GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Phaeobacter inhibens BS107

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate GFF2425 PGA1_c24560 carbamoyl-phosphate synthase large chain

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Phaeo:GFF2425
          Length = 1119

 Score = 1251 bits (3238), Expect = 0.0
 Identities = 673/1111 (60%), Positives = 805/1111 (72%), Gaps = 56/1111 (5%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDI+SI+I+GAGPI+IGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP +
Sbjct: 1    MPKRTDIQSIMIIGAGPIIIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGL 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI  EVV KIIEKERPDA+LPTMGGQT LN AL LE  GVL +F V MIGA  
Sbjct: 61   ADATYIEPITPEVVAKIIEKERPDALLPTMGGQTGLNTALALEEMGVLAKFDVEMIGAKR 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHT-------------MEEALAVAADVGFPCI 167
            +AI+ AEDR+ F  AM ++GLE  R+ I                ++ AL    D+G P I
Sbjct: 121  EAIEMAEDRKLFREAMDRLGLENPRATIITAPKKDNGNADLDAGVQMALDELEDIGLPAI 180

Query: 168  IRPSFTMGGSGGGIAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDN 227
            IRP+FT+GG+GGG+AYNRE++   C  G+D SP  ++L+DESL+GWKEYEMEVVRD  DN
Sbjct: 181  IRPAFTLGGTGGGVAYNREDYIHFCRSGMDASPVNQILVDESLLGWKEYEMEVVRDTADN 240

Query: 228  CIIVCSIENFDAMGIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFA 287
             IIVCSIEN D MG+HTGDSITVAPA TLTDKEYQ+MR+AS+AVLREIGVETGGSNVQ+A
Sbjct: 241  AIIVCSIENIDPMGVHTGDSITVAPALTLTDKEYQMMRSASIAVLREIGVETGGSNVQWA 300

Query: 288  VNPKNGRLIVIEMNPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPAS 347
            VNP +GR++VIEMNPRVSRSSALASKATGFPIAK+AAKLAVG+TLDEL NDIT G TPAS
Sbjct: 301  VNPADGRMVVIEMNPRVSRSSALASKATGFPIAKIAAKLAVGFTLDELDNDIT-GVTPAS 359

Query: 348  FEPSIDYVVTKIPRFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGAT 407
            FEP+IDYVVTKIPRF FEKFAG+   LTT MKSVGE MAIGRT  ESLQKAL  +E G T
Sbjct: 360  FEPTIDYVVTKIPRFAFEKFAGSEPYLTTAMKSVGETMAIGRTIHESLQKALASMETGLT 419

Query: 408  GFDPKV---SLDDPEALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLV 464
            GFD      + D+ +    + + +     DR+  IA A R GLS D +  +T  D WFL 
Sbjct: 420  GFDEVAIPGAEDETDGKAAVIKAISQQTPDRMRTIAQAMRHGLSDDDIHAVTKFDPWFLA 479

Query: 465  QIEELVRLEEKVAEVGITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHP 524
            +I E+V  E K+   G+   +   LR +K  GF DARLA L   RE +IR  R    ++ 
Sbjct: 480  RIREIVEAEAKIRAEGLP-QDEHGLRAIKMLGFTDARLAMLTDQREGDIRAARRALGVNA 538

Query: 525  VYKRVDTCAAEFATDTAYMYSTYEE------ECEANPSTDREKIMVLGGGPNRIGQGIEF 578
            V+KR+DTCAAEF   T YMYSTYE       ECEA PS D++K+++LGGGPNRIGQGIEF
Sbjct: 539  VFKRIDTCAAEFEAQTPYMYSTYEAPAFGDVECEARPS-DKKKVVILGGGPNRIGQGIEF 597

Query: 579  DYCCVHASLALREDGYETIMVNCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPK-- 636
            DYCC HA  AL + GYETIM+NCNPETVSTDYDTSDRLYFEP+T E V+EI+  E     
Sbjct: 598  DYCCCHACFALTDAGYETIMINCNPETVSTDYDTSDRLYFEPLTFEHVMEILTKELENGT 657

Query: 637  --GVIVQYGGQTPLKLARALEAAGVPVIGTSPDAIDRAEDRERFQHAVERLKLKQPANAT 694
              GVIVQ+GGQTPLKLA ALE  G+P++GTSPDAID AEDRERFQ  V +L LKQP N  
Sbjct: 658  LHGVIVQFGGQTPLKLANALEEEGIPILGTSPDAIDLAEDRERFQALVNQLGLKQPHNGI 717

Query: 695  VTAIEMAVEKAKEIGYPLVVRPSYVLGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDH 754
             +    A+E A+EIG+PLV+RPSYVLGGRAMEIV D   L+RY   AV VS D+PVLLD 
Sbjct: 718  ASTDAQALEIAEEIGFPLVIRPSYVLGGRAMEIVRDMDQLKRYIAEAVVVSGDSPVLLDS 777

Query: 755  FLDDAVEVDVDAICDGEMVLIGGIMEHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQ 814
            +L  AVE+DVDAICDG  V + GIM+HIE+AGVHSGDSACSLP Y+LS+E+   ++ Q  
Sbjct: 778  YLSGAVELDVDAICDGTEVHVAGIMQHIEEAGVHSGDSACSLPPYSLSKEVIAEVKTQTN 837

Query: 815  KLAFELQVRGLMNVQFAVK-----NNEVYLIEVNPRAARTVPFVSKATGVPLAKVAARVM 869
             LA  L V GLMN+QFAVK      + +YLIEVNPRA+RTVPFV+K+T   +A +AARVM
Sbjct: 838  ALAKALNVVGLMNIQFAVKPDADGKDVIYLIEVNPRASRTVPFVAKSTDSAIASIAARVM 897

Query: 870  AGKSL---------------------AEQGVTKEVIPPYYSVKEVVLPFNKFPGVDPLLG 908
            AG+ L                     A+     +   P++SVKE VLPF +FPGVD LLG
Sbjct: 898  AGEPLSNFPKRAPYEPDAGYDVNVPMADPMTLADPDMPWFSVKEAVLPFARFPGVDTLLG 957

Query: 909  PEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDLAAKLL-KQ 967
            PEMRSTGEVMG  R+FA AF KAQ+G+   +   GRA +S+++ DK  ++  AAK+L +Q
Sbjct: 958  PEMRSTGEVMGWDRSFARAFLKAQMGAGMVLPSEGRAFISIKDADKGTLMLDAAKILVEQ 1017

Query: 968  GFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGRRAIEDSR 1027
            GF L AT GT   L   G+   LVNKV+EGRPH+ D +K+G    ++NTT G +A++DS+
Sbjct: 1018 GFTLVATRGTQSWLDGHGVPCELVNKVYEGRPHVVDMLKDGNVQLLMNTTEGAQAVQDSK 1077

Query: 1028 VIRRSALQYKVHYDTTLNGGFATAMALNADA 1058
             +R  AL  K+ Y TT  G  A A A+ A A
Sbjct: 1078 DMRSVALYDKIPYFTTAAGANAAARAIKAQA 1108


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: 3105
Number of extensions: 157
Number of successful extensions: 23
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: 1119
Length adjustment: 46
Effective length of query: 1027
Effective length of database: 1073
Effective search space:  1101971
Effective search space used:  1101971
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 GFF2425 PGA1_c24560 (carbamoyl-phosphate synthase large chain)
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.15649.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15649.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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