GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Acidimicrobium ferrooxidans DSM 10331

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_015798369.1 AFER_RS04845 aspartate aminotransferase family protein

Query= curated2:O27392
         (390 letters)



>NCBI__GCF_000023265.1:WP_015798369.1
          Length = 431

 Score =  236 bits (602), Expect = 9e-67
 Identities = 145/423 (34%), Positives = 211/423 (49%), Gaps = 39/423 (9%)

Query: 5   EIIELERKFI---MQTYTRQPIVLSHGKGATVWDIEGNSYIDCFAGVAVNSIGHAHPKVA 61
           ++IE  R+ +   +  Y  +PI L  G+G  VWD  G  Y+DCF G+   S+GH  P++ 
Sbjct: 2   DLIERHRRVLPSWLSLYYDEPIELDRGEGCWVWDAHGERYLDCFGGILTTSVGHNVPEIV 61

Query: 62  LAICHQAQRLIHSSNIYYTREQVELAKLLTAIS--PHDRVFFANSGAEANEGAIKLARKF 119
            AI  QA R+IHSS +Y  R  +ELA+ L   S  P  +VFF  SG EAN+ A+ LA   
Sbjct: 62  SAISDQAARVIHSSTLYLNRPMIELAERLAKASGIPDAKVFFTTSGTEANDAALLLATAA 121

Query: 120 TGKSEIIAAENSFHGRTLATVTATGQKKYS-EPFRPLP--------------EGFKHVPY 164
            G +++ A  NS+HGR+   +  TG + +S   + PL                G     Y
Sbjct: 122 LGSNQVFALRNSYHGRSFTEIAVTGNRTWSPTSYSPLSVSWLQGGSRLRGPLAGLSDAEY 181

Query: 165 GDIG------AMADAVGDETAAIILEPVQGEGGVIIPPEGYLKDVQELARQNDVLLILDE 218
              G      A+        AA+I EP+QG GG  +PP+GY  ++  + ++  +L I DE
Sbjct: 182 VARGVADLEDALLTTTAGRVAALIAEPIQGVGGFCLPPDGYFGELWRVTQREGILWISDE 241

Query: 219 VQTGFGRTGAMF-ASQLFGVEPDITTVAKAMGGGYPIGAVLANERVAMAFEPGDHGSTFG 277
           VQTGFGRTG  F   +  G+ PD+ T AK +G G  +  V+    V  A       STFG
Sbjct: 242 VQTGFGRTGEHFWGYEAHGITPDLITFAKGVGNGMSLAGVIGRAEVMDALGTNSI-STFG 300

Query: 278 GNPWGCAAAIATIEVLMDEKLPERAAKMGSYFLGRLRQVLHGCDAVRDIRGVGLMIGIEI 337
           G+P   AA +AT + ++D  L   A   G+     L  +     A+ ++RG GLM G+E+
Sbjct: 301 GSPITAAAGVATFDYIIDHDLMANARARGAELREGLDAIARSTPAIGEVRGKGLMQGVEL 360

Query: 338 ---------DGECAGVVDAAREMGVLINCTA--GKVIRIVPPLVIKKEEIDAAVDVLGHV 386
                           ++AAR  GVLI      G V+RI PP+ I  E+I+ A++     
Sbjct: 361 VWPGTVEPAPELATRALEAARREGVLIGKGGLHGNVLRIAPPMTISAEQIEHALEAFRRS 420

Query: 387 ISD 389
            +D
Sbjct: 421 FAD 423


Lambda     K      H
   0.320    0.138    0.404 

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: 445
Number of extensions: 26
Number of successful extensions: 6
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: 390
Length of database: 431
Length adjustment: 31
Effective length of query: 359
Effective length of database: 400
Effective search space:   143600
Effective search space used:   143600
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 (21.8 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