RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780130|ref|YP_003064543.1| hypothetical protein
CLIBASIA_00045 [Candidatus Liberibacter asiaticus str. psy62]
         (205 letters)



>gnl|CDD|30899 COG0553, HepA, Superfamily II DNA/RNA helicases, SNF2 family
           [Transcription / DNA replication, recombination, and
           repair].
          Length = 866

 Score = 50.1 bits (118), Expect = 4e-07
 Identities = 31/105 (29%), Positives = 50/105 (47%), Gaps = 7/105 (6%)

Query: 100 TIQEWNEGKIPLLF-AHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQ 158
            I  +N  +   +F     + G GLNL    + ++ F  WW+     Q I+R    R  Q
Sbjct: 753 LIDRFNADEEEKVFLLSLKAGGLGLNLTGA-DTVILFDPWWNPAVELQAIDRA--HRIGQ 809

Query: 159 AGFKRAVFVYYLIAQNTIDELVLQRLRTKSTIQDLLLNALKKETI 203
              KR V VY LI + TI+E +L+    K  + D L++A  ++ +
Sbjct: 810 ---KRPVKVYRLITRGTIEEKILELQEKKQELLDSLIDAEGEKEL 851


>gnl|CDD|35611 KOG0390, KOG0390, KOG0390, DNA repair protein, SNF2 family
           [Replication, recombination and repair].
          Length = 776

 Score = 46.2 bits (109), Expect = 7e-06
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 6/86 (6%)

Query: 105 NEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRA 164
            E    +      + G GLNL  G + L+ F   W+    QQ + R       + G K+ 
Sbjct: 644 PESPSFVFLLSSKAGGEGLNL-IGASRLILFDPDWNPAVDQQAMARA-----WRDGQKKP 697

Query: 165 VFVYYLIAQNTIDELVLQRLRTKSTI 190
           V++Y L+A  TI+E + QR   K  +
Sbjct: 698 VYIYRLLATGTIEEKIYQRQTHKEGL 723


>gnl|CDD|35613 KOG0392, KOG0392, KOG0392, SNF2 family DNA-dependent ATPase
            domain-containing protein [Transcription].
          Length = 1549

 Score = 39.2 bits (91), Expect = 8e-04
 Identities = 36/144 (25%), Positives = 64/144 (44%), Gaps = 15/144 (10%)

Query: 55   KIKALEVIIEKANAAPIIVAYHFNSDLARLQKAFPQGRTLDKDPCTIQEWNEGK-IPLLF 113
            ++K++  ++EK     +   Y  +    RL  + P G         ++ +NE   I +L 
Sbjct: 1348 QLKSMLDLVEKD----LFKKYMPSVTYMRLDGSVPPGDRQK----IVERFNEDPTIDVLL 1399

Query: 114  AHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQ 173
                  G GLNL  G + +VF    W+     Q ++R       + G KR V VY LI +
Sbjct: 1400 LTTHVGGLGLNLT-GADTVVFVEHDWNPMRDLQAMDR-----AHRIGQKRVVNVYRLITR 1453

Query: 174  NTIDELVLQRLRTKSTIQDLLLNA 197
             T++E V+   + K  + + ++N 
Sbjct: 1454 GTLEEKVMGLQKFKMNVANTVINQ 1477


>gnl|CDD|36218 KOG1000, KOG1000, KOG1000, Chromatin remodeling protein
           HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure
           and dynamics].
          Length = 689

 Score = 39.3 bits (91), Expect = 8e-04
 Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 12/73 (16%)

Query: 118 SCGHGLNLQYGGNILVFFSLWWD---LEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQN 174
           + G GL L     + VF  L W+   L + +    RIG           +VFV YL+A+ 
Sbjct: 553 AAGVGLTLTAASVV-VFAELHWNPGVLLQAEDRAHRIGQKS--------SVFVQYLVAKG 603

Query: 175 TIDELVLQRLRTK 187
           T D+ +   L+ K
Sbjct: 604 TADDYMWPMLQQK 616


>gnl|CDD|39640 KOG4439, KOG4439, KOG4439, RNA polymerase II transcription
           termination factor TTF2/lodestar, DEAD-box superfamily
           [Transcription, Replication, recombination and repair].
          Length = 901

