GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Sphingomonas koreensis DSMZ 15582

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate Ga0059261_3926 Ga0059261_3926 L-proline dehydrogenase (EC 1.5.99.8)/delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)

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



>FitnessBrowser__Korea:Ga0059261_3926
          Length = 1199

 Score = 1573 bits (4072), Expect = 0.0
 Identities = 829/1224 (67%), Positives = 941/1224 (76%), Gaps = 31/1224 (2%)

Query: 16   APFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAATARKLITAL 75
            APFADFAPPIRP T LR+AITAAYRRPEPEC+P L EQASLP G   AA  TA  LITAL
Sbjct: 3    APFADFAPPIRPQTPLRSAITAAYRRPEPECVPPLVEQASLPEGTREAARITASTLITAL 62

Query: 76   RAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAGGDWQAHLG 135
            RAK +G GVEGL+ EY+LSSQEG+ALMCLAEALLRIPD ATRDALIRDKIA GDW++H+G
Sbjct: 63   RAKHKGTGVEGLVQEYALSSQEGVALMCLAEALLRIPDDATRDALIRDKIADGDWKSHIG 122

Query: 136  KGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFAMRMMGEQF 195
             G S+FVNAATWGL++TGKLT +  +  L +ALTRLIAR GEP+IRRGVD AMRMMGEQF
Sbjct: 123  DGRSLFVNAATWGLVVTGKLTGSVNDAGLGAALTRLIARAGEPVIRRGVDMAMRMMGEQF 182

Query: 196  VTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAIGTASAGRG 255
            VTG+TI EAL  ART+EA GF+YSYDMLGEAA T  DA RYY DY NA+ AIG ASAGRG
Sbjct: 183  VTGETIAEALKRARTLEARGFQYSYDMLGEAATTMADADRYYRDYENAVRAIGEASAGRG 242

Query: 256  VYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDAEEADRLEL 315
            V  GPGISIKLSA+HPRY+RAQA RVMDELLP+VKALA+LA+GYDIG NIDAEEADRLEL
Sbjct: 243  VVGGPGISIKLSALHPRYARAQAGRVMDELLPKVKALAVLARGYDIGFNIDAEEADRLEL 302

Query: 316  SLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIRLVKGAYWD 375
            SLDL+ESL  DPDL GW+G+GFVVQAYGKRCP+VID+++DLA+R+  R+M+RLVKGAYWD
Sbjct: 303  SLDLLESLALDPDLKGWDGLGFVVQAYGKRCPFVIDWIVDLAQRADRRIMVRLVKGAYWD 362

Query: 376  SEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQTLATIYEMA 435
            +EIKRAQ+DGLPDFPVYTRK+YTDV+Y+ACARKLLA  + +FPQFATHNAQTLATIY+MA
Sbjct: 363  AEIKRAQVDGLPDFPVYTRKIYTDVAYIACARKLLANRDRIFPQFATHNAQTLATIYQMA 422

Query: 436  GSDFQVGKYEFQCLHGMGEPLYKEVVG--PLKRPCRIYAPVGTHETLLAYLVRRLLENGA 493
            G DF VG YEFQCLHGMGEPLY EVVG   L RPCRIYAPVGTHETLLAYLVRRLLENGA
Sbjct: 423  GPDFSVGDYEFQCLHGMGEPLYDEVVGATKLNRPCRIYAPVGTHETLLAYLVRRLLENGA 482

Query: 494  NSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERANSAGIDLSD 553
            NSSFVNRIADP V + ELVADPV   R++   GA H LIALP  LY   R NS G+DLS+
Sbjct: 483  NSSFVNRIADPEVSIAELVADPVDQVRSMDVVGAKHPLIALPTGLYGARR-NSEGLDLSN 541

Query: 554  ETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTEASEALVAE 613
            E  LA L+A+L  SA   W A P     +R G ++PV NPAD +DVVG+V E +      
Sbjct: 542  ENVLAELAASLKVSAAAGWAAEP----ADRIGTSRPVYNPADGKDVVGTVVEVTPEAAQT 597

