GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Pseudomonas fluorescens FW300-N2E3

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate AO353_05635 AO353_05635 carbamoyl phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05635
          Length = 378

 Score =  344 bits (882), Expect = 3e-99
 Identities = 177/376 (47%), Positives = 242/376 (64%), Gaps = 11/376 (2%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L L DGSI+  ++ GA G  + E+VFNT++TGYQEILTDPSYA Q V +T P IGNTG
Sbjct: 5   AILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHIGNTG 64

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
             P+D ES + +  GLVIR+L +  SNWR T +L+DYL   +++ +  +DTR +TR LRE
Sbjct: 65  TTPEDAESDRVWSAGLVIRDLPLVASNWRNTMSLSDYLKANNVVAIAGIDTRRLTRILRE 124

Query: 178 DGSLIGVLSTEQSKTDDELLQMSRSW-DIVGIDLISDVSCKSPYEWVDKTNAEWDFNTNS 236
            G+  G +    + +D+  +  +R +  + G+DL   VS K  YEW    +  WD  T+S
Sbjct: 125 KGAQNGCIMAGDNISDEAAIAAARGFPGLKGMDLAKVVSTKKQYEW---RSTVWDLKTDS 181

Query: 237 R-----DGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNG 291
                     Y V+AYD+G+K NILR L   GC++TVVP+  PAA+ L + PDG+  SNG
Sbjct: 182 HATLDASDLPYHVVAYDYGVKVNILRMLVERGCRVTVVPAQTPAADVLALKPDGVFLSNG 241

Query: 292 PGDPSAVPYAVETVKELL-GKVPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNR 350
           PGDP    YA++ +K++L  ++PV+GIC+GHQLL  A G KT KM  GHHG NHPV++  
Sbjct: 242 PGDPEPCDYAIQAIKDILETEIPVFGICLGHQLLALASGAKTLKMGHGHHGANHPVQDLD 301

Query: 351 TGQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPH 410
           +G V I++QNH +AVD A+LPG V   H +L DG+  G+   + +  S Q HPEASPGP+
Sbjct: 302 SGVVMITSQNHGFAVDEATLPGNVRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGPN 361

Query: 411 DSDNAFREFI-ELMKR 425
           D    F  FI E+ KR
Sbjct: 362 DVAPLFDRFINEMAKR 377


Lambda     K      H
   0.316    0.134    0.403 

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: 449
Number of extensions: 13
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 430
Length of database: 378
Length adjustment: 31
Effective length of query: 399
Effective length of database: 347
Effective search space:   138453
Effective search space used:   138453
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate AO353_05635 AO353_05635 (carbamoyl phosphate synthase small subunit)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.24949.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24949.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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