GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Desulfacinum hydrothermale DSM 13146

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_212636831.1 B9A12_RS05520 aspartate aminotransferase family protein

Query= curated2:Q8TUZ5
         (389 letters)



>NCBI__GCF_900176285.1:WP_212636831.1
          Length = 449

 Score =  196 bits (499), Expect = 8e-55
 Identities = 140/433 (32%), Positives = 216/433 (49%), Gaps = 56/433 (12%)

Query: 10  YHMNTYSRFPVTLVPGEGARVWDDEGNEYIDLVAGIAVNVLGHCHPAVVEAVKEQVERLI 69
           ++ N    +PV +  GEG  +WD +GN YID   G  V  LGH  P ++EA+KEQ  R+ 
Sbjct: 11  FYRNLRKTYPV-VDRGEGIHIWDKDGNRYIDGSGGACVVSLGHGVPEILEAMKEQAARIS 69

Query: 70  HCSNLYYNEPQAE--AARLLAEAAPKDLNKVFFCNSGTESVECAIKLARKF------TGC 121
                ++    A   A RL+  A    L++V+F + G+E+VE A+K+ R++         
Sbjct: 70  FAHGSHFTSEAARECADRLVRLAPDPSLSRVYFLSGGSEAVETAVKVVRQYWREVGRPDK 129

Query: 122 TKFIAFEGGFHGRTMGALSATWKPEFREPFEPLVPEFEHV--------PYGD-------- 165
            K I+    FHG TMGA++       R  + P      H+        P+G         
Sbjct: 130 YKVISRWVSFHGNTMGAVALGGHTARRRHYHPHFLHTPHIEPAYCYRCPFGREPQTCSLE 189

Query: 166 -VNAVEKAID----DDTAAVIVEPVQGE-AGVRIPPEGFLRELRELCDEHGLLLIVDEVQ 219
               +E+ I     D  AA I EPV G  AG  +P +G+ + +RE+CD + + LI DEV 
Sbjct: 190 CAEQLERTIKYEGPDAVAAFIAEPVVGATAGALVPRDGYWQRIREICDTYEVKLIADEVM 249

Query: 220 SGMGRTGQFFAFEHEDVLPDIVCLAKGLGGG-VPVGATIAREEVAEAFEPGD----HGST 274
           +G+GRTG+ F  +H  V+PD++  AKGL  G  P+GA I +EE+ +A   G     HG T
Sbjct: 250 TGVGRTGRNFCLDHWSVVPDVIVSAKGLSSGYTPLGAVIVKEEIHDAIRSGSGAFVHGHT 309

Query: 275 FGGNPLACAAVCAAVSTVLEENLPEAAERKGKLAMRILSE--AEDVVEEVRGRGLMMGVE 332
           +  NPL+ A   A +  + E++L       G++ +  L       +V +VRG GL  GVE
Sbjct: 310 YSQNPLSVAVGAAVLRYLEEKDLIARCATMGEVFLEKLRGLLERPMVGDVRGLGLFAGVE 369

Query: 333 VGDDERAK-----------DVAREMLDRGAL-------VNVTSGDVIRLVPPLVIGEDEL 374
           +  ++  K            VA+E   RG +        +  +GD I L PP +I E+EL
Sbjct: 370 LVQNKETKAPFAPSGKISARVAQEAFRRGLITYPGSGGADGINGDHILLAPPFIITEEEL 429

Query: 375 EKALAELADALRA 387
           ++ +  L +A++A
Sbjct: 430 DEIVRILGEAIQA 442


Lambda     K      H
   0.318    0.137    0.405 

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: 482
Number of extensions: 29
Number of successful extensions: 8
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: 389
Length of database: 449
Length adjustment: 32
Effective length of query: 357
Effective length of database: 417
Effective search space:   148869
Effective search space used:   148869
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 Jul 25 2024. The underlying query database was built on Jul 25 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