 Score = 36.6 bits (84), Expect = 0.004
 Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 7/91 (7%)

Query: 105 NEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRA 164
             G   +L +  A  G GLNL  G N L+   L W+    QQ  +RI      + G K+ 
Sbjct: 796 KGGARVMLLSLTAG-GVGLNL-IGANHLILVDLHWNPALEQQACDRI-----YRMGQKKD 848

Query: 165 VFVYYLIAQNTIDELVLQRLRTKSTIQDLLL 195
           VF++ L+ + T+++ V      K  +   +L
Sbjct: 849 VFIHRLMCKGTVEQRVKSLQDKKLDLAKGVL 879


>gnl|CDD|36219 KOG1001, KOG1001, KOG1001, Helicase-like transcription factor
           HLTF/DNA helicase RAD5, DEAD-box superfamily
           [Transcription, Replication, recombination and repair].
          Length = 674

 Score = 35.4 bits (81), Expect = 0.013
 Identities = 32/197 (16%), Positives = 65/197 (32%), Gaps = 28/197 (14%)

Query: 4   YHKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVY----YDEEKHWKEVHDEKIKAL 59
            H F  E       ++I+   +A   +    L    +          +       KI A 
Sbjct: 472 GHDFCVECLK----KSIQQSENAPCPLCRNVLKEKKLLSANPLPSIINDLLPESSKIYAF 527

Query: 60  EVIIE--KANAAP-IIVAYHFNSDLARLQ----------KAFPQGRTLDKDPCTIQEWNE 106
             I++  + +  P I++       LA +             +     +     +  ++  
Sbjct: 528 LKILQAKEMSEQPKIVIFSQLIWGLALVCLRLFFKGFVFLRYDGEMLMKIRTKSFTDFPC 587

Query: 107 GKIPLLFAHPASCGH-GLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAV 165
             +          G  GLNL    ++L+    WW+    +Q I+R     Q      + V
Sbjct: 588 DPLVTALLMSLKAGKVGLNLTAASHVLLM-DPWWNPAVEEQAIDRAHRIGQT-----KPV 641

Query: 166 FVYYLIAQNTIDELVLQ 182
            V   I ++T++E +L+
Sbjct: 642 KVSRFIIKDTVEERILK 658


>gnl|CDD|144016 pfam00271, Helicase_C, Helicase conserved C-terminal domain.  The
           Prosite family is restricted to DEAD/H helicases,
           whereas this domain family is found in a wide variety of
           helicases and helicase related proteins. It may be that
           this is not an autonomously folding unit, but an
           integral part of the helicase.
          Length = 78

 Score = 34.8 bits (81), Expect = 0.018
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 2/53 (3%)

Query: 100 TIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIG 152
            ++++  GK  +L A     G G++L    N+++ + L W+   + Q I R G
Sbjct: 25  ILEDFRNGKSKVLVA-TDVAGRGIDLP-DVNVVINYDLPWNPASYIQRIGRAG 75


>gnl|CDD|28960 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
           with DEXDc-, DEAD-, and DEAH-box proteins, yeast
           initiation factor 4A, Ski2p, and Hepatitis C virus NS3
           helicases; this domain is found in a wide variety of
           helicases and helicase related proteins; may not be an
           autonomously folding unit, but an integral part of the
           helicase; 4 helicase superfamilies at present according
           to the organization of their signature motifs; all
           helicases share the ability to unwind nucleic acid
           duplexes with a distinct directional polarity; they
           utilize the free energy from nucleoside triphosphate
           hydrolysis to fuel their translocation along DNA,
           unwinding the duplex in the process.
          Length = 131

 Score = 34.1 bits (78), Expect = 0.027
 Identities = 25/137 (18%), Positives = 57/137 (41%), Gaps = 21/137 (15%)

Query: 45  EKHWKEVHDEKIKALEVIIEKANAAP--IIVAYHFNSDLARLQKAFP-----------QG 91
           +++   V DEK++AL  ++++       +++       L  L +               G
Sbjct: 3   KQYVLPVEDEKLEALLELLKEHLKKGGKVLIFCPSKKMLDELAELLRKPGIKVAALHGDG 62

