GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carB in Dinoroseobacter shibae DFL-12

Align Carbamoyl-phosphate synthase large chain, chloroplastic; Carbamoyl-phosphate synthetase ammonia chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate 3609253 Dshi_2639 carbamoyl-phosphate synthase, large subunit (RefSeq)

Query= SwissProt::Q42601
         (1187 letters)



>FitnessBrowser__Dino:3609253
          Length = 1105

 Score = 1178 bits (3047), Expect = 0.0
 Identities = 627/1120 (55%), Positives = 795/1120 (70%), Gaps = 57/1120 (5%)

Query: 94   KRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDPETAN 153
            KRTD+K IMI+GAGPI+IGQACEFDYSG QACKALREEGY VIL+NSNPATIMTDP  A+
Sbjct: 3    KRTDIKSIMIIGAGPIIIGQACEFDYSGAQACKALREEGYRVILVNSNPATIMTDPGLAD 62

Query: 154  RTYIAPMTPELVEQVIEKERPDALLPTMGGQTALNLAVALAESGALEKYGVELIGAKLGA 213
             TYI P+TPE+V ++IEKERPDALLPTMGGQT LN ++AL E G L KYGVE+IGAK  A
Sbjct: 63   ATYIEPITPEIVAKIIEKERPDALLPTMGGQTGLNTSLALEEMGVLAKYGVEMIGAKREA 122

Query: 214  IKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFTLGGTGGGI 273
            I+ AEDR+LF++AM  +G++ P + I TT+DEC    + IG  P IIRPAFTLGGTGGG+
Sbjct: 123  IEMAEDRKLFREAMDRLGIENPRATIATTMDECMAALDDIG-LPAIIRPAFTLGGTGGGV 181

Query: 274  AYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICSIENIDPMG 333
            AYN++++E  CKSGL AS  +Q+L+++SLLGWKE+E+EV+RD ADN +I+C+IEN+DPMG
Sbjct: 182  AYNRDDYEHFCKSGLDASPVNQILIDESLLGWKEFEMEVVRDKADNAIIVCAIENVDPMG 241

Query: 334  VHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDGEVMIIEMN 393
            VHTGDSITVAPA TLTD+EYQ +R+ SIA++REIGVE GGSNVQ+AVNP DG +++IEMN
Sbjct: 242  VHTGDSITVAPALTLTDKEYQIMRNGSIAVLREIGVETGGSNVQWAVNPADGRMVVIEMN 301

Query: 394  PRVSRSSALASKATGFPIAKMAAKLSVGYTLDQIPNDITRKTPASFEPSIDYVVTKIPRF 453
            PRVSRSSALASKATGFPIAK+AAKL+VGYTLD++ NDIT+ TPASFEP+IDYVVTKIPRF
Sbjct: 302  PRVSRSSALASKATGFPIAKIAAKLAVGYTLDELDNDITKVTPASFEPTIDYVVTKIPRF 361

Query: 454  AFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKALRSLECGFSGWGCAKIKELDWDWD 513
            AFEKFPG++P LTT MKSVGE+M++GRTF ES QKAL S+E G +G+    I  +  D  
Sbjct: 362  AFEKFPGAEPNLTTAMKSVGEAMSIGRTFHESVQKALASMETGLTGFDEIAIPGISADHR 421

Query: 514  Q-------LKYSLRVPNPDRIHAIYAAMKKGMKIDEIYELSMVDKWFLTQLKELVDVEQY 566
                    +  +L    PDR+  I  AM+ G+  DEI   +  D WFL +++E+V+ E  
Sbjct: 422  SDAPDTAAVVKALARQTPDRLRVIAQAMRHGLSDDEIQAATSYDPWFLARIREIVETEAQ 481

Query: 567  LMSGTLSEITKEDLYEVKKRGFSDKQIAFATKTTEEEVRTKRISLGVVPSYKRVDTCAAE 626
            +    L  +  E L ++K  GF+D ++A  T   E +VR  R  LGV   +KR+DTCAAE
Sbjct: 482  VRRDGL-PLEAEGLRKLKMMGFTDARLAKLTGRDEGQVRRARTRLGVTAQFKRIDTCAAE 540

