GapMind for catabolism of small carbon sources

 

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

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate 3608920 Dshi_2311 delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= reanno::Marino:GFF2744
         (1209 letters)



>FitnessBrowser__Dino:3608920
          Length = 1221

 Score = 1263 bits (3267), Expect = 0.0
 Identities = 665/1209 (55%), Positives = 848/1209 (70%), Gaps = 19/1209 (1%)

Query: 15   RQAIRDYYLADEHKVIHEMIAGAQLSQAERDAISARAAELVRSVRKNAKSTIMEKFLAEY 74
            R  +R +Y A+E  ++  + A  +LS  ER+  +A  A  V  VR   + ++ME FLAEY
Sbjct: 16   RAQVRAHYTAEETALLKSLAARIKLSAHEREKAAAAGARYVTRVRNETRPSMMEAFLAEY 75

Query: 75   GLTTKEGVALMCLAEALLRVPDNTTIHELIEDKITSGAWGTHVGKASSGLINTATVALLM 134
            GL+T EGV LMCLAEALLRVPD  TI +LIEDK+    WG H+G +SS L+N +T AL++
Sbjct: 76   GLSTSEGVGLMCLAEALLRVPDADTIDDLIEDKVAPSNWGAHLGHSSSSLVNASTWALML 135

Query: 135  TSNLLKDSERNTVGETLRKLLKRFGEPVIRTVAGQAMKEMGRQFVLGRDIDEAQDEAKEY 194
            T  +L +  R      LR L+KR GEPV+RT  GQ+MK +GRQFVLG+ I+E    A+E 
Sbjct: 136  TGKVLDEDPRGPA-RALRGLVKRLGEPVVRTAVGQSMKVLGRQFVLGQTIEEGLKNAREL 194

Query: 195  MAKGYTYSYDMLGEAARTDDDAKRYYDSYSNAIDSIAKASKGDVRKNPGISVKLSALLAR 254
              KG+TYSYDMLGEAARTD DA+RY+ +Y+ AI +IA+ + GDVR +PGISVKLSAL  R
Sbjct: 195  EKKGFTYSYDMLGEAARTDADARRYHAAYAQAITAIARQATGDVRSSPGISVKLSALHPR 254

Query: 255  YEYGNKERVMNELLPRARELVKKAAAANMGFNIDAEEQDRLDLSLDVIEELVADPELAGW 314
            YEY ++  VM +L+PRA  LVK+AA A +GFN+DAEEQDRLDLSLDVIE +++DP+L GW
Sbjct: 255  YEYTHRHSVMADLVPRAAALVKQAAQAGIGFNVDAEEQDRLDLSLDVIEAMMSDPDLDGW 314

Query: 315  DGFGVVVQAYGKRSSFVLDWLYGLAEKYDRKFMVRLVKGAYWDAEIKRAQVMGLNGFPVF 374
            DGFGVVVQAYG+R+  V++ LY +AE+YDRK MVRLVKGAYWD EIK AQ +G+  FPVF
Sbjct: 315  DGFGVVVQAYGRRAGPVIETLYDMAERYDRKIMVRLVKGAYWDTEIKLAQELGVERFPVF 374

Query: 375  TRKACSDVSFLSCATKLLNMTNRIYPQFATHNAHSVSAILEMAKTKGVDNYEFQRLHGMG 434
            TRK  +DVS+++CA  LL+  +RIYPQFATHNAH+ +A+L+MA     D +EFQRLHGMG
Sbjct: 375  TRKNNTDVSYMACAQMLLDRRDRIYPQFATHNAHTCAAVLQMAGNAR-DCFEFQRLHGMG 433

Query: 435  ESLHNEVLKVSGVPCRIYAPVGPHKDLLAYLVRRLLENGANSSFVNQIVDKRITPEEIAK 494
             SLH  V +  G  CRIYAPVG H+DLLAYLVRRLLENGANSSFVNQIVD  I  E I+ 
Sbjct: 434  ASLHQIVKETEGTRCRIYAPVGAHQDLLAYLVRRLLENGANSSFVNQIVDPDIPAEAISA 493

Query: 495  DPIVSVEEMGNNISSKAIVHPFKLFGDQRRNSKGWDITDPVTVNEIEKGRGAYKDYRWKG 554
            DP+  +E++G+ I + AI  P  LF   RRNS+G+ + +P ++  +   R A+ +  W  
Sbjct: 494  DPVSEMEKLGDQIPNPAIRQPSDLFAPDRRNSRGYRVNEPASILPLMTAREAFAETTWHA 553

Query: 555  GPLIAGEVAGT-EIQVVRNPADPDDLVGHVTQASDADVDTAITSAAAAFESWSAKSAEER 613
             P++AG    T   + V +PAD   LVG V +AS  DV  A+ +A   F  WSA+   ER
Sbjct: 554  RPMLAGGRDPTGPTREVHSPADKTRLVGTVQEASAEDVACALDAAETGFRDWSARPVSER 613

