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_1288 Ga0059261_1288 Aspartate/tyrosine/aromatic aminotransferase

Query= BRENDA::Q2RK33
         (390 letters)



>FitnessBrowser__Korea:Ga0059261_1288
          Length = 401

 Score =  330 bits (847), Expect = 3e-95
 Identities = 162/387 (41%), Positives = 235/387 (60%), Gaps = 3/387 (0%)

Query: 2   QEARRIRELPPYLFARIEKKIAEARERGVDIISLGIGDPDMPTPSHVIDKLVAEAHNPEN 61
           +E  RI+ LPPY+ A +    A AR  G DII LG+G+PD+P P HVIDKL   A  P  
Sbjct: 3   EEFYRIKRLPPYVIAEVNGMRAAARAAGEDIIDLGMGNPDLPPPQHVIDKLCEVAQKPSA 62

Query: 62  HRYPTSEGLLAFRQAVADWYQRLYGVDLDPRREVVTLIGSKEGIAHISLCYVDPGDINLV 121
           H Y  S+G+   R+A A++Y R +GVD+DP  EVV  +GSKEG+A ++     PGD+ L 
Sbjct: 63  HGYSQSKGIPGLRRAQANYYGRRFGVDVDPESEVVVTMGSKEGLASLATAITAPGDVILA 122

Query: 122 PDPGYPVYNIGTLLAGGESYFMPLTAANGFLPDLGAIPSDVARRAKLMFINYPNNPTGAV 181
           P+P YP++  G ++AG     +P T    +   L    +    R  ++ +NYP+NPT   
Sbjct: 123 PNPSYPIHTFGFIIAGATIRAVPTTPDEHYFESLERAMNFTVPRPSILVVNYPSNPTAET 182

Query: 182 ADLKFFQEVVEFARSYDLIVCHDAAYSEITYDGYRAPSFLQAPGAKEVGIEFNSVSKPYN 241
            DL F++ +V +A+   + +  D AYSE+ YDG    S LQ  GAK+V IEF S+SK Y+
Sbjct: 183 VDLAFYERLVAWAKENKVWIISDLAYSELYYDGKPTVSILQVKGAKDVAIEFTSLSKTYS 242

Query: 242 MTGWRLGWACGRADVIEALARIKSNIDSGAFQAVQYAGIAALTGPQEGLAEVRRVYQERR 301
           M GWR+G+A G   +I A+ R+KS +D GAF  VQ A  AAL GPQ+ +   R++Y +RR
Sbjct: 243 MAGWRIGFAVGNKQLIAAMTRVKSYLDYGAFTPVQAAACAALNGPQDIVEANRQLYHKRR 302

Query: 302 DIIVEGFNSLGWHLEKPKATFYVWAPVPRGYT---SASFAEMVLEKAGVIITPGNGYGNY 358
           D++VE F   GW +  P A+ + WAP+P       S  F++ +L  A V + PG GYG  
Sbjct: 303 DVLVESFGRAGWDIPAPPASMFAWAPLPPALAHLGSLEFSKQLLSHAKVAVAPGVGYGEN 362

Query: 359 GEGYFRIALTISKERMQEAIERLRRVL 385
           GEG+ RIA+  +++R+++A   +R+ L
Sbjct: 363 GEGFVRIAMVENEQRLRQAARNVRKYL 389


Lambda     K      H
   0.320    0.139    0.421 

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: 474
Number of extensions: 16
Number of successful extensions: 1
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: 401
Length adjustment: 31
Effective length of query: 359
Effective length of database: 370
Effective search space:   132830
Effective search space used:   132830
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