GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Shewanella amazonensis SB2B

Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate 6936138 Sama_0335 2-isopropylmalate synthase (RefSeq)

Query= curated2:Q8TYM1
         (509 letters)



>FitnessBrowser__SB2B:6936138
          Length = 522

 Score =  305 bits (780), Expect = 3e-87
 Identities = 182/502 (36%), Positives = 285/502 (56%), Gaps = 18/502 (3%)

Query: 12  DEVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIA 71
           D V IFDTTLRDGEQ    +L+ +EKL++A  L+ +GVD +E GF  +S G+ ++++ IA
Sbjct: 3   DRVIIFDTTLRDGEQALAASLSVKEKLQVALALERLGVDVMEVGFPVSSPGDFESVQTIA 62

Query: 72  REELDAEVCSMARMVKGDVDAAVE----AEADAVHIVVPTSEVHVKKKLRMDREEVLERA 127
           R   ++ VC+++R ++ D+DAA +    AE   +H  + TS +HV+ KL+   ++VL+ A
Sbjct: 63  RHIKNSRVCALSRALEKDIDAAAQALSVAEQFRIHTFISTSNIHVESKLKRSFDQVLDMA 122

Query: 128 REVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFL 187
              V+YAR     VE S ED  RT ++ L  + +A + AGA  +   DTVG   P     
Sbjct: 123 VGAVKYARRFTDDVEFSCEDAGRTPIDNLCRMVEAAISAGARTINIPDTVGYTVPSEFGG 182

Query: 188 AVKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALE 245
            ++ L  RV   +  ++SVHCHDD G++ AN++AAV+AGARQ+  TVNGIGERAGN +LE
Sbjct: 183 IIQTLFNRVPNIDQAVISVHCHDDLGLSVANSIAAVQAGARQIECTVNGIGERAGNCSLE 242

Query: 246 EVVVVL---EELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHAD 302
           E+ ++L   +++ G+ T I    +   S LV +L  + + PNKA+VG NAFTH SGIH D
Sbjct: 243 EIAMILATRKDMLGLYTNINAREIHRTSSLVSQLCNMPIQPNKAIVGSNAFTHSSGIHQD 302

Query: 303 GILKDESTYEPIPPEKVGHERRFV-LGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKR 361
           G+LK ++TYE + PE +G  R  + +    G  VI+ ++++MG    D  +  +     +
Sbjct: 303 GMLKAQNTYEIMTPESIGLNRNNLNMTSRSGRHVIKHRMEEMGYGAGDYDMDTLYAAFLK 362

Query: 362 LGDRGKRITEADLRAIAEDVLGRPAERDIEVEDFTTVTGKRT--IPTASIVVKIDGTRKE 419
           L D+  ++ + DL A+A  +  +  + D  V +   V    T    TA++ +++      
Sbjct: 363 LADKKGQVFDYDLEALA-FMEAQAEDDDHYVMEQLVVQSDSTEGKATATVRMRVGDEVIT 421

Query: 420 AASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIV 479
            A+TG GPVDA   A+ RA         +  Y+  A   G +A+  VD+  R  +     
Sbjct: 422 EAATGNGPVDAAYNAIARATHR---TINISSYKLGAKGEGQNALGQVDITARYDDRN--F 476

Query: 480 HSGSSREDIVVASLEAFIDGIN 501
           H      D+V AS +A +  +N
Sbjct: 477 HGVGLATDVVEASAQALVHVMN 498


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: 550
Number of extensions: 29
Number of successful extensions: 5
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: 522
Length adjustment: 35
Effective length of query: 474
Effective length of database: 487
Effective search space:   230838
Effective search space used:   230838
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:

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