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

GapMind for Amino acid biosynthesis

Aligments 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis