GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Pseudomonas fluorescens FW300-N2E2

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate Pf6N2E2_3452 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= reanno::pseudo13_GW456_L13:PfGW456L13_5146
         (508 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3452
          Length = 508

 Score =  959 bits (2480), Expect = 0.0
 Identities = 476/508 (93%), Positives = 503/508 (99%)

Query: 1   MNVSLTPNDTTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISA 60
           MNVSLTP+DTT+Q V+LLIDG+WVES+++EWHDI+NPATQQVLAKVPFATA EVDAAI+A
Sbjct: 1   MNVSLTPSDTTLQTVRLLIDGEWVESQSSEWHDIVNPATQQVLAKVPFATASEVDAAIAA 60

Query: 61  AHRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120
           A RAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV
Sbjct: 61  AQRAFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVV 120

Query: 121 EHACSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180
           EHACSIG+LQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT
Sbjct: 121 EHACSIGTLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNT 180

Query: 181 FVLKPSEQDPMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAV 240
           FVLKPSEQDP+STMLLVELAIEAG+PAGVLNVVHGGKDVVD LCTHKDIKAVSFVGSTAV
Sbjct: 181 FVLKPSEQDPLSTMLLVELAIEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAV 240

Query: 241 GTHVYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL 300
           GTHVYDLAG+HGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL
Sbjct: 241 GTHVYDLAGRHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVL 300

Query: 301 VGAAKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDG 360
           VGAAKQWLP+LKALAQKLKVNAGSEPGTDVGPVISK+AKARIL+LIESG+++GAKLELDG
Sbjct: 301 VGAAKQWLPELKALAQKLKVNAGSEPGTDVGPVISKRAKARILELIESGVQQGAKLELDG 360

Query: 361 REISVPGYEKGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGN 420
           R ISVPG+E+GNFVGPTLFSGVTTDM+IYT+EIFGPVLVVLEV+TLD+AIALVNANPFGN
Sbjct: 361 RGISVPGFEQGNFVGPTLFSGVTTDMRIYTEEIFGPVLVVLEVDTLDQAIALVNANPFGN 420

Query: 421 GTGLFTQSGAAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480
           GTGLFTQSGAAARKFQ+EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF
Sbjct: 421 GTGLFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQF 480

Query: 481 YTQTKTVTSRWFDDDSVNDGVNTTINLR 508
           YTQTKTVT+RWFDDDSVNDGVNTTINLR
Sbjct: 481 YTQTKTVTARWFDDDSVNDGVNTTINLR 508


Lambda     K      H
   0.318    0.135    0.395 

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: 921
Number of extensions: 25
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: 508
Length of database: 508
Length adjustment: 34
Effective length of query: 474
Effective length of database: 474
Effective search space:   224676
Effective search space used:   224676
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Pf6N2E2_3452 (Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.18588.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18588.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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