GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuD in Shewanella amazonensis SB2B

Align 3-isopropylmalate dehydratase small subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate 6936141 Sama_0338 isopropylmalate isomerase small subunit (RefSeq)

Query= SwissProt::P04787
         (201 letters)



>FitnessBrowser__SB2B:6936141
          Length = 201

 Score =  246 bits (627), Expect = 3e-70
 Identities = 120/200 (60%), Positives = 150/200 (75%), Gaps = 1/200 (0%)

Query: 3   EKFTQHTGLVVPLDAANVDTDAIIPKQFLQKVTRTGFGAHLFNDWRFLDEKGQQPNPEFV 62
           + FT HTGL V +D+AN+DTD IIPKQFL KVT+ GFG HLF+DWR+LD+ G  PNPEF 
Sbjct: 2   QAFTTHTGLAVAIDSANIDTDQIIPKQFLSKVTKDGFGIHLFHDWRYLDDAGDIPNPEFN 61

Query: 63  LNFPEYQGASILLARENFGCGSSREHAPWALTDYGFKVVIAPSFADIFYGNSFNNQLLPV 122
           LN P Y+GA+ILLA+ENFGCGSSREHAPWAL D+G + +IAP+FADIFYGN+ NN LLPV
Sbjct: 62  LNKPRYKGATILLAQENFGCGSSREHAPWALADFGLRAIIAPTFADIFYGNAINNGLLPV 121

Query: 123 TLSDAQVDELFALVKANPGIKFEVDLE-AQVVKAGDKTYSFKIDDFRRHCMLNGLDSIGL 181
            L +A V +L   V+AN G +  VDLE  +VV      +SF + +  R  +L GLD+IGL
Sbjct: 122 RLPEAAVRQLMDEVEANEGAEVTVDLENLKVVSPSGAEFSFTLAESARQNLLKGLDAIGL 181

Query: 182 TLQHEDAIAAYENKQPAFMR 201
           TL HE AI+ YE++ PA+ R
Sbjct: 182 TLAHEAAISEYESRIPAWRR 201


Lambda     K      H
   0.321    0.138    0.416 

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: 156
Number of extensions: 4
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: 201
Length of database: 201
Length adjustment: 21
Effective length of query: 180
Effective length of database: 180
Effective search space:    32400
Effective search space used:    32400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)

Align candidate 6936141 Sama_0338 (isopropylmalate isomerase small subunit (RefSeq))
to HMM TIGR00171 (leuD: 3-isopropylmalate dehydratase, small subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.20547.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20547.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.