RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

Query= gi|254780129|ref|YP_003064542.1| hypothetical protein
CLIBASIA_00040 [Candidatus Liberibacter asiaticus str. psy62]
         (220 letters)



>gnl|CDD|128763 smart00487, DEXDc, DEAD-like helicases superfamily. 
          Length = 201

 Score = 76.4 bits (188), Expect = 6e-15
 Identities = 42/177 (23%), Positives = 70/177 (39%), Gaps = 14/177 (7%)

Query: 5   LKPHQIVMVNWLLSHDR-CALWASMGSGKT-VSVLFALSTIKILDPRPVLIIAPLRVAQY 62
           L+P+Q   +  LLS  R   L A  GSGKT  ++L AL  +K    + VL++ P R    
Sbjct: 9   LRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGKGKRVLVLVPTRELAE 68

Query: 63  VWKDEVERWSAFSDMTVSSLIGS---ERQRIKALNTPAHLYIINFENIP-WLVKMKLDHW 118
            W +E+++      + V  L G      Q  K  +    + +     +   L    L+  
Sbjct: 69  QWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDLLELS 128

Query: 119 DFATIVVDES--TKLKSFRTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDLW 173
           +   +++DE+       F       Q   L K+    V+  + L+ TP       L 
Sbjct: 129 NVDLVILDEAHRLLDGGFG-----DQLEKLLKLLPKNVQLLL-LSATPPEEIENLLE 179


>gnl|CDD|162193 TIGR01078, arcA, arginine deiminase.  Arginine deiminase is the
           first enzyme of the arginine deiminase pathway of
           arginine degradation.
          Length = 405

 Score = 31.6 bits (72), Expect = 0.16
 Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 4/45 (8%)

Query: 84  GSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFATIVVDES 128
           G E + +    TP++L  + F++IPW+   + +H  FA  + D  
Sbjct: 17  GRELENL----TPSNLDELLFDDIPWVEDAQKEHDQFANTLRDNG 57


>gnl|CDD|178452 PLN02861, PLN02861, long-chain-fatty-acid-CoA ligase.
          Length = 660

 Score = 31.0 bits (70), Expect = 0.23
 Identities = 14/38 (36%), Positives = 19/38 (50%)

Query: 166 PNGLIDLWGQIWFLDKGKRLGLSFKSFVERWFHTQQVG 203
           P G I L G   F    KR  L+ +  ++ WFHT  +G
Sbjct: 464 PRGEICLRGNTLFSGYHKRQDLTEEVLIDGWFHTGDIG 501


>gnl|CDD|178687 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
           chain; Provisional.
          Length = 1033

 Score = 29.0 bits (65), Expect = 0.86
 Identities = 47/195 (24%), Positives = 84/195 (43%), Gaps = 40/195 (20%)

Query: 5   LKPHQIVMVNWLL---SHDRCALWA-SMGSGKTVSVLFALSTIKIL----DPR----PVL 52
           ++ +Q+  +NWL+    +    + A  MG GKT      L TI +L    + R    P +
Sbjct: 170 MRDYQLAGLNWLIRLYENGINGILADEMGLGKT------LQTISLLGYLHEYRGITGPHM 223

Query: 53  IIAPLRVAQYVWKDEVERWSAFSDMTVSSLIGS--ERQRIKALNTPAHLYIINFENIPWL 110
           ++AP +     W +E+ R+     +      G+  ER   +     A  + +   +    
Sbjct: 224 VVAP-KSTLGNWMNEIRRFCPV--LRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMA 280

Query: 111 VK----MKLDHWDFATIVVDESTKLKSFRTHQGTKQTRALGKVA--FSKVKRFIELTGTP 164
           +K    +K   W +  I++DE+ ++K+        +   L K    FS   R + +TGTP
Sbjct: 281 IKEKTALKRFSWRY--IIIDEAHRIKN--------ENSLLSKTMRLFSTNYRLL-ITGTP 329

Query: 165 SPNGLIDLWGQIWFL 179
             N L +LW  + FL
Sbjct: 330 LQNNLHELWALLNFL 344


>gnl|CDD|179290 PRK01388, PRK01388, arginine deiminase; Provisional.
          Length = 406

 Score = 28.6 bits (65), Expect = 1.2
 Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 4/40 (10%)

Query: 84  GSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWDFATI 123
           G E +R+    TP++   + F+++PW+ + + +H  FA  
Sbjct: 24  GLELERL----TPSNCDELLFDDVPWVERAQKEHDAFAQT 59


>gnl|CDD|184388 PRK13909, PRK13909, putative recombination protein RecB;
          Provisional.
          Length = 910

 Score = 28.4 bits (64), Expect = 1.3
 Identities = 13/19 (68%), Positives = 13/19 (68%), Gaps = 4/19 (21%)

Query: 23 ALWASMGSGKTVSVLFALS 41
          AL AS GSGKT    FALS
Sbjct: 2  ALKASAGSGKT----FALS 16


>gnl|CDD|169949 PRK09536, btuD, corrinoid ABC transporter ATPase; Reviewed.
          Length = 402

