GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatB in Marinobacter adhaerens HP15

Align glutamyl-tRNAGln amidotransferase subunit B (EC 6.3.5.7) (characterized)
to candidate GFF2514 HP15_2458 aspartyl/glutamyl-tRNA amidotransferase subunit B

Query= metacyc::MONOMER-13956
         (476 letters)



>FitnessBrowser__Marino:GFF2514
          Length = 483

 Score =  421 bits (1081), Expect = e-122
 Identities = 221/481 (45%), Positives = 314/481 (65%), Gaps = 8/481 (1%)

Query: 1   MNFETVIGLEVHVELKTKSKIFSSSPTPFGAEANTQTSVIDLGYPGVLPVLNKEAVEFAM 60
           M ++ VIGLE+HV+L TK+KIFS S T +GAE NTQ + +DL  PG LPV N++A  +A+
Sbjct: 1   MQWDIVIGLEIHVQLATKTKIFSGSSTAYGAEPNTQANAVDLAMPGTLPVPNEQAFRYAV 60

Query: 61  KAAMALNCEIATDTKFDRKNYFYPDNPKAYQISQFDKPIGENGWIEIEV-GGKTKRIGIT 119
              +A+N EI   + F+RKNYFYPD PK YQ +Q ++PI   G+++I++  G+TKR+ I 
Sbjct: 61  MFGLAVNAEIERRSVFERKNYFYPDLPKGYQTTQLERPIVGPGFVDIDLPNGETKRVRIH 120

Query: 120 RLHLEEDAGKLTHTG-DGYSLVDFNRQGTPLVEIVSEPDIRTPEEAYAYLEKLKSIIQYT 178
             HLEEDAGK  H    G + VD NR GTPL+E+V+EPD+   EEA A+ +KL SI+   
Sbjct: 121 HAHLEEDAGKSLHEDFHGMTGVDLNRAGTPLIEVVTEPDMNNAEEAVAFAKKLHSIVTSL 180

Query: 179 GVSDCKMEEGSLRCDANISLRPIGQEEFGTKTELKNLNSFAFVQKGLEHEEKRQEQVLLS 238
           G+ D  M +GS+R D NISL+P G +  GT+TE KNLNSF F+++ + HE +RQ  +L  
Sbjct: 181 GICDGDMSQGSMRFDVNISLKPKGSDTLGTRTETKNLNSFRFMEQAIAHEVERQMDILED 240

Query: 239 GFFIQQETRRYDEATKKTILMRVKEGSDDYRYFPEPDLVELYIDDEWKERVKASIPELPD 298
           G  I QETR Y+    ++  MR KE ++DYRYFP PDL+ + IDD + E  + S+PELPD
Sbjct: 241 GGNIVQETRLYNGDRDESRSMRTKEEANDYRYFPCPDLLPVEIDDSFIEEARNSLPELPD 300

Query: 299 ERRKRYIEELGFAAYDAMVLTLTKEMADFFEETVQKGAEAKQASNWLMGEVSAYLNAEQK 358
            R+ R++E+ G   YDA +L+   ++A FFEE   +G +AK  +NW+ GE SA LNAE+K
Sbjct: 301 ARKARFMEQYGLNDYDAGLLSGDSKLATFFEEAASQGKDAKLVANWIQGEFSARLNAEEK 360

Query: 359 ELADVALTPEGLAGMIKLIEKGTISSKIAKKVFKELIEKGGDA-EKIVKEKGLVQISDEG 417
            +AD  ++   L  ++  I   TISS  AKKVF+ L     D+ + I+  KGL Q+SD G
Sbjct: 361 SVADSPISGAQLGDLVVRIADNTISSAGAKKVFEALWSGENDSVDAIIDAKGLKQVSDTG 420

Query: 418 VLLKLVTEALDNNPQSIEDFKNGKD-----RAIGFLVGQIMKASKGQANPPMVNKILLEE 472
            L  +V E L   P  +  ++N +D     + +G  +G +MKASKGQ NP + N+IL+ +
Sbjct: 421 ALEAMVDEVLAGMPDQVAQYQNEEDPKKRKKMLGGFMGPLMKASKGQGNPKLFNEILVRK 480

Query: 473 I 473
           +
Sbjct: 481 L 481


Lambda     K      H
   0.314    0.134    0.373 

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: 620
Number of extensions: 29
Number of successful extensions: 6
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: 476
Length of database: 483
Length adjustment: 34
Effective length of query: 442
Effective length of database: 449
Effective search space:   198458
Effective search space used:   198458
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)

Align candidate GFF2514 HP15_2458 (aspartyl/glutamyl-tRNA amidotransferase subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))

Software error:

../bin/blast/fastacmd -i /tmp/list.5554.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5554.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.