GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Cupriavidus basilensis 4G11

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate RR42_RS37440 RR42_RS37440 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Cup4G11:RR42_RS37440
          Length = 608

 Score =  736 bits (1901), Expect = 0.0
 Identities = 370/597 (61%), Positives = 448/597 (75%), Gaps = 1/597 (0%)

Query: 2   HPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLR 61
           HP +  VT R+VARS ATR+ Y+   R  A    +R +L C N AH VA    + K  L+
Sbjct: 4   HPVLERVTARIVARSAATRQTYMDRTRAMAGQKVERAQLSCTNLAHAVAAMPEQAKIRLK 63

Query: 62  MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121
                N+AIVSSYNDMLSAHQP   +P+ +K+A  E G   QFAGGTPAMCDGVTQG+ G
Sbjct: 64  AQERPNLAIVSSYNDMLSAHQPLAEYPQWLKEAALEAGGTAQFAGGTPAMCDGVTQGQDG 123

Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181
           M+LSL SR+VIALSTAVALSH MFD AL LG+CDKIVPGL+MGAL FGHLP IFVPGGPM
Sbjct: 124 MDLSLFSRDVIALSTAVALSHQMFDGALYLGVCDKIVPGLVMGALSFGHLPAIFVPGGPM 183

Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241
            +GI N+EKA VRQRYAEGK +R ELLE+E +SYH PGTCTFYGTAN+NQ+LME+MGLHL
Sbjct: 184 TTGIGNEEKARVRQRYAEGKLSRAELLEAESQSYHGPGTCTFYGTANSNQMLMEIMGLHL 243

Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301
           PG +FVNP TPLR+ALT E+A+Q  RL      +TP+ +++DER+ VN IV L ATGGST
Sbjct: 244 PGTAFVNPNTPLREALTRESARQALRLVHGGDRYTPVADVLDERAFVNGIVGLLATGGST 303

Query: 302 NHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELL 361
           NHTLH+ A+A+ AGI L W D A+LSEVVP L+ VYPNG AD+N FQAAGG+  +IR LL
Sbjct: 304 NHTLHLVAMARTAGIMLGWDDFAELSEVVPLLARVYPNGSADVNQFQAAGGLGLVIRGLL 363

Query: 362 EAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLR 421
           + GLLH+DV TV G+GL+ YT+EP L +G+L W DGP   LD+ I+R   + F+PEGG+R
Sbjct: 364 QLGLLHDDVTTVVGKGLADYTREPVLRDGQLTWIDGPEAPLDDTIVRAAGQPFAPEGGIR 423

Query: 422 VMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRS 481
           +++GN+GR V+K+SAV  +H IV+APA+VF  Q  L +AFK GELE+DFVAV+ +QGP +
Sbjct: 424 LLDGNIGRAVLKISAVKPEHHIVQAPAMVFHTQDALIEAFKRGELERDFVAVLPWQGPAA 483

Query: 482 NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDG 541
            GMPELHK+TP L VLQDRGF VALVTDGRMSGASGK+PAAIHV PEA  GG +ARVRDG
Sbjct: 484 CGMPELHKLTPTLTVLQDRGFHVALVTDGRMSGASGKVPAAIHVCPEALSGGGIARVRDG 543

Query: 542 DIIRVDGVKGTLELKVDADEFAARE-PAKGLLGNNVGSGRELFGFMRMAFSSAEQGA 597
           D +RVD   G L + V   E+AAR      L  N  G GR+LF   R   S+AE GA
Sbjct: 544 DPMRVDAHAGVLTVLVPQAEWAARSVTPPDLSANRHGVGRDLFANFRRHVSTAEAGA 600


Lambda     K      H
   0.318    0.134    0.386 

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: 1142
Number of extensions: 54
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: 608
Length of database: 608
Length adjustment: 37
Effective length of query: 571
Effective length of database: 571
Effective search space:   326041
Effective search space used:   326041
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate RR42_RS37440 RR42_RS37440 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.18130.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18130.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.