Query: 92  RTLDKDPCTIQEWNEGKIPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERI 151
              +++   ++++ EG+I +L A       G++L    ++++ + L W    + Q I R 
Sbjct: 63  SQEEREE-VLKDFREGEIVVLVATDVI-ARGIDLP-NVSVVINYDLPWSPSSYLQRIGRA 119

Query: 152 GVTRQRQAGFKRAVFVY 168
           G     +AG K    + 
Sbjct: 120 G-----RAGQKGTAILL 131


>gnl|CDD|36233 KOG1015, KOG1015, KOG1015, Transcription regulator XNP/ATRX, DEAD-box
            superfamily [Transcription].
          Length = 1567

 Score = 33.6 bits (76), Expect = 0.042
 Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 6/66 (9%)

Query: 122  GLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNTIDELVL 181
            G+NL    N ++ F   W+     Q I R+      + G  + V++Y  IAQ T++E + 
Sbjct: 1231 GINL-VAANRVIIFDASWNPSYDTQSIFRV-----YRFGQTKPVYIYRFIAQGTMEEKIY 1284

Query: 182  QRLRTK 187
            +R  TK
Sbjct: 1285 KRQVTK 1290


>gnl|CDD|35606 KOG0385, KOG0385, KOG0385, Chromatin remodeling complex WSTF-ISWI,
           small subunit [Transcription].
          Length = 971

 Score = 32.7 bits (74), Expect = 0.075
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 12/79 (15%)

Query: 120 GHGLNLQYGGNILVFFSLW---WDLEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNTI 176
           G G+NL     ++++ S W    DL+       RIG  +         V VY LI +NT+
Sbjct: 551 GLGINLTAADTVILYDSDWNPQVDLQA-MDRAHRIGQKKP--------VVVYRLITENTV 601

Query: 177 DELVLQRLRTKSTIQDLLL 195
           +E +++R   K  +  L++
Sbjct: 602 EEKIVERAAAKLRLDKLVI 620


>gnl|CDD|35608 KOG0387, KOG0387, KOG0387, Transcription-coupled repair protein
           CSB/RAD26 (contains SNF2 family DNA-dependent ATPase
           domain) [Transcription, Replication, recombination and
           repair].
          Length = 923

 Score = 32.3 bits (73), Expect = 0.10
 Identities = 25/87 (28%), Positives = 37/87 (42%), Gaps = 7/87 (8%)

Query: 98  PCTIQEWNEGK-IPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQ 156
              +  +NE + I +        G GLNL  G N ++ F   W+     Q  ER      
Sbjct: 587 QKLVDRFNEDESIFVFLLTTRVGGLGLNLT-GANRVIIFDPDWNPSTDNQARERA----- 640

Query: 157 RQAGFKRAVFVYYLIAQNTIDELVLQR 183
            + G K+ V VY L+   TI+E +  R
Sbjct: 641 WRIGQKKDVVVYRLMTAGTIEEKIYHR 667


>gnl|CDD|35519 KOG0298, KOG0298, KOG0298, DEAD box-containing helicase-like
            transcription factor/DNA repair protein [Replication,
            recombination and repair].
          Length = 1394

 Score = 28.1 bits (62), Expect = 2.0
 Identities = 12/47 (25%), Positives = 20/47 (42%)

Query: 148  IERIGVTRQRQAGFKRAVFVYYLIAQNTIDELVLQRLRTKSTIQDLL 194
             E   + R  + G KR  FV+  I   T++E +L  + +K       
Sbjct: 1300 DEAQAIGRVHRIGQKRPTFVHRFIVNETVEENILSLITSKEETLTKS 1346


>gnl|CDD|35610 KOG0389, KOG0389, KOG0389, SNF2 family DNA-dependent ATPase
           [Chromatin structure and dynamics].
          Length = 941

 Score = 28.0 bits (62), Expect = 2.0
 Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 7/88 (7%)

Query: 101 IQEWNEGK-IPLLFAHPASCGHGLNLQYGGNILVFFSLWWDLEEHQQMIERIGVTRQRQA 159
           I E+N  K I +      + G G+NL    N ++   + ++  + +Q  +R       + 
Sbjct: 820 IDEFNTDKDIFVFLLSTKAGGFGINLT-CANTVIIHDIDFNPYDDKQAEDRC-----HRV 873

