RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780689|ref|YP_003065102.1| flagellar motor switch protein
G [Candidatus Liberibacter asiaticus str. psy62]
         (345 letters)



>gnl|CDD|31725 COG1536, FliG, Flagellar motor switch protein [Cell motility and
           secretion].
          Length = 339

 Score =  186 bits (474), Expect = 7e-48
 Identities = 85/325 (26%), Positives = 163/325 (50%), Gaps = 4/325 (1%)

Query: 21  SLTQKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQ 80
            LT  +KA  +LLA+ ++++ ++L+H +  E++ +      L  +SPEE E +++EFE  
Sbjct: 10  PLTGTEKAAILLLALGEEIAAEVLKHLSPEEIQRLSTEMATLKTVSPEEKEQVLEEFEEL 69

Query: 81  FIAGIGLTENSKNIESILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFL 140
           F    G+ + +      L E     E  + L +         S +D L++ DP  +AD +
Sbjct: 70  FTEQAGINKGADEYARELLEKALGEEKAESLLERITGSAIQTSPFDLLRKLDPSQLADLI 129

Query: 141 SKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEKCI--- 197
             EHPQT A +LS +PP   A +L   P ++ AD++KR   L  +SP     +E  +   
Sbjct: 130 KNEHPQTIALILSYLPPDQAAEILSTLPEELRADVVKRIATLEGVSPEALAELENVLEKK 189

Query: 198 VEMLPQSNSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVFLFDDLIT 257
           ++ L   + +   G +  A ++N L++     +L SL+E   E  ++++ K+F+F+D++ 
Sbjct: 190 LQSLVNEDYSKLGGIKAAAEILNLLDRGTEKTILESLEEEDPELAEEIKEKMFVFEDIVL 249

Query: 258 LSSHDLSIVFNNISLEVLGKALHGTSIETQNAILHCLSNRQRKIIEENIVLNDSSIAPRE 317
           L    +  +   +  E L  AL G S E +  IL  +S R  ++++E +      +   +
Sbjct: 250 LDDRSIQRLLREVDKEDLAIALKGASEELREKILSNMSKRAAEMLKEELE-FLGPVRLSD 308

Query: 318 VAMARRSIVQEAISLLKTNKIELSN 342
           V  A+++I+     L ++ +I +  
Sbjct: 309 VETAQKAILNIVRRLAESGEIVIKR 333


>gnl|CDD|145059 pfam01706, FliG_C, FliG C-terminal domain.  FliG is a component of
           the flageller rotor, present in about 25 copies per
           flagellum. This domain functions specifically in motor
           rotation.
          Length = 110

 Score = 71.4 bits (176), Expect = 4e-13
 Identities = 31/110 (28%), Positives = 55/110 (50%), Gaps = 1/110 (0%)

Query: 231 LTSLQEVSKEAFDKVRPKVFLFDDLITLSSHDLSIVFNNISLEVLGKALHGTSIETQNAI 290
           L +L+E   E  +++R  +F F+DL+ L   D+  +   +  +VL  AL G S E +  I
Sbjct: 1   LEALEERDPELAEEIRKLMFTFEDLVRLDDRDIQRLLREVDKDVLALALKGASEELREKI 60

Query: 291 LHCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIVQEAISLLKTNKIEL 340
           L  +S R  +++ E +      +   +V  A++ IV     L +  +IEL
Sbjct: 61  LSNMSKRAAEMLREELEALG-PVRLSDVEAAQKEIVAIVRELAEEGEIEL 109


>gnl|CDD|32420 COG2239, MgtE, Mg/Co/Ni transporter MgtE (contains CBS domain)
           [Inorganic ion transport and metabolism].
          Length = 451

 Score = 33.3 bits (76), Expect = 0.11
 Identities = 24/127 (18%), Positives = 52/127 (40%), Gaps = 11/127 (8%)

Query: 117 SQENNNSIWDHLKETDPGVIADFLSKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHADIM 176
              +  ++ D L++ D  V+   L++ HP   A +L  +P      V    P +  A++ 
Sbjct: 5   QLLDIENLIDLLEDKDLSVLRKLLARLHPADVAEILEELPGRERVVVWRLLPKEDAAEV- 63

Query: 177 KRTVNLPKISPYIQKTIEKCIVEMLPQSNSNTSTG--PEKVANLINELEKPQVDKLLTSL 234
                L ++   +++ I   I  +  +  +        +  A+L++EL     D+LL+ L
Sbjct: 64  -----LGELDDEVREEI---IEALSDEELAAAIEELDIDDAADLLDELPDEVRDELLSLL 115