Query: 614  AFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPNAIAEVREA 673
            A   A AAA+ WAA  P ERAA L RAAD MQ+RM  L+GLI+REAGKS PNAIAEVREA
Sbjct: 598  AVATAQAAAADWAAVAPAERAACLDRAADIMQDRMQILMGLIIREAGKSAPNAIAEVREA 657

Query: 674  IDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNPVLAKPAEE 733
            IDFLRYY  Q R     A H+PLG V CISPWNFPLAIF+GQ+AAAL AGN VLAKPAEE
Sbjct: 658  IDFLRYYAEQARAML-GAAHKPLGAVTCISPWNFPLAIFTGQVAAALVAGNTVLAKPAEE 716

Query: 734  TPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEVARLIQRQL 793
            TPLIAA+ V ILH AGIPA ALQL+PG G +GAALV     + VMFTGSTEVAR+IQ++L
Sbjct: 717  TPLIAAQGVSILHEAGIPAAALQLVPGDGRIGAALVAAPGTQAVMFTGSTEVARIIQKEL 776

Query: 794  AGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRILCLQE 853
            A RL   G P+P IAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALR+LCLQ+
Sbjct: 777  AKRLTDGGDPVPFIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSALRVLCLQD 836

Query: 854  DVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKGRNVEFLPL 913
            DVADR L MLKGA+ EL IG  D L+ D+GPVI+ EA+A I  HI  M   GR VE + L
Sbjct: 837  DVADRILVMLKGALHELSIGRTDSLSTDIGPVITAEAKANIEGHIARMLGMGRGVEQIEL 896

Query: 914  PAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINATGYGLTFGL 973
              ETA GTF+ PT+IE+  I +LEREVFGPVLHVVR+ R DLD ++D+INATGYGLTFGL
Sbjct: 897  AGETAQGTFVPPTIIELQSIADLEREVFGPVLHVVRYKRRDLDRVIDAINATGYGLTFGL 956

Query: 974  HTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPLYLSRLLSR 1033
            HTR+D TI  V+ R+ AGN+Y+NRN IGAVVGVQPFGG GLSGTGPKAGGPLYL RL+  
Sbjct: 957  HTRLDETIAHVSQRVEAGNLYINRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYLGRLVQT 1016

Query: 1034 R--PKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAELNGPVGE 1091
               P G        A R   L    WL  +G   EA+R AG    S +G   EL GPVGE
Sbjct: 1017 ATVPPGVASDTSDPALRDFAL----WLGEQG---EAARAAG--EASLLGAEVELPGPVGE 1067

Query: 1092 RNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPALAARVR 1151
            RN+Y LH RG VLLLP+TR GL+ Q+ A LATGN A +       E L GLP  +AAR+ 
Sbjct: 1068 RNIYALHPRGSVLLLPKTREGLIAQVSAALATGNRAVIGNTALRGE-LAGLPERVAARLS 1126

Query: 1152 TTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGEGYDLDL 1211
               DWR  GP    L+EGD    +A    +A LPGPI+L QA T             LD 
Sbjct: 1127 WADDWRKAGPYGGALIEGDAAARSAALAEIAALPGPIVLAQAGTPR-----------LDW 1175

Query: 1212 LLNERSVSVNTAAAGGNASLVAMS 1235
            L+ E S SVNT AAGGNASL+A++
Sbjct: 1176 LVEEVSTSVNTTAAGGNASLMAVA 1199


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: 3787
Number of extensions: 157
Number of successful extensions: 8
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: 1199
Length adjustment: 47
Effective length of query: 1188
Effective length of database: 1152
Effective search space:  1368576
Effective search space used:  1368576
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 Ga0059261_3926 Ga0059261_3926 (L-proline dehydrogenase (EC 1.5.99.8)/delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12))
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.32535.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32535.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.