Query: 160 GFKRAVFVYYLIAQNTIDELVLQRLRTK 187
           G  + V VY LI ++TI+E +L+  +TK
Sbjct: 874 GQTKPVTVYRLITKSTIEEGILRLAKTK 901


>gnl|CDD|35554 KOG0333, KOG0333, KOG0333, U5 snRNP-like RNA helicase subunit [RNA
           processing and modification].
          Length = 673

 Score = 27.3 bits (60), Expect = 3.2
 Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)

Query: 45  EKHWKEV-HDEKIKALEVIIEKANAAPIIV 73
           E+  + V  DEK K L  I+E     PII+
Sbjct: 493 EQKVEMVSEDEKRKKLIEILESNFDPPIII 522


>gnl|CDD|30596 COG0247, GlpC, Fe-S oxidoreductase [Energy production and
           conversion].
          Length = 388

 Score = 26.8 bits (58), Expect = 3.9
 Identities = 22/105 (20%), Positives = 33/105 (31%), Gaps = 13/105 (12%)

Query: 3   QYHKFQRELYCDLQGENIEAFNSASKTVKCLQLANGAVYYDEEKHWKEVHDEKIKALEVI 62
            Y     E    L  +NIEAF    +    +     A Y   +K + E+  E+   +  +
Sbjct: 193 AYRSGFLERAKKLAKKNIEAFKKLIEGGDPIVTVCPACYGALKKEYPELLGERALKVVDL 252

Query: 63  IE-------------KANAAPIIVAYHFNSDLARLQKAFPQGRTL 94
           +E                    IV YH    L R      + R L
Sbjct: 253 VELLAELLREGKLKLLPKLKGKIVTYHDPCHLRRGGGVVDEPREL 297


>gnl|CDD|147517 pfam05373, Pro_3_hydrox_C, L-proline 3-hydroxylase, C-terminal.
          Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases
          catalyse oxidative reactions in a range of metabolic
          processes. Proline 3-hydroxylase hydroxylates proline
          at position 3, the first of a 2-OG oxygenase catalysing
          oxidation of a free alpha-amino acid. The structure
          contains conserved motifs present in other 2-OG
          oxygenases including a jelly roll strand core and
          residues binding iron and 2-oxoglutarate, consistent
          with divergent evolution within the extended family.
          The structure differs significantly from many other
          2-OG oxygenases in possessing a discrete C-terminal
          helical domain.
          Length = 101

 Score = 26.7 bits (59), Expect = 4.9
 Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 3/43 (6%)

Query: 42 YDEEKHWKEVHDEKIKALEVIIEKANAAPIIV---AYHFNSDL 81
           DE K + +   E+I A   II +AN   I+      HF   +
Sbjct: 19 VDERKPFTDETKERILAFSGIISEANFRDIVFILSKLHFTYKV 61


>gnl|CDD|30833 COG0486, ThdF, Predicted GTPase [General function prediction only].
          Length = 454

 Score = 26.7 bits (59), Expect = 5.1
 Identities = 13/54 (24%), Positives = 27/54 (50%), Gaps = 5/54 (9%)

Query: 141 LEEHQQMIERIGVTRQRQAGFKRAVFVYYLIAQNT----IDELVLQRLRTKSTI 190
           + E   ++ERIG+ R ++A  + A  V +++  +      D  +++ L  K  I
Sbjct: 275 IRETDDVVERIGIERAKKA-IEEADLVLFVLDASQPLDKEDLALIELLPKKKPI 327


>gnl|CDD|38873 KOG3669, KOG3669, KOG3669, Uncharacterized conserved protein,
           contains dysferlin, TECPR and PH domains [General
           function prediction only].
          Length = 705

 Score = 26.6 bits (58), Expect = 5.6
 Identities = 8/23 (34%), Positives = 12/23 (52%)

Query: 139 WDLEEHQQMIERIGVTRQRQAGF 161
           W + E+  +  R GV+RQ   G 
Sbjct: 241 WAVTENGAVFYREGVSRQNPEGD 263


>gnl|CDD|34816 COG5219, COG5219, Uncharacterized conserved protein, contains RING
           Zn-finger [General function prediction only].
          Length = 1525

