 135 FHGRSIATMSATGN-PKIRSGFGPLVEGFIRVP-------------LNDIDAIKQATEGN 180

Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248
            +V A  FE +QGEGG       + + LR+ CDER  L++IDE+Q G GRTG+ FA    
Sbjct: 181 PNVVAVFFETIQGEGGINPARSEYLRDLRKLCDERDWLMMIDEVQCGMGRTGKWFAHQWA 240

Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308
           GI PD++ LAK +  G+P+GAVV   +    L  G  G T+ GNP++  A + ++  M +
Sbjct: 241 GIVPDVMPLAKGLGSGVPIGAVVAGPKAADVLQPGNHGTTFGGNPLAMRAGVETIRIMEE 300

Query: 309 ----ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQL 364
               EN AT G   + ++       +A G  P +  + G G M G+E       P  A +
Sbjct: 301 DGLLENAATVGAHLKASLE------RALGSLPGVKEIRGQGLMLGVEL----DRPCGALI 350

Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEE 403
            +  EA    GLLL  S  A  +IR++ PL +     +E
Sbjct: 351 GQAAEA----GLLL--SVTADSVIRIVPPLILTTAEADE 383


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: 431
Number of extensions: 15
Number of successful extensions: 4
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: 398
Length adjustment: 31
Effective length of query: 385
Effective length of database: 367
Effective search space:   141295
Effective search space used:   141295
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 24 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