GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Sphingomonas koreensis DSMZ 15582

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate Ga0059261_3677 Ga0059261_3677 methylmalonic acid semialdehyde dehydrogenase

Query= reanno::Caulo:CCNA_01360
         (500 letters)



>FitnessBrowser__Korea:Ga0059261_3677
          Length = 503

 Score =  775 bits (2002), Expect = 0.0
 Identities = 384/498 (77%), Positives = 427/498 (85%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           +R+I HFIG     G   R  +VFDPNTG VQA+V L +  +L+ A+ANA  AQ +WAAT
Sbjct: 5   VREISHFIGNAATAGTGTRRSDVFDPNTGAVQAQVTLGAQADLDAAMANAVRAQISWAAT 64

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQRRARVMF FK L+E +M+ELA LLSSEHGKVIAD+KGDIQRGLEVIEF CG+PH+LK
Sbjct: 65  NPQRRARVMFNFKALIEKNMEELAHLLSSEHGKVIADAKGDIQRGLEVIEFVCGIPHVLK 124

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
           GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFG AIA GNAFILKPSERDPS
Sbjct: 125 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGVAIACGNAFILKPSERDPS 184

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           VPVRLAELM+EAGLP GVL VV GDK+ V+AILDHP+IKAVSFVGSSDIA  V++R  AA
Sbjct: 185 VPVRLAELMLEAGLPEGVLQVVQGDKEMVDAILDHPEIKAVSFVGSSDIAHYVYRRGVAA 244

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
           GKRVQAMGGAKNHG+VMPDADLDQ V D+ GAA+GSAGERCMALPVVVPVG+KTA ALR 
Sbjct: 245 GKRVQAMGGAKNHGIVMPDADLDQVVNDLAGAAFGSAGERCMALPVVVPVGDKTADALRA 304

Query: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361
           KL+ AI  LRVGVSTD  AHYGPVV+AAHKA+IESYIQMGVDEGAELVVDGRGF+LQGHE
Sbjct: 305 KLLPAIEALRVGVSTDAGAHYGPVVTAAHKAKIESYIQMGVDEGAELVVDGRGFTLQGHE 364

Query: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421
           +GFFVGPTLFD V P  +SY +EIFGPVLQ+VRA   E  + L S HQYGNGVAIFTRNG
Sbjct: 365 QGFFVGPTLFDRVTPQMQSYQEEIFGPVLQIVRAPDFETALRLPSEHQYGNGVAIFTRNG 424

Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481
            AAREFA +V VGMVGINVPIPVPVAYH+FGGWKRS FGD NQ+GM+G++F+T+ KTVTQ
Sbjct: 425 HAAREFAARVNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGMEGIKFFTKVKTVTQ 484

Query: 482 RWPKGGAVLDQSFVIPTM 499
           RWP G      +FVIPTM
Sbjct: 485 RWPDGSPDGGNAFVIPTM 502


Lambda     K      H
   0.320    0.137    0.409 

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: 908
Number of extensions: 30
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: 500
Length of database: 503
Length adjustment: 34
Effective length of query: 466
Effective length of database: 469
Effective search space:   218554
Effective search space used:   218554
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 Ga0059261_3677 Ga0059261_3677 (methylmalonic acid semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.27143.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27143.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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