Query: 235 QEVSKEA 241
               +  
Sbjct: 116 DPEERAR 122


>gnl|CDD|36330 KOG1114, KOG1114, KOG1114, Tripeptidyl peptidase II
            [Posttranslational modification, protein turnover,
            chaperones].
          Length = 1304

 Score = 32.6 bits (74), Expect = 0.18
 Identities = 17/71 (23%), Positives = 29/71 (40%), Gaps = 5/71 (7%)

Query: 68   EELEDIIDEFESQFIAGIGLTENSKNIESILEE-----GLEQNELEKLLNKSDISQENNN 122
            EE  + I + +  +++ +   E  K    +         L +  L KL+ KSD  +E N 
Sbjct: 1072 EECAEAIRDLQVSWLSKLADEEAEKIYNYLKSSYPDYLPLLEVRLAKLMQKSDAVKETNK 1131

Query: 123  SIWDHLKETDP 133
             I + L   D 
Sbjct: 1132 KIEEILSAADS 1142


>gnl|CDD|37150 KOG1939, KOG1939, KOG1939, Oxoprolinase [Amino acid transport and
            metabolism].
          Length = 1247

 Score = 30.3 bits (68), Expect = 0.74
 Identities = 37/155 (23%), Positives = 67/155 (43%), Gaps = 24/155 (15%)

Query: 191  KTIEKCIVEMLPQSNSNTSTGPEKVANLINELEKPQVDKLLTSLQEVSKEAFDKVRPKVF 250
            + +   I ++  Q  +N   G + V +LI E     V   +  +Q  ++ A  ++  KV 
Sbjct: 906  RNLSDNISDLKAQIAANHK-GIQLVTSLIEEYGLDVVQAYMKHIQNNAELAVREMLKKVG 964

Query: 251  LFDDLITLSSHDLSIVFNNISLEVL-----GKAL---HGTSIE-----------TQNAIL 291
                  TLS+ D     + I L+V      G+A+    GT  E           T +A++
Sbjct: 965  RRVLEKTLSAEDFMDDGSPIKLKVTIDPEKGEAIFDFTGTGPEVYGNCNAPEAVTYSAVI 1024

Query: 292  HCLSNRQRKIIEENIVLNDSSIAPREVAMARRSIV 326
            +CL    R ++ E+I LN   +AP ++ +   S +
Sbjct: 1025 YCL----RCLVNEDIPLNQGCLAPIQIKIPAGSFL 1055


>gnl|CDD|146204 pfam03448, MgtE_N, MgtE intracellular N domain.  This domain is
           found at the N-terminus of eubacterial magnesium
           transporters of the MgtE family pfam01769. This domain
           is an intracellular domain that has an alpha-helical
           structure. The crystal structure of the MgtE transporter
           shows two of 5 magnesium ions are in the interface
           between the N domain and the CBS domains. In the absence
           of magnesium there is a large shift between the N and
           CBS domains.
          Length = 102

 Score = 29.4 bits (67), Expect = 1.6
 Identities = 23/105 (21%), Positives = 45/105 (42%), Gaps = 13/105 (12%)

Query: 144 HPQTTAYVLSMMPPSIGASVLLRFPNKIHADIMKRTVNLPKISPYIQKTIEKCIVEMLPQ 203
           HP   A +L  +PP    ++L   P +  A++      L ++   +Q  +    +E LP 
Sbjct: 2   HPADIAELLEELPPEERLALLRLLPPERAAEV------LEELDEDVQAEL----LEALPP 51

Query: 204 SNSNTSTG---PEKVANLINELEKPQVDKLLTSLQEVSKEAFDKV 245
                      P+  A+L+ EL +   ++LL+ L    +E   ++
Sbjct: 52  EELAELLEELDPDDAADLLEELPEEVREELLSLLDPEEREEIREL 96



 Score = 28.3 bits (64), Expect = 3.6
 Identities = 12/54 (22%), Positives = 27/54 (50%), Gaps = 6/54 (11%)

Query: 25 KDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFE 78
           ++A  +L  +++ V  +LL      EL E++       E+ P++  D+++E  
Sbjct: 27 PERAAEVLEELDEDVQAELLEALPPEELAELLE------ELDPDDAADLLEELP 74


