RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

Searching..................................................done

Query= gi|254780772|ref|YP_003065185.1| surface antigen (D15)
[Candidatus Liberibacter asiaticus str. psy62]
         (781 letters)



>gnl|CDD|34388 COG4775, COG4775, Outer membrane protein/protective antigen OMA87
           [Cell envelope biogenesis, outer membrane].
          Length = 766

 Score =  492 bits (1268), Expect = e-139
 Identities = 244/769 (31%), Positives = 395/769 (51%), Gaps = 17/769 (2%)

Query: 25  MGFIILFYAIFGLSAVYGSNTSIVRRIEIRGATNVGKEVILSRIPVVVGQSISDADLDHA 84
           M  ++    +F  ++   +   +V+ I + G   V     LS +PV VG ++SD D+D A
Sbjct: 3   MKKLLSALLLFASASAVAAEAFVVKDIRVEGLQRVSSGTALSYLPVRVGDTVSDEDIDEA 62

Query: 85  VKNIYAMGYFSNVKIKIVDSVLIIDLIERKIINHLFFSGNNNLKDDQLKMIVRSRSAAAY 144
           +K +YA GYF +V+++     L++ + ER +IN + FSGN ++KDD LK  ++ +     
Sbjct: 63  IKALYATGYFEDVRVEREGGTLVVTVKERPVINSVVFSGNKSIKDDALKKNLKIKPGEVL 122

Query: 145 DEDTVNADVHNIKQAYASIGYLNVMVKVQHHSISPTTLNITYVIEEGVKAKINSIRFVGN 204
           +   + ADV  +K+AY S GY +V V  +   +    +++ +VI EG  AKI  I F GN
Sbjct: 123 NRAKLEADVEALKEAYLSRGYYSVKVTYKVTPLPRNRVDVVFVINEGPSAKIKQINFEGN 182

Query: 205 KNYSHARLERVISIRTSGYFS-FGKTDVYSKERMSFDEEAIRAFYHDRGYAAVKVSS-QV 262
             +S + LE V+  + S  +    + D Y  +++  D E +R+FY +RGYA  +VSS QV
Sbjct: 183 TAFSDSDLESVVQTKESNIWGWLTRLDKYDPDKLEADLETLRSFYLNRGYADFRVSSTQV 242

Query: 263 LFDKQKSGYVLIFQIDEGEIYTVGNISIQSTLQEIQKKTLLSLIRIRSGNLYNPQEIKES 322
             D  K G  + + + EG  Y  G++ I+  L  +  + L  L++++ G L+N ++I++ 
Sbjct: 243 SLDPDKKGVTVTYTVKEGPQYKFGSVLIEGNLAGVS-EELEKLLKVKPGKLFNRKKIEDD 301

Query: 323 SEKISKYFFSGERPFVRVKTRINRDFAKRIVDIEYLIDQGSPLYVKRIEIEGNDQSYDSV 382
           ++KI + +      F  V  + + +   + VD+ + +D+G  +YV+RI I GN ++ D V
Sbjct: 302 ADKIKERYARYGYAFANVSPQPDANDENKTVDVVFRVDEGDRVYVRRIRIRGNTRTKDYV 361

Query: 383 IRRELELSEGDPINYSMIERAKRRIMATGYFSEVNISQLPANDVSDYVILRVSVKQLSAG 442
           IRRE+ L EGD  N  +++R KRR+   GYF  VNI   P +  SD V + V VK+ S G
Sbjct: 362 IRREMRLKEGDVFNRKLVQRGKRRLRRLGYFESVNIDTAPGSG-SDQVDVVVDVKERSTG 420

Query: 443 SVGIATNYEVDKGMGVEGHIDDNNFFGQGYRARLAAGFGRHAVQNYTFSVEDPYFLGSPI 502
           S+     Y  D G+     + + NF G G    L A  G     +Y+ S  DPYFL   +
Sbjct: 421 SINFGLGYGSDSGLSGFASLSERNFLGTGQSLSLNANLGDKQ-TSYSLSFTDPYFLDDRV 479

Query: 503 SAGFDLQKTH-------LEDGSLDINDESAAVRMIVPITESISTSFKYDLRFLQYGAISE 555
           S GF+L             + S  +      V +  PITE++S    Y         +++
Sbjct: 480 SLGFNLFSNRYDTFDADTANDSYRVKTYGGGVSLGRPITENLSLGLGYGYEQNSLSLLNK 539

Query: 556 KEKIPSIYTTL-IEHGKFSSHSISQSIIYNTLDNPIVPRKGMLISSSYDYAGFGGDSQYH 614
                     + ++ GK    S+S    Y+T DN + P KG  +S + + AG GGD +Y+
Sbjct: 540 SPPDEYASLGVKLQGGKSDLSSLSLGWTYDTRDNALFPTKGSYLSLTQEVAGLGGDIKYY 599

