GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Magnetospirillum magneticum AMB-1

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate WP_050750618.1 AMB_RS03600 carbamoyl-phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>NCBI__GCF_000009985.1:WP_050750618.1
          Length = 401

 Score =  318 bits (814), Expect = 2e-91
 Identities = 172/374 (45%), Positives = 234/374 (62%), Gaps = 12/374 (3%)

Query: 60  LVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTGVN 119
           LVL DGS+   K  GA G+ + E+VF T +TGYQE LTDPS+AGQ +  T P +GN G N
Sbjct: 30  LVLADGSVLWGKGIGATGSNVGEVVFTTGMTGYQETLTDPSFAGQVITFTFPHVGNVGTN 89

Query: 120 PDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLREDG 179
            +D E+      GL++R      +NWR  K L  +L   +I+G+  +DTRA+TRR+R  G
Sbjct: 90  VEDLETTTPAARGLILRADITDPANWRSAKHLDSWLKANNIVGLCGVDTRALTRRIRAKG 149

Query: 180 SLIGVLSTEQSKTDD--ELLQMSRSWD-IVGIDLISDVSCKSPYEWVDKTNAEWDFNTN- 235
           +  GV+        D   L   +  W  + G+DL  DV+C   Y W D+T  EW      
Sbjct: 150 APNGVIVNAPDGAFDLPALWGKAAGWPGLEGMDLARDVTCAQTYSW-DET--EWSLRGGY 206

Query: 236 SRDGKS-YKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGPGD 294
            R  K  + V+A DFG K+NILR L+  GC++TV+P+   A + L + PDG+  SNGPGD
Sbjct: 207 GRQAKPRFHVVAVDFGAKRNILRCLAETGCKVTVLPAEATAEQVLALEPDGVFLSNGPGD 266

Query: 295 PSAV-PYAVETVKELL--GKVPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRT 351
           P+A   YAV  ++ ++  GK P++GIC+GHQ+LG ALG KTFKM  GH G NHPV++  T
Sbjct: 267 PAATGTYAVPMIQGVIKSGK-PLFGICLGHQMLGLALGAKTFKMDTGHRGANHPVKDLET 325

Query: 352 GQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPHD 411
           G+VEI++QNH + VD  SLP GV+VTH +L DGS  G++     V S+QYHPEASPGP D
Sbjct: 326 GKVEITSQNHGFVVDEKSLPAGVKVTHRSLFDGSVEGIAVDGKPVFSVQYHPEASPGPQD 385

Query: 412 SDNAFREFIELMKR 425
           +   F  F+ LM++
Sbjct: 386 AHYLFERFVGLMEK 399


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: 514
Number of extensions: 20
Number of successful extensions: 4
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: 430
Length of database: 401
Length adjustment: 31
Effective length of query: 399
Effective length of database: 370
Effective search space:   147630
Effective search space used:   147630
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 WP_050750618.1 AMB_RS03600 (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.15492.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15492.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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