GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisC in Denitrovibrio acetiphilus DSM 12809

Align Histidinol-phosphate aminotransferase; EC 2.6.1.9; Imidazole acetol-phosphate transaminase (uncharacterized)
to candidate WP_013009503.1 DACET_RS00755 class I and II aminotransferase

Query= curated2:A4XMY1
         (358 letters)



>NCBI__GCF_000025725.1:WP_013009503.1
          Length = 323

 Score =  106 bits (265), Expect = 7e-28
 Identities = 97/350 (27%), Positives = 159/350 (45%), Gaps = 44/350 (12%)

Query: 15  GKPISEVKRELGL--EKVIKLASNENPLGPSENVKKAIKESLDDLSLYPDGNCTELKLKL 72
           G  I EV   LG+    V   +SN +P     +V K+       LS  P+     L    
Sbjct: 7   GGDIHEVANYLGVPASDVYDYSSNVSPYPIDISVDKSA------LSRLPEPYSRTLAKAF 60

Query: 73  AKKLNVKPTQIIFGAGSDEITQLIASIFINPGDNSIMARPSFPRYETVTK-----VMGGI 127
           A+K       +   AG+ E   +I  IF   G ++ +  P++  Y+   K     V   +
Sbjct: 61  AEKYGYDEKMVCITAGTTEAIDIICRIFA--GKSACIKNPTYADYKKFCKNNKITVRNSL 118

Query: 128 PIEIPLKNYTHDLEEFSKHINERTRVIWICNPNNPTGTIVKKDELYNFIKSVPSEIAVVV 187
           P+E+                       +ICNPNNPTG    ++ L  + K+ PS + V+ 
Sbjct: 119 PVEL----------------------YFICNPNNPTGQTCPREFLPTYFKTSPSTLFVID 156

Query: 188 DQAYKEYIDDPEYPDAIHWLDEFKNLIVLQTFSKIYGLASLRIGYAIASEEIIEKLNRVR 247
           +     +ID+P        LD   N+ +L++FSKIYGL  LR+G  IA+E++IEK+    
Sbjct: 157 ESYMPFHIDEPMQTLMGEKLD---NIAILRSFSKIYGLPGLRLGAVIANEKLIEKMKNQM 213

Query: 248 PPFNVNHVAQIAAIAALDDQEHIEKAKELNKKSLEFFYKSFEEMK-LPYIKSYGNFVMVD 306
            P++VN +AQ A +  L D +    AK LN   ++F  K  E +  L  + S  N++M  
Sbjct: 214 SPWSVNSLAQSAGLELL-DVDTAPIAKRLNDIKVQFL-KELESIDFLEAVDSDVNYMMCK 271

Query: 307 VTK-DAVEVFKKLLLKGIIVRPGDIFDMPTYIRVTTGLESDNMEFIKALK 355
           + +  + E+F+  L + +++R    F+      V   +  D    ++ALK
Sbjct: 272 MKRGTSDELFRHCLNQRVLIRDCSNFEGLDNRHVRFAMADDMSPLLEALK 321


Lambda     K      H
   0.318    0.138    0.392 

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: 268
Number of extensions: 14
Number of successful extensions: 2
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: 358
Length of database: 323
Length adjustment: 28
Effective length of query: 330
Effective length of database: 295
Effective search space:    97350
Effective search space used:    97350
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: 49 (23.5 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