GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Echinicola vietnamensis KMM 6221, DSM 17526

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate Echvi_1869 Echvi_1869 mannonate dehydratase

Query= BRENDA::P24215
         (394 letters)



>FitnessBrowser__Cola:Echvi_1869
          Length = 387

 Score =  425 bits (1093), Expect = e-123
 Identities = 212/388 (54%), Positives = 276/388 (71%), Gaps = 7/388 (1%)

Query: 3   QTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVV 62
           QTWRWYGPNDPVSL DVRQAGATGVV+ALH IP+G+ W ++ I +RKA IE AGL WSVV
Sbjct: 5   QTWRWYGPNDPVSLQDVRQAGATGVVSALHQIPHGDEWPIQLIQERKATIEAAGLEWSVV 64

Query: 63  ESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDG 122
           ESVP+HE IKT   + E ++ NY++TLRNL++CGI+TVCYNFMPVLDWTRTDL   L +G
Sbjct: 65  ESVPVHEAIKTRNDHAEYYLENYRKTLRNLSKCGIKTVCYNFMPVLDWTRTDLALPLANG 124

Query: 123 SKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGLP 182
           +KAL  D  + A F++ IL R G EA Y  E +A+  ER+A M+ E +A L   ++ G+P
Sbjct: 125 AKALYLDWTDLAVFDLKILGRAGGEAFYKPEILAKVEERYAAMTKEQQAALQEIVLMGVP 184

Query: 183 GAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPIL 242
             E G TL+  ++ +E+Y  I K  L+EN   FL+ I  V EE G+RM +HPDDPP PIL
Sbjct: 185 -TEGGVTLEALQESIEVYSSIGKHGLQENLTYFLENIAEVCEEEGIRMTIHPDDPPFPIL 243

Query: 243 GLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRST 302
           GLPRI S+ ED+++++  V+   NG   CTGS G    NDL  M+   G R+YF HLR+ 
Sbjct: 244 GLPRIASSKEDLEFILQAVDRPFNGICFCTGSLGAGDHNDLPAMLDAVGDRVYFAHLRN- 302

Query: 303 MREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKK 362
           +++D    FHE+ HL+GDVDM  +++ +V+   +R        IP RPDHGHQMLDDL+K
Sbjct: 303 VKKDALGNFHESDHLDGDVDMCAIMERLVKLNAQR-----HQAIPFRPDHGHQMLDDLQK 357

Query: 363 KTNPGYSAIGRLKGLAEVRGVELAIQRA 390
            TNPGYSAIGRLKGLAE+RG+E+ I+ +
Sbjct: 358 VTNPGYSAIGRLKGLAELRGLEMGIKNS 385


Lambda     K      H
   0.320    0.136    0.410 

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: 453
Number of extensions: 23
Number of successful extensions: 4
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: 394
Length of database: 387
Length adjustment: 31
Effective length of query: 363
Effective length of database: 356
Effective search space:   129228
Effective search space used:   129228
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: 50 (23.9 bits)

Align candidate Echvi_1869 Echvi_1869 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.7434.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7434.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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