GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Shewanella oneidensis MR-1

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate 200322 SO1142 carbamoyl-phosphate synthase, large subunit (NCBI ptt file)

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__MR1:200322
          Length = 1074

 Score = 1793 bits (4644), Expect = 0.0
 Identities = 895/1072 (83%), Positives = 974/1072 (90%), Gaps = 1/1072 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI WEVVR II KERPDA+LPTMGGQTALNCALELE +GVL EF V MIGATA
Sbjct: 61   ADATYIEPIQWEVVRNIIAKERPDAILPTMGGQTALNCALELEAKGVLAEFNVEMIGATA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            DAIDKAEDR RFD AMK IGLE  R+GIAH+MEEA  V   VGFPCIIRPSFTMGGSGGG
Sbjct: 121  DAIDKAEDRSRFDKAMKSIGLECPRAGIAHSMEEAYGVLEQVGFPCIIRPSFTMGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYN+EEFEEIC++GLDLSPTKELLIDESLIGWKEYEMEVVRD+NDNCIIVCSIENFD M
Sbjct: 181  IAYNKEEFEEICSQGLDLSPTKELLIDESLIGWKEYEMEVVRDRNDNCIIVCSIENFDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQF +NPK+GR+++IEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFGINPKDGRMVIIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAK+AAKLAVG+TLDELMNDITGGRTPASFEP+IDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKIAAKLAVGFTLDELMNDITGGRTPASFEPAIDYVVTKVP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RFNFEKFAG+NDRLTTQMKSVGEVMAIGRT QESLQKALRGLEV   G DP   +  PEA
Sbjct: 361  RFNFEKFAGSNDRLTTQMKSVGEVMAIGRTFQESLQKALRGLEVNRHGLDPITDMSKPEA 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            + +IR ELK+ G DRIWYIADA RAGL++D +F LTNID WFLVQIEEL++LE +VAE G
Sbjct: 421  MARIRLELKEPGCDRIWYIADAMRAGLTLDEIFRLTNIDPWFLVQIEELIKLEGQVAEAG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            + GLN + LR+LKRKGFADARLA + GV E+E+RKLRD++D+HPVYKRVDTCAAEFATDT
Sbjct: 481  LAGLNEELLRKLKRKGFADARLAVVLGVNESEVRKLRDRFDIHPVYKRVDTCAAEFATDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AYMYSTYEEECEANPS +R+KIMVLGGGPNRIGQGIEFDYCCVHA+LALREDGYETIMVN
Sbjct: 541  AYMYSTYEEECEANPS-NRDKIMVLGGGPNRIGQGIEFDYCCVHAALALREDGYETIMVN 599

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 659

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPDAIDRAEDRERFQ A++RL++KQP N TVT +E AV  A+ IGYPLVVRPSYVL
Sbjct: 660  IIGTSPDAIDRAEDRERFQQAIQRLEMKQPENDTVTTVEGAVIAAERIGYPLVVRPSYVL 719

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVYD+ DL RYF  AVSVSN +PVLLDHFLDDA+EVD+DA+CDGE V+IG IME
Sbjct: 720  GGRAMEIVYDQQDLLRYFNEAVSVSNASPVLLDHFLDDAIEVDIDAVCDGETVVIGAIME 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDS CSLP YTLSQEIQD MR QV KLA EL V GLMNVQFAVKNNE+Y+I
Sbjct: 780  HIEQAGVHSGDSGCSLPPYTLSQEIQDRMRVQVGKLAMELGVVGLMNVQFAVKNNEIYMI 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRAARTVPFVSKATGVPLAK+AARVMAG+SL  Q  T+EVIPP+YSVKEVVLPFNKF
Sbjct: 840  EVNPRAARTVPFVSKATGVPLAKIAARVMAGQSLKAQNFTQEVIPPFYSVKEVVLPFNKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDPLLGPEMRSTGEVMGVG TFAEA+AKAQLG+ S + K GRALLSVR  DK+RV DL
Sbjct: 900  PGVDPLLGPEMRSTGEVMGVGDTFAEAYAKAQLGATSEVPKSGRALLSVRNSDKKRVADL 959

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            AAKL++ G+++DATHGTA++LGEAGINPRLVNKVHEGRPHI DRIKNGEYTYI+NTT GR
Sbjct: 960  AAKLIELGYQIDATHGTAVILGEAGINPRLVNKVHEGRPHILDRIKNGEYTYIVNTTEGR 1019

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQI 1072
            +AIEDSR +RR AL+YKV+Y TT+N  FAT MA  AD    V SVQE+H +I
Sbjct: 1020 QAIEDSRQLRRGALRYKVNYTTTMNAAFATCMAHAADDRTNVTSVQELHKRI 1071


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: 3363
Number of extensions: 120
Number of successful extensions: 12
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: 1074
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1029
Effective search space:  1057812
Effective search space used:  1057812
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 200322 SO1142 (carbamoyl-phosphate synthase, large subunit (NCBI ptt file))
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.20034.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20034.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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