GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Shewanella loihica PV-4

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate 5210397 Shew_2838 carbamoyl phosphate synthase large subunit (RefSeq)

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__PV4:5210397
          Length = 1073

 Score = 1770 bits (4585), Expect = 0.0
 Identities = 883/1073 (82%), Positives = 974/1073 (90%), Gaps = 1/1073 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM
Sbjct: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPIHWEVVR II KERPDA+LPTMGGQTALNCAL LE +GVL EF V MIGATA
Sbjct: 61   ADATYIEPIHWEVVRNIIAKERPDAILPTMGGQTALNCALRLEAEGVLAEFNVDMIGATA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            DAIDKAEDR RFD AMKKIGLE  R+GIA +ME+A  V   VGFPCIIRPSFTMGGSGGG
Sbjct: 121  DAIDKAEDRSRFDAAMKKIGLECPRAGIARSMEDAYEVLEQVGFPCIIRPSFTMGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYN+EEFEEIC++GL+LSPT ELLIDESLIGWKEYEMEVVRD+NDN IIVCSIENFD M
Sbjct: 181  IAYNKEEFEEICSQGLELSPTNELLIDESLIGWKEYEMEVVRDRNDNSIIVCSIENFDPM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQ+MRNAS+AVLREIGVETGGSNVQF +NPK+GR+++IEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQLMRNASLAVLREIGVETGGSNVQFGINPKDGRMVIIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAK+AAKLAVG+TLDEL NDITGG TPASFEP+IDYVVTK+P
Sbjct: 301  NPRVSRSSALASKATGFPIAKIAAKLAVGFTLDELSNDITGGATPASFEPAIDYVVTKVP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKVSLDDPEA 420
            RFNFEKFAGANDRLTTQMKSVGEVMAIGRT QESLQKALRGLEVG  G DP V ++D +A
Sbjct: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGVNGLDPIVDVEDNDA 420

Query: 421  LTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEVG 480
            L++IR ELK+ GA+RIWYIADAFRAGLS+D +F LTNID WFLVQIEEL+ LE +V E G
Sbjct: 421  LSRIRHELKEPGAERIWYIADAFRAGLSLDAIFKLTNIDPWFLVQIEELLSLENQVKEAG 480

Query: 481  ITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATDT 540
            +  ++ DFL +LKRKGF+DARLA L GV E+E+RKLR +++++PVYKRVDTCAAEF+TDT
Sbjct: 481  MASMDKDFLYKLKRKGFSDARLAALMGVSESEMRKLRYRHEVYPVYKRVDTCAAEFSTDT 540

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

Query: 601  CNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGVP 660
            CNPETVSTDYDTSDRLYFE VTLEDVLEIVRIE+PKGVIVQYGGQTPLKLAR LEAAGVP
Sbjct: 600  CNPETVSTDYDTSDRLYFESVTLEDVLEIVRIEQPKGVIVQYGGQTPLKLARDLEAAGVP 659

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

Query: 721  GGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIME 780
            GGRAMEIVYDE DLRRYF  AVSVSN +PVLLDHFLD+A EVD+DA+CDG  V++G IME
Sbjct: 720  GGRAMEIVYDEQDLRRYFNEAVSVSNASPVLLDHFLDNATEVDIDAVCDGTTVVVGAIME 779

Query: 781  HIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYLI 840
            HIEQAGVHSGDS CSLP YTLSQEIQD MR+QV+KLA EL V GLMNVQFAV++N +Y+I
Sbjct: 780  HIEQAGVHSGDSGCSLPPYTLSQEIQDQMREQVRKLAMELGVVGLMNVQFAVQDNTIYMI 839

Query: 841  EVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNKF 900
            EVNPRAARTVPFVSKATGVPLAK+AARVMAG+SL EQG TKEVIPP+YSVKEVVLPFNKF
Sbjct: 840  EVNPRAARTVPFVSKATGVPLAKIAARVMAGQSLEEQGFTKEVIPPFYSVKEVVLPFNKF 899

Query: 901  PGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVDL 960
            PGVDPLLGPEMRSTGEVMGVG TFAEA+AKA+LG+ S + K GRALLSVR  DK+RV DL
Sbjct: 900  PGVDPLLGPEMRSTGEVMGVGATFAEAYAKAELGATSEVPKSGRALLSVRNSDKKRVADL 959

Query: 961  AAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSGR 1020
            AAKL++ G+E+DATHGTA+VLGEAGINPRLVNKVHEGRPHI DRIKN EYTYI+NTT GR
Sbjct: 960  AAKLIELGYEIDATHGTAVVLGEAGINPRLVNKVHEGRPHILDRIKNDEYTYIVNTTEGR 1019

Query: 1021 RAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHAQIK 1073
            +AIEDSR +RR AL+YKV+Y TTLN  FAT MA +AD+   V SVQE+H +IK
Sbjct: 1020 QAIEDSRQLRRGALRYKVNYTTTLNAAFATCMAHSADSRTNVTSVQELHQRIK 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: 3284
Number of extensions: 127
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 5210397 Shew_2838 (carbamoyl phosphate synthase large subunit (RefSeq))
to HMM TIGR01369 (carB: carbamoyl-phosphate synthase, large subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.30353.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30353.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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