GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Phaeobacter inhibens BS107

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate GFF974 PGA1_c09900 malate synthase GlcB

Query= reanno::psRCH2:GFF353
         (726 letters)



>FitnessBrowser__Phaeo:GFF974
          Length = 710

 Score =  862 bits (2228), Expect = 0.0
 Identities = 427/715 (59%), Positives = 536/715 (74%), Gaps = 16/715 (2%)

Query: 10  LQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDLQAQIDAWHQ 69
           +QVA  L  F+ ++A+PGTGV A AFWAG   +++ +  +NRALLAKR DLQ QIDAWH 
Sbjct: 10  MQVADTLVSFIEDKALPGTGVTADAFWAGLAGLVNGMGDENRALLAKRADLQGQIDAWHI 69

Query: 70  ARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVPIMNARFALN 129
            R GQAHDA AY++FL++IGYLLPE +DF+  T+NVD+EIA + GPQLVVPI NARFALN
Sbjct: 70  ERKGQAHDATAYEAFLRDIGYLLPEGDDFEIETQNVDDEIANVPGPQLVVPITNARFALN 129

Query: 130 AANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAAPLETGSHVD 189
           AANARWGSLYDALYGTDA+ +     +G GY+  RG +VIA+ R FL++  PL  GS  D
Sbjct: 130 AANARWGSLYDALYGTDAMGDLP---EGKGYDAGRGARVIAWGRGFLDQTFPLAEGSWND 186

Query: 190 STGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHFEIQIDPASP 249
             G  +EGG LV +LKD         AQ  G++G+A+ P  +LLKNNG+H  I +D    
Sbjct: 187 CVGLSVEGGALVPALKDA--------AQFAGYEGDAATPGKILLKNNGLHAVIVVDANGN 238

Query: 250 IGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDLVEELEKGGK 309
           IG+ D AG+ DI++ESAL+TIMDCEDS+A VD +DK   Y NWLGLMK DL EE+ KGG+
Sbjct: 239 IGKGDQAGINDIVLESALSTIMDCEDSVACVDGEDKVTAYANWLGLMKRDLAEEVTKGGE 298

Query: 310 RITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEVPEGIMDGLF 369
             TR +N D+ +T  DG+ +L L GRSLL +RNVGHLMTN A+ D  G E  EG +D + 
Sbjct: 299 TFTRVLNDDQTFTAPDGS-DLVLKGRSLLLVRNVGHLMTNPAVRDSAGREAGEGFIDAMV 357

Query: 370 TSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLGLPRNTLKVG 429
           T L A+H+L       N+  GS+Y+VKPKMHGPEEVAF   +F  VED LGLPR+T+K+G
Sbjct: 358 TVLCAMHDLQAEGG--NSLHGSVYVVKPKMHGPEEVAFTDRIFTHVEDALGLPRHTVKIG 415

Query: 430 IMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKAAMKAEKWIS 489
           IMDEERRT++NLK+CI+ A+ RV FINTGFLDRTGDEIHTSMEAG M+RK  MK+  WI+
Sbjct: 416 IMDEERRTSVNLKSCIRAAKHRVAFINTGFLDRTGDEIHTSMEAGAMMRKGEMKSTPWIA 475

Query: 490 AYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAWVPSPTAATL 549
           +YE+ NVD+GLACGL+G+AQIGKGMWAMPD M  MLE K+GHP +GA  AWVPSPTAATL
Sbjct: 476 SYEDRNVDIGLACGLKGRAQIGKGMWAMPDRMGEMLEAKIGHPKSGATCAWVPSPTAATL 535

Query: 550 HAMHYHKIDVQARQVEL-AKREKASIDDILTIPLAQDTNWSEEEKRNELDNNSQGILGYM 608
           HA HYH+++V   Q +L A   + ++DD+LTIP+ Q  N S+ E   E++NN+QGILGY+
Sbjct: 536 HATHYHRVNVHEVQDQLKAGGARGTLDDLLTIPVMQGENLSDAEIAQEIENNAQGILGYV 595

Query: 609 VRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVESLKRMAPVV 668
           VRWV+QGVGCSKVPDI+++ LMEDRAT RISSQ +ANW+ HG+V + QV+ ++++MA VV
Sbjct: 596 VRWVDQGVGCSKVPDIHNVGLMEDRATCRISSQALANWLHHGIVDETQVMAAMQKMAAVV 655

Query: 669 DRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRREFKAK 723
           D QN  D  Y PMAP FD  +AFQAA +LV  G  QP+GYTEPVLH RR E KA+
Sbjct: 656 DGQNASDASYTPMAPGFD-GIAFQAACDLVFRGRIQPSGYTEPVLHARRLELKAQ 709


Lambda     K      H
   0.316    0.133    0.386 

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: 1475
Number of extensions: 65
Number of successful extensions: 7
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: 726
Length of database: 710
Length adjustment: 40
Effective length of query: 686
Effective length of database: 670
Effective search space:   459620
Effective search space used:   459620
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: 55 (25.8 bits)

Align candidate GFF974 PGA1_c09900 (malate synthase GlcB)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.24270.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24270.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.