GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvC in Shewanella loihica PV-4

Align ketol-acid reductoisomerase [NAD(P)+] (EC 1.1.1.383) (characterized)
to candidate 5207767 Shew_0288 ketol-acid reductoisomerase (RefSeq)

Query= BRENDA::A0KS29
         (492 letters)



>FitnessBrowser__PV4:5207767
          Length = 493

 Score =  895 bits (2312), Expect = 0.0
 Identities = 439/490 (89%), Positives = 466/490 (95%)

Query: 1   MANYFNSLNLRQQLAQLGQCRFMDRSEFSDGCNYIKDWNIVILGCGAQGLNQGLNMRDSG 60
           MANYFNSLNLRQQL QLGQCRFMDRSEFS GC+YIK WNIVILGCGAQGLNQGLNMRDSG
Sbjct: 1   MANYFNSLNLRQQLEQLGQCRFMDRSEFSQGCDYIKGWNIVILGCGAQGLNQGLNMRDSG 60

Query: 61  LNIAYALRPEAIAQKRASWQKATDNGFKVGTFEELIPTADLVLNLTPDKQHSNVVSAVMP 120
           LNI++ALR +AIA++R S+QKAT NGF+VGTFEELIP ADLVLNLTPDKQH++ V+AVMP
Sbjct: 61  LNISFALREQAIAEQRPSYQKATGNGFRVGTFEELIPDADLVLNLTPDKQHTDAVNAVMP 120

Query: 121 LMKQGATLSYSHGFNIVEEGMQIRPDITVVMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180
           LMKQGA LSYSHGFNIVEEGMQ+RPDITV+MVAPKCPGTEVREEYKRGFGVPTLIAVHPE
Sbjct: 121 LMKQGAVLSYSHGFNIVEEGMQVRPDITVIMVAPKCPGTEVREEYKRGFGVPTLIAVHPE 180

Query: 181 NDPNGDGLEIAKAYASATGGDRAGVLQSSFIAEVKSDLMGEQTILCGMLQTGAILGYDKM 240
           NDP GDGLE+AKAYASATGGDRAGVL SSFIAEVKSDLMGEQTILCGMLQTGAILGY+KM
Sbjct: 181 NDPKGDGLEVAKAYASATGGDRAGVLHSSFIAEVKSDLMGEQTILCGMLQTGAILGYEKM 240

Query: 241 VADGVEPGYAAKLIQQGWETVTEALKHGGITNMMDRLSNPAKIKAFEIAEDLKEILQPLF 300
           VADG+EPGYAAKLIQQGWET TEALKHGGIT+MMDRLSNPAKIKAFE+AE+LK ILQPLF
Sbjct: 241 VADGIEPGYAAKLIQQGWETTTEALKHGGITHMMDRLSNPAKIKAFEMAEELKAILQPLF 300

Query: 301 EKHMDDIISGEFSRTMMQDWANDDANLLRWRAETAETGFENAPVSSEHIDEQTYFDKGIF 360
           EKHMDDIISGEFS+TMM+DWANDDANLL+WRAET ETGFENAP   E IDEQTYFDKGIF
Sbjct: 301 EKHMDDIISGEFSKTMMEDWANDDANLLKWRAETNETGFENAPACDEAIDEQTYFDKGIF 360

Query: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420
           LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG
Sbjct: 361 LVAMIKAGVELAFDTMVSAGIVEESAYYESLHETPLIANTIARKRLYEMNVVISDTAEYG 420

Query: 421 CYLFNHAAVPMLRDYVNAMSPEYLGAGLKDSSNNVDNLQLIAINDAIRHTSVEYIGAELR 480
           CYLFNHAAVP+LRDYVN MSPEYLG GLKDS N VDNL+LI +NDAIRHT+VEYIGAELR
Sbjct: 421 CYLFNHAAVPLLRDYVNQMSPEYLGGGLKDSGNGVDNLRLIEVNDAIRHTAVEYIGAELR 480

Query: 481 GYMTDMKSIV 490
           GYMT+MK IV
Sbjct: 481 GYMTEMKRIV 490


Lambda     K      H
   0.317    0.134    0.389 

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: 928
Number of extensions: 14
Number of successful extensions: 1
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: 492
Length of database: 493
Length adjustment: 34
Effective length of query: 458
Effective length of database: 459
Effective search space:   210222
Effective search space used:   210222
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: 52 (24.6 bits)

Align candidate 5207767 Shew_0288 (ketol-acid reductoisomerase (RefSeq))
to HMM TIGR00465 (ilvC: ketol-acid reductoisomerase (EC 1.1.1.86))

Software error:

../bin/blast/fastacmd -i /tmp/list.16192.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16192.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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