>gnl|CDD|33843 COG4086, COG4086, Predicted secreted protein [Function unknown].
          Length = 299

 Score = 29.2 bits (65), Expect = 1.9
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 5/45 (11%)

Query: 50  AELKEIVASAKLLPEISPEELEDIIDEFESQFIAGIGLTENSKNI 94
           AE+KE VA  K+     P ++  ++D+  + +   + LT+   N 
Sbjct: 198 AEVKEEVAKQKVD---DPADIRKVVDDVANNY--NVNLTDTQVNQ 237


>gnl|CDD|119333 cd06563, GH20_chitobiase-like, The chitobiase of Serratia
           marcescens is a beta-N-1,4-acetylhexosaminidase with a
           glycosyl hydrolase family 20 (GH20) domain that
           hydrolyzes the beta-1,4-glycosidic linkages in oligomers
           derived from chitin.  Chitin is degraded by a two step
           process: i) a chitinase hydrolyzes the chitin to
           oligosaccharides and disaccharides such as
           di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase
           then further degrades these oligomers into monomers.
           This GH20 domain family includes an
           N-acetylglucosamidase (GlcNAcase A) from
           Pseudoalteromonas piscicida and an
           N-acetylhexosaminidase (SpHex) from Streptomyces
           plicatus. SpHex lacks the C-terminal PKD (polycystic
           kidney disease I)-like domain found in the chitobiases.
           The GH20 hexosaminidases are thought to act via a
           catalytic mechanism in which the catalytic nucleophile
           is not provided by solvent or the enzyme, but by the
           substrate itself..
          Length = 357

 Score = 29.1 bits (66), Expect = 2.1
 Identities = 10/25 (40%), Positives = 15/25 (60%), Gaps = 5/25 (20%)

Query: 46  HFTHAELKEIVASAK-----LLPEI 65
            +T  E++EIVA A      ++PEI
Sbjct: 82  FYTQEEIREIVAYAAERGITVIPEI 106


>gnl|CDD|133299 cd01899, Ygr210, Ygr210 subfamily.  Ygr210 is a member of Obg-like
           family and present in archaea and fungi.  They are
           characterized by a distinct glycine-rich motif
           immediately following the Walker B motif.  The Ygr210
           and YyaF/YchF subfamilies appear to form one major
           branch of the Obg-like family.  Among eukaryotes, the
           Ygr210 subfamily is represented only in fungi.  These
           fungal proteins form a tight cluster with their archaeal
           orthologs, which suggests the possibility of horizontal
           transfer from archaea to fungi.
          Length = 318

 Score = 28.3 bits (64), Expect = 3.2
 Identities = 22/85 (25%), Positives = 32/85 (37%), Gaps = 24/85 (28%)

Query: 74  IDEFESQFIAGIGLTENSKNIESILEEGLE--------QNELEKL--------------L 111
           I E  S+ ++G G+ E  K++   LEE             +L +L               
Sbjct: 164 IVEALSEQLSGFGVNE--KDVIEALEELELPEDLSKWTDEDLLRLARALRKRSKPMVIAA 221

Query: 112 NKSDISQENNNSIWDHLKETDPGVI 136
           NK+DI    NN     LK  D  V+
Sbjct: 222 NKADIPDAENNISKLRLKYPDEIVV 246


>gnl|CDD|144739 pfam01255, Prenyltransf, Putative undecaprenyl diphosphate
           synthase.  Previously known as uncharacterized protein
           family UPF0015, a single member of this family has been
           identified as an undecaprenyl diphosphate synthase.
          Length = 222

 Score = 27.9 bits (63), Expect = 4.2
 Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 3/45 (6%)

Query: 36  EKQVSGKLLRHFTHAELKEIVASAKLLPEISPEELEDIIDEFESQ 80
           EK++S  LL    +AEL     +  L P+ + E+L   I +++S+
Sbjct: 175 EKRLSNFLLWQSAYAEL---YFTDTLWPDFTKEDLLRAIRDYQSR 216


>gnl|CDD|73400 cd04738, DHOD_2_like, Dihydroorotate dehydrogenase (DHOD) class 2.
           DHOD catalyzes the oxidation of (S)-dihydroorotate to
           orotate. This is the fourth step and the only redox
           reaction in the de novo biosynthesis of UMP, the
           precursor of all pyrimidine nucleotides. DHOD requires
           FMN as co-factor. DHOD divides into class 1 and class 2
           based on their amino acid sequences, their cellular
           location and their natural electron acceptor used to
           reoxidize the flavin group. Members of class 1 are
           cytosolic enzymes and multimers, while class 2 enzymes
           are membrane associated, monomeric and use respiratory
           quinones as their physiological electron acceptors..
          Length = 327

