GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Sulfurihydrogenibium subterraneum DSM 15120

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_028949923.1 Q385_RS0101285 2-isopropylmalate synthase

Query= BRENDA::Q58787
         (491 letters)



>NCBI__GCF_000619805.1:WP_028949923.1
          Length = 516

 Score =  384 bits (987), Expect = e-111
 Identities = 227/501 (45%), Positives = 323/501 (64%), Gaps = 25/501 (4%)

Query: 5   IFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKEGL 64
           IFDTTLRDGEQ PG S+T  +K+++A +L++LGVDVIEAG A  S+G+ E +K + +E  
Sbjct: 6   IFDTTLRDGEQAPGFSMTVEEKVKMALQLEKLGVDVIEAGFAAASEGDFEAVKRVAEEIK 65

Query: 65  NAEICSFVRALPVDIDAALE----CDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALKAV 120
           NA++CS  RAL  DID A E     +   +H  + TSPIHM+YKL+ + DEV+E A+ AV
Sbjct: 66  NAKVCSLARALQSDIDKAGEALTPAENRRIHTFIATSPIHMQYKLKMSPDEVVERAIAAV 125

Query: 121 EYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELFKK 180
           +YA ++   VE SAEDA RS+  FL ++F    K GA  + V DTVG   P++  +L   
Sbjct: 126 KYALKYTDDVEFSAEDAFRSEREFLYRVFEAVIKAGAKTINVPDTVGYAIPEEFGQLIAD 185

Query: 181 ITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEVVA 236
           I  NV       +SVHCHND G+A AN+ SAV  GA Q H TVNGIGERAGNA++EEVV 
Sbjct: 186 IKNNVPNIDKAVISVHCHNDLGLAVANSLSAVKNGARQVHATVNGIGERAGNAAVEEVVM 245

Query: 237 ALKILYGY----DTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGLI 292
           A+K+ + Y     T +  +++Y+ SR++ R+    V PNKAIVGDNAFAHEAGIH  G++
Sbjct: 246 AIKVRHDYFKGIYTTVNTKEIYKTSRLLCRITGSFVQPNKAIVGDNAFAHEAGIHQHGIL 305

Query: 293 KNTETYEPIKPEMVG-NRRRIILGKHSGRKALKYKLDLMG-INVSDEQLNKIYERVKEFG 350
            + ETYE ++ E VG  + +I+LGKHSGR A K +L  +G  N++D +++ ++ + K+  
Sbjct: 306 AHRETYEIMRAEDVGVPKSKIVLGKHSGRHAFKTRLQELGYTNLTDAEIDSLFIKFKKLA 365

Query: 351 DLGKYISDADLLAIVREVTGKLVEEKIKLDELTVVSGNKITPIASVKLHYKGEDITLIET 410
           D  K + D D+ A++ E      E K+K++   VVSG+ + P A+VK+   GE+I  + T
Sbjct: 366 DKKKEVFDEDIEALILE-EFSFFENKVKVNYFHVVSGDNVIPSATVKIEKDGEEI--VST 422

Query: 411 AYGVGPVDAAINAVRKAISGVADI--KLVEYRVEAIGGGTDALIEVVVKLR-KGTEIVEV 467
           A G GP+D+ INAV KA+    DI  KL++Y + ++  G DA+ EV V +R   T+ V  
Sbjct: 423 ASGDGPIDSVINAVEKAL----DIKGKLLDYTIRSLSSGKDAMGEVRVLVRFDDTDYVAS 478

Query: 468 RK-SDADIIRASVDAVMEGIN 487
            K +  DII AS+ A ++  N
Sbjct: 479 GKGTSTDIIEASLKAYVDAYN 499


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: 619
Number of extensions: 31
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: 516
Length adjustment: 34
Effective length of query: 457
Effective length of database: 482
Effective search space:   220274
Effective search space used:   220274
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