Query: 614  AACVRKVGDLYEENYAELFALTTREAGKSLLDAVAEIREAVDFSQYYANEAIRYK--DSG 671
            A  +RK+ D+YE+N AEL A+TTREAGK++LD +AE+REAVDF ++YANEA R +  D G
Sbjct: 614  ADMLRKLADMYEDNIAELTAITTREAGKTVLDGIAEVREAVDFLRFYANEAERLEEEDPG 673

Query: 672  DARGVMCCISPWNFPLAIFTGQILANLAAGNTVVAKPAEQTSLLAIRAVELMHQAGIPKD 731
              RG+  CISPWNFPLAIFTGQI A L  GN V+AKPAEQT ++A RAV++M   G+P  
Sbjct: 674  RPRGIFVCISPWNFPLAIFTGQIAAALVMGNAVLAKPAEQTPIIAARAVQMMRDCGLPDA 733

Query: 732  AIQLVPGTGATVGAALTSDSRVSGVCFTGSTATAQRINKVMTENMAPDAPLVAETGGLNA 791
            A+QL+PG G  VG  LTSD R++GVCFTGST  A  I+K + +N  P+A LVAETGGLNA
Sbjct: 734  ALQLLPGDGPMVGGPLTSDPRIAGVCFTGSTEVAMIIHKALAKNAGPEAVLVAETGGLNA 793

Query: 792  MIVDSTALPEQVVRDVLASSFQSAGQRCSALRMLYVQRDIADGLLEMLYGAMEELGIGDP 851
            MIVDSTAL EQ VRD+L SSFQSAGQRCSALR+LYVQ D+ D L+EML GA++ L IGD 
Sbjct: 794  MIVDSTALHEQAVRDILISSFQSAGQRCSALRILYVQEDVHDKLMEMLSGALDALVIGDS 853

Query: 852  WLLSTDVGPVIDENARKKIVDHCEKFERNGKLLKKMKVPEKGLFVSPAVLSVSGIEELEE 911
            W L  DV PVID +A+  I+ + ++  + G L+K +  P+ G +V+PA++ V GI ++E 
Sbjct: 854  WNLDVDVSPVIDADAQSDILGYIDQHRKAGTLIKTLAAPDSGTYVTPAIVKVGGIADMER 913

Query: 912  EIFGPVLHVATFEAKNIDKVVDDINAKGYGLTFGIHSRVDRRVERITSRIKVGNTYVNRN 971
            EIFGPVLHVATF+A  ID+VVD INA+ YGLTFG+H+R+D RVE+I  RI+VGN YVNRN
Sbjct: 914  EIFGPVLHVATFKANEIDQVVDAINARRYGLTFGLHTRIDDRVEQIVERIQVGNVYVNRN 973

Query: 972  QIGAIVGSQPFGGEGLSGTGPKAGGPQYVRRFLK-GETVEREADSNARKVDAKQLQKLIG 1030
            QIGAIVGSQPFGGEGLSGTGPKAGGP Y+ RF K G++    A   A  +    L   + 
Sbjct: 974  QIGAIVGSQPFGGEGLSGTGPKAGGPLYLTRFRKVGKSTSHPAPQGA-VLGKAALNTALS 1032

Query: 1031 QLDKLK-ASRPE----ARMDAIRPIFGNVPEPL------DAHVEALPGPTGETNRLSNHA 1079
             LD    A+RP+     RM A+    G V   L      D   + LPGPTGE+NRLS   
Sbjct: 1033 SLDARNWAARPDRVHILRM-ALSGSTGVVRRALSETAAFDMSPQTLPGPTGESNRLSMVP 1091

Query: 1080 RGVVLCLGPDKETALEQAGTALSQGNKVVVIAPGTQDVVDQANKAGLPIVGAQGLLEPEA 1139
            RG VLCLGP  E A+ QA  AL  G  VV+  PG+  +    + AG P+V   G ++   
Sbjct: 1092 RGTVLCLGPTPEIAMAQAVQALGAGCAVVIALPGSTPLSQPLSDAGAPVVTLDGTVDCVT 1151

Query: 1140 LATIDGFEAVVSCGDQPLLKAYREALAKRDGALLPLITEHTLDQRFVIERHLCVDTTAAG 1199
            L  + G E V + G     +  R AL++RDG ++PLI +    +R+V+ERHLC+DTTAAG
Sbjct: 1152 LTELTGIEVVAAAGASDWTRTLRVALSQRDGPIIPLIVDEIAPERYVLERHLCIDTTAAG 1211

Query: 1200 GNASLIAAS 1208
            GNA L+AAS
Sbjct: 1212 GNAKLLAAS 1220


Lambda     K      H
   0.316    0.133    0.378 

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: 3465
Number of extensions: 168
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: 1209
Length of database: 1221
Length adjustment: 47
Effective length of query: 1162
Effective length of database: 1174
Effective search space:  1364188
Effective search space used:  1364188
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 (21.6 bits)
S2: 59 (27.3 bits)

Align candidate 3608920 Dshi_2311 (delta-1-pyrroline-5-carboxylate dehydrogenase (RefSeq))
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

Software error:

../bin/blast/fastacmd -i /tmp/list.31793.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31793.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.