GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Cupriavidus basilensis 4G11

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate RR42_RS25635 RR42_RS25635 methylmalonate-semialdehyde dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1229
         (505 letters)



>FitnessBrowser__Cup4G11:RR42_RS25635
          Length = 507

 Score =  804 bits (2076), Expect = 0.0
 Identities = 394/493 (79%), Positives = 440/493 (89%), Gaps = 1/493 (0%)

Query: 13  KLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGA 72
           KLLIDG++VES + +W ++VNPATQQV+ +VPFAT  EVDAAI++A RAF  W+ TP+GA
Sbjct: 16  KLLIDGKFVESDSNQWGNVVNPATQQVIGRVPFATVEEVDAAIASAQRAFLAWRNTPLGA 75

Query: 73  RMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACSIGSLQMGEFA 132
           R+R+MLK Q L+R + +RIA  L+ EQGKT+ DA+GDIFRGLEVVEHACS+G+LQMGEFA
Sbjct: 76  RLRVMLKFQDLVRRNMERIARTLTAEQGKTLPDAQGDIFRGLEVVEHACSVGTLQMGEFA 135

Query: 133 ENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTML 192
           ENVAGGVDTYTLRQPIGVCAGITPFNFP MIPLWMFPMAI CGNTFVLKPSEQDP+STM 
Sbjct: 136 ENVAGGVDTYTLRQPIGVCAGITPFNFPGMIPLWMFPMAIVCGNTFVLKPSEQDPLSTME 195

Query: 193 LVELAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKRV 252
           LVELA+EAG+PPGVLNVVHGGK VVD LCTH D+KA+SFVGST VGTHVY+L  KHGKRV
Sbjct: 196 LVELAMEAGVPPGVLNVVHGGKTVVDMLCTHPDVKAISFVGSTHVGTHVYNLGSKHGKRV 255

Query: 253 QSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLPDLKALA 312
           QSMMGAKNHAVVLPDANR+Q LNALVGAGFGAAGQRCMATSVVVLVG ++ WLP+L A A
Sbjct: 256 QSMMGAKNHAVVLPDANRQQTLNALVGAGFGAAGQRCMATSVVVLVGQSRDWLPELVAKA 315

Query: 313 QKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGNFVG 372
           + LKVNAG EPGTDVGPV+SK A ARI  LIE G++ GA L LDGR++ VPGYE GNFVG
Sbjct: 316 KLLKVNAGHEPGTDVGPVMSKAAHARITGLIEEGVQAGAALLLDGRNVKVPGYENGNFVG 375

Query: 373 PTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAAARKF 432
           PT+FSGV+P+M IYTQEIFGPV+VVLEVDTLD+AIALVN NP GNG GLFTQSGAAARKF
Sbjct: 376 PTIFSGVSPDMSIYTQEIFGPVVVVLEVDTLDEAIALVNRNPMGNGVGLFTQSGAAARKF 435

Query: 433 QTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFDDD 492
           Q+EIDVGQVGINIPIPVPVP+FSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFDD 
Sbjct: 436 QSEIDVGQVGINIPIPVPVPYFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFDDT 495

Query: 493 SVNDGVNTTIHLR 505
              +GVNTTI LR
Sbjct: 496 PA-EGVNTTIALR 507


Lambda     K      H
   0.319    0.135    0.397 

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: 834
Number of extensions: 25
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 505
Length of database: 507
Length adjustment: 34
Effective length of query: 471
Effective length of database: 473
Effective search space:   222783
Effective search space used:   222783
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 RR42_RS25635 RR42_RS25635 (methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.7291.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7291.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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