GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Marinobacter adhaerens HP15

Align Methylmalonate-semialdehyde dehydrogenase [acylating]; MMSDH; EC 1.2.1.27 (characterized)
to candidate GFF927 HP15_906 methylmalonate-semialdehyde dehydrogenase

Query= SwissProt::P28810
         (497 letters)



>FitnessBrowser__Marino:GFF927
          Length = 497

 Score =  728 bits (1879), Expect = 0.0
 Identities = 358/490 (73%), Positives = 407/490 (83%), Gaps = 1/490 (0%)

Query: 9   IAGAFVEGLGAQRIPVSNPLDNSTLAEIACASAEQVEQAVASARETFASWKETPVSERAR 68
           IAG F++      I V+NP  N  +A+    +  ++EQA+  A E F +WKE PVSERAR
Sbjct: 8   IAGEFIQSQTKDWIEVTNPATNEVIAKAPNTTHAEMEQAIKYAGEVFKTWKEVPVSERAR 67

Query: 69  VMLRYQALLKEHHDELAKIVSSELGKTFEDAKGDVWRGIEVVEHACNVPSLLMGETVENV 128
           VMLRYQALLK+HHDE+A+I+S E GKTFEDAKGDVWRGIEVVEHA NV SL+MGETVENV
Sbjct: 68  VMLRYQALLKKHHDEIAEILSQETGKTFEDAKGDVWRGIEVVEHAGNVASLMMGETVENV 127

Query: 129 ARNIDTYSITQPLGVCVGITPFNFPAMIPLWMFPLAIACGNAFILKPSEQVPLTSVRLAE 188
           AR +DT+S  QPLGVC GITPFNFPAMIPLWMFP+AIACGN FILKPSEQ PLT +RLAE
Sbjct: 128 AREVDTHSWIQPLGVCAGITPFNFPAMIPLWMFPMAIACGNTFILKPSEQDPLTPMRLAE 187

Query: 189 LFLEAGAPKGVLQVVHGGKEQVDQLLKHPQVKAVSFVGSVAVGQYVYHTGTAHNKRVQSF 248
           LF EAGAPKGVLQVVHGGKEQVD LL  P +KAVSFVGSV VG+Y+Y TGT + KRVQSF
Sbjct: 188 LFEEAGAPKGVLQVVHGGKEQVDVLLTDPAIKAVSFVGSVPVGRYIYETGTRNMKRVQSF 247

Query: 249 AGAKNHMVIMPDADKAQVISNLVGASVGAAGQRCMAISVAVLVGAAREWIPEIRDALAKV 308
           AGAKNHMVI+PDADK QVI+ LVGASVGAAGQRCMAISVAV VG A++WIPE+++A+AKV
Sbjct: 248 AGAKNHMVILPDADKQQVINALVGASVGAAGQRCMAISVAVFVGEAQQWIPELKEAMAKV 307

Query: 309 RPGPWDDSGASYGPVINPQAKARIERLIGQGVEEGAQLLLDGRGYKVEGYPDGNWVGPTL 368
           RPG W+DSGASYGP+I+ +AK RIE LI  G  +GA LLLDGRG  V+G PDGNWVGPTL
Sbjct: 308 RPGAWNDSGASYGPIISAKAKDRIESLIATGEAQGANLLLDGRGCTVDGLPDGNWVGPTL 367

Query: 369 FAGVRPDMAIYREEVFGPVLCLAEVDSLEQAIRLINESPYGNGTSIFTSSGAAARTFQHH 428
           F+GV  +M IY EE+FGPVL   E D+L  AI L+N SPYGNG SIFTSSG AAR FQH 
Sbjct: 368 FSGVTTEMDIYNEEIFGPVLSCMETDTLGDAIELVNNSPYGNGVSIFTSSGGAARRFQHE 427

Query: 429 IEVGQVGINIPIPVPLPFFSFTGWKGSFYGDLHAYGKQGVRFYTETKTVTARWFDSDSVA 488
           I+VGQVG+NIPIPVPLPFFSFTGWKGSFYGD HAYGKQ VRFYTETKTVT+RWF S++ +
Sbjct: 428 IDVGQVGVNIPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYTETKTVTSRWFSSEATS 487

Query: 489 G-TNFSIQMR 497
              NFSIQ+R
Sbjct: 488 SEANFSIQLR 497


Lambda     K      H
   0.319    0.135    0.406 

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: 870
Number of extensions: 26
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
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 GFF927 HP15_906 (methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.4670.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4670.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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