GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Synechococcus elongatus PCC 7942

Align Probable 2-isopropylmalate synthase; EC 2.3.3.13; Alpha-IPM synthase; Alpha-isopropylmalate synthase (uncharacterized)
to candidate Synpcc7942_0428 Synpcc7942_0428 putative alpha-isopropylmalate/homocitrate synthase family transferase

Query= curated2:Q8TYB1
         (499 letters)



>FitnessBrowser__SynE:Synpcc7942_0428
          Length = 542

 Score =  217 bits (552), Expect = 9e-61
 Identities = 163/519 (31%), Positives = 259/519 (49%), Gaps = 36/519 (6%)

Query: 5   VRIFDTTLRDGEQTPGVSLTVEEKVEIARKLDEFGVDTIEAGFPVASEGEFEAVRAIAGE 64
           + ++DTTLRDG Q  G+SL++E+K+ IA  LD  GV  IE G+P A+  + +    +   
Sbjct: 9   IAVYDTTLRDGAQREGLSLSLEDKLRIAHCLDRLGVKFIEGGWPGANPKDVQFFWELQQR 68

Query: 65  ELD-AEI---CGLARC--VKGD---IDAAIDADVDCVHVFIATSDIHLRYKLEMSREEAL 115
            L  AE+   C   R   + G+   + A + A    V +F  + D+H+   L+ S +E L
Sbjct: 69  PLQQAEVVAFCSTRRPGQIAGEDELLKALLAAGTTWVTIFGKSWDLHVVEGLKTSLDENL 128

Query: 116 ERAIEGVEYASDHGVTVEFSAE---DATRTDRDYLLEVYKATVEAGADRVNVPDTVGVMT 172
               + + Y       V + AE   D    + DY L+   A +EAGA+ + + DT G   
Sbjct: 129 VMISDSIAYLRTCDRRVIYDAEHWFDGYLANPDYALQTLAAAIEAGAEWIVLCDTNGGCL 188

Query: 173 PPEMYRLTAEVVDA--------VDVPVSVHCHNDFGMAVANSLAAVEAGAEQVHVTVNGI 224
           P ++  + A V+D             + +H HND   AVAN++AAV+AGA  VH T+NG 
Sbjct: 189 PHQISEIVAAVLDRFPSLAPDQTGPQLGIHTHNDSETAVANAIAAVQAGARMVHGTINGY 248

Query: 225 GERAGNASLEQVV--MALKALYDIELDVRTEMLVEL---SRLVERLTGVVVPPNTPIVGE 279
           GER GNA+L  V+  + LK  YD    V TE L++L   SRLV  +  +    +   VG+
Sbjct: 249 GERCGNANLCSVIPNLQLKLGYDC---VETEQLMQLTATSRLVSEIVNLAPDDHAAYVGQ 305

Query: 280 NAFAHESGIHSHGVIKKAETYEPIRPEDVGHRRRIVLGKHAGRHAIKKKLEEMGIEV--T 337
           +AFAH+ GIH   V +   TYE IRPE VG+ RRIV+ + +G   +  K    G+++   
Sbjct: 306 SAFAHKGGIHVSAVERNPLTYEHIRPEQVGNLRRIVISEQSGLSNVLAKARSFGLDLQRN 365

Query: 338 EEQLDEIVRRVKELGDKGKR--VTEDDLEAIARDVVGEVPESEAAVKLEEIAVMTGNKFT 395
           +    +++ R+KEL  +G +    E   + + R+  G+ P                 +  
Sbjct: 366 DPACRDLLARLKELESQGYQFEAAEASFDLLMREATGDRPHFFDLKDFHVHCSKQRQELN 425

Query: 396 PTASVRVYLDGEEHEAASTGVGSVDAAIRALREAIEEL---GMDVELKEYRLEAITGGTD 452
             A+V+V + G +   ++ G G V A   ALR+AI       M   L +Y++  + G   
Sbjct: 426 ALATVKVAVTGRDILESAEGNGPVSALDAALRKAIGSFYPAVMQFHLSDYKVRILDGAAG 485

Query: 453 ALAEVTVRLEDEDGNVT-TARGAAEDIVMASVKAFVRGV 490
             A+  V +E  +G+   +  G + +I+ AS +A V G+
Sbjct: 486 TSAKTRVLVESSNGSQRWSTVGVSGNIIEASYQAVVEGI 524


Lambda     K      H
   0.315    0.133    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: 512
Number of extensions: 22
Number of successful extensions: 4
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: 499
Length of database: 542
Length adjustment: 35
Effective length of query: 464
Effective length of database: 507
Effective search space:   235248
Effective search space used:   235248
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 (21.5 bits)
S2: 52 (24.6 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