Query: 615 RIGSRASYFYLLSDDSDIVGSLRFGYGCVIP-SNKNLQLFDQFSVSSNYYLRGFAYKGIG 673
           ++    S +Y L  D     SLR   G       K L ++++F +  +  +RGF   G+G
Sbjct: 600 KLELDGSKYYPL-TDYIFTLSLRGEVGYGKGYGTKLLPIYERFYLGGSNSVRGFESGGLG 658

Query: 674 PRVDKKYAIGGKIYSSASAAVSFPMPLVPERAGLRGAFFVDSATLYANHVALGADK-LEG 732
           P+     A+GG  Y  ASA + FP+P V   +G+RGA F D+ +++         +   G
Sbjct: 659 PKDGYTDALGGTSYFVASAELRFPLPKVIG-SGVRGALFFDAGSVWNTGTDPSTVRNFYG 717

Query: 733 NDSFWRVSTGVEIMWNSPLGMMGVYYGIPLRHREGDKIQQFGFRIGNRM 781
           + S  R S GV + W SPLG +   Y  P++ +EGD  Q+F F +G R 
Sbjct: 718 SGSELRASAGVGLRWASPLGPLRFDYAFPIKKKEGDDTQRFQFGLGTRF 766


>gnl|CDD|144626 pfam01103, Bac_surface_Ag, Surface antigen.  This entry includes
           the following surface antigens; D15 antigen from
           H.influenzae, OMA87 from P.multocida, OMP85 from
           N.meningitidis and N.gonorrhoeae. The family also
           includes a number of eukaryotic proteins that are
           members of the UPF0140 family. There also appears to be
           a relationship to pfam03865 (personal obs: C Yeats). In
           eukaryotes, it appears that these proteins are not
           surface antigens; S. cerevisiae YNL026W (SAM50) is an
           essential component of the Sorting and Assembly
           Machinery (SAM) of the mitochondrial outer membrane. The
           protein was localized to the mitochondria.
          Length = 317

 Score =  178 bits (453), Expect = 5e-45
 Identities = 91/324 (28%), Positives = 155/324 (47%), Gaps = 15/324 (4%)

Query: 466 NFFGQGYRARLAAGFGRHAVQNYTFSVEDPYFLGSPISAGFDLQKTHLEDG---SLDIND 522
           N  G+G    ++  + ++  Q+++ S  DPYFLG  +S G+ L     ++    S D   
Sbjct: 1   NLLGRGQSLSVSLSYSQYE-QSFSLSFTDPYFLGDGLSLGYSLFYNTYDEDEYDSYDTKS 59

Query: 523 ESAAVRMIVPITESISTSFKYDLRFLQYGAISEKEKIPSIYTTLIEHGKFSSHSISQSII 582
              ++ +  PI+E+ S S        +           +I     + GK    S+S  + 
Sbjct: 60  VGFSLSLGYPISENWSLSLGLSYSRDKIRDEDGS---DNIRNYASQTGKSLLSSLSFGLS 116

Query: 583 YNTLDNPIVPRKGMLISSSYDYAG--FGGDSQYHRIGSRASYFYLLSDDSDIVGSLR--F 638
           Y+T DN + P +G  +  + ++AG   GGD ++ ++   AS++Y L +D D V + R   
Sbjct: 117 YDTRDNGLFPTRGYYLRFNLEFAGPILGGDVKFLKLTGDASWYYPLGEDHDFVLAARVGL 176

Query: 639 GYGCVIPSNKNLQLFDQFSVSSNYYLRGFAYKGIGPRVDKKYAIGGKIYSSASAAVSFPM 698
           GY     +   L   ++F    +  +RG+ Y  IGPR +   A+GG+ Y +ASA + +P+
Sbjct: 177 GYLLGYGAKDKLPPSERFFAGGSNSVRGYGYGSIGPRDEDGDALGGRSYFTASAELRYPL 236

Query: 699 PLVPERAGLRGAFFVDSATLYANHVALGADKLEGNDSFWRVSTGVEIMWNSPLGMMGVYY 758
           P +P    LRGA FVD+  ++ +                R S GV + W+SP G +   Y
Sbjct: 237 PFIPN---LRGALFVDAGNVWNSGGDTPGGSDGVRSKNIRASVGVGLRWDSPFGPLRFDY 293

Query: 759 GIPLRHREGDKIQ-QFGFRIGNRM 781
            IPL+  +GD+ + +F F IG   
Sbjct: 294 AIPLKKPDGDRTEFRFYFGIGTEF 317


>gnl|CDD|31073 COG0729, COG0729, Outer membrane protein [Cell envelope biogenesis,
           outer membrane].
          Length = 594

 Score =  113 bits (284), Expect = 2e-25
 Identities = 104/553 (18%), Positives = 202/553 (36%), Gaps = 52/553 (9%)

