GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Phaeobacter inhibens BS107

Align Dihydrolipoyl dehydrogenase; EC 1.8.1.4; Dihydrolipoamide dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes (uncharacterized)
to candidate GFF3862 PGA1_78p00260 dihydrolipoyl dehydrogenase LpdA

Query= curated2:P95596
         (454 letters)



>FitnessBrowser__Phaeo:GFF3862
          Length = 460

 Score =  492 bits (1266), Expect = e-143
 Identities = 257/461 (55%), Positives = 337/461 (73%), Gaps = 8/461 (1%)

Query: 1   MAEFDVIIIGGGPGGYVCAIRCAQLGLKTACVEGRGALGGTCLNVGCIPSKALLHATHEL 60
           M+ +D+I+IGGGPGGYV AIR AQLGLK ACVEGRG LGGTCLNVGCIPSKA+L ++ + 
Sbjct: 1   MSLYDLIVIGGGPGGYVAAIRAAQLGLKVACVEGRGTLGGTCLNVGCIPSKAMLSSSGKY 60

Query: 61  HEV-HENFEKMGLMGAKVKVDWA-----KIDGN-TKGIEFLFKKNKVTYLRGWGSIPAPG 113
             + H     + + GA++ +D       KI G+ TKGI FLF+KN V  + GW SIPA G
Sbjct: 61  ESLSHLAGHGIAIEGARLDLDAMMARKDKIVGDLTKGIAFLFQKNGVDLIEGWASIPAVG 120

Query: 114 QVKVGDEVHTAKNIVIATGSESSGLPGIEIDEQTVVTSTGALSLAKVPKSMVVIGAGVIG 173
           +VKVGDE+H  KNI+IATGSE + LPG+EIDE  VV+STGAL+L +VPK +VV+GAGVIG
Sbjct: 121 KVKVGDEIHETKNILIATGSEPTPLPGVEIDEGDVVSSTGALTLPEVPKHLVVVGAGVIG 180

Query: 174 LELGSVYARLGAEVTVVEYLDAITPGMDAEVAKGLQRILTRQGLKFVLGAAVQGVDKAKG 233
           LELG V++RLGA+VTVVEYLD I PG+D E+AK  QR L+++GLKF LG A++ +D++  
Sbjct: 181 LELGQVWSRLGAKVTVVEYLDRILPGIDGEIAKLAQRALSKRGLKFQLGRALKFIDRSDE 240

Query: 234 KNTVRYTLRKDESAHAIEAEVVLVATGRKPFTKGLGLEALGVEMLPRGQVKADSHWATNV 293
             T+       +    + A+ VL+A GR+P  +GLGLEALGV +  RG V+ D  ++T+V
Sbjct: 241 GLTLTLDRVGKDKEEQLVADKVLIAIGRRPVIRGLGLEALGVSVNARGFVEVDERFSTSV 300

Query: 294 PGLYAIGDAIVGPMLAHKAEDEGMAVAEVIAGKHGHVNYDVIPGVIYTTPEVAAVGKTED 353
            G+YAIGD + GPMLAHKAE++G+A  E++AG+ GHV+Y+ +PG++YT PEVA+VGKTE+
Sbjct: 301 EGIYAIGDCVPGPMLAHKAEEDGVACVEMLAGQAGHVDYNTVPGIVYTDPEVASVGKTEE 360

Query: 354 ALKQEGRAYKVGKFSFMGNGRAKAVFQAEGFVKILADAATDRILGAHIIGPSAGDMIHEI 413
           ALK  G  Y VGKF FM N RA+A  + +G VK+LA     +ILGAHI G   GD+I E+
Sbjct: 361 ALKDAGTDYIVGKFIFMANSRARAQGETDGAVKVLA-TPEGQILGAHICGAHGGDLIAEL 419

Query: 414 CVAMEFGASAQDLALTCHAHPTYSEAVREAALACGDGAIHA 454
            +AM  GA+  ++A TCHAHP  +EAV+EA L     AIHA
Sbjct: 420 VLAMTKGATVAEVAATCHAHPAMAEAVKEACLDAMGRAIHA 460


Lambda     K      H
   0.318    0.136    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: 783
Number of extensions: 30
Number of successful extensions: 4
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: 454
Length of database: 460
Length adjustment: 33
Effective length of query: 421
Effective length of database: 427
Effective search space:   179767
Effective search space used:   179767
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: 51 (24.3 bits)

Align candidate GFF3862 PGA1_78p00260 (dihydrolipoyl dehydrogenase LpdA)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.2862.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2862.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.