GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pseudomonas fluorescens FW300-N1B4

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Pf1N1B4_1976 Dihydrolipoamide dehydrogenase (EC 1.8.1.4)

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1976
          Length = 466

 Score =  712 bits (1838), Expect = 0.0
 Identities = 346/465 (74%), Positives = 403/465 (86%)

Query: 2   MESYDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELY 61
           M +YDV+++GAGPGGYNAAIRAGQLGLK ACVEGR TLGGTCLNVGCMPSKALLHASELY
Sbjct: 1   MSTYDVVILGAGPGGYNAAIRAGQLGLKAACVEGRATLGGTCLNVGCMPSKALLHASELY 60

Query: 62  AAASGGEFARLGIRVSPELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGE 121
            AA G EFA LGI V P L+LAQMMKQKDESV  LT+G+EFLFRK+KV WIKGW  + G 
Sbjct: 61  DAAMGAEFANLGIEVKPVLNLAQMMKQKDESVTGLTKGIEFLFRKNKVDWIKGWGHIDGP 120

Query: 122 GRVGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVI 181
           G V V  + GG  QL A+DIVIATGSEP PLPGV +DN+RILDSTGAL L+EVP+HLVVI
Sbjct: 121 GSVTVTDSQGGKTQLTAKDIVIATGSEPTPLPGVDIDNKRILDSTGALSLSEVPKHLVVI 180

Query: 182 GAGVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRVVA 241
           GAGVIGLELGSVWRRLGAQVTV+E+L+RICPG+DGE  +TLQR+L++QG+RF+L ++V +
Sbjct: 181 GAGVIGLELGSVWRRLGAQVTVVEFLDRICPGVDGEAGKTLQRSLSKQGIRFKLSSKVTS 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLENQG 301
           A +   GV+L ++PAAGG  E L+ADYVLVAIGRRPYT+GLGLE VGLA+D+RGML N+G
Sbjct: 241 ATTSASGVQLSVEPAAGGTAELLEADYVLVAIGRRPYTQGLGLENVGLATDKRGMLANKG 300

Query: 302 QRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVASV 361
            R+ A GVWVIGDVTSGPMLAHKAE+EA+ CIE+I G A E+N ++IPSVIYT+PE+ASV
Sbjct: 301 HRTEAAGVWVIGDVTSGPMLAHKAEDEAMACIEQIVGKAGEVNYDLIPSVIYTKPELASV 360

Query: 362 GLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVSE 421
           G  EEQL+A  R YKVG+FPF+ANSRAKINHE+EGF K+L+D R+D+VLGVH++GP VSE
Sbjct: 361 GKTEEQLKAEGRAYKVGKFPFTANSRAKINHETEGFAKVLADERTDEVLGVHLVGPSVSE 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: 800
Number of extensions: 26
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 Pf1N1B4_1976 (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.1799.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1799.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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