GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Synechococcus elongatus PCC 7942

Align Arginine biosynthesis bifunctional protein ArgJ, chloroplastic; EC 2.3.1.35; EC 2.3.1.1 (characterized)
to candidate Synpcc7942_1896 Synpcc7942_1896 bifunctional ornithine acetyltransferase/N-acetylglutamate synthase protein

Query= SwissProt::Q9ZUR7
         (468 letters)



>FitnessBrowser__SynE:Synpcc7942_1896
          Length = 414

 Score =  436 bits (1120), Expect = e-127
 Identities = 233/417 (55%), Positives = 301/417 (72%), Gaps = 8/417 (1%)

Query: 56  QGSWKQIAGGVTAAKGFKAAGMYAGLRAAGKKPDLALVTCDVEAVAAGVFTTNVVAAAPV 115
           Q +W++I+GG+TA +GF+AAG+ AGL+A+G+ PDLAL+  + +A+AA VFTT+ V AA V
Sbjct: 2   QAAWQEISGGLTAPRGFQAAGITAGLKASGQ-PDLALIVSESDAIAAAVFTTSQVRAACV 60

Query: 116 VYCKKVLETSKTARAVLINAGQANAATGDAGYQDMLDCVGSIATLLKVKPEEVLIESTGV 175
            + ++ L+ +  ARA+L N+GQANAATGD G+ D ++    +A  L++   +VL+ STGV
Sbjct: 61  DFSRQQLDGNSIARAILCNSGQANAATGDQGWSDAVESAEQLAQALQIPSHQVLVASTGV 120

Query: 176 IGQRIKKEELLHALPTLVNSRSDSVEEADSAAVAITTTDLVSKSVAVESQVGGIKIRVGG 235
           IGQRIK E L   +P  + + S   E   +AA AI TTDLV+K +A+E  +G   +R+GG
Sbjct: 121 IGQRIKMEALRTGIPQAIAALSP--EGGPAAAQAILTTDLVAKQIALELPLGDRTVRIGG 178

Query: 236 MAKGSGMIHPNMATMLGVITTDALVESDIWRKMVKVAVNRSFNQITVDGDTSTNDTVIAL 295
           +AKGSGMIHPNMATML  IT DA V   +W++M+  AV+RSFNQITVDGDTSTND V AL
Sbjct: 179 IAKGSGMIHPNMATMLSFITCDAAVSPQLWQEMLSRAVDRSFNQITVDGDTSTNDCVFAL 238

Query: 296 ASGLSGSPSISSLNCKEAAQLQACLDAVMQGLAKSIAWDGEGATCLIEVTVKGTETEAEA 355
           A+G S +P+I+      A QL+A L AV Q LAK+IA DGEGATCLIEV VKGT  +A A
Sbjct: 239 ANGQSRTPAITERG-PIADQLEAMLTAVCQHLAKAIARDGEGATCLIEVQVKGTADDAAA 297

Query: 356 AKIARSVASSSLVKAAVYGRDPNWGRIAAAAGYAGVSFQMDKLKISLGEFSLMESGQPLP 415
             IAR++A SSLVK+A++GRDPNWGRIAAAAG AGV F  + L + LGEF L+ +GQPLP
Sbjct: 298 RAIARTIAGSSLVKSAIFGRDPNWGRIAAAAGRAGVQFNSENLGVRLGEFELLRNGQPLP 357

Query: 416 FDRDGASNYLKKTGE----VHGTVTIDISVGDGAAIGKAWGCDLSYDYVKINAEYTS 468
           FDR+ AS YL+           TV I + VG G   G AWGCDLSYDYV+INAEYT+
Sbjct: 358 FDRNAASQYLRDRAAGAYLQDDTVLIQVDVGAGTGQGVAWGCDLSYDYVRINAEYTT 414


Lambda     K      H
   0.315    0.129    0.364 

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: 504
Number of extensions: 15
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: 468
Length of database: 414
Length adjustment: 32
Effective length of query: 436
Effective length of database: 382
Effective search space:   166552
Effective search space used:   166552
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 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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