 Score = 28.7 bits (64), Expect = 1.4
 Identities = 10/19 (52%), Positives = 14/19 (73%)

Query: 72  SAFSDMTVSSLIGSERQRI 90
           + F+D  V+SL G ERQR+
Sbjct: 130 AQFADRPVTSLSGGERQRV 148


>gnl|CDD|140243 PTZ00216, PTZ00216, acyl-CoA synthetase; Provisional.
          Length = 700

 Score = 28.4 bits (64), Expect = 1.5
 Identities = 27/65 (41%), Positives = 31/65 (47%), Gaps = 13/65 (20%)

Query: 161 TGTPSPNGLIDLWGQIWFLDKG--KRLGLSFKSFVER-WFHTQQVGSS--------IGAV 209
           T TP P G I L G   FL KG  K+  L+ +   E  WFHT  VGS         IG V
Sbjct: 501 TDTPEPRGEILLRGP--FLFKGYYKQEELTREVLDEDGWFHTGDVGSIAANGTLRIIGRV 558

Query: 210 KHIPK 214
           K + K
Sbjct: 559 KALAK 563


>gnl|CDD|181290 PRK08206, PRK08206, diaminopropionate ammonia-lyase; Provisional.
          Length = 399

 Score = 27.5 bits (62), Expect = 3.1
 Identities = 14/65 (21%), Positives = 21/65 (32%), Gaps = 9/65 (13%)

Query: 135 RTHQGTKQTRALGKVAFSKVKRFIELTGTPSPNGLIDL--------WGQIWFLDKGKRLG 186
                      L +    K + F +     +P  L+ L         G I   D+  R G
Sbjct: 13  NKPYDGADLPLLSQEEAKKARAFHQSFPGYAPTPLVALPDLAAELGVGSILVKDESYRFG 72

Query: 187 L-SFK 190
           L +FK
Sbjct: 73  LNAFK 77


>gnl|CDD|161871 TIGR00420, trmU, tRNA
           (5-methylaminomethyl-2-thiouridylate)-methyltransferase.
            tRNA
           (5-methylaminomethyl-2-thiouridylate)-methyltransferase
           (trmU, asuE, or mnmA) is involved in the biosynthesis of
           the modified nucleoside
           5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in
           the wobble position of some tRNAs. This enzyme appears
           not to occur in the Archaea.
          Length = 352

 Score = 27.4 bits (61), Expect = 3.3
 Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 8/54 (14%)

Query: 152 SKVKRFIELTGTPSPNGLIDLWGQ--------IWFLDKGKRLGLSFKSFVERWF 197
            K + F++      P  +I + GQ        +WF   G+R GL      E WF
Sbjct: 201 RKFRDFLKKYLPVKPGVIITVDGQSVIGEHDGLWFYTIGQRKGLGIGGAAEPWF 254


>gnl|CDD|132298 TIGR03254, oxalate_oxc, oxalyl-CoA decarboxylase.  In a number of
           bacteria, including Oxalobacter formigenes from the
           human gut, a two-gene operon of oxc (oxalyl-CoA
           decarboxylase) and frc (formyl-CoA transferase) encodes
           a system for degrading and therefore detoxifying
           oxalate. Members of this family are the thiamine
           pyrophosphate (TPP)-containing enzyme oxalyl-CoA
           decarboxylase.
          Length = 554

 Score = 27.1 bits (60), Expect = 3.9
 Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 5/29 (17%)

Query: 3   LVLKPHQIVMV-----NWLLSHDRCALWA 26
             L    +VM+     NWLLSH +  LW 
Sbjct: 261 FALAEADVVMLVGARLNWLLSHGKGKLWG 289


>gnl|CDD|166255 PLN02614, PLN02614, long-chain acyl-CoA synthetase.
          Length = 666

 Score = 26.9 bits (59), Expect = 4.3
 Identities = 13/39 (33%), Positives = 20/39 (51%)

Query: 165 SPNGLIDLWGQIWFLDKGKRLGLSFKSFVERWFHTQQVG 203
           +P G I + G+  F    KR  L+ +  ++ W HT  VG
Sbjct: 466 TPRGEICIRGKTLFSGYYKREDLTKEVLIDGWLHTGDVG 504


>gnl|CDD|163585 TIGR03873, F420-0_ABC_ATP, proposed F420-0 ABC transporter,
           ATP-binding protein.  This small clade of ABC-type
           transporter ATP-binding protein components is found as a
           three gene cassette along with a periplasmic
           substrate-binding protein (TIGR03868) and a permease
           (TIGR03869). The organisms containing this cassette are
           all Actinobacteria and all contain numerous genes
           requiring the coenzyme F420. This model was defined
           based on five such organisms, four of which are lacking
           all F420 biosynthetic capability save the final
           side-chain polyglutamate attachment step (via the gene
           cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and
           marine actinobacterium PHSC20C1 this cassette is in an
           apparent operon with the cofE gene and, in PHSC20C1,
           also with a F420-dependent glucose-6-phosphate
           dehydrogenase (TIGR03554). Based on these observations
           we propose that this ATP-binding protein is a component
           of an F420-0 (that is, F420 lacking only the
           polyglutamate tail) transporter.
          Length = 256

