GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysJ in Dinoroseobacter shibae DFL-12

Align [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate 3609962 Dshi_3343 aminotransferase class-III (RefSeq)

Query= curated2:Q976K0
         (387 letters)



>FitnessBrowser__Dino:3609962
          Length = 413

 Score =  148 bits (374), Expect = 2e-40
 Identities = 106/343 (30%), Positives = 172/343 (50%), Gaps = 29/343 (8%)

Query: 4   IQLYGDRGLTIVKGEGQYVWDISGTKYLDLHTGIGVAFLGHRNRRVIEYLSRQMENIMTL 63
           +  + D  L IV+GEG ++WD  G +YLD +    V  +GH + RV++ ++RQ   + T 
Sbjct: 16  VPTFYDPPLHIVRGEGVWLWDAGGRRYLDCYNN--VPHVGHCHPRVVDAIARQARVLNTH 73

Query: 64  STSFSTPIRDEMLKELDPLKPDKMDNIILLNSGTEAVEAALKTARKITGRKKIIAFKNSF 123
           +      + D  ++ L     + +D  +L+ +G+EAV+ AL+ AR  TG+  +IA  N++
Sbjct: 74  TRYLHEGVLD-YIERLTGTMDNGLDQALLVCTGSEAVDVALRMARAATGKTGLIATDNTY 132

Query: 124 HGRTAGSLSVTWNK----------RYREPFEPLMSPVQFLTY--NNIDELKNIDEQTAAV 171
           HG T     ++  +          R     EP      F  +      EL+      AA+
Sbjct: 133 HGNTTAVAQLSTRRPPIGGYSDHVRLVPAPEPGTDGAAFGAHVARAAAELETAGHGVAAL 192

Query: 172 IVEPIQGESGVIPANEDFMKALREQTQKVGALLVVDEVQTGFGRTGKV-WAYQHYGIIPD 230
           IV PI    G+      F++      +  G LL+ DEVQ GFGR G V W YQ  GI PD
Sbjct: 193 IVCPIFANEGLPCLPRGFLEPAVAALRTRGGLLISDEVQPGFGRLGDVFWGYQALGIAPD 252

Query: 231 LLTAGKAIGGGFPVSALFLPDWIAEKLEEG-DHGSTYGGNPMAMAAVTAASKVLKEDNVV 289
           ++T GK++G G+PV+ +     I     E   + +T+GG+P+A AA  A   VL+++ +V
Sbjct: 253 VVTLGKSMGNGYPVAGVVARTEIMGAFREAFGYFNTFGGSPVAAAAAMAVLDVLEDEGLV 312

Query: 290 EQASIKGEIFKKILREKLSDLKSVRE-----IRGKGLMIGIEI 327
           E A       K++ R  L  L+++R      +RG GL   +++
Sbjct: 313 ENA-------KRVGRYTLERLQALRHPAIDGVRGYGLAFALDL 348


Lambda     K      H
   0.318    0.135    0.383 

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: 350
Number of extensions: 19
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: 387
Length of database: 413
Length adjustment: 31
Effective length of query: 356
Effective length of database: 382
Effective search space:   135992
Effective search space used:   135992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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