GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Lentibacillus jeotgali Grbi

Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_010532009.1 ON01_RS15965 2-isopropylmalate synthase

Query= BRENDA::Q58787
         (491 letters)



>NCBI__GCF_000224785.1:WP_010532009.1
          Length = 515

 Score =  353 bits (907), Expect = e-102
 Identities = 206/499 (41%), Positives = 305/499 (61%), Gaps = 18/499 (3%)

Query: 3   VRIFDTTLRDGEQTPGVSLTPNDKLEIAKKLDELGVDVIEAGSAITSKGEREGIKLITKE 62
           ++IFDTTLRDGEQ+PGV+L   +KLEIAK+L+++G+D +EAG   +SKG+ E +K I K 
Sbjct: 4   IKIFDTTLRDGEQSPGVNLNKPEKLEIAKQLEKMGIDRMEAGFPASSKGDFEAVKEIAKT 63

Query: 63  GLNAEICSFVRALPVDIDAALE----CDVDSVHLVVPTSPIHMKYKLRKTEDEVLETALK 118
             N  +    R +  DID A E     +   +HL V TSPIHM YKL+++ ++V+E A+ 
Sbjct: 64  IKNTSVTGLARTVKSDIDTAWEALKYAEEPRLHLFVATSPIHMTYKLKQSPEQVIENAVS 123

Query: 119 AVEYAKEHGLIVELSAEDATRSDVNFLIKLFNEGEKVGADRVCVCDTVGVLTPQKSQELF 178
            V YA E    VE SAEDA+RSD+ FL ++  +    GA  + + DTVG  TP +   +F
Sbjct: 124 MVSYASEKFPQVEWSAEDASRSDLTFLAQIIEKVIDAGATVINLPDTVGYTTPAEYGAMF 183

Query: 179 KKITENV----NLPVSVHCHNDFGMATANTCSAVLGGAVQCHVTVNGIGERAGNASLEEV 234
           + I ENV     + +S HCHND G+A AN+ +AV  G  Q   T+NGIGERAGNASLEEV
Sbjct: 184 RYIRENVPNIDKVELSCHCHNDLGLAVANSIAAVENGVTQVEGTINGIGERAGNASLEEV 243

Query: 235 VAALKI---LYGYDTKIKMEKLYEVSRIVSRLMKLPVPPNKAIVGDNAFAHEAGIHVDGL 291
             AL++    Y Y T++K+++    S ++++L  + V  NKAIVG NAF HEAGIH DG+
Sbjct: 244 AVALRVRSDYYPYTTRLKLDETKRTSDLIAKLSGMYVQANKAIVGRNAFQHEAGIHQDGV 303

Query: 292 IKNTETYEPIKPEMVGNRR-RIILGKHSGRKALKYKLDLMGINVSDEQLNKIYERVKEFG 350
           +KN ETYE + PEMVG +   + LGKHSGR A K +++ +G+ +S+++L + +   K+  
Sbjct: 304 LKNKETYEIMTPEMVGVKADTLFLGKHSGRHAFKDRVNELGVQLSEDKLKEAFTMFKQLT 363

Query: 351 DLGKYISDADLLAIVREV-TGKLVEEKIKLDELTVVSGNKITPIASVKLHYKGEDITLIE 409
           D  + ++D DL  I+ E+ T      K +L+   V  G    P A+V L     D   ++
Sbjct: 364 DRKREVTDDDLYTILMEIQTDTSAVNKYQLEMFQVQYGTSNIPTATVSL--TAPDGKTVQ 421

Query: 410 TAY-GVGPVDAAINAVRKAISGVADIKLVEYRVEAIGGGTDALIEVVVKLRKGTEIVEVR 468
           TA  G G V+A    +   I    +++L +Y++ ++G G DAL E  V+L    E +  R
Sbjct: 422 TAQTGQGSVEALYKTLDALIK--EELQLTDYQLNSVGRGKDALAESHVQLIVNGETMNGR 479

Query: 469 KSDADIIRASVDAVMEGIN 487
            +  D+++ASV+A +  +N
Sbjct: 480 GTAQDVLQASVNAFLNAVN 498


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: 577
Number of extensions: 22
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: 491
Length of database: 515
Length adjustment: 34
Effective length of query: 457
Effective length of database: 481
Effective search space:   219817
Effective search space used:   219817
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 26 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