GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Desulforamulus ruminis DSM 2154

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_013840144.1 DESRU_RS00330 2-isopropylmalate synthase

Query= BRENDA::Q58787
         (491 letters)



>NCBI__GCF_000215085.1:WP_013840144.1
          Length = 501

 Score =  340 bits (872), Expect = 7e-98
 Identities = 204/498 (40%), Positives = 301/498 (60%), Gaps = 19/498 (3%)

Query: 5   IFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKEGL 64
           IFDTTLRDGEQ+ G++L  ++KLEIA++L  LGVDVIEAG   +S G+   +K I +E  
Sbjct: 6   IFDTTLRDGEQSLGITLNTHEKLEIARQLVRLGVDVIEAGFPASSPGDMNSVKTIAREIK 65

Query: 65  NAEICSFVRALPVDIDAALECDVDS----VHLVVPTSPIHMKYKLRKTEDEVLETALKAV 120
            A IC   RA+  DIDA  E   D+    +H  +  SP+HM+ KLR + ++V+E A+ AV
Sbjct: 66  GAVICGLTRAVAKDIDACAEALRDAEQPRIHTGIAVSPVHMEKKLRLSPEQVVEAAVAAV 125

Query: 121 EYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKK 180
           ++AK++   VE  AEDA+RS+  FL K+  +  + GA  V + DTVG +TP +  EL   
Sbjct: 126 KHAKKYVSDVEFYAEDASRSEPAFLAKILEKVIEAGATVVNIPDTVGYVTPWQYGELISF 185

Query: 181 ITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVA 236
           +T+NV    +  +S HCHND GMATANT +AV  GA Q   T+NGIGERAGN +LEEV+ 
Sbjct: 186 LTKNVKNIDSAIISTHCHNDLGMATANTLAAVKAGASQVEGTINGIGERAGNTALEEVMM 245

Query: 237 AL---KILYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLIK 293
           A+     LYG +  +K +++   SR+VS +  +PVP +KAIVG NAF H +GIH DG++K
Sbjct: 246 AVYSQPSLYGVELGVKTKEIAATSRLVSGITGVPVPSHKAIVGANAFMHASGIHQDGVLK 305

Query: 294 NTETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFGDL 352
              TYE I PE VG  R +I+L   SGR ALK++L+ +G +     +  +Y+   +  D 
Sbjct: 306 EKRTYEIIDPETVGILRNKIVLSARSGRHALKHRLEELGYSPEQYDVETVYKEFLQLADQ 365

Query: 353 GKYISDADLLAIVREVTGKLVEEKIKLDELTVVSGNKITPIASVKLHYKGEDITLIETAY 412
            K + D DL A++     +     I +  ++V +    T  A+V L     D  L + AY
Sbjct: 366 KKEVFDEDLHALMGYTEKE--RNSISIKNISVATNGAATATATVSLAM--NDQILTDAAY 421

Query: 413 GVGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKG-TEIVEVRKSD 471
           G GPVDA   A+ + I+G+  +KL +Y + ++  G++AL   +VK+R G + +V  R   
Sbjct: 422 GNGPVDAVFKAIER-ITGIT-VKLEDYNLSSVSRGSEALGNAIVKVRYGESGLVIGRGVS 479

Query: 472 ADIIRASVDAVMEGINML 489
            D+I A+  A +  ++ +
Sbjct: 480 PDVIEATAKAYVNALSKI 497


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: 596
Number of extensions: 34
Number of successful extensions: 8
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: 501
Length adjustment: 34
Effective length of query: 457
Effective length of database: 467
Effective search space:   213419
Effective search space used:   213419
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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