GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Pseudomonas simiae WCS417

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate GFF4637 PS417_23725 methylmalonate-semialdehyde dehydrogenase

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



>FitnessBrowser__WCS417:GFF4637
          Length = 505

 Score =  944 bits (2441), Expect = 0.0
 Identities = 471/505 (93%), Positives = 493/505 (97%)

Query: 1   MNASLETTVQKVKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHR 60
           MNAS + +VQ+VKLLI+GEWVES+TTEW DIVNPATQ+VLAKVPFATA EV+AAI AAHR
Sbjct: 1   MNASADISVQQVKLLINGEWVESKTTEWQDIVNPATQEVLAKVPFATADEVNAAIDAAHR 60

Query: 61  AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA 120
           AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA
Sbjct: 61  AFQTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHA 120

Query: 121 CSIGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180
           CSIG+LQMGEF+ENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL
Sbjct: 121 CSIGTLQMGEFSENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 180

Query: 181 KPSEQDPMSTMLLVELAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH 240
           KPSEQDP+STMLLVELA+EAG+P GVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH
Sbjct: 181 KPSEQDPLSTMLLVELALEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH 240

Query: 241 VYDLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGA 300
           VYDLAGKHGKRVQSMMGAKNHAVVLPDANRE  LNALVGAGFGAAGQRCMATSVVVLVGA
Sbjct: 241 VYDLAGKHGKRVQSMMGAKNHAVVLPDANREHTLNALVGAGFGAAGQRCMATSVVVLVGA 300

Query: 301 AKQWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDI 360
           +KQWLPDLKALAQKLKVNAGSE GTDVGPVISKRAKARIL+LIESG+KEGAKLELDGRDI
Sbjct: 301 SKQWLPDLKALAQKLKVNAGSEAGTDVGPVISKRAKARILELIESGVKEGAKLELDGRDI 360

Query: 361 SVPGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTG 420
            VPG+E+GNFVGPTLFSGVTP MQIYTQEIFGPVLVVLEV TLD+AIALVNANPFGNGTG
Sbjct: 361 KVPGFEQGNFVGPTLFSGVTPSMQIYTQEIFGPVLVVLEVATLDEAIALVNANPFGNGTG 420

Query: 421 LFTQSGAAARKFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ 480
           LFTQSGAAARKFQ+EIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ
Sbjct: 421 LFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ 480

Query: 481 TKTVTARWFDDDSVNDGVNTTIHLR 505
           TKTVT+RWFDDD+VNDGVNTTI+LR
Sbjct: 481 TKTVTSRWFDDDTVNDGVNTTINLR 505


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: 923
Number of extensions: 22
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: 505
Length of database: 505
Length adjustment: 34
Effective length of query: 471
Effective length of database: 471
Effective search space:   221841
Effective search space used:   221841
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 GFF4637 PS417_23725 (methylmalonate-semialdehyde dehydrogenase)
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.2237.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2237.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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