GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mhpE in Cupriavidus basilensis 4G11

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate RR42_RS27900 RR42_RS27900 4-hyroxy-2-oxovalerate aldolase

Query= metacyc::MONOMER-11384
         (352 letters)



>FitnessBrowser__Cup4G11:RR42_RS27900
          Length = 338

 Score =  622 bits (1604), Expect = 0.0
 Identities = 306/333 (91%), Positives = 322/333 (96%)

Query: 3   QQKLYISDVTLRDGSHAIRHQYTVEQVKQIARALDDAKVDSIEVAHGDGLQGGSFNYGFG 62
           Q+K+YISDVTLRDGSHA+RHQY+VEQ +QIA+ALDDAKVDSIEVAHGDGLQG SFNYGFG
Sbjct: 4   QKKIYISDVTLRDGSHAVRHQYSVEQARQIAKALDDAKVDSIEVAHGDGLQGSSFNYGFG 63

Query: 63  AHTDLEWIEAAASVVKHAKIATLLLPGIGTVHDLKAVYEAGVRVVRVATHCTEADISRQH 122
           AHTDLEWIEA ASVVKHAKIATLLLPGIGTVHDLKA Y+AG R+VRVATHCTEAD+SRQH
Sbjct: 64  AHTDLEWIEAVASVVKHAKIATLLLPGIGTVHDLKAAYDAGARIVRVATHCTEADVSRQH 123

Query: 123 IEYARHLGMEAVGFLMMSHMTTPQHLAQQAKLMESYGATVCYVVDSGGALSMNDVRDRFR 182
           IEYARHLGMEAVGFLMMSHMTTPQ+LA QAKLMESYGAT CYVVDSGGAL+MNDVRDRFR
Sbjct: 124 IEYARHLGMEAVGFLMMSHMTTPQNLAAQAKLMESYGATCCYVVDSGGALTMNDVRDRFR 183

Query: 183 AFKDVLKPETQTGMHAHHNLSLGVANSIVAVENGCDRVDASLAGMGAGAGNAPLEVFIAA 242
           AFK VLKPETQTGMHAHHNLSLGVANSIVAVE GCDR+DASLAGMGAGAGNAPLEVFIAA
Sbjct: 184 AFKAVLKPETQTGMHAHHNLSLGVANSIVAVEEGCDRIDASLAGMGAGAGNAPLEVFIAA 243

Query: 243 AERMGWNHGTDLYKLMDAADDLVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEMAASKY 302
           AERMGW+HG DLYKLMDAADD+VRPLQDRPVRVDRETLALGYAGVYSSFLRHSE AASKY
Sbjct: 244 AERMGWDHGCDLYKLMDAADDIVRPLQDRPVRVDRETLALGYAGVYSSFLRHSEAAASKY 303

Query: 303 GLKTVDILVELGRRRMVGGQEDMIIDVALDLLK 335
           GLKTVD+LVELGRRRMVGGQEDMI+DVALDLLK
Sbjct: 304 GLKTVDVLVELGRRRMVGGQEDMIVDVALDLLK 336


Lambda     K      H
   0.319    0.133    0.383 

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: 527
Number of extensions: 15
Number of successful extensions: 1
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: 352
Length of database: 338
Length adjustment: 29
Effective length of query: 323
Effective length of database: 309
Effective search space:    99807
Effective search space used:    99807
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate RR42_RS27900 RR42_RS27900 (4-hyroxy-2-oxovalerate aldolase)
to HMM TIGR03217 (dmpG: 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))

Software error:

../bin/blast/fastacmd -i /tmp/list.10517.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10517.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.