GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Paraburkholderia bryophila 376MFSha3.1

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_01202 H281DRAFT_01202 methylmalonate-semialdehyde dehydrogenase [acylating]

Query= reanno::pseudo3_N2E3:AO353_05990
         (507 letters)



>FitnessBrowser__Burk376:H281DRAFT_01202
          Length = 502

 Score =  845 bits (2184), Expect = 0.0
 Identities = 416/494 (84%), Positives = 454/494 (91%)

Query: 14  VKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAAHRAFQTWKLTPIG 73
           VKLLI+G++V+S+TTEW D+VNPATQQVLA+VPFAT  EVD AI +AH AF+TWK TPIG
Sbjct: 9   VKLLINGEFVDSRTTEWRDVVNPATQQVLARVPFATAGEVDEAIRSAHAAFKTWKDTPIG 68

Query: 74  ARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEF 133
           ARMRIMLK QALIREH  RIA  LSAEQGKTI DAEGDIFRGLEVVEHACSIGSLQ GEF
Sbjct: 69  ARMRIMLKYQALIREHMPRIAKTLSAEQGKTIPDAEGDIFRGLEVVEHACSIGSLQQGEF 128

Query: 134 AENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTM 193
           AENVAGGVDTYTLRQP+GVCAGITPFNFPAMIPLWMFPMAI CGNTFVLKPSEQDPMSTM
Sbjct: 129 AENVAGGVDTYTLRQPLGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQDPMSTM 188

Query: 194 LLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKR 253
            LVELA+EAG+P GVLNVVHGGKDVVDALCTH+ +KAVSFVGSTAVGTHVY L  +HGKR
Sbjct: 189 QLVELALEAGVPKGVLNVVHGGKDVVDALCTHELVKAVSFVGSTAVGTHVYRLGSEHGKR 248

Query: 254 VQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPDLKAL 313
           VQSMMGAKNHAVVLPDANREQ LNAL GAGFGAAGQRCMATSVVVLVGAA+QWLP++ A 
Sbjct: 249 VQSMMGAKNHAVVLPDANREQTLNALAGAGFGAAGQRCMATSVVVLVGAAQQWLPEIVAK 308

Query: 314 AQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDITVPGYEKGNFV 373
           A+ LKVNAG+EP TD+GPV+S+ AK RIL LIE+G+KEGA L LDGRD+TVPGYE+GNF+
Sbjct: 309 AKTLKVNAGNEPNTDIGPVVSRAAKERILGLIEAGVKEGATLALDGRDVTVPGYEQGNFI 368

Query: 374 GPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARK 433
           GPT+FS V+T+M+IY  EIFGPVL+VL   TLD AIALVN+NPFGNG GLFTQSGAAARK
Sbjct: 369 GPTIFSDVSTEMEIYRTEIFGPVLLVLNAATLDDAIALVNSNPFGNGVGLFTQSGAAARK 428

Query: 434 FQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTSRWFDD 493
           FQ+EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVT+RWFDD
Sbjct: 429 FQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFDD 488

Query: 494 DSVNDGVNTTINLR 507
           D+VNDGVNTTI+LR
Sbjct: 489 DTVNDGVNTTISLR 502


Lambda     K      H
   0.319    0.135    0.396 

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: 830
Number of extensions: 23
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: 507
Length of database: 502
Length adjustment: 34
Effective length of query: 473
Effective length of database: 468
Effective search space:   221364
Effective search space used:   221364
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate H281DRAFT_01202 H281DRAFT_01202 (methylmalonate-semialdehyde dehydrogenase [acylating])
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.15187.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15187.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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