GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Desulfurobacterium atlanticum DSM 15668

Align alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_089323728.1 CHB58_RS08740 succinyldiaminopimelate transaminase

Query= BRENDA::D2Z0I0
         (402 letters)



>NCBI__GCF_900188395.1:WP_089323728.1
          Length = 387

 Score =  169 bits (427), Expect = 2e-46
 Identities = 120/383 (31%), Positives = 195/383 (50%), Gaps = 20/383 (5%)

Query: 10  VKKLPKYVFAMVNELKYQLRREGEDIVDLGMGNPDIPPSQHIIDKLCEVANRPNVHGYSA 69
           ++ +  Y    + + K  L+++G+ I D G G+P  P +  I + +      P V  Y  
Sbjct: 5   LRNMKPYPMDELVKAKELLKKDGKKIYDFGTGDPKEPTAPFIREAVKTAI--PEVSQYPT 62

Query: 70  SKGIPRLRKAICDFYKRRYGVELDPERNAIMTIGAKEGYSHLMLAMLEPGD---TVIVPN 126
            KG   LR+AI  ++KRR+ VELD E+  I + G+KE   H  L  ++       VI   
Sbjct: 63  VKGRKDLREAISSWFKRRFDVELDSEKEIIPSAGSKEAIFHFPLVFIDADSDKKRVIFGT 122

Query: 127 PTYPIHYYAPIICGGDAISVPILPEEDFPEVFLRRLYDLIKTSFRKPKAVVLSFPHNPTT 186
           P YP++    +   G    +P      + E FL RL  + +   ++ K V L++PHNPT 
Sbjct: 123 PAYPVYERGTLFAQG----IPTSYTLKYEEGFLLRLDKMPEEILKETKIVWLNYPHNPTG 178

Query: 187 LCVDLEFFQEVVKLAKQEGIWIVHDFAYADLGFDGYTPPSILQVEGALDVAVELYSMSKG 246
               L +F+++ ++ ++  I +  D  Y ++ F+   PPS LQV G  +V V  +S+SK 
Sbjct: 179 ATAPLSYFEDMYQICREYDIIMCSDECYTEIYFE-EKPPSALQV-GKENVVV-FHSLSKR 235

Query: 247 FSMAGWRVAFVVGNEMLIKNLAHLKSYLDYGVFTP--IQVASIIALESPYEVVEKNREIY 304
             M G+R  FV G+  +I+     +S   +GV +P  IQV +  A +     VE+ R I+
Sbjct: 236 SGMTGYRSGFVAGDSRIIQEYLRFRS--SFGVGSPDFIQVGAREAWKDESH-VEERRLIF 292

Query: 305 RRRRDVLVEGLNRVGWEVKKPKGSMFVWAKVPEEVGMNSLDFSLFLLREAKVAVSPGIGF 364
           R+++++  +     G+E    K S + W KVP   G+ S D++  LL+   + VSPG  F
Sbjct: 293 RKKKEIFEKFFKEEGFEFLDVKASFYFWVKVP--FGLTSKDYAFHLLKYG-IVVSPGEFF 349

Query: 365 GEYGEGYVRFALVENEHRIRQAV 387
           G  GEG+ R ALV +     +AV
Sbjct: 350 GSGGEGFFRIALVPSVDECEEAV 372


Lambda     K      H
   0.322    0.141    0.425 

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: 7
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: 402
Length of database: 387
Length adjustment: 31
Effective length of query: 371
Effective length of database: 356
Effective search space:   132076
Effective search space used:   132076
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 (21.9 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

Links

Downloads

Related tools

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