 Score = 26.7 bits (59), Expect = 4.5
 Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 3/35 (8%)

Query: 72  SAFSDMTVSSLIGSERQRI---KALNTPAHLYIIN 103
           S  +D  +S+L G ERQR+   +AL     L +++
Sbjct: 128 SHLADRDMSTLSGGERQRVHVARALAQEPKLLLLD 162


>gnl|CDD|129256 TIGR00152, TIGR00152, dephospho-CoA kinase.  This model produces
           scores in the range of 0-25 bits against adenylate,
           guanylate, uridine, and thymidylate kinases.
          Length = 188

 Score = 26.6 bits (59), Expect = 5.6
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 60  AQYVWKDEVERWSAFSDMTVSSLIGSERQRIKALNTPAHLYIINFENIPWLVKMKLDHWD 119
            + V+ D  E     +++    LI    +++ A       Y++   ++P L + KL    
Sbjct: 69  GERVFNDPEEL-KWLNNLL-HPLIREWMKKLLAQFQSKLAYVL--LDVPLLFENKLRSLC 124

Query: 120 FATIVVDESTKLKSFRTHQGTKQTRA 145
              IVVD S +L+  R  Q    T  
Sbjct: 125 DRVIVVDVSPQLQLERLMQRDNLTEE 150


>gnl|CDD|150299 pfam09586, YfhO, Bacterial membrane protein YfhO.  This protein is
           a conserved membrane protein. The yfhO gene is
           transcribed in Difco sporulation medium and the
           transcription is affected by the YvrGHb two-component
           system. Some members of this family have been annotated
           as glycosyl transferases of the PMT family.
          Length = 835

 Score = 26.4 bits (59), Expect = 6.4
 Identities = 8/26 (30%), Positives = 14/26 (53%)

Query: 59  VAQYVWKDEVERWSAFSDMTVSSLIG 84
           + + ++KD   RW  F    +SSL+ 
Sbjct: 198 LYRLIFKDIKSRWKQFLRFIISSLLS 223


>gnl|CDD|161832 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
           family.  Members of this family are assumed to differ
           from each other in DNA site specificity.
          Length = 667

 Score = 26.2 bits (58), Expect = 6.8
 Identities = 17/66 (25%), Positives = 25/66 (37%), Gaps = 14/66 (21%)

Query: 3   LVLKPHQIVMVNWLL--------------SHDRCALWASMGSGKTVSVLFALSTIKILDP 48
           LV KP+Q  M    +                    +W + GSGKT+++LFA      L  
Sbjct: 233 LVTKPYQRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALELLK 292

Query: 49  RPVLII 54
            P +  
Sbjct: 293 NPKVFF 298


>gnl|CDD|183924 PRK13258, PRK13258, 7-cyano-7-deazaguanine reductase; Provisional.
          Length = 115

 Score = 26.3 bits (59), Expect = 7.2
 Identities = 14/32 (43%), Positives = 15/32 (46%), Gaps = 12/32 (37%)

Query: 119 DFATIVVD--------ESTKLK----SFRTHQ 138
           DFATIV+D        E   LK    SFR H 
Sbjct: 36  DFATIVIDYIPDKKCVELKSLKLYLFSFRNHG 67


>gnl|CDD|149650 pfam08664, YcbB, YcbB domain.  YcbB is a DNA-binding domain.
          Length = 133

 Score = 26.1 bits (58), Expect = 7.4
 Identities = 10/24 (41%), Positives = 13/24 (54%), Gaps = 5/24 (20%)

Query: 88  QRI-----KALNTPAHLYIINFEN 106
           QRI     KALN  A L + ++ N
Sbjct: 68  QRIRRAIKKALNNLASLGLEDYSN 91


>gnl|CDD|163398 TIGR03686, pupylate_PafA, proteasome accessory factor PafA.
           Members of this family are PafA (proteasome accessory
           factor A), a protein shown to regulate steady-state
           levels of certain proteasome targets in Mycobacterium
           tuberculosis. Iyer, et al (2008) suggest that PafA is
           the ligase for Pup, a ubiquitin analog attached to an
           epsilon-amino group of a Lys side-chain to direct the
           target to the proteasome.
          Length = 453

 Score = 25.9 bits (57), Expect = 7.7
 Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 6/40 (15%)

Query: 141 KQTRALG--KVAFSKVKRFIELTGTPSPNGLI----DLWG 174
           +   AL   +  + KVK F+E  G  +PN  I    DLWG
Sbjct: 269 RSASALEIQREYYEKVKAFLETRGDGTPNAEIPRVVDLWG 308


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.323    0.136    0.426 

Gapped
Lambda     K      H
   0.267   0.0636    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,612,891
Number of extensions: 220968
Number of successful extensions: 355
Number of sequences better than 10.0: 1
Number of HSP's gapped: 353
Number of HSP's successfully gapped: 23
Length of query: 220
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 130
Effective length of database: 4,049,753
Effective search space: 526467890
Effective search space used: 526467890
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.2 bits)