Query: 241 EEAIRAFYHDRGYAAVKVSSQVLFDKQKSGYVLIFQIDEGEIYTVGNISIQ-----STLQ 295
            + +RA  + +          V   + K    LI ++  GE   +  + +       T  
Sbjct: 76  RDGLRALGYLQPKGRFGGKVSVTEKRGK----LIAKVTPGEPTPIAVVIVVLPGPAFTDG 131

Query: 296 EIQKKTLLSLIRIRSGNLYNPQEIKESSEKISKYFFSGERPFVRV-KTRINRDFAKRIVD 354
           + +   L      + G   N    + +   I +          R  K+R+  D A    D
Sbjct: 132 DYRL--LGDAAGPKEGEDLNQGTYENAKSSIVRALLRKGYFLARFTKSRLVVDPATHTAD 189

Query: 355 IEYLIDQGSPLYVKRIEIEGNDQSYDSVIRRELELSEGDPINYSMIERAKRRIMATGYFS 414
           ++   D G       + +EG+ +  +  ++  +    G P +   +    +R+  TGYFS
Sbjct: 190 VDLNYDSGRRYRFGPVTVEGSQRIDEEYLQNLVPFKYGLPYDPEDLAELNQRLRQTGYFS 249

Query: 415 EVNISQLPANDVSDYVI-LRVSVKQLSAGSVGIATNYEVDKGMGVEGHIDDNNFFGQGYR 473
            V +         D ++ ++VSV +    +  +   Y  D G G+E   +  N FG+G+ 
Sbjct: 250 SVVVQPADKQAGPDGLLPVKVSVSERKENTFELGVGYSTDVGAGLEAGWEKRNLFGRGHS 309

Query: 474 ARLAAGFGRHAVQNYTFSVEDPYFLGSP-----ISAGFDLQKTHLEDGSLDINDESAAVR 528
            R+ +      +Q    + + P           +SAGFD          LD+ D  +   
Sbjct: 310 LRIESEISA-PLQTLEATYKAPLLFNPLGQYNPVSAGFD---------RLDLYDTESDA- 358

Query: 529 MIVPITESISTSFKYDLRFLQYGAISEKEKIPSIYTTLIEHG-KFSSHSISQSIIYNTLD 587
                TES+S S  +D       +++ +    +     I       +  +  S   +T D
Sbjct: 359 ----YTESLSASRGWDASLGWQRSLALRFSYDNFRQGDISGKTSLLTPGVEFSYTRDT-D 413

Query: 588 NPIVPRKGMLISSSYDYA--GFGGDSQYHRIGSRASYFYLLSDDSDIVGSLRFGYGCVIP 645
           + + P  G  +  +   +    G D  +  + +R+ Y      D  + G    G   +  
Sbjct: 414 DGLFPTWGDRLDLTIGPSYEALGSDVDFRLVQARSGYLRTGGADHRLAGRGELGA-ILTG 472

Query: 646 SNKNLQLFDQFSVSSNYYLRGFAYKGIGPRVDKKYAIGGKIYSSASAAVSFPMPLVPERA 705
              ++    +F    +  +RG+ Y+ IGP+      +GG+   + S    + +       
Sbjct: 473 DLDDVPPSLRFFAGGDRSVRGYGYQSIGPQDANGDLLGGRSLVTGSLEYQYLV-----TD 527

Query: 706 GLRGAFFVDSATLYANHVALGADKLEGNDSFWRVSTGVEIMWNSPLGMMGVYYGIPLRHR 765
               A FVD+ +   N   L +D         +   G+ + W+SP+G +     +PL  +
Sbjct: 528 PWGLAVFVDAGSAGNNFTRLFSD--------LKKGAGIGVRWDSPVGPIRFDIAVPLEDK 579

Query: 766 EGDKIQQFGFRIG 778
           +  K  QF   IG
Sbjct: 580 DDKKF-QFYIGIG 591


>gnl|CDD|37813 KOG2602, KOG2602, KOG2602, Predicted cell surface protein
           homologous to bacterial outer membrane proteins [General
           function prediction only].
          Length = 457

 Score = 89.3 bits (221), Expect = 3e-18
 Identities = 88/424 (20%), Positives = 181/424 (42%), Gaps = 21/424 (4%)

Query: 367 VKRIEIEGNDQSYDSVIRREL-ELSEGDPINYSMIER--AKRRIMATGYFSEVNI---SQ 420
           V  + + G +++ D  I +E+  + +   +   ++    A   + A G F  VNI   ++
Sbjct: 38  VDHVIVSGLERTKDDFIMKEVDLVFKAKNLQELLLASHEAASNLRALGIFDSVNILIDTK 97

Query: 421 LPANDVSDYVILRVSVKQLSAGSVGIATNYEVDKGMGVEGHIDDNNFFGQGYRARLAAGF 480
             ++ +   +++   V +    +    T+    +G  VE ++   N  G+G        +
Sbjct: 98  EGSDALPGGLVVTFLVTEPKRLTGSTGTDVGNREG-SVELNLKLPNILGRGENLSGQVSY 156