 Score = 27.8 bits (62), Expect = 4.9
 Identities = 13/29 (44%), Positives = 17/29 (58%)

Query: 60  KLLPEISPEELEDIIDEFESQFIAGIGLT 88
           K+ P++S EELEDI D      + GI  T
Sbjct: 208 KIAPDLSDEELEDIADVALEHGVDGIIAT 236


>gnl|CDD|145673 pfam02637, GatB_Yqey, GatB domain.  This domain is found in GatB.
           It is about 140 amino acid residues long. This domain is
           found at the C terminus of GatB, which transamidates
           Glu-tRNA to Gln-tRNA.
          Length = 148

 Score = 27.5 bits (62), Expect = 5.4
 Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 14/72 (19%)

Query: 65  ISPEELEDIIDEFESQFIAG-------IGLTENSKNIESILEE-GLEQ----NELEKLLN 112
           ++PE L ++I   +   I+G         L EN K+ E I+EE GL Q     ELEK+++
Sbjct: 40  LTPEHLAELIKLIDEGTISGKIAKEVLEELLENGKSPEEIVEEKGLVQISDEEELEKIVD 99

Query: 113 KSDISQENNNSI 124
             ++  EN  ++
Sbjct: 100 --EVIAENPKAV 109


>gnl|CDD|163687 cd08056, MPN_PRP8, Mpr1p, Pad1p N-terminal (MPN) domains without
           isopeptidase activity found in splicing factor Prp8.
           Members of this family are found in pre-mRNA-processing
           factor 8 (Prp8) which is a critical splicing factor,
           interacting with several other spliceosomal proteins,
           snRNAs, and the pre-mRNA, thus organizing and
           stabilizing the spliceosome catalytic core. Prp8 is one
           of the largest and most highly conserved of nuclear
           proteins, occupying a central  position in the catalytic
           core of the spliceosome. Its C-terminal domain exhibits
           a JAB1/MPN-like core similar to deubiquitinating
           enzymes, but does not show catalytic isopeptidase
           activity, possibly because the putative isopeptidase
           center is covered by insertions and terminal appendices
           that are grafted onto this core, thus impairing the
           metal binding site. It is proposed that this domain is a
           protein interaction domain instead of a Zn(2+)-dependent
           metalloenzyme as proposed for some MPN proteins. The
           DEAD-box protein Brr2 and the GTPase Snu114 bind to the
           Prp8 C-terminus, a region where mutations in human Prp8
           (hPrp8) cause a severe form of the genetic disorder
           retinitis pigmentosa, RP13, which leads to progressive
           photoreceptor degeneration in the retina and eventual
           blindness. At the N-terminus of Prp8, there are several
           domains, including a highly variable nuclear
           localization signal (NLS) motif rich in prolines, a
           conserved RNA recognition motif (RRM), and U5 and U6
           snRNA binding sites.
          Length = 252

 Score = 27.6 bits (62), Expect = 5.4
 Identities = 29/137 (21%), Positives = 52/137 (37%), Gaps = 41/137 (29%)

Query: 76  EFESQFIAGIGLTENSKNI----ESILEEG----LEQNELEKLLNKSDI-SQENNNSIWD 126
           ++  + IA   L   +KNI    + I E G    L +N L+K ++ SD+ +Q        
Sbjct: 6   DWRVRAIAATNLHLRTKNIYVSSDDIKETGYTYILPKNLLKKFISISDLRTQ-------- 57

Query: 127 HLKETDPGVIADFL----SKEHPQTTAYVLSMMPPSIGASVLLRFPNKIHAD-------- 174
                    IA +L      ++PQ       ++ P +G    +  P ++           
Sbjct: 58  ---------IAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQLPQHEYLEDLEP 108

Query: 175 ---IMKRTVNLPKISPY 188
              I  +   LP++SP 
Sbjct: 109 LGWIHTQPNELPQLSPQ 125


>gnl|CDD|30898 COG0552, FtsY, Signal recognition particle GTPase [Intracellular
           trafficking and secretion].
          Length = 340

 Score = 27.5 bits (61), Expect = 5.4
 Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 2/63 (3%)