Query: 627  FEAHTPYMYSSY------DVECESAPNNKKKVLILGGGPNRIGQGIEFDYCCCHTSFALQ 680
            FEA TPYMYS+Y      + ECES P +  KV+ILGGGPNRIGQGIEFDYCCCH  FAL 
Sbjct: 541  FEAQTPYMYSTYETPVMGEAECESRPTDATKVVILGGGPNRIGQGIEFDYCCCHACFALT 600

Query: 681  DAGYETIMLNSNPETVSTDYDTSDRLYFEPLTIEDVLNVIDLEKPD----GIIVQFGGQT 736
            +AGYETIM+N NPETVSTDYDTSDRLYFEPLT E V+ ++  E+ +    G+IVQFGGQT
Sbjct: 601  EAGYETIMVNCNPETVSTDYDTSDRLYFEPLTFEHVMEILRAEQENGTLHGVIVQFGGQT 660

Query: 737  PLKLALPIKHYLDKHMPMSLSGAGPVRIWGTSPDSIDAAEDRERFNAILDELKIEQPKGG 796
            PLKLA  ++             A  + I GT+PD+ID AEDRERF A++++L ++QP   
Sbjct: 661  PLKLANALE-------------AEGIPILGTTPDAIDLAEDRERFQALVNDLGLKQPHNA 707

Query: 797  IAKSEADALAIAKEVGYPVVVRPSYVLGGRAMEIVYDDSRLITYLENAVQVDPERPVLVD 856
            IA ++A+A A A ++G+P+V+RPSYVLGGRAMEIV D  +L  Y+  AV V  + PVL+D
Sbjct: 708  IASTDAEAFAAAGDIGFPLVIRPSYVLGGRAMEIVRDMGQLERYIAEAVVVSGDSPVLLD 767

Query: 857  KYLSDAIEIDVDTLTDSYGNVVIGGIMEHIEQAGVHSGDSACMLPTQTIPASCLQTIRTW 916
             YL+ A+E+DVD L D   NV + GIM+HIE+AGVHSGDSAC LP  ++    L  IR  
Sbjct: 768  SYLAGAVELDVDALCDG-ENVHVAGIMQHIEEAGVHSGDSACSLPPYSLSDDVLARIRVQ 826

Query: 917  TTKLAKKLNVCGLMNCQYAITTSGDVFLLEANPRASRTVPFVSKAIGHPLAKYAALVMSG 976
            T  LA+ L V GLMN Q+AI    +++L+E NPRASRTVPFV+KA    +A  AA +M+G
Sbjct: 827  TEALARALRVKGLMNVQFAI-KDDEIYLIEVNPRASRTVPFVAKATDSAIASIAARLMAG 885

Query: 977  KSLKDLNF---------EKEVIP------------KHVSVKEAVFPFEKFQGCDVILGPE 1015
            + L +            E + +P               SVKEAV PF +F G D ILGPE
Sbjct: 886  EPLSNFPLRDPLPHDAPEDQHLPIGDPMTLAHPDTPWFSVKEAVLPFARFPGVDTILGPE 945

Query: 1016 MRSTGEVMSISSEFSSAFAMAQIAAGQKLPLSGTVFLSLNDMTKPH-LEKIAVSFLELGF 1074
            MRSTGEVM     F  AF  AQ+ AG  LP  GTVFLS+ +  K   L + A    ELG 
Sbjct: 946  MRSTGEVMGWDRSFPRAFLKAQMGAGTVLPTEGTVFLSIKEADKTEMLVETAAMLTELGL 1005

Query: 1075 KIVATSGTAHFLELKGIPVERVLKLHEGRPHAADMVANGQIHLMLITSSGDALDQKDGRQ 1134
             IVAT GTA FL+  GI  + V K++EGRP   DM+ +G+I L++ T+ G A    D R+
Sbjct: 1006 DIVATRGTAAFLKDHGIASKVVNKVYEGRPDVVDMLKDGRIALVMNTTEG-AQAVNDSRE 1064