Query: 481 GRHAVQNYTFSVEDPYFLGSP---ISAGFDLQKTHLEDGSLDINDESAAVRMIVPITESI 537
           G     +   S   P F G      S      +  ++  SLD     A++ +       +
Sbjct: 157 GCTRSTDMGLSFYKPRFHGLKTPFSSFSIFRTQDWMKWSSLDETHRGASLELSAEDWFLL 216

Query: 538 STSFKYDLRFLQYGAISEKEKIPSIYTTLIEHGKFSSHSISQSIIYNTLDNPIVPRKGML 597
               KY++ +   G +S+            + G     S+S + +++  D+ I+P +G+L
Sbjct: 217 FHELKYEIAWRNLGDLSQGASFS----VRRQAGHSLKSSLSYTFVFDKRDSSIIPTRGIL 272

Query: 598 ISSSYDYAGFGGDSQYHRIGSRASYFYLLSDDSDIVGSLRFGYGCVIP-SNKNLQLFDQF 656
           + S+ + AG  GD  + +  S       +    D   S  F  G + P  ++ + + D+F
Sbjct: 273 LKSTSELAGLFGDVSFLK--SELDLQKAVPLGFDATLSFSFSGGVLKPLGSRPVSIADRF 330

Query: 657 SVSSNYYLRGFAYKGIGPRVDKKYAIGGKIYSSASAAVSFPMPLVP-ERAGLRGAFFVDS 715
            +     LRGF  +GIGP+ +  + +GG  + +A A + FP+P     ++G RG  F ++
Sbjct: 331 YLGGPSDLRGFKTRGIGPKDEGDF-LGGDAFVAAGAHLYFPLPFAKGFKSGFRGHVFANA 389

Query: 716 ATLYANHVALGADKLEGNDSFWRVSTGVEIMWNSP-LGMMGVYYGIPLRHREGDKIQQFG 774
             L         + +      +R S G  ++  +P    + + Y +PL+ +E D+I++ G
Sbjct: 390 GNLANLSSEAPKNTIPKLLETFRTSVGAGLVVPTPRAARLELNYCLPLKKQENDRIRK-G 448

Query: 775 FRIG 778
           F+ G
Sbjct: 449 FQFG 452


>gnl|CDD|32659 COG2831, FhaC, Hemolysin activation/secretion protein
           [Intracellular trafficking and secretion].
          Length = 554

 Score = 44.6 bits (105), Expect = 1e-04
 Identities = 54/324 (16%), Positives = 101/324 (31%), Gaps = 37/324 (11%)

Query: 366 YVKRIEIEGNDQSYDSVIRRELELSEGDPINYSMIERA----KRRIMATGYFSEVNISQL 421
            ++ I I G+       +R       GDP+N   +E+      R         + +  +L
Sbjct: 149 RIEDIRITGDSDLRSVALRSLFPAHRGDPLNLRDLEQGLELLNRLPGV-----QADA-EL 202

Query: 422 PANDVSDYVILRVSVKQLSAGSVGIATNYEVDKGMG---VEGHIDDNNFFGQGYRARLAA 478
                     L + V+Q     V  + +    K  G   +   +  +N  G G +  L+ 
Sbjct: 203 VPGSEPGESDLVIKVQQGKPWRVSASADNYGSKSTGRYRLGVGLSLDNPLGLGDQLSLSY 262

Query: 479 --GFGRHAVQNYTFSVEDPY-FLGSPISAGF--DLQKTHLEDGSLDINDESAAVR----- 528
                     NY+ S   P  +    + A +    Q        LD   +S  +      
Sbjct: 263 SRSLDGQTTNNYSLSYSVPLGYWTFSLGASYSEYRQVLEGPFDVLDYQGKSQNLSLRLSH 322

Query: 529 -MIVPITESISTSFKYDLRFLQYGAISEKEKIPSIYTTLIEHGKFSSHSISQSIIYNTLD 587
            ++   +  +S       R  +      + ++     T +E G      +    +  +L 
Sbjct: 323 PLLRNRSSKLSLGLGLSHRRSENYLDDTEIEVQRRRLTAVELGLSGRRYLGGGTLDASLG 382

Query: 588 NPIVPRKG--MLISSSYDYAGFG-GDSQYHRIGSRASYFYLLSDDS-DIVGSLRFGYGCV 643
                R+G   L +S  D    G   S++ ++   AS                   Y   
Sbjct: 383 Y----RRGLGALGASKDDEETNGEPTSRFKKLNGNASLLQPFGLGPFLYATQFNAQY--- 435

Query: 644 IPSNKNLQLFDQFSVSSNYYLRGF 667
             S   L   ++FS+   Y +RGF
Sbjct: 436 --SGDPLLSSEKFSIGGRYSVRGF 457



 Score = 31.5 bits (71), Expect = 0.91
 Identities = 17/97 (17%), Positives = 43/97 (44%), Gaps = 9/97 (9%)

