GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Caulobacter crescentus NA1000

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate CCNA_02357 CCNA_02357 methylmalonic acid semialdehyde dehydrogenase

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



>FitnessBrowser__Caulo:CCNA_02357
          Length = 498

 Score =  765 bits (1976), Expect = 0.0
 Identities = 376/499 (75%), Positives = 429/499 (85%), Gaps = 1/499 (0%)

Query: 2   MRDIPHFIGGQKVDGASGRFGEVFDPNTGKVQARVALASAGELNTAIANAKVAQAAWAAT 61
           MRDI HF+ GQ + GASGRFG+VF+PNTG+VQARV  A+  EL+ A+  A  AQ  WA T
Sbjct: 1   MRDIAHFVKGQTLVGASGRFGDVFNPNTGEVQARVQFATDAELDAAVQVAAKAQVGWAQT 60

Query: 62  NPQRRARVMFEFKRLLEVHMDELAALLSSEHGKVIADSKGDIQRGLEVIEFACGVPHLLK 121
           NPQRRARVMFEFKRL+E  M+ LA +LSSEHGKVIADSKGDIQRGLEVIEFACG+PH+LK
Sbjct: 61  NPQRRARVMFEFKRLIERDMNTLAEILSSEHGKVIADSKGDIQRGLEVIEFACGIPHILK 120

Query: 122 GEYTQGAGPGIDVYSMRQPLGVVAGITPFNFPAMIPMWMFGPAIATGNAFILKPSERDPS 181
           GEYT+GAGPGIDVYSMRQPLGV AGITPFNFPAMIPMWMFG +IA GN+FILKPSE+DP+
Sbjct: 121 GEYTEGAGPGIDVYSMRQPLGVCAGITPFNFPAMIPMWMFGISIAVGNSFILKPSEKDPT 180

Query: 182 VPVRLAELMIEAGLPPGVLNVVHGDKDCVEAILDHPDIKAVSFVGSSDIAQSVFQRAGAA 241
           VPV+LAELM+EAG P GVLNVVHGDK  V+AIL HP I+AVSFVGSSDIA  V+Q   A 
Sbjct: 181 VPVKLAELMMEAGAPAGVLNVVHGDKSAVDAILTHPLIRAVSFVGSSDIAHYVYQTGTAH 240

Query: 242 GKRVQAMGGAKNHGLVMPDADLDQAVADIIGAAYGSAGERCMALPVVVPVGEKTATALRE 301
           GKRVQAMGGAKNHG+V+PDAD+DQ V D+ GAA+GSAGERCMALPVVVPVG+KTA  LRE
Sbjct: 241 GKRVQAMGGAKNHGIVLPDADMDQVVKDLSGAAFGSAGERCMALPVVVPVGQKTADELRE 300

Query: 302 KLVAAIGGLRVGVSTDPDAHYGPVVSAAHKARIESYIQMGVDEGAELVVDGRGFSLQGHE 361
           ++VA I  L+VGVSTDPDAHYGPVVSA H+ +I  YI++G +EGAELVVDGR F LQG E
Sbjct: 301 RMVAEIASLKVGVSTDPDAHYGPVVSAQHRDKIADYIRIGQEEGAELVVDGRDFQLQGFE 360

Query: 362 EGFFVGPTLFDHVKPTSRSYHDEIFGPVLQMVRAESLEEGIALASRHQYGNGVAIFTRNG 421
           +GFF+GP+LFD VK   ++YH+EIFGPVLQ+VRAE+LEE IAL S HQYGNGVAIFTRNG
Sbjct: 361 KGFFIGPSLFDGVKKGMKTYHEEIFGPVLQIVRAETLEEAIALPSEHQYGNGVAIFTRNG 420

Query: 422 DAAREFADQVEVGMVGINVPIPVPVAYHSFGGWKRSGFGDLNQYGMDGVRFYTRTKTVTQ 481
            AAREFA  V VGMVGINVPIPVPVAYH+FGGWKRS FGD NQ+G++GV+FYT+ KTVT 
Sbjct: 421 RAAREFAANVNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGVEGVKFYTKVKTVTA 480

Query: 482 RWPKGGAVLDQSFVIPTMR 500
           RWP+ G V D SFVIPTM+
Sbjct: 481 RWPE-GEVADSSFVIPTMK 498


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: 913
Number of extensions: 35
Number of successful extensions: 2
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: 498
Length adjustment: 34
Effective length of query: 466
Effective length of database: 464
Effective search space:   216224
Effective search space used:   216224
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 CCNA_02357 CCNA_02357 (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.23639.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23639.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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