GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Limnohabitans curvus MWH-C5

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_108401693.1 B9Z44_RS03080 aspartate aminotransferase family protein

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



>NCBI__GCF_003063475.1:WP_108401693.1
          Length = 398

 Score =  174 bits (442), Expect = 3e-48
 Identities = 132/406 (32%), Positives = 200/406 (49%), Gaps = 49/406 (12%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPH 74
           P+ L+HGR   VWDT+GK Y+D + GI V  LGH +P +  A+Q Q  ++ H       +
Sbjct: 18  PVALTHGRGLRVWDTNGKAYLDALAGIAVNTLGHAHPQLTPALQDQVGKMIHSC-----N 72

Query: 75  GPYLALMEQLS-QFVPVSYPLAGMLTNSGAEAAENALKVARG-----ATGKRAIIAFDGG 128
             ++ L E L+ + V +S        NSG EA E A+K+AR         K  I+ ++  
Sbjct: 73  YYHIPLQEALAAKLVELSGMTNAFFCNSGLEANEAAIKLARKFGHMKGIEKPEIVVYEKA 132

Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVY--HLPYPSADTGVTCEQALKAMDRLFSVEL 186
           FHGR+LATL   G      +++ E  GP+   ++  P     V   +ALK          
Sbjct: 133 FHGRSLATLAATGN-----EKIKEGFGPMMEGYIRVP-----VNNIEALKKATE------ 176

Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246
              +VAA  FE +QGEGG   ++  + Q +R+ CD+R  L++IDE+Q G GRTG+ FA  
Sbjct: 177 GNPNVAAVFFETIQGEGGVKPMNTDYLQQVRQLCDKRDWLLMIDEVQCGMGRTGKWFAHQ 236

Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM 306
             GI PD++ LAK +  G+P+GAVV   +       G  G T+ GNP++  A + ++  M
Sbjct: 237 WSGIVPDVMPLAKGLGSGVPVGAVVAGPKAAHIFQPGNHGTTFGGNPLAMRAGVETIRIM 296

Query: 307 TD----ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPA 362
            +    +N+   G     A+    +  K       +  + G G M GI+     G     
Sbjct: 297 EEDKLLDNVLKVGAHLHAALHRELDGVKG------VKEIRGQGLMIGIDLDRPCG----- 345

Query: 363 QLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDIL 408
               +M+ A   GLLL  S  A  ++RL+ PL I     +E + IL
Sbjct: 346 ---VLMQRALDAGLLL--SVTADSVVRLVPPLIITEAEADEVVAIL 386


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: 432
Number of extensions: 17
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