GapMind for Amino acid biosynthesis

 

Aligments for a candidate for lysN in Dyella japonica UNC79MFTsu3.2

Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate N515DRAFT_3308 N515DRAFT_3308 acetylornithine/N-succinyldiaminopimelate aminotransferase

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



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3308 N515DRAFT_3308
           acetylornithine/N-succinyldiaminopimelate
           aminotransferase
          Length = 411

 Score =  202 bits (513), Expect = 2e-56
 Identities = 140/406 (34%), Positives = 203/406 (50%), Gaps = 33/406 (8%)

Query: 16  ITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHG 75
           + L HG+ A VWDT+G+ Y+D   GI V  LGH +P +V+A+  QA +L H + N     
Sbjct: 27  VVLDHGKGARVWDTEGRDYVDLGAGIAVNALGHQDPDLVDALVTQARKLWHSS-NVFYTE 85

Query: 76  PYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARG-------ATGKRAIIAFDGG 128
           P L L E+L Q     +     L NSG EA E A+K+ R        A  +R I+ F G 
Sbjct: 86  PPLHLAEELVQ--ASGFAERVFLCNSGTEANEAAIKLVRKWAASKGRAPEQRVILTFRGS 143

Query: 129 FHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAV 188
           FHGRTLA +    +   Y++    LPG   +L +            +  ++  F    A 
Sbjct: 144 FHGRTLAAVTATAQ-PKYQENYEPLPGGFRYLDFND----------VAGLEAAF----AQ 188

Query: 189 EDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRL 248
            DVAA + EPVQGEGG L   PAF +  R  CD    L+++DEIQ G GRTG  FA  + 
Sbjct: 189 GDVAAVMLEPVQGEGGVLPASPAFIRRARELCDTHEALLVLDEIQCGMGRTGTLFAHAQD 248

Query: 249 GIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTD 308
           G+ PD++ LAK++  G P+GA++   ++   +  G  G T+ GNP++ A A  +L ++  
Sbjct: 249 GVTPDIVTLAKALGCGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALRKLAS 308

Query: 309 ENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVM 368
             L     +Q QA+  R       G       + G G M G   A A       +  +V+
Sbjct: 309 AELMANVAKQAQAL--RDGLAAIDGELKLFAEVRGRGLMLGAVLAEA----YKGRAGEVL 362

Query: 369 EAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414
           + A A GLL++ +G    ++R + PL I    L EGL  L   LA+
Sbjct: 363 DHAAAHGLLVLQAGP--DVLRFVPPLNITDADLAEGLARLRAALAD 406


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: 435
Number of extensions: 23
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: 411
Length adjustment: 31
Effective length of query: 385
Effective length of database: 380
Effective search space:   146300
Effective search space used:   146300
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 Aug 03 2021. The underlying query database was built on Aug 03 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 paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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