GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Sphingomonas koreensis DSMZ 15582

Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (characterized)
to candidate Ga0059261_3674 Ga0059261_3674 adenosylmethionine-8-amino-7-oxononanoate transaminase

Query= SwissProt::Q93R93
         (395 letters)



>FitnessBrowser__Korea:Ga0059261_3674
          Length = 415

 Score =  166 bits (420), Expect = 1e-45
 Identities = 127/395 (32%), Positives = 189/395 (47%), Gaps = 32/395 (8%)

Query: 30  LIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQTLPTPMR 89
           L+   +GA +  A+G   ID +  + V   GHGNP +V A++ QAE L  +     T   
Sbjct: 21  LVTHAEGAVLHTADGRRVIDAISSWWVTTHGHGNPRIVAAIRDQAEKLDQLIFAGWTHEP 80

Query: 90  GEFY-RTLTAILPPELNRVFPVNSGTEANEAALKFARAHTG-----RKKFVAAMRGFSGR 143
            E   R L A++P  L+ VF  +SG+ + E A+K A  H       R + +     + G 
Sbjct: 81  AETVARDLVAMMPRPLDHVFFSDSGSTSVEVAIKMALGHFANRGEPRHRIIVMQGSYHGD 140

Query: 144 TMGSLSVTWEPKYREPFLPLVEPVEFIP-------YNDVEALKRAVDEET--AAVILEP- 193
           T+G +SV     +   + PL+  V+ IP       Y  ++AL++   +    AA+I+EP 
Sbjct: 141 TIGGMSVGARGVFNRSYAPLLFDVDTIPFPEGANEYRALDALEQLCAQSPLPAAMIVEPL 200

Query: 194 VQGEGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLA 253
           V G GG++   P  LRA REI    G L I DE+ TG GRTG   A E   +VPD+L L+
Sbjct: 201 VLGAGGMKMYPPGVLRAMREICAAHGVLFIADEVMTGWGRTGTLLACEQAAVVPDLLCLS 260

Query: 254 KAL-GGGVPLGVAVMREEVARSMPKGG------HGTTFGGNPLAMAAGVAAIRYLERTRL 306
           K L GG +PL V +   E+  S           H +++  NP+A AA  A +       +
Sbjct: 261 KGLTGGSLPLAVTMATPEIFESHRSKDRSKMFFHSSSYTANPIACAAAAANLAIWREEPV 320

Query: 307 WERAAELGPWFMEKLRAIPSPKIREVRGMGLMVGLELKEKAAPYIARLE-------KEHR 359
            ER A L        RA+ + K+  +R +G +V +E++     Y++ L        +E  
Sbjct: 321 LERVAHLAHRQRSYSRAL-AGKVNNLRQLGTIVAMEVQAPQGAYLSVLGPRLMSFFRERN 379

Query: 360 VLALQAGPTVIRFLPPLVIEKEDLERVVEAVRAVL 394
           VL    G TV   +PP  I  EDL RV   +   L
Sbjct: 380 VLLRPLGNTVY-VMPPYCISDEDLARVYTVIGEAL 413


Lambda     K      H
   0.319    0.137    0.403 

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: 377
Number of extensions: 15
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: 395
Length of database: 415
Length adjustment: 31
Effective length of query: 364
Effective length of database: 384
Effective search space:   139776
Effective search space used:   139776
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