GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Marinobacter adhaerens HP15

Align carbamoyl-phosphate synthase (glutamine-hydrolysing) (EC 6.3.5.5) (characterized)
to candidate GFF3135 HP15_3077 carbamoyl-phosphate synthase, large subunit

Query= BRENDA::P00968
         (1073 letters)



>FitnessBrowser__Marino:GFF3135
          Length = 1072

 Score = 1574 bits (4076), Expect = 0.0
 Identities = 804/1071 (75%), Positives = 900/1071 (84%), Gaps = 2/1071 (0%)

Query: 1    MPKRTDIKSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPEM 60
            MPKRTDI+SILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDP M
Sbjct: 1    MPKRTDIQSILILGAGPIVIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPVM 60

Query: 61   ADATYIEPIHWEVVRKIIEKERPDAVLPTMGGQTALNCALELERQGVLEEFGVTMIGATA 120
            ADATYIEPI W+ V KIIEKE+PDA+LPTMGGQTALNCAL+LER G+LE+ GV MIGA A
Sbjct: 61   ADATYIEPITWKTVEKIIEKEQPDALLPTMGGQTALNCALDLERHGILEKHGVEMIGANA 120

Query: 121  DAIDKAEDRRRFDVAMKKIGLETARSGIAHTMEEALAVAADVGFPCIIRPSFTMGGSGGG 180
            D IDKAEDR RFD AMKKIGLE  R+ IAH+MEEA  VA D+GFPCIIRPSFTMGGSGGG
Sbjct: 121  DTIDKAEDRDRFDKAMKKIGLECPRATIAHSMEEAWKVADDIGFPCIIRPSFTMGGSGGG 180

Query: 181  IAYNREEFEEICARGLDLSPTKELLIDESLIGWKEYEMEVVRDKNDNCIIVCSIENFDAM 240
            IAYNR+EFEEIC RGLDLSPT ELLIDESLIGWKEYEMEVVRDKNDNCIIVC+IENFDAM
Sbjct: 181  IAYNRDEFEEICTRGLDLSPTNELLIDESLIGWKEYEMEVVRDKNDNCIIVCAIENFDAM 240

Query: 241  GIHTGDSITVAPAQTLTDKEYQIMRNASMAVLREIGVETGGSNVQFAVNPKNGRLIVIEM 300
            G+HTGDSITVAPAQTLTDKEYQIMRNAS+AVLREIGVETGGSNVQF +NP  GR++VIEM
Sbjct: 241  GVHTGDSITVAPAQTLTDKEYQIMRNASLAVLREIGVETGGSNVQFGMNPDTGRMVVIEM 300

Query: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELMNDITGGRTPASFEPSIDYVVTKIP 360
            NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDEL N+ITGG TPASFEPSIDYVVTKIP
Sbjct: 301  NPRVSRSSALASKATGFPIAKVAAKLAVGYTLDELRNEITGGVTPASFEPSIDYVVTKIP 360

Query: 361  RFNFEKFAGANDRLTTQMKSVGEVMAIGRTQQESLQKALRGLEVGATGFDPKV-SLDDPE 419
            RF FEKF  A+ RLTTQMKSVGEVMAIGRT QESLQKALRGLEVG+ GFD K+  LD   
Sbjct: 361  RFTFEKFPQADARLTTQMKSVGEVMAIGRTFQESLQKALRGLEVGSEGFDEKLEDLDSEN 420

Query: 420  ALTKIRRELKDAGADRIWYIADAFRAGLSVDGVFNLTNIDRWFLVQIEELVRLEEKVAEV 479
            +   + REL   GADRIWYI DAFRAG++V+ +   T++D W+LVQIE+L+R E+ +   
Sbjct: 421  SRETLTRELNVPGADRIWYIGDAFRAGMTVEDLHEHTHVDPWYLVQIEDLIREEQALKSA 480

Query: 480  GITGLNADFLRQLKRKGFADARLAKLAGVREAEIRKLRDQYDLHPVYKRVDTCAAEFATD 539
            G   ++   L +LKRKGF+DARLAKL G+ E  +RKLR   D+ PVYKRVDTCAAEFA+D
Sbjct: 481  GKADIDQATLFRLKRKGFSDARLAKLLGISEVSLRKLRHDLDIRPVYKRVDTCAAEFASD 540

