GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Klebsiella michiganensis M5al

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate BWI76_RS02840 BWI76_RS02840 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= reanno::Koxy:BWI76_RS03070
         (501 letters)



>FitnessBrowser__Koxy:BWI76_RS02840
          Length = 503

 Score =  458 bits (1179), Expect = e-133
 Identities = 229/480 (47%), Positives = 317/480 (66%), Gaps = 5/480 (1%)

Query: 7   FIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAFESWSRTTPLRRA 66
           F+ G+   S + + M V++P+TG+V+ +    T QEV DA+  AR AF +WS T  ++R+
Sbjct: 10  FVDGQWRVSQTERYMDVYNPSTGEVMAQAPCCTEQEVLDAVAAARKAFPAWSDTPAIKRS 69

Query: 67  RVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEVVEFACGIPHLIKGEFSSD 126
           ++MF  + LL QH + L  ++  E+GK + DA G++ +  E  E AC IP L+ GE   D
Sbjct: 70  QIMFRVRELLIQHQDRLTELVAKENGKAWGDAQGDVLKAKEGTELACSIPTLMAGENLMD 129

Query: 127 VGTGVDSYSLMQPLGVVAGITPFNFPAMVPM-WMFPLALACGNSFVLKPPALAPTAAVRL 185
              G+D+    +P+GV AGI PFNFPAM+PM WM PL +A GN+ V+K  ++ P   + +
Sbjct: 130 ASAGIDTNLYREPIGVFAGIVPFNFPAMIPMGWMAPLCVASGNTMVIKAASMTPMTCMEI 189

Query: 186 AELLKEAGLPDGVFNVVHCSNEDAEQLYRDPRIAAVSFVGSSGVAEHIYKTASAYGKRVQ 245
            +L +EAG+PDGV NVV CS  +A+ L   P +  VSFVGS+ V  H+Y  A+A+GKRVQ
Sbjct: 190 TKLYQEAGVPDGVINVVTCSRNEADILLTHPDVNGVSFVGSTSVGLHVYSKAAAHGKRVQ 249

Query: 246 AFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETADKLIARLKPL 305
           A   AKNHA+V+ DA ++ T   I+  AFG AGERCMALPVVV V +E ADKLIA +   
Sbjct: 250 ALCEAKNHALVLADAPINRTAAGIINAAFGCAGERCMALPVVV-VQEEIADKLIAAVVEK 308

Query: 306 VESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGATLVVDGRKPQVPGFEEG 365
            + LK+GPG +R   + +MGPV+S  H++ V+G+I+KG+ EGA LV+DGR  +VPG E G
Sbjct: 309 AKQLKIGPGYLR---DTDMGPVISKDHKRSVIGWINKGIEEGAKLVLDGRDIKVPGQENG 365

Query: 366 YYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNSHEFGNGSAVFTSNGHT 425
           +YVG T+ D VT EM++  +EIFGPVL   RV  +   L+L+N++ F NGS +FT +G+ 
Sbjct: 366 FYVGPTILDRVTEEMSVGTQEIFGPVLCFKRVKTFEEGLQLMNNNPFANGSVIFTQSGYY 425

Query: 426 AREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKTATVRW 485
           AREF      GMVG+NV +PVP+    F G K+S FG L+  G DGVRFYT  K  T RW
Sbjct: 426 AREFQKRTHGGMVGINVGIPVPVGVFPFSGHKQSFFGDLHCLGKDGVRFYTESKCVTSRW 485


Lambda     K      H
   0.319    0.135    0.404 

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: 616
Number of extensions: 21
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: 501
Length of database: 503
Length adjustment: 34
Effective length of query: 467
Effective length of database: 469
Effective search space:   219023
Effective search space used:   219023
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: 52 (24.6 bits)

Align candidate BWI76_RS02840 BWI76_RS02840 (methylmalonate-semialdehyde dehydrogenase (CoA acylating))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.12606.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12606.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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