GapMind for catabolism of small carbon sources

 

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

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Pf6N2E2_4251 Dihydrolipoamide dehydrogenase (EC 1.8.1.4)

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4251
          Length = 466

 Score =  719 bits (1857), Expect = 0.0
 Identities = 351/465 (75%), Positives = 402/465 (86%)

Query: 2   MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61
           M +YDVI++G GPGGYNAAIRAGQLGLK ACVEGR TLGGTCLNVGCMPSKALLHASELY
Sbjct: 1   MSNYDVIILGGGPGGYNAAIRAGQLGLKAACVEGRATLGGTCLNVGCMPSKALLHASELY 60

Query: 62  AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121
            AA+G EFA LGI VSP L+LAQMMKQKDESVA LT+G+EFLFRK+KV WIKGW  + G 
Sbjct: 61  EAATGAEFANLGIEVSPTLNLAQMMKQKDESVAGLTKGIEFLFRKNKVDWIKGWGHIDGP 120

Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181
           G+V V   DG   +L A+DIVIATGSEP PLPGVP+DNQRILDSTGAL L EVPRHLVVI
Sbjct: 121 GKVIVTGDDGAKTELSAKDIVIATGSEPMPLPGVPIDNQRILDSTGALSLGEVPRHLVVI 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           GAGVIGLELGSVWRRLGAQVTV+EYL+RICPG+DGE  +TLQRAL +QG++F+L ++V  
Sbjct: 181 GAGVIGLELGSVWRRLGAQVTVVEYLDRICPGVDGEAGKTLQRALAKQGIQFKLSSKVTG 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301
           A +   GV+L ++PAAGG  + L ADYVLVAIGRRPYT+GLGLE VGL+ D+RGML NQ 
Sbjct: 241 ATTSASGVQLQIEPAAGGEAQPLDADYVLVAIGRRPYTQGLGLENVGLSPDQRGMLANQN 300

Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361
            R+ APGVWVIGDVTSGPMLAHKAE+EA+ CIE+IAG AAE+N  +IPSVIYT+PE+ASV
Sbjct: 301 HRTEAPGVWVIGDVTSGPMLAHKAEDEAMACIEQIAGKAAEVNYALIPSVIYTRPELASV 360

Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421
           G  EEQL+A  R YKVG+FPF+ANSRAKINHE+EGF K+L+D R+D++LGVH++GP VSE
Sbjct: 361 GKTEEQLKAEGRAYKVGKFPFTANSRAKINHETEGFAKVLADERTDEILGVHLVGPSVSE 420

Query: 422 MIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGRAMQ 466
           MIGE CVAMEFSASAED+ALTCHPHPTRSEALRQAAMDV G A Q
Sbjct: 421 MIGEYCVAMEFSASAEDIALTCHPHPTRSEALRQAAMDVEGMATQ 465


Lambda     K      H
   0.318    0.135    0.390 

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: 809
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: 467
Length of database: 466
Length adjustment: 33
Effective length of query: 434
Effective length of database: 433
Effective search space:   187922
Effective search space used:   187922
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 Pf6N2E2_4251 (Dihydrolipoamide dehydrogenase (EC 1.8.1.4))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.25860.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25860.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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