 Score = 25.9 bits (56), Expect = 8.3
 Identities = 17/77 (22%), Positives = 30/77 (38%), Gaps = 1/77 (1%)

Query: 39  AVYYDEEKHWKEVHDEKIKALEVIIEKANAAPIIVAYHFNSDLARLQKAFPQGRTLDKDP 98
           A+     K+ ++V +EKI+  + +          VA HF S  + L++   +        
Sbjct: 685 ALLPLVLKYPEDVFEEKIRLYKTLPVILFEDDGHVAAHFESIFSLLKEKALEDSGFSLKL 744

Query: 99  CT-IQEWNEGKIPLLFA 114
           C   QE    K+   F 
Sbjct: 745 CKDSQELKLNKVLNGFM 761


>gnl|CDD|133148 cd05481, retropepsin_like_LTR_1, Retropepsins_like_LTR; pepsin-like
           aspartate protease from retrotransposons with long
           terminal repeats.  Retropepsin of retrotransposons with
           long terminal repeats are pepsin-like aspartate
           proteases. While fungal and mammalian pepsins are
           bilobal proteins with structurally related N and
           C-terminals, retropepsins are half as long as their
           fungal and mammalian counterparts. The monomers are
           structurally related to one lobe of the pepsin molecule
           and retropepsins function as homodimers. The active site
           aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it
           does in pepsin. Retroviral aspartyl protease is
           synthesized as part of the POL polyprotein that contains
           an aspartyl protease, a reverse transcriptase, RNase H,
           and an integrase. The POL polyprotein undergoes specific
           enzymatic cleavage to yield the mature proteins. In
           aspartate peptidases, Asp residues are ligands of an
           activated water molecule in all examples where catalytic
           residues have been identified. This group of aspartate
           peptidases is classified by MEROPS as the peptidase
           family A2 (retropepsin family, clan AA), subfamily A2A.
          Length = 93

 Score = 25.7 bits (57), Expect = 9.5
 Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 2/45 (4%)

Query: 84  LQKAFPQGRT-LDKDPCTIQEWNEGKIPLLFAHPASCGHGLNLQY 127
           L+   P     L   P  +  +    IP+       C +  N +Y
Sbjct: 29  LKSLTPDKDPELRPSPVRLTAYGGSTIPVEGGVKLKCRYR-NPKY 72


>gnl|CDD|133364 cd04164, trmE, TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found
           in bacteria and eukaryotes.  It controls modification of
           the uridine at the wobble position (U34) of tRNAs that
           read codons ending with A or G in the mixed codon family
           boxes.  TrmE contains a GTPase domain that forms a
           canonical Ras-like fold.  It functions a molecular
           switch GTPase, and apparently uses a conformational
           change associated with GTP hydrolysis to promote the
           tRNA modification reaction, in which the conserved
           cysteine in the C-terminal domain is thought to function
           as a catalytic residue.  In bacteria that are able to
           survive in extremely low pH conditions, TrmE regulates
           glutamate-dependent acid resistance.
          Length = 157

 Score = 25.5 bits (57), Expect = 9.8
 Identities = 16/56 (28%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 141 LEEHQQMIERIGVTRQRQAGFKRAVFVYYLI-AQNTIDELVLQRLRTKSTIQDLLL 195
           + E +  IE+IG+ R R+A  + A  V ++I A   +DE  L+ L   +    +++
Sbjct: 59  IRETEDEIEKIGIERAREA-IEEADLVLFVIDASRGLDEEDLEILELPADKPIIVV 113


  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
   0.322    0.137    0.414 

Gapped
Lambda     K      H
   0.267   0.0630    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,532,327
Number of extensions: 130593
Number of successful extensions: 308
Number of sequences better than 10.0: 1
Number of HSP's gapped: 304
Number of HSP's successfully gapped: 27
Length of query: 205
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 116
Effective length of database: 4,340,536
Effective search space: 503502176
Effective search space used: 503502176
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 (21.9 bits)
S2: 55 (25.2 bits)