GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Pseudomonas fluorescens FW300-N2E2

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate Pf6N2E2_3364 Carbamoyl-phosphate synthase large chain (EC 6.3.5.5)

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3364
          Length = 1073

 Score = 1601 bits (4146), Expect = 0.0
 Identities = 808/1073 (75%), Positives = 918/1073 (85%), Gaps = 1/1073 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP M
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPAM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI W+ V KIIEKERPDA+LPTMGGQTALNCAL+LER+GVLE+FGV MIGA A
Sbjct: 61   ADATYIEPIKWQTVAKIIEKERPDALLPTMGGQTALNCALDLEREGVLEKFGVEMIGANA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            D IDKAEDR RFD AMK IGL+  RSGIAH+MEEA AV   +GFPCIIRPSFTMGG+GGG
Sbjct: 121  DTIDKAEDRSRFDKAMKSIGLDCPRSGIAHSMEEANAVLERLGFPCIIRPSFTMGGTGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDK DNCIIVCSIENFD M
Sbjct: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKKDNCIIVCSIENFDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQI+RNAS+AVLREIGVETGGSNVQF + P  GR++VIEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQILRNASLAVLREIGVETGGSNVQFGICPNTGRMVVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL NDITGG+TPASFEPSIDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELSNDITGGKTPASFEPSIDYVVTKLP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RF FEKFA A+ RLTTQMKSVGEVMAIGRT QESLQKALRGLEVG  G DPK+ L DPE+
Sbjct: 361  RFAFEKFAKADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVCGLDPKLDLADPES 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            ++ ++REL   GA+RIWY+ADAFRAG++V+ +F +  ID WFLVQIE+L++ EEKV  +G
Sbjct: 421  MSVLKRELTVPGAERIWYVADAFRAGMTVEQIFGMNMIDPWFLVQIEDLIKEEEKVKTLG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            ++ ++ D + +LKRKGF+D RLAKL GV E  +R  R + ++ PVYKRVDTCAAEFATDT
Sbjct: 481  MSSIDRDTMFRLKRKGFSDMRLAKLLGVTEKSLRAHRHKLEVFPVYKRVDTCAAEFATDT 540

Query: 541  AYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMVN 600
            AY+YSTYEEECEA PST R+KIM+LGGGPNRIGQGIEFDYCCVHA+LALR+DGYETIMVN
Sbjct: 541  AYLYSTYEEECEAAPST-RDKIMILGGGPNRIGQGIEFDYCCVHAALALRDDGYETIMVN 599

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFEPVTLEDVLEIVR+EKPKGVIVQYGGQTPLKLARALEAAGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRVEKPKGVIVQYGGQTPLKLARALEAAGVP 659

Query: 661  VIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYVL 720
            +IGTSPDAIDRAEDRERFQ  VERL L+QP NATV + + A+  A +IGYPLVVRPSYVL
Sbjct: 660  IIGTSPDAIDRAEDRERFQQMVERLNLRQPPNATVRSEDEAIRAAAKIGYPLVVRPSYVL 719

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVY E +L+RY + AV VSND+PVLLDHFL+ A+E+DVDA+ DG+ V+IG IM+
Sbjct: 720  GGRAMEIVYQEDELKRYLREAVQVSNDSPVLLDHFLNCAIEMDVDAVSDGKDVVIGAIMQ 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDSACSLP Y+L   IQD MR+QV+K+A EL V GLMNVQ A++  ++Y+I
Sbjct: 780  HIEQAGVHSGDSACSLPPYSLPAHIQDEMREQVKKMALELGVVGLMNVQLALQGEDIYVI 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRA+RTVPFVSK  GV LA +AARVMAGK+L E   TKE+IP +YSVKE V PF KF
Sbjct: 840  EVNPRASRTVPFVSKCIGVSLAMIAARVMAGKTLKELNFTKEIIPNFYSVKEAVFPFAKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDP+LGPEM+STGEVMGVG TF EAFAKAQ+G++  +   G A +SVR+ DK  V  +
Sbjct: 900  PGVDPILGPEMKSTGEVMGVGDTFGEAFAKAQMGASEVLPTGGTAFISVRDDDKPLVAGV 959

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            A  L+  GFE+ AT GTA ++  AG+  R VNKV EGRPH+ D IKN E T IINTT GR
Sbjct: 960  ARDLINLGFEVVATAGTARLIEAAGLKVRRVNKVTEGRPHVVDMIKNDEVTLIINTTEGR 1019

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            ++I DS  IRR+ALQ+K++  TT+  G A   AL     + V  +Q++HA +K
Sbjct: 1020 QSIADSYSIRRNALQHKIYCTTTIAAGEAICEALKFGPEKTVRRLQDLHAGLK 1072


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: 3125
Number of extensions: 135
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: 1073
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1028
Effective search space:  1056784
Effective search space used:  1056784
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 Pf6N2E2_3364 (Carbamoyl-phosphate synthase large chain (EC 6.3.5.5))
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.20827.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20827.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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