GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Sinorhizobium meliloti 1021

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate SMc02181 SMc02181 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase

Query= reanno::azobra:AZOBR_RS23695
         (1235 letters)



>FitnessBrowser__Smeli:SMc02181
          Length = 1233

 Score = 1637 bits (4239), Expect = 0.0
 Identities = 860/1227 (70%), Positives = 964/1227 (78%), Gaps = 9/1227 (0%)

Query: 10   AAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATAR 69
            AAP   APFADFAPP+RP + LR AITAAYRRPE ECLP L E A+    +  AAA+TAR
Sbjct: 13   AAP---APFADFAPPVRPQSTLRRAITAAYRRPETECLPPLVEAATQSKEIRDAAASTAR 69

Query: 70   KLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGD 129
            KLI ALR K  G GVEGL+ EYSLSSQEG+ALMCLAEALLRIPD ATRDALIRDKIA G+
Sbjct: 70   KLIEALRGKHSGSGVEGLVQEYSLSSQEGVALMCLAEALLRIPDTATRDALIRDKIADGN 129

Query: 130  WQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMR 189
            W++HLG   S+FVNAATWGL++TGKLTS   +++L++ALTRLI+R GEP+IRRGVD AMR
Sbjct: 130  WKSHLGGSRSLFVNAATWGLVVTGKLTSTVNDRSLAAALTRLISRCGEPVIRRGVDMAMR 189

Query: 190  MMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGT 249
            MMGEQFVTG+TI+EAL  ++ +E +GF YSYDMLGEAA TA DA RYY DY +AIHAIG 
Sbjct: 190  MMGEQFVTGETIREALKRSKELEEKGFSYSYDMLGEAATTAADAERYYRDYESAIHAIGK 249

Query: 250  ASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEE 309
            ASAGRG+YEGPGISIKLSA+HPRYSRAQA RVM ELLPRVKALALLAK YDIGLNIDAEE
Sbjct: 250  ASAGRGIYEGPGISIKLSALHPRYSRAQAARVMGELLPRVKALALLAKNYDIGLNIDAEE 309

Query: 310  ADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLV 369
            ADRLELSLDL+E LC D DL+GWNG+GFVVQAYGKRCP+V+DF+IDLARRSG R+M+RLV
Sbjct: 310  ADRLELSLDLLEVLCLDGDLSGWNGMGFVVQAYGKRCPFVLDFIIDLARRSGRRIMVRLV 369

Query: 370  KGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLA 429
            KGAYWD+EIKRAQLDGL DFPV+TRK++TDVSY+ACA KLLAA + VFPQFATHNAQTLA
Sbjct: 370  KGAYWDAEIKRAQLDGLADFPVFTRKIHTDVSYIACAAKLLAATDVVFPQFATHNAQTLA 429

Query: 430  TIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVV--GPLKRPCRIYAPVGTHETLLAYLVRR 487
             IY MAG DF VGKYEFQCLHGMGEPLY+EVV  G L RPCRIYAPVGTHETLLAYLVRR
Sbjct: 430  AIYHMAGKDFHVGKYEFQCLHGMGEPLYEEVVGRGKLDRPCRIYAPVGTHETLLAYLVRR 489

Query: 488  LLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSA 547
            LLENGANSSFV+RI DP V +DEL+ADPV V RA+   GA H  IALP  L+   R NSA
Sbjct: 490  LLENGANSSFVHRINDPKVSIDELIADPVEVVRAMPVVGAKHDRIALPAELFGDARTNSA 549

Query: 548  GIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEAS 607
            G+DLS+E  LA L+ AL  SA M WTA P LA G  AG+ + V NP D RDVVGSVTE S
Sbjct: 550  GLDLSNEETLASLTEALRESAAMKWTALPQLATGPAAGETRTVLNPGDHRDVVGSVTETS 609

Query: 608  EALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAI 667
            E     A   A  AA  WAA PP ERAA L RAA+ MQ RMPTLLGLI+REAGKS  NAI
Sbjct: 610  EEDARRAVRLAADAAPDWAAVPPSERAACLDRAAELMQARMPTLLGLIIREAGKSALNAI 669

Query: 668  AEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVL 727
            AEVREAIDFLRYY  Q R R     H PLGP+VCISPWNFPLAIF+GQIAAAL AGNPVL
Sbjct: 670  AEVREAIDFLRYYAEQTR-RTLGPGHGPLGPIVCISPWNFPLAIFTGQIAAALVAGNPVL 728

Query: 728  AKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVAR 787
            AKPAEETPLIAAE VRIL  AGIPA ALQLLPG G VGAALV      GVMFTGSTEVAR
Sbjct: 729  AKPAEETPLIAAEGVRILREAGIPASALQLLPGDGRVGAALVAAAETAGVMFTGSTEVAR 788

Query: 788  LIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALR 847
            LIQ QLA RL P G PIPLIAETGGQNAMIVDSSALAEQVVGDVI SAFDSAGQRCSALR
Sbjct: 789  LIQAQLADRLSPAGRPIPLIAETGGQNAMIVDSSALAEQVVGDVITSAFDSAGQRCSALR 848

Query: 848  ILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRN 907
            +LCLQEDVADR L MLKGA+ EL IG  DRL+VDVGPVI+ EA+  I  HIE MR  GR 
Sbjct: 849  VLCLQEDVADRILTMLKGALHELHIGRTDRLSVDVGPVITSEAKDNIEKHIERMRGLGRK 908

Query: 908  VEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGY 967
            VE + L +ET  GTF+ PT+IE+  + +L+REVFGPVLHV+R+ RDDLD LVD +NATGY
Sbjct: 909  VEQIGLASETGVGTFVPPTIIELEKLSDLQREVFGPVLHVIRYRRDDLDRLVDDVNATGY 968

Query: 968  GLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYL 1027
            GLTFGLHTR+D TI  VT RI AGN+Y+NRN IGAVVGVQPFGG GLSGTGPKAGGPLYL
Sbjct: 969  GLTFGLHTRLDETIAHVTSRIKAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYL 1028

Query: 1028 SRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNG 1087
             RL++  P                L + +WL  KG  AEA       + SA+G   EL G
Sbjct: 1029 GRLVTTAPVP--PQHSSVHTDPVLLDFAKWLDGKGARAEAEAARNAGSSSALGLDLELPG 1086

Query: 1088 PVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALA 1147
            PVGERNLY LH RGR+LL+P T +GL  QL A LATGNS A+DA   L   L+ LP  + 
Sbjct: 1087 PVGERNLYTLHARGRILLVPATESGLYHQLAAALATGNSVAIDAASGLQASLKNLPQTVG 1146

Query: 1148 ARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGY 1207
             RV  + DW   GP A  LVEGD ER+ A+N+ +A LPGP+LLVQAA++  +A    + Y
Sbjct: 1147 LRVSWSKDWAADGPFAGALVEGDAERIRAVNKAIAALPGPLLLVQAASSGEIAR-NPDAY 1205

Query: 1208 DLDLLLNERSVSVNTAAAGGNASLVAM 1234
             L+ L+ E S S+NTAAAGGNASL+A+
Sbjct: 1206 CLNWLVEEVSASINTAAAGGNASLMAI 1232


Lambda     K      H
   0.319    0.136    0.396 

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: 3806
Number of extensions: 156
Number of successful extensions: 6
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: 1235
Length of database: 1233
Length adjustment: 48
Effective length of query: 1187
Effective length of database: 1185
Effective search space:  1406595
Effective search space used:  1406595
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)

Align candidate SMc02181 SMc02181 (bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.10455.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10455.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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