Query: 68  EELEDIIDEFESQFIAGIGLTENSKNIESILEEGLEQNELEKLLNKSDISQENNNSIWDH 127
           E L+  + + +  F  GI      K  E + E+ LE  ELE+LL ++D+  E    I + 
Sbjct: 35  ERLKQGLSKTKKNFGKGIKGLFLKKIKEKLDEDLLE--ELEELLIEADVGVETAEEIIEE 92

Query: 128 LKE 130
           L++
Sbjct: 93  LRK 95


>gnl|CDD|30955 COG0610, COG0610, Type I site-specific restriction-modification
           system, R (restriction) subunit and related helicases
           [Defense mechanisms].
          Length = 962

 Score = 27.3 bits (60), Expect = 6.9
 Identities = 16/129 (12%), Positives = 43/129 (33%), Gaps = 1/129 (0%)

Query: 24  QKDKATAILLAMEKQVSGKLLRHFTHAELKEIVASAKLLPEIS-PEELEDIIDEFESQFI 82
             ++    L  + K    K  +      +  +  + ++  + S   +L+DI  E E    
Sbjct: 751 TLEEEIQYLEDLLKARLEKDYQSKYLDLIDNLNDAREIKDKESKAIDLDDIDFELELIGK 810

Query: 83  AGIGLTENSKNIESILEEGLEQNELEKLLNKSDISQENNNSIWDHLKETDPGVIADFLSK 142
             I +    + +++  ++      L++L+ +       +      L E     I  + +K
Sbjct: 811 QEINIDYILELLQTFNDKNGAYESLKELIERIIKEWIEDLRQKKKLIERLIEAINQYRAK 870

Query: 143 EHPQTTAYV 151
           +        
Sbjct: 871 KLDTAEKLE 879


>gnl|CDD|36947 KOG1736, KOG1736, KOG1736, Glia maturation factor beta
          [Extracellular structures].
          Length = 143

 Score = 26.9 bits (59), Expect = 7.7
 Identities = 14/30 (46%), Positives = 19/30 (63%)

Query: 53 KEIVASAKLLPEISPEELEDIIDEFESQFI 82
           EIV   + L EISPEEL D + E + +F+
Sbjct: 42 YEIVLDEEELDEISPEELADELPERQPRFV 71


>gnl|CDD|153247 cd07985, LPLAT_GPAT, Lysophospholipid Acyltransferases (LPLATs) of
           Glycerophospholipid Biosynthesis: GPAT.
           Lysophospholipid acyltransferase (LPLAT) superfamily
           member: glycerol-3-phosphate 1-acyltransferase (GPAT,
           PlsB). LPLATs are acyltransferases of de novo and
           remodeling pathways of glycerophospholipid biosynthesis
           which catalyze the incorporation of an acyl group from
           either acylCoAs or acyl-acyl carrier proteins (acylACPs)
           into acceptors such as glycerol 3-phosphate,
           dihydroxyacetone phosphate or lyso-phosphatidic acid.
           This subgroup includes glycerol-3-phosphate
           1-acyltransferase (GPAT, PlsB).
          Length = 235

 Score = 27.0 bits (60), Expect = 7.7
 Identities = 10/21 (47%), Positives = 12/21 (57%)

Query: 126 DHLKETDPGVIADFLSKEHPQ 146
           +H  E DP VI+  L K HP 
Sbjct: 29  NHQTEADPAVISLLLEKTHPY 49


>gnl|CDD|111365 pfam02459, Adeno_terminal, Adenoviral DNA terminal protein.  This
           protein is covalently attached to the terminii of
           replicating DNA in vivo.
          Length = 548

 Score = 26.5 bits (59), Expect = 9.5
 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 8/35 (22%)

Query: 64  EISPEELEDIIDEFESQFIAGIGLTENSKNIESIL 98
           E+  EE E        QF++ I   ENS ++E IL
Sbjct: 471 ELDEEEQE--------QFLSDIAYRENSGDVEEIL 497


  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
   0.312    0.130    0.346 

Gapped
Lambda     K      H
   0.267   0.0732    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,819,403
Number of extensions: 197204
Number of successful extensions: 646
Number of sequences better than 10.0: 1
Number of HSP's gapped: 640
Number of HSP's successfully gapped: 41
Length of query: 345
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 250
Effective length of database: 4,210,882
Effective search space: 1052720500
Effective search space used: 1052720500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.1 bits)