GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Dinoroseobacter shibae DFL-12

Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate 3607175 Dshi_0596 2-isopropylmalate synthase (RefSeq)

Query= curated2:Q8TYM1
         (509 letters)



>FitnessBrowser__Dino:3607175
          Length = 525

 Score =  357 bits (915), Expect = e-103
 Identities = 212/511 (41%), Positives = 301/511 (58%), Gaps = 16/511 (3%)

Query: 7   DADPPDEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKA 66
           D    D V IFDTTLRDGEQ+PG  +T +EKL IA  LDE+GVD IEAGF  AS+G+  A
Sbjct: 3   DKTDQDRVLIFDTTLRDGEQSPGATMTHDEKLEIAALLDEMGVDIIEAGFPIASDGDFAA 62

Query: 67  IRRIAREELDAEVCSMARMVKGDVDAAVEAEADA----VHIVVPTSEVHVKKKLRMDREE 122
           +  IA+  +++ +C +AR    D+D   EA   A    +H  + TS +H +    +  +E
Sbjct: 63  VSEIAKNSVNSVICGLARANFKDIDRCWEAVRHARQPRIHTFIGTSPLH-RAIPNLTMDE 121

Query: 123 VLERAREVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAP 182
           + +R  + V +AR+    V+ S  D TRTE +YL  V +  ++AGA  +   DTVG  AP
Sbjct: 122 MADRIHDTVTHARNLCDNVQWSPMDATRTEYDYLCRVIEIAIKAGATTINIPDTVGYTAP 181

Query: 183 -EGMFLAVKKLRERVG-EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAG 240
            E   L  + + +  G EDV  + HCH+D GMATAN +AAV AGARQV  T+NG+GERAG
Sbjct: 182 RESADLIARLIADVPGAEDVTFATHCHNDLGMATANALAAVDAGARQVECTINGLGERAG 241

Query: 241 NAALEEVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHES 297
           N ALEEVV+ L    ++    T I T ++  +S+ V  ++G  V  NKA+VG+NAF HES
Sbjct: 242 NTALEEVVMALRVRNDIMPYQTRIDTRKIMNISRRVAAVSGFAVQFNKAIVGKNAFAHES 301

Query: 298 GIHADGILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEIL 356
           GIH DG+LK+  T+E + PE +G  E   V+GKH G + +R KLK +G ++ D QL ++ 
Sbjct: 302 GIHQDGMLKNAETFEIMRPEDIGLSETNLVMGKHSGRAALRAKLKDLGYELADNQLKDVF 361

Query: 357 RRLKRLGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRTIPTASIVVKIDGT 416
            R K L DR K I + DL A+  +    PA   + V+    + G     +A + + IDG 
Sbjct: 362 VRFKALADRKKEIYDEDLVALMSESSSDPARERLSVKFLRVICGTEAPQSADLTLSIDGV 421

Query: 417 RKEAASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETG 476
            K+  + G GPVDAT  A+ +AL       +L  Y+  A+T GTDA   V V++   E G
Sbjct: 422 DKQVTAQGDGPVDATFNAV-KALFPHTARLQL--YQVHAVTEGTDAQATVTVRME--EDG 476

Query: 477 DIVHSGSSREDIVVASLEAFIDGINSLMARK 507
            IV   ++  D VVAS +A++  +N L+ R+
Sbjct: 477 RIVSGQAADTDTVVASAKAYVAALNRLILRR 507


Lambda     K      H
   0.315    0.134    0.367 

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: 622
Number of extensions: 32
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: 509
Length of database: 525
Length adjustment: 35
Effective length of query: 474
Effective length of database: 490
Effective search space:   232260
Effective search space used:   232260
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: 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