GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Sphingomonas koreensis DSMZ 15582

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate Ga0059261_2226 Ga0059261_2226 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q3MDN5
         (390 letters)



>FitnessBrowser__Korea:Ga0059261_2226
          Length = 399

 Score =  158 bits (400), Expect = 2e-43
 Identities = 117/399 (29%), Positives = 188/399 (47%), Gaps = 19/399 (4%)

Query: 1   MQFAKRLEKIPPYLFAEINRKREALIAQGVDIINIGVGDPDKPTPAHILQAMREAIDEAS 60
           MQ +  L +I P     +  +   L  QG+D+I +G G+PD  TP  + +A  EAI +  
Sbjct: 1   MQTSAALNRIQPSATLAMTSRVFELKRQGIDVIGLGAGEPDFDTPDFVKEAAIEAIRKGI 60

Query: 61  NHNYPPYEGTQEFREAAVKWMERRFGVVDLNPNTEVVSSIGSKEAIHNTFLAFVEAGDYT 120
              Y   +GT E + A V    R  G+        V S  G K  + N F A ++AGD  
Sbjct: 61  T-KYTNVDGTPELKAAIVGKFARDNGLTYAENQISVNS--GGKHTLFNAFCATIDAGDEV 117

Query: 121 LIPDPGYPVYRTSTIFAGGEPFTMPLKAENKFLPDLDLIPEEVARKAKMLWVNYPNNPTG 180
           +IP P +  Y     FAGG+P  +   AE  +    + +   +  + K + +N P+NPTG
Sbjct: 118 VIPAPYWVSYPDVVEFAGGKPVFIAAGAEANYKIKPEQLEAAITARTKWVVLNSPSNPTG 177

Query: 181 ALATLEFFEELVAFCQQH-SILLCHDHAYSEMAYDGYKPPSVLQI-PGAKDIAIEFHSLS 238
           A  +    + L    ++H ++L+  D  Y  + YDG++  ++ Q+ P   +  +  + +S
Sbjct: 178 AAYSAAELKALGEVLERHPNVLIYADDMYEHILYDGFEFATIAQVCPSLYERTLTANGVS 237

Query: 239 KSYNMTGWRIGFAVGNAYAIQGLSQVKTNVDSGVFKAIQKAAIAAYNTDEVELQAVMSVY 298
           K+Y MTGWRIG+A G  + I+ + ++++   S      Q A++AA N D+  L+   + +
Sbjct: 238 KAYAMTGWRIGYAGGPQWLIKAMGKLQSQSTSNPCSVSQAASVAALNGDQSFLKDRAAAF 297

Query: 299 QNRRDIIVKGL-QSLGWPIEPPKATLYVW--------VPVPPGY---TSTEFTTLLLDKC 346
           Q RRD++V  L Q  G     P+   YV+           P G    T       LLD  
Sbjct: 298 QKRRDLVVSMLGQINGMNCPRPEGAFYVYPEFSQLIGKTTPKGLVIDTDETMVGYLLDDA 357

Query: 347 GIVVPPGVGYGVSGEGYFRIALTICEERLHEAIQRMQDA 385
            +    G  +G S     RI+    E+ L EA  R+Q+A
Sbjct: 358 KVAAVHGGAFGFSPA--LRISYATSEDVLAEACGRIQEA 394


Lambda     K      H
   0.319    0.137    0.414 

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: 366
Number of extensions: 19
Number of successful extensions: 3
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: 390
Length of database: 399
Length adjustment: 31
Effective length of query: 359
Effective length of database: 368
Effective search space:   132112
Effective search space used:   132112
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 (21.7 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