GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asd in Klebsiella michiganensis M5al

Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate BWI76_RS12880 BWI76_RS12880 aspartate-semialdehyde dehydrogenase

Query= BRENDA::C5BB06
         (367 letters)



>FitnessBrowser__Koxy:BWI76_RS12880
          Length = 372

 Score =  420 bits (1079), Expect = e-122
 Identities = 208/369 (56%), Positives = 265/369 (71%), Gaps = 4/369 (1%)

Query: 1   MKNVGFIGWRGMVGSVLMQRMSEERDFDAIRPLFFSTSQHGQPAPTFGGHGGTLQDASDI 60
           MK VG +GWRGMVGSVL+QRM EE DFD I   FFSTS  G   P   G   TL+DA+ +
Sbjct: 1   MKQVGIVGWRGMVGSVLLQRMIEENDFDNISAHFFSTSSAGAAGPVIDGISYTLKDANSV 60

Query: 61  DALKALDIIITCQGGDYTHAVYPRLRAAGWQGYWIDAASALRMQDDAIIILDPVNRAVID 120
            AL  +DIIITCQGGDYT A+YP L   GW GYWIDAASALRM + A IILDPVNR  ID
Sbjct: 61  SALAEMDIIITCQGGDYTKAIYPNLLNHGWGGYWIDAASALRMDEKACIILDPVNRNNID 120

Query: 121 RGLENGVKTFVGGNCTVSLMLMSLGGLFAADLVEWVSVATYQAASGGGARHMRELLTQMG 180
           R ++ G+K FVGGNC+++L LM L GL  ADL+EW+SV TYQ+ASG GA+++REL+ Q  
Sbjct: 121 RAIKEGIKLFVGGNCSITLSLMGLAGLIKADLIEWMSVMTYQSASGAGAQYVRELIAQSA 180

Query: 181 MLHGQVAPALENPASAILDIERQVTDLMRNGTLPTDNFGVPLAGSLIPWIDKALDNGQSR 240
            +   ++P     + ++L +  +V++L+ +  +PT NFG PL GS+IPWID  L +G SR
Sbjct: 181 YISRHLSPDELASSGSVLPLVNKVSELINSADMPTQNFGAPLMGSIIPWIDSDLGDGNSR 240

Query: 241 EEWKGQAETNKILA-SPQTIPIDGLCVRVGALRCHSQAFTVKLKRDIAIPEVEQLLARHN 299
           EEWKG+AETNKIL  SP TIP++GLC+RVG +RCHS A T+KLKR++   E  +L+   +
Sbjct: 241 EEWKGEAETNKILGLSPGTIPVNGLCIRVGVIRCHSAAITLKLKREVNEEEFAELVMNSH 300

Query: 300 EWVRVIPNDRELSMRELTPAAVTGTLATPVGRLRK--LNMGPQYLSAFTVGDQLLWGAAE 357
            WV  +PN++E S+  LTPA ++G+L   +GR +K  LN  P Y S  TVGDQLLWGAAE
Sbjct: 301 PWVNYVPNNKEESVSTLTPAHISGSLKVGIGRYKKMSLNNEPIY-SVLTVGDQLLWGAAE 359

Query: 358 PLRRMLRLL 366
           PLRRML +L
Sbjct: 360 PLRRMLNIL 368


Lambda     K      H
   0.321    0.137    0.418 

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: 395
Number of extensions: 10
Number of successful extensions: 3
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: 367
Length of database: 372
Length adjustment: 30
Effective length of query: 337
Effective length of database: 342
Effective search space:   115254
Effective search space used:   115254
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: 49 (23.5 bits)

Align candidate BWI76_RS12880 BWI76_RS12880 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01745 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.7904.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7904.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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