GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cimA in Escherichia coli BW25113

Align Putative (R)-citramalate synthase CimA; EC 2.3.1.182 (uncharacterized)
to candidate 14220 b0074 2-isopropylmalate synthase (NCBI)

Query= curated2:Q8TYM1
         (509 letters)



>FitnessBrowser__Keio:14220
          Length = 523

 Score =  305 bits (780), Expect = 3e-87
 Identities = 186/503 (36%), Positives = 286/503 (56%), Gaps = 19/503 (3%)

Query: 13  EVRIFDTTLRDGEQTPGVALTPEEKLRIARKLDEIGVDTIEAGFAAASEGELKAIRRIAR 72
           +V IFDTTLRDGEQ    +L+ +EKL+IA  L+ +GVD +E GF  +S G+ ++++ IAR
Sbjct: 4   QVIIFDTTLRDGEQALQASLSVKEKLQIALALERMGVDVMEVGFPVSSPGDFESVQTIAR 63

Query: 73  EELDAEVCSMARMVKGDVDAAVE----AEADAVHIVVPTSEVHVKKKLRMDREEVLERAR 128
           +  ++ VC++AR V+ D+D A E    AEA  +H  + TS +H+  KLR   +EV+ERA 
Sbjct: 64  QVKNSRVCALARCVEKDIDVAAESLKVAEAFRIHTFIATSPMHIATKLRSTLDEVIERAI 123

Query: 129 EVVEYARDHGLTVEISTEDGTRTELEYLYEVFDACLEAGAERLGYNDTVGVMAPEGMFLA 188
            +V+ AR++   VE S ED  RT +  L  V +A + AGA  +   DTVG   P      
Sbjct: 124 YMVKRARNYTDDVEFSCEDAGRTPIADLARVVEAAINAGATTINIPDTVGYTMPFEFAGI 183

Query: 189 VKKLRERVG--EDVILSVHCHDDFGMATANTVAAVRAGARQVHVTVNGIGERAGNAALEE 246
           +  L ERV   +  I+SVH HDD G+A  N++AAV AGARQV   +NGIGERAGN +LEE
Sbjct: 184 ISGLYERVPNIDKAIISVHTHDDLGLAVGNSLAAVHAGARQVEGAMNGIGERAGNCSLEE 243

Query: 247 VVV---VLEELYGVDTGIRTERLTELSKLVERLTGVRVPPNKAVVGENAFTHESGIHADG 303
           V++   V +++  V T I  + +   S+LV ++  + +P NKA+VG  AF H SGIH DG
Sbjct: 244 VIMAIKVRKDILNVHTAINHQEIWRTSQLVSQICNMPIPANKAIVGSGAFAHSSGIHQDG 303

Query: 304 ILKDESTYEPIPPEKVG-HERRFVLGKHVGTSVIRKKLKQMGVDVDDEQLLEILRRLKRL 362
           +LK+   YE + PE +G ++ +  L    G + ++ ++ +MG    +  L  +     +L
Sbjct: 304 VLKNRENYEIMTPESIGLNQIQLNLTSRSGRAAVKHRMDEMGYKESEYNLDNLYDAFLKL 363

Query: 363 GDRGKRITEADLRAIAEDVLGRPAE--RDIEVEDFTTVTGKRTIPTASIVVKIDGTRKEA 420
            D+  ++ + DL A+A   +G+  E      ++ F+  +G   I TA++ +      K  
Sbjct: 364 ADKKGQVFDYDLEALA--FIGKQQEEPEHFRLDYFSVQSGSNDIATAAVKLACGEEVKAE 421

Query: 421 ASTGVGPVDATIKALERALKDQGIDFELVEYRAEALTGGTDAITHVDVKLRDPETGDIVH 480
           A+ G GPVDA  +A+ R  +    + ELV+Y   A   G DA+  VD+       G   H
Sbjct: 422 AANGNGPVDAVYQAINRITE---YNVELVKYSLTAKGHGKDALGQVDIVAN--YNGRRFH 476

Query: 481 SGSSREDIVVASLEAFIDGINSL 503
                 DIV +S +A +  +N++
Sbjct: 477 GVGLATDIVESSAKAMVHVLNNI 499


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: 31
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: 523
Length adjustment: 35
Effective length of query: 474
Effective length of database: 488
Effective search space:   231312
Effective search space used:   231312
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