Query: 540  TAYMYSTYEEECEANPSTDREKIMVLGGGPNRIGQGIEFDYCCVHASLALREDGYETIMV 599
            TAYMYSTYEEECE++ S DREKI+V+GGGPNRIGQGIEFDYCCVHA+LA+REDGYETIM+
Sbjct: 541  TAYMYSTYEEECESDAS-DREKIVVIGGGPNRIGQGIEFDYCCVHAALAMREDGYETIMI 599

Query: 600  NCNPETVSTDYDTSDRLYFEPVTLEDVLEIVRIEKPKGVIVQYGGQTPLKLARALEAAGV 659
            NCNPETVSTDYDTSDRLYFEP+TLEDVLEI+ +EKPKGVIVQYGGQTPLKLAR LEAAGV
Sbjct: 600  NCNPETVSTDYDTSDRLYFEPITLEDVLEIIHVEKPKGVIVQYGGQTPLKLARGLEAAGV 659

Query: 660  PVIGTSPDAIDRAEDRERFQHAVERLKLKQPANATVTAIEMAVEKAKEIGYPLVVRPSYV 719
            P+IGTSPDAIDRAEDRERFQ  + RL LKQP NATV + E  +  A+EIGYPLVVRPSYV
Sbjct: 660  PIIGTSPDAIDRAEDRERFQQMITRLGLKQPENATVRSHEEGILAAREIGYPLVVRPSYV 719

Query: 720  LGGRAMEIVYDEADLRRYFQTAVSVSNDAPVLLDHFLDDAVEVDVDAICDGEMVLIGGIM 779
            LGGRAMEIVYDE +L RY + AV VSND+PVLLDHFL+ A+EVD+DAI DG+ V+IGGIM
Sbjct: 720  LGGRAMEIVYDEEELVRYMRNAVLVSNDSPVLLDHFLNAAIEVDIDAISDGKDVVIGGIM 779

Query: 780  EHIEQAGVHSGDSACSLPAYTLSQEIQDVMRQQVQKLAFELQVRGLMNVQFAVKNNEVYL 839
            +HIEQAGVHSGDSACSLP YTLSQ++QD MR  V+K+A EL V GLMNVQ A ++ E+Y+
Sbjct: 780  QHIEQAGVHSGDSACSLPPYTLSQQVQDEMRDAVKKMAIELDVVGLMNVQLAWQDGEIYV 839

Query: 840  IEVNPRAARTVPFVSKATGVPLAKVAARVMAGKSLAEQGVTKEVIPPYYSVKEVVLPFNK 899
            IEVNPRA+RTVPFVSKA GV LAKVAARVMAGK+L E   T+E+IP YY+VKE V PFNK
Sbjct: 840  IEVNPRASRTVPFVSKAIGVSLAKVAARVMAGKTLKELEFTQEIIPSYYAVKESVFPFNK 899

Query: 900  FPGVDPLLGPEMRSTGEVMGVGRTFAEAFAKAQLGSNSTMKKHGRALLSVREGDKERVVD 959
            FP VDP+LGPEM+STGEVMG+G +F EAFAKA L     +   G A +SVR+ DK     
Sbjct: 900  FPAVDPILGPEMKSTGEVMGLGDSFDEAFAKAALAVGERLPAKGTAFMSVRDVDKPGAAK 959

Query: 960  LAAKLLKQGFELDATHGTAIVLGEAGINPRLVNKVHEGRPHIQDRIKNGEYTYIINTTSG 1019
            +A  L+  GF+L AT GTA  L EAGI    VNKV EGRPHI D IKNG+   IINTT G
Sbjct: 960  VARDLVDAGFKLVATTGTAKALKEAGIEVDRVNKVREGRPHIVDAIKNGQVQLIINTTEG 1019

Query: 1020 RRAIEDSRVIRRSALQYKVHYDTTLNGGFATAMALNADATEKVISVQEMHA 1070
            R+AI DS  IR+SALQ KV Y TTL GG A   A+       V  +Q++HA
Sbjct: 1020 RKAISDSAQIRQSALQTKVTYTTTLAGGEAFCRAIKFGPERTVRRLQDLHA 1070


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: 3265
Number of extensions: 140
Number of successful extensions: 13
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: 1072
Length adjustment: 45
Effective length of query: 1028
Effective length of database: 1027
Effective search space:  1055756
Effective search space used:  1055756
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 GFF3135 HP15_3077 (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.2657.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2657.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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