Query: 48  VRRIEIRGATNVGKEVILSRIPVVVGQSISDADLDHAVKNI----YAMGY-FSNVKIK-- 100
           + RIE+ G T +    + + +   +G+ +  ADL+     +       GY  +   +   
Sbjct: 75  INRIELEGNTLLDALELQAILAPYLGRCLGLADLNQLASALTNLYIDRGYVTTRALLPPQ 134

Query: 101 -IVDSVLIIDLIERKIINHLFFSGNNNLKDDQLKMIV 136
            +    L + ++E + I  +  +G+++L+   L+ + 
Sbjct: 135 DLKSGTLRLQVVEGR-IEDIRITGDSDLRSVALRSLF 170


>gnl|CDD|143423 cd07105, ALDH_SaliADH, Salicylaldehyde dehydrogenase, DoxF-like.
           Salicylaldehyde dehydrogenase (DoxF, SaliADH,
           EC=1.2.1.65) involved in the upper naphthalene catabolic
           pathway of Pseudomonas strain C18 and other similar
           sequences are present in this CD.
          Length = 432

 Score = 32.9 bits (76), Expect = 0.39
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 16/62 (25%)

Query: 48  VRRIEIRGATNVGKEVILSRI------PVVV---GQSIS----DADLDHAVKNIYAMGYF 94
           VR++   G+T VG+  I++        PV++   G++ +    DADLD A       G F
Sbjct: 181 VRKVNFTGSTRVGR--IIAETAAKHLKPVLLELGGKAPAIVLEDADLDAAANAA-LFGAF 237

Query: 95  SN 96
            N
Sbjct: 238 LN 239


>gnl|CDD|143411 cd07092, ALDH_ABALDH-YdcW, Escherichia coli NAD+-dependent
           gamma-aminobutyraldehyde dehydrogenase YdcW-like.
           NAD+-dependent, tetrameric, gamma-aminobutyraldehyde
           dehydrogenase (ABALDH), YdcW of Escherichia coli K12,
           catalyzes the oxidation of gamma-aminobutyraldehyde to
           gamma-aminobutyric acid. ABALDH can also oxidize n-alkyl
           medium-chain aldehydes, but with a lower catalytic
           efficiency.
          Length = 450

 Score = 32.7 bits (75), Expect = 0.45
 Identities = 24/81 (29%), Positives = 32/81 (39%), Gaps = 20/81 (24%)

Query: 31  FYAIFGLSAVYGS---NTSIVRRIEIRGATNVGKEVI------LSRI--------PVVVG 73
              + G  A  G        VR + + G+   GK+V       L R+        PV+V 
Sbjct: 177 VNVVCGGGASAGDALVAHPRVRMVSLTGSVRTGKKVARAAADTLKRVHLELGGKAPVIV- 235

Query: 74  QSISDADLDHAVKNIYAMGYF 94
               DADLD AV  I   GY+
Sbjct: 236 --FDDADLDAAVAGIATAGYY 254


>gnl|CDD|32462 COG2308, COG2308, Uncharacterized conserved protein [Function
           unknown].
          Length = 488

 Score = 32.1 bits (73), Expect = 0.57
 Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 31  FYAIFGLSAVYGSNTSIVRRIEIRGATNVGKEVI-LSRIPVVVGQSISDADLD 82
           +  + G +A      +   RI+      + + V+ LS +P  V   ++   +D
Sbjct: 379 YGMLVGPAASKAELAAFAERIKADPENYIAQPVLQLSTVPTFVDGGLAPRHVD 431


>gnl|CDD|143422 cd07104, ALDH_BenzADH-like, ALDH subfamily: NAD(P)+-dependent
           benzaldehyde dehydrogenase II, vanillin dehydrogenase,
           p-hydroxybenzaldehyde dehydrogenase and related
           proteins.  ALDH subfamily which includes the
           NAD(P)+-dependent, benzaldehyde dehydrogenase II (XylC,
           BenzADH, EC=1.2.1.28)  involved in the oxidation of
           benzyl alcohol to benzoate; p-hydroxybenzaldehyde
           dehydrogenase (PchA, HBenzADH) which catalyzes the
           oxidation of p-hydroxybenzaldehyde to p-hydroxybenzoic
           acid; vanillin dehydrogenase (Vdh, VaniDH) involved in
           the metabolism of ferulic acid as seen in Pseudomonas
           putida KT2440; and other related sequences.
          Length = 431

 Score = 30.2 bits (69), Expect = 2.4
 Identities = 20/62 (32%), Positives = 28/62 (45%), Gaps = 18/62 (29%)

Query: 47  IVRRIEIRGATNVGKEV------ILSRI--------PVVVGQSISDADLDHAVKNIYAMG 92
            VR I   G+T VG+ +       L ++        P++V   + DADLD AV    A G
Sbjct: 178 RVRMISFTGSTAVGRHIGELAGRHLKKVALELGGNNPLIV---LDDADLDLAVSAA-AFG 233

