GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Marinobacter adhaerens HP15

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate GFF3915 HP15_3855 2,4-diaminobutyrate 4-transaminase

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



>FitnessBrowser__Marino:GFF3915
          Length = 422

 Score =  159 bits (401), Expect = 2e-43
 Identities = 126/411 (30%), Positives = 202/411 (49%), Gaps = 26/411 (6%)

Query: 15  PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNP----AVVEAIQAQATRLTHYAFN 70
           P+  +  +NA ++  DGK Y+DF+ G G LN GH N     A++E I+A         F 
Sbjct: 19  PVIFNRAKNAHLYTEDGKEYLDFLAGAGSLNYGHNNDTLKKALLEYIEADGVSQGLDMFT 78

Query: 71  AAPHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFH 130
            A H    +  + +     + Y +      +G    E ALK+AR   G+  II+F  GFH
Sbjct: 79  TAKHDFMESYKKHILDPRGLDYKMQ-FTGPTGTNCVEAALKLARKVKGRSGIISFTNGFH 137

Query: 131 GRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCE-QALKAMDRLFSV-ELAV 188
           G T+  +   G     K   G +  P+ ++ +   D  +  +   L  MD+L S      
Sbjct: 138 GVTMGAVATTGN----KHHRGGVGTPLGNVDFMFYDGYLGDDVDTLAIMDKLLSDGSSGF 193

Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248
           E  AA I E VQGEGG  A    + + L   C +  IL+I+D+IQ+G GRTG+ F+F   
Sbjct: 194 ELPAAVIVEAVQGEGGLNACRAEWLKGLSELCKKHDILLILDDIQAGNGRTGEFFSFEFA 253

Query: 249 GIEPDLLLLAKSIAG-GMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQ-M 306
           GI+PD++ ++KS++G G+P+  V+ + EL    P G   GT+ GN ++   A A++    
Sbjct: 254 GIKPDIVTVSKSLSGYGLPMALVLFKPELDVWDP-GEHNGTFRGNNMAFITARAAVENYW 312

Query: 307 TDENLATWGERQEQAIVSRYERWKASGLSPYIG--RLTGVGAMRGIEFANADGSPAPAQL 364
            D+  A   + + + +    +    S    Y G  ++ G G MRGIE  +AD +      
Sbjct: 313 KDDAFANEVKAKTEVLGDALQ----SICDKYPGQFKMKGRGLMRGIEAKHADIT------ 362

Query: 365 AKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
             + + A   GL++  SG    +I+ L PLT   E L++G  +L + + E+
Sbjct: 363 GPITKRAFEHGLIIETSGPNDEVIKCLMPLTTSEEDLKKGAALLAKSVDEI 413


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: 425
Number of extensions: 30
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: 422
Length adjustment: 32
Effective length of query: 384
Effective length of database: 390
Effective search space:   149760
Effective search space used:   149760
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:

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