GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Pedobacter sp. GW460-11-11-14-LB5

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate CA265_RS15830 CA265_RS15830 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Pedo557:CA265_RS15830
          Length = 470

 Score =  544 bits (1401), Expect = e-159
 Identities = 273/466 (58%), Positives = 340/466 (72%), Gaps = 3/466 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M+KTL EK++DAHVV   E    +LYID HL+HEVTSPQAFDGLR  G PV +P +T AT
Sbjct: 1   MSKTLVEKIWDAHVVKSEEGFPDILYIDTHLIHEVTSPQAFDGLRKRGLPVFRPKQTVAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  + +    E++R Q+  L KNC EFGVELY L HP+QGIVHV+GPE G+TLP
Sbjct: 61  ADHNVPTLNQLLPIKEELSRYQVDMLTKNCAEFGVELYGLGHPFQGIVHVIGPELGITLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           G T+VCGDSHT+THGAFGA+AFGIGTS+VE V ATQ L Q + KTMKIEV G+   G+ A
Sbjct: 121 GKTMVCGDSHTSTHGAFGAIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDI+L II K  +AGGTG+ +E+ G AI  LSME RMT+CNM+IEMGA+ GL+APD+TTF
Sbjct: 181 KDIILYIIAKISAAGGTGYFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTF 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
           +Y+KGR  AP G+++D A+AYWKTL +D  A FD+V+T  A +I+P +T+GTNPG  + +
Sbjct: 241 DYIKGREFAPAGEEWDKALAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGI 300

Query: 301 NDNIPDPASFADP-VERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
            ++I  PA+ A P  E+ S +KAL YMG      L    +D VFIGSCTNSRIEDLR  A
Sbjct: 301 QEHI--PATGAQPEKEKLSYQKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVA 358

Query: 360 EIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLN 419
           +  K ++ A  V   +VPGS  V+ QA+ EGLDKIF  AGF+ R PGCS CL MN D++ 
Sbjct: 359 DFVKDKRKADNVTVWIVPGSKQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIP 418

Query: 420 PGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
            G+ C STSNRNFEGRQG+  RT L SP  AAAAAVTG   D+R++
Sbjct: 419 AGKYCVSTSNRNFEGRQGQNARTLLASPLTAAAAAVTGKITDVRDL 464


Lambda     K      H
   0.317    0.134    0.396 

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: 670
Number of extensions: 28
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: 466
Length of database: 470
Length adjustment: 33
Effective length of query: 433
Effective length of database: 437
Effective search space:   189221
Effective search space used:   189221
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate CA265_RS15830 CA265_RS15830 (3-isopropylmalate dehydratase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.19829.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19829.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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