Query: 1135 LRQMALAYKVPVITTVAGALATAEGIKSLKSSAIKMTALQ 1174
            +R +AL  ++P  TT+A + A A+ + + +   I + ALQ
Sbjct: 1065 IRSVALYDRIPYFTTLAASHAAAQAMIARREGEIGVRALQ 1104



 Score =  230 bits (587), Expect = 4e-64
 Identities = 151/417 (36%), Positives = 220/417 (52%), Gaps = 28/417 (6%)

Query: 90  EIVGKRTDLKKIMILGAGPIVIGQACEFDYSGTQACKALREEGYEVILINSNPATIMTDP 149
           E   + TD  K++ILG GP  IGQ  EFDY    AC AL E GYE I++N NP T+ TD 
Sbjct: 561 ECESRPTDATKVVILGGGPNRIGQGIEFDYCCCHACFALTEAGYETIMVNCNPETVSTDY 620

Query: 150 ETANRTYIAPMTPELVEQVIEKERPD----ALLPTMGGQTALNLAVALAESGALEKYGVE 205
           +T++R Y  P+T E V +++  E+ +     ++   GGQT L LA       ALE  G+ 
Sbjct: 621 DTSDRLYFEPLTFEHVMEILRAEQENGTLHGVIVQFGGQTPLKLA------NALEAEGIP 674

Query: 206 LIGAKLGAIKKAEDRELFKDAMKNIGLKTPPSGIGTTLDECFDIAEKIGEFPLIIRPAFT 265
           ++G    AI  AEDRE F+  + ++GLK P + I +T  E F  A  IG FPL+IRP++ 
Sbjct: 675 ILGTTPDAIDLAEDRERFQALVNDLGLKQPHNAIASTDAEAFAAAGDIG-FPLVIRPSYV 733

Query: 266 LGGTGGGIAYNKEEFESICKSGLAASATSQVLVEKSLLGWKEYELEVMRDLADNVVIICS 325
           LGG    I  +  + E      +  S  S VL++  L G  E +++ + D  +NV +   
Sbjct: 734 LGGRAMEIVRDMGQLERYIAEAVVVSGDSPVLLDSYLAGAVELDVDALCD-GENVHVAGI 792

Query: 326 IENIDPMGVHTGDSITVAPAQTLTDREYQRLRDYSIAIIREIGVECGGSNVQFAVNPVDG 385
           +++I+  GVH+GDS    P  +L+D    R+R  + A+ R + V+ G  NVQFA+   D 
Sbjct: 793 MQHIEEAGVHSGDSACSLPPYSLSDDVLARIRVQTEALARALRVK-GLMNVQFAIK--DD 849

Query: 386 EVMIIEMNPRVSRSSALASKATGFPIAKMAAKLSVGYTL------DQIPNDITRKTPASF 439
           E+ +IE+NPR SR+    +KAT   IA +AA+L  G  L      D +P+D         
Sbjct: 850 EIYLIEVNPRASRTVPFVAKATDSAIASIAARLMAGEPLSNFPLRDPLPHDAPEDQHLPI 909

Query: 440 -------EPSIDYVVTKIPRFAFEKFPGSQPLLTTQMKSVGESMALGRTFQESFQKA 489
                   P   +   K     F +FPG   +L  +M+S GE M   R+F  +F KA
Sbjct: 910 GDPMTLAHPDTPWFSVKEAVLPFARFPGVDTILGPEMRSTGEVMGWDRSFPRAFLKA 966


Lambda     K      H
   0.317    0.133    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: 3005
Number of extensions: 135
Number of successful extensions: 22
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 1187
Length of database: 1105
Length adjustment: 46
Effective length of query: 1141
Effective length of database: 1059
Effective search space:  1208319
Effective search space used:  1208319
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 3609253 Dshi_2639 (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.11440.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11440.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.