Query: 93  YF 94
            F
Sbjct: 234 AF 235


>gnl|CDD|38933 KOG3729, KOG3729, KOG3729, Mitochondrial glycerol-3-phosphate
           acyltransferase GPAT [Lipid transport and metabolism].
          Length = 715

 Score = 29.6 bits (66), Expect = 3.4
 Identities = 10/46 (21%), Positives = 20/46 (43%), Gaps = 2/46 (4%)

Query: 721 NHVALGADKLEGNDSFWRVSTGVEIMWNSPLGMMGVYYGIPLRHRE 766
            H  +G  K+   +S   V  G+    +   G++ + +G P+   E
Sbjct: 301 LHEQMGIPKV--RESVLGVFRGIFSGLSKNYGVVRMDFGRPISLTE 344


>gnl|CDD|34740 COG5139, COG5139, Uncharacterized conserved protein [Function
           unknown].
          Length = 397

 Score = 29.4 bits (65), Expect = 3.9
 Identities = 12/69 (17%), Positives = 26/69 (37%)

Query: 338 VRVKTRINRDFAKRIVDIEYLIDQGSPLYVKRIEIEGNDQSYDSVIRRELELSEGDPINY 397
            R +  I+ DF+   +  +   DQ      + ++   + Q +      EL  +    +  
Sbjct: 78  ERKRKHISTDFSDMSLLRKRKNDQSLQPTREPMDSRDSGQDFTEAQSGELGDTGDRQLKA 137

Query: 398 SMIERAKRR 406
               RA+R+
Sbjct: 138 PAASRARRK 146


>gnl|CDD|143468 cd07150, ALDH_VaniDH_like, Pseudomonas putida vanillin
           dehydrogenase-like.  Vanillin dehydrogenase (Vdh,
           VaniDH) involved in the metabolism of ferulic acid and
           other related  sequences are included in this CD.  The
           E. coli vanillin dehydrogenase (LigV) preferred NAD+ to
           NADP+  and exhibited a broad substrate preference,
           including vanillin,  benzaldehyde, protocatechualdehyde,
           m-anisaldehyde, and p-hydroxybenzaldehyde.
          Length = 451

 Score = 29.2 bits (66), Expect = 4.1
 Identities = 21/61 (34%), Positives = 31/61 (50%), Gaps = 18/61 (29%)

Query: 48  VRRIEIRGATNVGKEVI------LSRI--------PVVVGQSISDADLDHAVKNIYAMGY 93
           VR +   G+T VG+E+       L +I        P++V   ++DADLD+AV    A G 
Sbjct: 199 VRMVTFTGSTAVGREIAEKAGRHLKKITLELGGKNPLIV---LADADLDYAV-RAAAFGA 254

Query: 94  F 94
           F
Sbjct: 255 F 255


>gnl|CDD|146706 pfam04209, HgmA, homogentisate 1,2-dioxygenase.  Homogentisate
           dioxygenase cleaves the aromatic ring during the
           metabolic degradation of Phe and Tyr. Homogentisate
           dioxygenase deficiency causes alkaptonuria. The
           structure of homogentisate dioxygenase shows that the
           enzyme forms a hexamer arrangement comprised of a dimer
           of trimers. The active site iron ion is coordinated near
           the interface between the trimers.
          Length = 424

 Score = 29.3 bits (66), Expect = 4.2
 Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 1/27 (3%)

Query: 541 FKYDLR-FLQYGAISEKEKIPSIYTTL 566
           +KYDL  F    ++S     PSI+T L
Sbjct: 267 YKYDLSRFNPINSVSFDHPDPSIFTVL 293


>gnl|CDD|37218 KOG2007, KOG2007, KOG2007, Cysteinyl-tRNA synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 586

 Score = 29.2 bits (65), Expect = 4.5
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 1   MHKSTEDFRRIKRLLEKYFPRSFQMGFI 28
           M KS ++F  IK  L+KY PR  ++ F+
Sbjct: 306 MSKSLKNFITIKEALKKYSPRQLRLAFL 333


>gnl|CDD|177040 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
          Length = 1364

 Score = 28.8 bits (65), Expect = 6.1
 Identities = 14/59 (23%), Positives = 22/59 (37%)

Query: 277 IDEGEIYTVGNISIQSTLQEIQKKTLLSLIRIRSGNLYNPQEIKESSEKISKYFFSGER 335
           I      T+   S    L  I+KK     ++I SG+++ P E  + S         G  
Sbjct: 686 IGVDTQITLNIRSKVGGLVRIEKKKKRIELKIFSGDIHFPGETDKISRHSGILIPPGTG 744


