GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD in Caldicellulosiruptor kronotskyensis 2002

Align Acetylornithine aminotransferase; ACOAT; EC 2.6.1.11 (uncharacterized)
to candidate WP_013430453.1 CALKRO_RS07580 glutamate-1-semialdehyde 2,1-aminomutase

Query= curated2:O30156
         (375 letters)



>NCBI__GCF_000166775.1:WP_013430453.1
          Length = 426

 Score =  165 bits (418), Expect = 2e-45
 Identities = 104/307 (33%), Positives = 161/307 (52%), Gaps = 14/307 (4%)

Query: 21  VIERGEGCYVYDVNGKRYLDLVAGIATVSIGHCNSHLVERLKEQLEKLIHISNLYYTTPQ 80
           +I +G+GC+++DV+G  Y+D V     + +GHC+  +V R+KE +E+ I       T  +
Sbjct: 37  IISKGKGCHIFDVDGNEYIDFVLSWGAMILGHCDPDVVNRIKEVVEEQIAFG--APTEIE 94

Query: 81  VELAEKLSEIAGMDRFFFCNSGAEAVEAALKFARRATGRKKFVSFTGDFHGR----TMGA 136
            E+A+ + E A +D   F NSG EA   A++ A+  TG+KK V F G +HG        A
Sbjct: 95  YEMAKLVCETAQIDMVRFVNSGTEATMTAVRLAKGYTGKKKIVKFAGCYHGHHDIFLKEA 154

Query: 137 LSVTHKEKFRKPFEPLVSPVEFAEFNNPESLEKVVDE---ETAAVIVELVQGEAGVYPAD 193
            S   + + +   E +V      E+NN +S+EK   E   E AAVI+E V G  G   + 
Sbjct: 155 GSAVAELRLKGIDEDIVQNTIVVEYNNLDSVEKAFKENKDEIAAVIIEPVAGNMGTVASK 214

Query: 194 REFVKAIEELREKYGFLLIVDEVQTGFGRTGRWFAKDHYGIEPDMITMAKAMGSGVPIGC 253
           +EF++ + E+   YG +LI DEV TGF R     A+  Y +EPD+IT+ K +G G+P G 
Sbjct: 215 KEFLQTLREICNFYGSVLIFDEVITGF-RLSLKGARALYNVEPDLITLGKIIGGGLPCGA 273

Query: 254 CALKEEVAEKIQVGDH---GSTFGGNPLACTAALATIEVI-EREGLVENSARMGEYFVKR 309
              K+E+ + +    +     T  GNP+  +   ATI+ + E      N   +   F K 
Sbjct: 274 VGGKKEIMQCLAPQGNVFQAGTMSGNPIVMSVGYATIKKLKENPHFYSNLEMLAGKFEKE 333

Query: 310 LKESFEN 316
           L + F N
Sbjct: 334 LTQVFSN 340


Lambda     K      H
   0.320    0.138    0.398 

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: 405
Number of extensions: 25
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: 375
Length of database: 426
Length adjustment: 31
Effective length of query: 344
Effective length of database: 395
Effective search space:   135880
Effective search space used:   135880
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 26 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