GapMind for catabolism of small carbon sources

 

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

Align Isocitrate dehydrogenase [NADP]; IDH; Oxalosuccinate decarboxylase; EC 1.1.1.42 (characterized)
to candidate Pf1N1B4_4051 Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42)

Query= SwissProt::P16100
         (741 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4051
          Length = 690

 Score =  981 bits (2537), Expect = 0.0
 Identities = 493/597 (82%), Positives = 543/597 (90%), Gaps = 1/597 (0%)

Query: 5   KIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISD 64
           KIIYT TDEAPALATYSLLPI++AFT S+ IAVETRDISLAGR++A+FPE L D + ++D
Sbjct: 6   KIIYTFTDEAPALATYSLLPIVEAFTASADIAVETRDISLAGRILASFPEQLGD-KAVAD 64

Query: 65  DLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKA 124
            LAELG LA TP+ANIIKLPNISASVPQL+AAIKELQ QG+ LPDYPE   +D +K  K+
Sbjct: 65  HLAELGDLAVTPEANIIKLPNISASVPQLQAAIKELQAQGFALPDYPETVTSDADKLAKS 124

Query: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGS 184
           RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAW+ DSKSHVAHM  GDFYGS
Sbjct: 125 RYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWAKDSKSHVAHMSTGDFYGS 184

Query: 185 EKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAK 244
           EKAALI A  +VKIELIA+DG++TVLK KT+VQAGEI+D +VMSKNALR+FIAAEIEDAK
Sbjct: 185 EKAALIDAADAVKIELIAQDGTTTVLKEKTTVQAGEILDCAVMSKNALRSFIAAEIEDAK 244

Query: 245 KQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARI 304
            +GVLLSVHLKATMMKVSDPIMFGQIV+EFYKDAL KHA+VL QIGF++NNGIGDLYARI
Sbjct: 245 AKGVLLSVHLKATMMKVSDPIMFGQIVAEFYKDALAKHADVLAQIGFNLNNGIGDLYARI 304

Query: 305 KTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364
           K LP  +Q +IEADIQAVYA RP LAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW
Sbjct: 305 KALPAEQQAQIEADIQAVYAVRPSLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMW 364

Query: 365 GPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHD 424
           G DG+LHDTKAVIPDRCYA +YQ VIEDCK +GAFDPTTMGSVPNVGLMA+KAEEYGSHD
Sbjct: 365 GTDGQLHDTKAVIPDRCYATIYQAVIEDCKANGAFDPTTMGSVPNVGLMAKKAEEYGSHD 424

Query: 425 KTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPA 484
           KTFQI A+GVVRV+D +G+ LLEQSVEAGDI+RMCQ KDAPIQDWVKLAVNRARA+ TPA
Sbjct: 425 KTFQIKANGVVRVSDSAGRTLLEQSVEAGDIFRMCQTKDAPIQDWVKLAVNRARASATPA 484

Query: 485 VFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGN 544
           +FWLDP RAHD  VI KV+ YLKD+DTSGLDIRI+SPV+A +F+L R REGKDTISVTGN
Sbjct: 485 IFWLDPMRAHDGVVIEKVQAYLKDHDTSGLDIRIMSPVDAMKFTLDRTREGKDTISVTGN 544

Query: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRW 601
           VLRDYLTDLFPIMELGTSAKMLSIVPLM+GGGLFETGAGGSAPKHVQQ LEE +LRW
Sbjct: 545 VLRDYLTDLFPIMELGTSAKMLSIVPLMNGGGLFETGAGGSAPKHVQQLLEENFLRW 601


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: 1381
Number of extensions: 52
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: 690
Length adjustment: 39
Effective length of query: 702
Effective length of database: 651
Effective search space:   457002
Effective search space used:   457002
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 Pf1N1B4_4051 (Isocitrate dehydrogenase [NADP] (EC 1.1.1.42); Monomeric isocitrate dehydrogenase [NADP] (EC 1.1.1.42))
to HMM TIGR00178 (isocitrate dehydrogenase, NADP-dependent (EC 1.1.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.20352.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20352.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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