GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Burkholderia phytofirmans PsJN

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate BPHYT_RS09815 BPHYT_RS09815 malate synthase

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



>FitnessBrowser__BFirm:BPHYT_RS09815
          Length = 724

 Score =  979 bits (2530), Expect = 0.0
 Identities = 476/726 (65%), Positives = 590/726 (81%), Gaps = 10/726 (1%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT+    GGLQVA  L  FV  EA+PGTG+D+AAFW+G D+++H+LAPKNRALLA+RD L
Sbjct: 1   MTQMNTRGGLQVAANLDQFVETEALPGTGIDSAAFWSGFDALVHELAPKNRALLAERDRL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q ++D WH+A  G   D  AY++FL+ IGY++P     +ATT+NVD EIA  AGPQLVVP
Sbjct: 61  QTELDNWHRANPGPVRDLRAYRAFLEGIGYIVPAPASVKATTDNVDTEIAEQAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           + N R+ALNAANARWGSLYDALYGTDAI E  GA K   +N +RG  VIAYAR FL++AA
Sbjct: 121 LSNQRYALNAANARWGSLYDALYGTDAIPETGGAEKQKAFNPVRGAAVIAYARKFLDQAA 180

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL  GSH D+T Y ++GGKLVV+LK+G T+ LK PAQ  G+QGE SAP AVLLK+NG+HF
Sbjct: 181 PLANGSHADATRYSVDGGKLVVTLKNG-TSELKTPAQFIGYQGEESAPSAVLLKHNGLHF 239

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           EIQID +  IG+TDAA VKD+++E+A++TI+DCEDS+AAVDADDK ++YRNWLGLM GDL
Sbjct: 240 EIQIDASDSIGRTDAAHVKDVVVEAAVSTIIDCEDSVAAVDADDKVLLYRNWLGLMTGDL 299

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
            EE+ K GK  TR +N DRVYT A+G   + LHGRSLLFIRNVGHLMTN A+L K+G+E+
Sbjct: 300 TEEVTKNGKTFTRRLNADRVYTAANGTAPVVLHGRSLLFIRNVGHLMTNPAVLTKDGHEI 359

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+D + T+L A+H+      + N+RTGS+YIVKPKMHGP EVAFA+ELF RVED+L 
Sbjct: 360 PEGILDAVITTLCALHD---RKHQLNSRTGSIYIVKPKMHGPAEVAFASELFSRVEDLLK 416

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           LPRNT+K+GIMDEERRT++NL ACI EA ERV FINTGFLDRTGDE+H++MEAGPM+RK 
Sbjct: 417 LPRNTIKMGIMDEERRTSVNLLACIAEASERVAFINTGFLDRTGDEMHSAMEAGPMMRKG 476

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MK+  WI+AYE +NV VGL+ GL+G++QIGKGMWAMPDLM AMLEQK+ HP AGANTAW
Sbjct: 477 DMKSSAWIAAYERSNVLVGLSAGLRGRSQIGKGMWAMPDLMHAMLEQKIAHPKAGANTAW 536

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASI-----DDILTIPLAQDTNWSEEEKRN 595
           VPSPTAATLHA+HYH++DVQA Q EL + + A++     D +LTIP+  +  WS++E R+
Sbjct: 537 VPSPTAATLHALHYHQVDVQAVQRELERTDYATVRDELLDGLLTIPVVAEAKWSDDEIRS 596

Query: 596 ELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKD 655
           E+DNN+QGILGY+VRW++QGVGCSKVPDI+D+ LMEDRATLRISSQH+ANW+ HGVV ++
Sbjct: 597 EIDNNAQGILGYVVRWIDQGVGCSKVPDIHDVGLMEDRATLRISSQHIANWLYHGVVKRE 656

Query: 656 QVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHR 715
            V E+ KRMA VVD QN GDPLY+PMAP FD ++AF+AA  LV EG +QP+GYTEP+LH+
Sbjct: 657 LVEETFKRMAKVVDEQNAGDPLYKPMAPGFD-TIAFKAAQALVFEGRQQPSGYTEPLLHK 715

Query: 716 RRREFK 721
            R E K
Sbjct: 716 FRLEVK 721


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: 1463
Number of extensions: 67
Number of successful extensions: 5
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: 724
Length adjustment: 40
Effective length of query: 686
Effective length of database: 684
Effective search space:   469224
Effective search space used:   469224
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 BPHYT_RS09815 BPHYT_RS09815 (malate synthase)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.19878.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19878.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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