>gnl|CDD|143401 cd07082, ALDH_F11_NP-GAPDH, NADP+-dependent non-phosphorylating
           glyceraldehyde 3-phosphate dehydrogenase and ALDH family
           11.  NADP+-dependent non-phosphorylating glyceraldehyde
           3-phosphate dehydrogenase (NP-GAPDH, EC=1.2.1.9)
           catalyzes the irreversible oxidation of glyceraldehyde
           3-phosphate to 3-phosphoglycerate generating NADPH for
           biosynthetic reactions.  This CD also includes the
           Arabidopsis thaliana osmotic-stress-inducible ALDH
           family 11, ALDH11A3  and similar sequences. In
           autotrophic eukaryotes, NP-GAPDH generates NADPH for
           biosynthetic processes from photosynthetic
           glyceraldehyde-3-phosphate exported from the chloroplast
           and catalyzes one of the classic glycolytic bypass
           reactions unique to plants.
          Length = 473

 Score = 28.7 bits (65), Expect = 6.4
 Identities = 14/50 (28%), Positives = 20/50 (40%), Gaps = 10/50 (20%)

Query: 55  GATNVGKEV--ILSRIPVVVGQS-------ISDADLDHAVKNIYAMGYFS 95
           G+T VG  +        +V+          + DADL+ A K I   G  S
Sbjct: 228 GSTEVGNRLKKQHPMKRLVLELGGKDPAIVLPDADLELAAKEI-VKGALS 276


>gnl|CDD|33973 COG4250, COG4250, Predicted sensor protein/domain [Signal
           transduction mechanisms].
          Length = 226

 Score = 28.5 bits (63), Expect = 6.6
 Identities = 16/69 (23%), Positives = 30/69 (43%), Gaps = 8/69 (11%)

Query: 574 SHSISQSIIYNTLDNPIVPRKGMLISSSYDYAGFGGD-SQYHRIGSRASYFYLLS-DDSD 631
           SH++   ++  T D P+V      I++      +  +  +YHRI   +S  Y+LS  ++ 
Sbjct: 36  SHAMEDQVLAVTADAPLV------IAAFQRERFYRQEAHRYHRIADESSQIYVLSAPETT 89

Query: 632 IVGSLRFGY 640
                R   
Sbjct: 90  FASYDRSQM 98


>gnl|CDD|143421 cd07103, ALDH_F5_SSADH_GabD, Mitochondrial succinate-semialdehyde
           dehydrogenase and ALDH family members 5A1 and 5F1-like. 
           Succinate-semialdehyde dehydrogenase, mitochondrial
           (SSADH, GabD, EC=1.2.1.24) catalyzes the NAD+-dependent
           oxidation of succinate semialdehyde (SSA) to succinate.
           This group includes the human aldehyde dehydrogenase
           family 5 member A1 (ALDH5A1) which is a mitochondrial
           homotetramer that converts SSA to succinate in the last
           step of 4-aminobutyric acid (GABA) catabolism. This CD
           also includes the Arabidopsis SSADH gene product
           ALDH5F1. Mutations in this gene result in the
           accumulation of H2O2, suggesting a role in plant defense
           against the environmental stress of elevated reactive
           oxygen species.
          Length = 451

 Score = 28.6 bits (65), Expect = 7.0
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 17/54 (31%)

Query: 47  IVRRIEIRGATNVGKEVI------LSRI--------PVVVGQSISDADLDHAVK 86
            VR+I   G+T VGK ++      + R+        P +V     DADLD AV 
Sbjct: 196 RVRKISFTGSTAVGKLLMAQAADTVKRVSLELGGNAPFIV---FDDADLDKAVD 246


>gnl|CDD|31101 COG0758, Smf, Predicted Rossmann fold nucleotide-binding protein
           involved in DNA uptake [DNA replication, recombination,
           and repair / Intracellular trafficking and secretion].
          Length = 350

 Score = 28.4 bits (63), Expect = 7.2
 Identities = 13/47 (27%), Positives = 19/47 (40%)

Query: 119 LFFSGNNNLKDDQLKMIVRSRSAAAYDEDTVNADVHNIKQAYASIGY 165
           LF+ GN +L +     IV SR  + Y  D        + Q   +I  
Sbjct: 100 LFYKGNLDLLEAPSVAIVGSRKPSKYGLDYTRDLAEYLAQNGITIVS 146


>gnl|CDD|39584 KOG4383, KOG4383, KOG4383, Uncharacterized conserved protein
           [Function unknown].
          Length = 1354

 Score = 28.6 bits (63), Expect = 7.4
 Identities = 17/57 (29%), Positives = 27/57 (47%)

Query: 72  VGQSISDADLDHAVKNIYAMGYFSNVKIKIVDSVLIIDLIERKIINHLFFSGNNNLK 128
           +G+ ++D   D A       G  S     I+D V IID ++   I  ++FS  + LK
Sbjct: 799 IGERLADEACDQAFSGQIFCGLVSLHYEAILDIVRIIDGLDNACIRFVYFSKEDELK 855


