GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Synechococcus elongatus PCC 7942

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Synpcc7942_1198 Synpcc7942_1198 dihydrolipoamide dehydrogenase

Query= BRENDA::A0A0K9R8G5
         (565 letters)



>FitnessBrowser__SynE:Synpcc7942_1198
          Length = 479

 Score =  556 bits (1434), Expect = e-163
 Identities = 284/474 (59%), Positives = 358/474 (75%), Gaps = 9/474 (1%)

Query: 81  FDYDLLIIGAGVGGHGAALHAVEKGLKTAIIEGDVMGGTCVNRGCVPSKALLAVSGRMRE 140
           FDYD+++IGAG GG  AA HA EKGLKTAI+E   +GGTCVNRGCVPSKALLA SGR+RE
Sbjct: 5   FDYDVIVIGAGYGGFDAAKHACEKGLKTAIVEARDLGGTCVNRGCVPSKALLAASGRVRE 64

Query: 141 LQNEQHLKSFGIQVGAANYDRQGVADHASNLASKIRGNLTNSLKALGVDILTGFGTILGP 200
           + +  HL++FGIQV   ++DRQ +ADHA+NL   +R NL N+LK LG +IL G G + G 
Sbjct: 65  ITDTDHLQNFGIQVQGVSFDRQAIADHAANLVDTVRTNLGNTLKRLGAEILMGRGRLAGS 124

Query: 201 QKVQF----GKDNIVTAKDIIIATGSVPFVPRGIEVDGKTVITSDHALKLESVPDWIAIV 256
           Q+V      G +   +A+D+I+ATGS PFVP GIE+DGKTV TSD ALKLE++P WIAI+
Sbjct: 125 QRVTVTAADGTEKTYSARDVILATGSDPFVPPGIEIDGKTVFTSDDALKLETLPQWIAII 184

Query: 257 GSGYIGLEFSDVYTALGSEVTFIEALDQLMPGFDPEVSKLAQRILINPRKIDYHTGVFAT 316
           GSGYIGLEFSDVYTALG EVT IEALD+L+P FDP+V+K+AQR L++ R I+  TGV A 
Sbjct: 185 GSGYIGLEFSDVYTALGCEVTMIEALDRLLPTFDPDVAKVAQRSLLDGRDIETRTGVLAR 244

Query: 317 KITPAKDGKPVTIELTDAKTKEHKDTLEVDAALIATGRAPYTQGLGLESINV-VTQRGFV 375
           KITP   G PV IEL D +TKE  + LEVDA L+ATGR P T+ LGLE++ V V +RGF+
Sbjct: 245 KITP---GSPVVIELADFETKELVEVLEVDACLVATGRIPSTKNLGLETVAVEVDRRGFI 301

Query: 376 PVDDRMRVIDANGKLVPNLYCIGDANGKMMLAHAASAQGISVVEQVTGRDHVLNHLSIPA 435
           PVDD MRV+  + K VP+L+ +GDA GK+MLAHAA+AQG+  +E +TG    +++ SIPA
Sbjct: 302 PVDDGMRVL-RDSKPVPHLFAVGDATGKLMLAHAAAAQGVVAIENITGHPRSVDYRSIPA 360

Query: 436 ACFTHPEISMVGLTEPQAREKAEKEGFPVSVAKTSFKANSKALAENEAEGIAKLIYRPDN 495
           A FTHPEIS VGL+E  A+    +EGF V   ++ FKANSKALAE +A+G AK+++R D 
Sbjct: 361 ATFTHPEISSVGLSEADAKALGGQEGFEVGSVRSYFKANSKALAEADADGFAKVLFRKDT 420

Query: 496 GEILGVHIFGLHAADLIHEASNAIAMGTPIQDLKLAVHAHPTLSEVLDELYKAA 549
           GE+LG HIFGLHAADLI E +NAIA    +++L   VH HPTLSEV++  YK A
Sbjct: 421 GEVLGAHIFGLHAADLIQEVANAIARRQSVKELAFEVHTHPTLSEVIESAYKQA 474


Lambda     K      H
   0.316    0.133    0.377 

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: 709
Number of extensions: 28
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: 565
Length of database: 479
Length adjustment: 35
Effective length of query: 530
Effective length of database: 444
Effective search space:   235320
Effective search space used:   235320
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 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate Synpcc7942_1198 Synpcc7942_1198 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.27373.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27373.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.