GapMind for Amino acid biosynthesis

 

Alignments for a candidate for agx1 in Methylocapsa aurea KYG T

Align alanine—glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate WP_036257785.1 DL86_RS02895 1-aminocyclopropane-1-carboxylate deaminase

Query= metacyc::MONOMER-21143
         (387 letters)



>NCBI__GCF_000746085.1:WP_036257785.1
          Length = 396

 Score =  155 bits (392), Expect = 2e-42
 Identities = 115/381 (30%), Positives = 183/381 (48%), Gaps = 22/381 (5%)

Query: 15  AFSVLAEAKKLEAQGKPMIHLGLGQPDFKTPQHVVDAAKKALDEGHHGYVLSNGILECRQ 74
           A  VLA A++ EAQG+ +IHL +G+P    P+ V +AA  ALD    GY  + G    R+
Sbjct: 28  ALDVLANARRREAQGQDIIHLEIGEPGSPPPRAVREAAMAALDGRRIGYTEALGRPSLRE 87

Query: 75  AVTRKIKKLYNKDIDPERVLIMPGGKPTMYYAIQCFGEPGAEIIHPTPAFPIYESMINYT 134
            + R  +  Y   + PE +++  G       A     + GA +    P +P Y +++   
Sbjct: 88  RIARHYRDAYGLAVAPEHIVVTNGSSGGFLLAFLSLFDAGARVAIAAPGYPAYRNILEAL 147

Query: 135 GSTPVPYDLTEDKDLKFDPEKILSLITDKTRL--LILINPNNPTGSFVEKSAI-DVLAEG 191
           G   V  +++E       P  ++  +  KTRL  ++L++P NP+G+ +   A+ DV A  
Sbjct: 148 GIETVTIEVSEATRFVVTP-SMIEAVHAKTRLDGILLMSPANPSGTMMSAEALRDVCA-- 204

Query: 192 LKKHPHVAILSDEIYSRQIYDGKEMPTFFNYPDLQDRLIVLDGWSKAYAMTGWRMGWSVW 251
             +   VA +SDE+Y    Y G+   T   +      +IV + +SK + MTGWR+GW V 
Sbjct: 205 ACERLGVAFISDEVYHGLTY-GQPARTALEF---SSEVIVANSFSKYFCMTGWRIGWLVL 260

Query: 252 PEELIPHVNKLIINSVSCVNAPSQFAGIAALDGPDDAIHEMMVKFDQRRKLIHEGLNSLP 311
           P  ++  V +L  N    V   SQ    A  D  +D +  ++  + + R ++   LN LP
Sbjct: 261 PGHMVRTVERLQQNLAVSVGLLSQIGAEAVFDAQED-LQRVLSGYARNRAIL---LNELP 316

Query: 312 GVECSLPG-----GAFYAFPKVIGTGMNGSEFAKKCMHEAGVAIVPGTAFGKT-CQDYVR 365
             +  L G     GAFY +  V     +   F  K + E GVA  PG  F +T  +  VR
Sbjct: 317 --DMGLGGFHPVDGAFYIYVDVSRLTDDSGHFCAKMLDEIGVAATPGLDFDRTRGRGAVR 374

Query: 366 FSYAASQDNISNALENIKKML 386
           FS+A  + +I  A+  +K  L
Sbjct: 375 FSFAGPEGDIVEAMRRLKSWL 395


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: 351
Number of extensions: 26
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: 396
Length adjustment: 31
Effective length of query: 356
Effective length of database: 365
Effective search space:   129940
Effective search space used:   129940
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 Apr 10 2024. The underlying query database was built on Apr 09 2024.

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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