GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Paraburkholderia bryophila 376MFSha3.1

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate H281DRAFT_04403 H281DRAFT_04403 carbamoyl-phosphate synthase large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Burk376:H281DRAFT_04403
          Length = 1084

 Score = 1454 bits (3765), Expect = 0.0
 Identities = 749/1089 (68%), Positives = 871/1089 (79%), Gaps = 23/1089 (2%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILI+GAGPI+IGQACEFDYSGAQACKALREEGY+VILVNSNPATIMTDP  
Sbjct: 1    MPKRTDIKSILIIGAGPIIIGQACEFDYSGAQACKALREEGYKVILVNSNPATIMTDPNT 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            AD TYIEPI WEVV +II KERPDA+LPTMGGQTALNCAL+L   GVLE++ V +IGA+ 
Sbjct: 61   ADVTYIEPITWEVVERIIAKERPDAILPTMGGQTALNCALDLHAHGVLEKYKVELIGASP 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADV-------GFPCIIRPSFT 173
            +AIDKAEDR++F  AM KIGL +A+SG AH+MEEAL V A +       G+P +IRPSFT
Sbjct: 121  EAIDKAEDRQKFKDAMTKIGLGSAKSGTAHSMEEALQVQARIAVETGSGGYPVVIRPSFT 180

Query: 174  MGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCS 233
            +GGSGGGIAYNREEFEEIC RGLDLSPT+ELLI+ESL+GWKEYEMEVVRDK DNCIIVCS
Sbjct: 181  LGGSGGGIAYNREEFEEICKRGLDLSPTRELLIEESLLGWKEYEMEVVRDKKDNCIIVCS 240

Query: 234  IENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNG 293
            IEN D MGIHTGDSITVAPAQTLTDKEYQ++RNAS+AVLREIGV+TGGSNVQF++NPK+G
Sbjct: 241  IENLDPMGIHTGDSITVAPAQTLTDKEYQVLRNASLAVLREIGVDTGGSNVQFSINPKDG 300

Query: 294  RLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSID 353
            R+IVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL N+ITGG+TPASFEP+ID
Sbjct: 301  RMIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELKNEITGGQTPASFEPTID 360

Query: 354  YVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV 413
            YVVTKIPRF FEKF  A+ RLTTQMKSVGEVMAIGRT QES QKALRGLEVG  G D K 
Sbjct: 361  YVVTKIPRFAFEKFREADSRLTTQMKSVGEVMAIGRTFQESFQKALRGLEVGVDGLDEKT 420

Query: 414  SLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLE 473
               D     +I RE+ +AG DRIWY+ DAFR G++   +F  T+ID WFL QIE+++  E
Sbjct: 421  DNRD-----EIIREIGEAGPDRIWYVGDAFRIGMTAQEIFEETSIDPWFLAQIEQIILKE 475

Query: 474  EKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCA 533
            + +A   +  L+ + L+ LK+ GF+D RLAKL G + AE+R  R + ++ PVYKRVDTCA
Sbjct: 476  KALAGRTLASLSKEELKYLKQSGFSDRRLAKLVGAKPAEVRARRIELNVRPVYKRVDTCA 535

Query: 534  AEFATDTAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDG 593
            AEFAT TAYMYSTYEEECEANP T+ +KIMVLGGGPNRIGQGIEFDYCCVHA+LA+REDG
Sbjct: 536  AEFATKTAYMYSTYEEECEANP-TNNKKIMVLGGGPNRIGQGIEFDYCCVHAALAMREDG 594

Query: 594  YETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARA 653
            YETIMVNCNPETVSTDYDTSDRLYFE +TLEDVLEIV  EKP GVIVQYGGQTPLKLA  
Sbjct: 595  YETIMVNCNPETVSTDYDTSDRLYFESLTLEDVLEIVDKEKPVGVIVQYGGQTPLKLALD 654

Query: 654  LEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLV 713
            LEA GVP+IGTSPD ID AEDRERFQ  ++ L L+QP N T  A + A++ A EIGYPLV
Sbjct: 655  LEANGVPIIGTSPDMIDAAEDRERFQKLLQDLGLRQPPNRTARAEDEALKLADEIGYPLV 714

Query: 714  VRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMV 773
            VRPSYVLGGRAMEIV++  DL RY + AV VSND+PVLLD FL+DA+E DVD I DGE V
Sbjct: 715  VRPSYVLGGRAMEIVHEPRDLERYMREAVKVSNDSPVLLDRFLNDAIECDVDCISDGEAV 774

Query: 774  LIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAV- 832
             IGG+MEHIEQAGVHSGDSACSLP Y+LS E    +++Q   +A  L V GLMNVQFA+ 
Sbjct: 775  FIGGVMEHIEQAGVHSGDSACSLPPYSLSGETIAELKRQTGAMAKALNVVGLMNVQFAIQ 834

Query: 833  --------KNNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVI 884
                    K + +Y++EVNPRA+RTVP+VSKAT +PLAK+AAR M G+ LA QGVTKE+ 
Sbjct: 835  QVPQADGSKQDIIYVLEVNPRASRTVPYVSKATSLPLAKIAARAMVGQKLAAQGVTKEID 894

Query: 885  PPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGR 944
            PPY+SVKE V PF KFP VDP+LGPEMRSTGEVMGVG+TF EA  K+QL + S + + G 
Sbjct: 895  PPYFSVKEAVFPFVKFPAVDPVLGPEMRSTGEVMGVGQTFGEALFKSQLAAGSRLPESGT 954

Query: 945  ALLSVREGDKERVVDLAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDR 1004
             LL+V + DK + V++A  L + G+ + AT GTA  +  AG+  ++VNKV +GRPHI D 
Sbjct: 955  VLLTVMDADKPKAVEVARMLHELGYPIVATKGTAAAIEAAGVPVKVVNKVKDGRPHIVDM 1014

Query: 1005 IKNGEYTYIINTT-SGRRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVI 1063
            IKNGE   +  T    R AI DSR IR SA   KV Y TT++G  A    L      +V 
Sbjct: 1015 IKNGEIALVFTTVDETRAAIADSRSIRMSAQANKVTYYTTMSGARAAVEGLRYLKDLEVY 1074

Query: 1064 SVQEMHAQI 1072
             +Q +HA++
Sbjct: 1075 DLQGLHARL 1083


Lambda     K      H
   0.318    0.135    0.383 

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: 3133
Number of extensions: 134
Number of successful extensions: 18
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: 1073
Length of database: 1084
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1038
Effective search space:  1066026
Effective search space used:  1066026
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: 58 (26.9 bits)

Align candidate H281DRAFT_04403 H281DRAFT_04403 (carbamoyl-phosphate synthase large subunit)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.28609.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28609.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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