GapMind for catabolism of small carbon sources

 

Alignments for a candidate for icd in Burkholderia phytofirmans PsJN

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate BPHYT_RS20300 BPHYT_RS20300 isocitrate dehydrogenase

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__BFirm:BPHYT_RS20300
          Length = 742

 Score = 1211 bits (3134), Expect = 0.0
 Identities = 608/742 (81%), Positives = 662/742 (89%), Gaps = 1/742 (0%)

Query: 1   MSTP-KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDT 59
           MSTP KIIYTLTDEAPALATYSLLPI+KAFT SS + VETRDISLAGR+IA FP+YL+  
Sbjct: 1   MSTPPKIIYTLTDEAPALATYSLLPIVKAFTRSSDVIVETRDISLAGRIIAAFPDYLSAE 60

Query: 60  QKISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTE 119
           QK  DDLAELG L+T P+AN+IKLPNISASVPQLKAAI EL+ QGYKLP YP+   TD E
Sbjct: 61  QKGPDDLAELGGLSTRPEANVIKLPNISASVPQLKAAITELRDQGYKLPAYPDVANTDAE 120

Query: 120 KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNG 179
           KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHM  G
Sbjct: 121 KDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMSGG 180

Query: 180 DFYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAE 239
           DFYGSEK+ALIGA GSVKIEL A DGS TVLK KT+VQAGEIID+SV+SKNALR+FI AE
Sbjct: 181 DFYGSEKSALIGAAGSVKIELTATDGSKTVLKEKTAVQAGEIIDASVLSKNALRSFIEAE 240

Query: 240 IEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGD 299
           I DAK +GVL SVHLKATMMKVSDPI+FG +VS FYKD LTKHA+ L Q GF+ NNGIGD
Sbjct: 241 IADAKAKGVLFSVHLKATMMKVSDPIIFGHVVSVFYKDVLTKHADALAQAGFNPNNGIGD 300

Query: 300 LYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRD 359
           LYAR+K LP      IEADI+A Y QRPQLAMVNSDKGIT+LHVPSDVIVDASMPAMIR+
Sbjct: 301 LYARLKDLPAETVAAIEADIKAQYEQRPQLAMVNSDKGITSLHVPSDVIVDASMPAMIRE 360

Query: 360 SGKMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEE 419
           SGKMWG DG LHD KAVIPDRCYAGVYQ VIEDCK+HGAFDP TMG+VPNVGLMAQ AEE
Sbjct: 361 SGKMWGADGALHDAKAVIPDRCYAGVYQAVIEDCKKHGAFDPVTMGTVPNVGLMAQAAEE 420

Query: 420 YGSHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARA 479
           YGSHDKTFQIPA+GVVRVTD +G +L+EQ VEAGDIWRMCQ KDAP+QDWVKLAVNRARA
Sbjct: 421 YGSHDKTFQIPANGVVRVTDAAGTVLIEQQVEAGDIWRMCQTKDAPVQDWVKLAVNRARA 480

Query: 480 TNTPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTI 539
           TNTPAVFWLD ARAHDAQ+I KVE+YLK++DT+GLDIR+++PVEAT+FS+ RIR GKDTI
Sbjct: 481 TNTPAVFWLDAARAHDAQIIKKVEQYLKNHDTTGLDIRVMTPVEATKFSIERIRAGKDTI 540

Query: 540 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYL 599
           SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLM+GGG+FETGAGGSAPKHVQQ +EEG+L
Sbjct: 541 SVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMAGGGMFETGAGGSAPKHVQQLVEEGFL 600

Query: 600 RWDSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGS 659
           RWDSLGEFLALAASLEHL +AY NPKA VLA TLDQATGK LDN+KSPARKVG IDNRGS
Sbjct: 601 RWDSLGEFLALAASLEHLSSAYHNPKAQVLAKTLDQATGKFLDNDKSPARKVGGIDNRGS 660

Query: 660 HFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPN 719
           HFYLALYWA+ALAAQTED  LQAQF G+AKAL +NE KIV ELAAAQGKPVDI GYY PN
Sbjct: 661 HFYLALYWAEALAAQTEDAALQAQFAGVAKALAENEAKIVEELAAAQGKPVDIGGYYRPN 720

Query: 720 TDLTSKAIRPSATFNAALAPLA 741
            +LTSKA+RPSAT N  +  +A
Sbjct: 721 VELTSKAMRPSATLNKIVDAIA 742


Lambda     K      H
   0.315    0.131    0.374 

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: 1549
Number of extensions: 50
Number of successful extensions: 2
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: 741
Length of database: 742
Length adjustment: 40
Effective length of query: 701
Effective length of database: 702
Effective search space:   492102
Effective search space used:   492102
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 (21.5 bits)
S2: 55 (25.8 bits)

Align candidate BPHYT_RS20300 BPHYT_RS20300 (isocitrate dehydrogenase)
to HMM TIGR00178 (isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.26475.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26475.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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