>gnl|CDD|143397 cd07078, ALDH, NAD(P)+ dependent aldehyde dehydrogenase family.
           The aldehyde dehydrogenase family (ALDH) of NAD(P)+
           dependent enzymes, in general, oxidize a wide range of
           endogenous and exogenous aliphatic and aromatic
           aldehydes to their corresponding carboxylic acids and
           play an  important role in detoxification. Besides
           aldehyde detoxification, many ALDH isozymes possess
           multiple additional catalytic and non-catalytic
           functions such as participating in  metabolic pathways,
           or as  binding proteins, or as osmoregulants, to mention
           a few. The enzyme has three domains, a NAD(P)+
           cofactor-binding domain, a catalytic domain, and a
           bridging domain; and the active enzyme  is generally
           either homodimeric or homotetrameric. The catalytic
           mechanism is proposed to involve cofactor binding,
           resulting in a conformational change and activation of
           an invariant catalytic cysteine nucleophile. The
           cysteine and aldehyde substrate form an oxyanion
           thiohemiacetal intermediate resulting in hydride
           transfer to the cofactor and formation of a
           thioacylenzyme intermediate. Hydrolysis of the
           thioacylenzyme and release of the carboxylic acid
           product occurs, and in most cases, the reduced cofactor
           dissociates from the enzyme. The evolutionary
           phylogenetic tree of ALDHs appears to have an initial
           bifurcation between what has been characterized as the
           classical aldehyde dehydrogenases, the ALDH family
           (ALDH) and extended family members or aldehyde
           dehydrogenase-like (ALDH-like) proteins. The ALDH
           proteins are represented by enzymes which share a number
           of highly conserved residues necessary for catalysis and
           cofactor binding and they include such proteins as
           retinal dehydrogenase, 10-formyltetrahydrofolate
           dehydrogenase, non-phosphorylating glyceraldehyde
           3-phosphate dehydrogenase,
           delta(1)-pyrroline-5-carboxylate dehydrogenases,
           alpha-ketoglutaric semialdehyde dehydrogenase,
           alpha-aminoadipic semialdehyde dehydrogenase, coniferyl
           aldehyde dehydrogenase and succinate-semialdehyde
           dehydrogenase.  Included in this larger group are all
           human, Arabidopsis, Tortula, fungal, protozoan, and
           Drosophila ALDHs identified in families ALDH1 through
           ALDH22 with the exception of families ALDH18, ALDH19,
           and ALDH20 which are present in the ALDH-like group.
          Length = 432

 Score = 28.3 bits (64), Expect = 8.5
 Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 18/56 (32%)

Query: 55  GATNVGKEVI------LSRI--------PVVVGQSISDADLDHAVKNIYAMGYFSN 96
           G+T VGK ++      L R+        P++V     DADLD AVK     G F N
Sbjct: 183 GSTAVGKAIMRAAAENLKRVTLELGGKSPLIVF---DDADLDAAVKGA-VFGAFGN 234


>gnl|CDD|31450 COG1258, COG1258, Predicted pseudouridylate synthase [Translation,
           ribosomal structure and biogenesis].
          Length = 398

 Score = 28.3 bits (63), Expect = 8.9
 Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 7/62 (11%)

Query: 316 PQEIKESSEKISKYF--FSGERPFVRVKTRINRDFAKRIVD-IEYLIDQGSPLYVKRIEI 372
           P+E+KE+  +I + F    GE     +K   NR+  KR+        D  +P  V  +++
Sbjct: 98  PEEVKEAESEIWEEFGIGYGES----IKHEFNREVGKRLASKTGKEPDFDNPDIVIVVDL 153

Query: 373 EG 374
           E 
Sbjct: 154 ET 155


>gnl|CDD|30564 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 464

 Score = 28.3 bits (63), Expect = 9.4
 Identities = 18/78 (23%), Positives = 30/78 (38%), Gaps = 7/78 (8%)

Query: 676 VDKKYAIGGKIYSSASAAVSFPMPLVPERAGLRGAFFVDSATLYANHVALGADKLEGND- 734
           ++K YA     Y +    V F +    +   L G   ++     A  V +  +K    D 
Sbjct: 129 IEKGYA-----YVADDGDVYFDVSKFKDYGKLSGRDSLEELQAGA-RVEVDEEKRNPLDF 182

Query: 735 SFWRVSTGVEIMWNSPLG 752
             W+ +   E  W+SP G
Sbjct: 183 VLWKAAKPGEPSWDSPWG 200


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.320    0.138    0.390 

Gapped
Lambda     K      H
   0.267   0.0771    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 9,388,792
Number of extensions: 520125
Number of successful extensions: 1234
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1195
Number of HSP's successfully gapped: 39
Length of query: 781
Length of database: 6,263,737
Length adjustment: 101
Effective length of query: 680
Effective length of database: 4,081,228
Effective search space: 2775235040
Effective search space used: 2775235040
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: 61 (27.2 bits)