GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Dyella79:N515DRAFT_3308
          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:

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