GapMind for Amino acid biosynthesis

 

Aligments for a candidate for cimA in Desulfovibrio vulgaris Hildenborough

Align (R)-citramalate synthase CimA; EC 2.3.1.182 (characterized)
to candidate 208494 DVU2981 2-isopropylmalate synthase

Query= SwissProt::Q58787
         (491 letters)



>lcl|MicrobesOnline__882:208494 DVU2981 2-isopropylmalate synthase
          Length = 509

 Score =  378 bits (971), Expect = e-109
 Identities = 218/501 (43%), Positives = 306/501 (61%), Gaps = 18/501 (3%)

Query: 3   VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62
           +RIFDTTLRDGEQ+PG ++   +KL +A +L  LGVD+IEAG    S G+ E ++ I K 
Sbjct: 5   IRIFDTTLRDGEQSPGATMNIKEKLRLAHQLQTLGVDIIEAGFPAASPGDFESVRAIAKT 64

Query: 63  GLNAEICSFVRALPVDIDAALE--CDVDS--VHLVVPTSPIHMKYKLRKTEDEVLETALK 118
                +    RALP DID A +  C  +S  +H  + TSP+HM+YKLRKT DEV+     
Sbjct: 65  VKGMTVAGLCRALPADIDRAWDAVCVAESPRLHTFLATSPVHMQYKLRKTPDEVVRMVDA 124

Query: 119 AVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELF 178
           AV +A  H   VE SAEDA+RSD +FL+++F    + GA  + + DTVG   P++   L 
Sbjct: 125 AVRHAAGHTSNVEFSAEDASRSDRDFLVRVFTTAIEAGATTINIPDTVGYAQPEEFGALV 184

Query: 179 KKITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEV 234
           + + EN         SVHCHND G+  ANT +A+  GA Q  VT++GIGERAGNA+LEE+
Sbjct: 185 RYVIENTPNAHKAVFSVHCHNDLGLGVANTLAALRAGARQAEVTISGIGERAGNAALEEL 244

Query: 235 VAALKI---LYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGL 291
           V AL+     +G DT I  E+LY   R++S ++  P+P NKAIVG NAFAHE+GIH DG+
Sbjct: 245 VMALRTRHDYFGLDTGIVTEQLYPTCRLLSMIIGQPIPANKAIVGANAFAHESGIHQDGM 304

Query: 292 IKNTETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFG 350
           +K+ ETYE + PE +G  R  ++LGKHSGR A+K KL+ +G  + ++QLN +++ VK+  
Sbjct: 305 LKHRETYEIMTPESIGRTRTELVLGKHSGRNAVKNKLEELGYRLEEDQLNTVFDAVKQLA 364

Query: 351 DLGKYISDADLLAIVREVTGKLVEEKIKLDELTV-VSGNKITPIASVKLHYKGEDITLIE 409
           D  K I D D+ A+V E   + + ++ +L  L+V  S   + P A+V +   GE  T+  
Sbjct: 365 DKKKQIHDEDVEALVLEEVYR-IPDRYRLVNLSVQCSDTGMPPTAAVVMEVDGE--TMRH 421

Query: 410 TAYGVGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKGTEIVEVRK 469
             +G GP+DA  NA+   +      +L  Y V AI GGTDA  EV V++R+       R 
Sbjct: 422 AGFGAGPIDAVFNAIAHIVGRTP--QLERYSVTAITGGTDAQGEVTVRVRENGGTAVGRG 479

Query: 470 SDADIIRASVDAVMEGINMLL 490
           S  DII AS  A +  +N L+
Sbjct: 480 SHPDIIIASARAYLNALNRLV 500


Lambda     K      H
   0.316    0.136    0.373 

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: 29
Number of successful extensions: 7
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: 491
Length of database: 509
Length adjustment: 34
Effective length of query: 457
Effective length of database: 475
Effective search space:   217075
Effective search space used:   217075
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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