RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780748|ref|YP_003065161.1| integration host factor, beta
subunit [Candidatus Liberibacter asiaticus str. psy62]
         (100 letters)



>gnl|CDD|143973 pfam00216, Bac_DNA_binding, Bacterial DNA-binding protein. 
          Length = 90

 Score = 98.0 bits (245), Expect = 4e-22
 Identities = 41/91 (45%), Positives = 56/91 (61%), Gaps = 1/91 (1%)

Query: 1  MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
          M K  LI  IA+K   L+ +D E IV+  L+ +T+AL  G +VE+RGFG+F VR+R AR 
Sbjct: 1  MTKKELIKAIAEKTG-LSKKDAEAIVDAFLDVITEALKKGEKVELRGFGTFEVRERKART 59

Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLN 91
           R P   + I +  K V  F+ GK LKE +N
Sbjct: 60 GRNPKTGEEIKIPAKKVVKFKPGKELKEAVN 90


>gnl|CDD|31119 COG0776, HimA, Bacterial nucleoid DNA-binding protein [DNA
          replication, recombination, and repair].
          Length = 94

 Score = 91.0 bits (226), Expect = 6e-20
 Identities = 46/93 (49%), Positives = 61/93 (65%), Gaps = 1/93 (1%)

Query: 1  MIKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARL 60
          M KS LI  IA+K   L+ +D E+ V+  LEE+T+ALA G RVE+RGFG+F VR+RAAR 
Sbjct: 2  MTKSELIDAIAEKA-GLSKKDAEEAVDAFLEEITEALAKGERVELRGFGTFEVRERAART 60

Query: 61 ARAPLAQKVISVEEKMVPFFRAGKNLKERLNSP 93
           R P   + I +  K VP F+ GK LK+ +N  
Sbjct: 61 GRNPKTGEEIKIPAKKVPKFKPGKALKDAVNGA 93


>gnl|CDD|29683 cd00591, HU_IHF, Integration host factor (IHF) and HU are small
          heterodimeric members of the DNABII protein family that
          bind and bend DNA, functioning as architectural factors
          in many cellular processes including transcription,
          site-specific recombination, and higher-order
          nucleoprotein complex assembly. The dimer subunits
          associate to form a compact globular core from which
          two beta ribbon arms (one from each subunit) protrude.
          The beta arms track and bind the DNA minor groove.
          Despite sequence and structural similarity, IHF and HU
          can be distinguished by their different DNA substrate
          preferences..
          Length = 87

 Score = 87.4 bits (217), Expect = 7e-19
 Identities = 39/87 (44%), Positives = 54/87 (62%), Gaps = 1/87 (1%)

Query: 3  KSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLAR 62
          KS LI  IA+K   L+ +D E  V+  L+ +T+ALA G +VE+ GFG+F VR+RAAR  R
Sbjct: 2  KSELIEAIAEKT-GLSKKDAEAAVDAFLDVITEALAKGEKVELPGFGTFEVRERAARTGR 60

Query: 63 APLAQKVISVEEKMVPFFRAGKNLKER 89
           P   + I +  K V  F+ GK LK+ 
Sbjct: 61 NPKTGEEIKIPAKKVVKFKPGKALKDA 87


>gnl|CDD|31304 COG1107, COG1107, Archaea-specific RecJ-like exonuclease, contains
           DnaJ-type Zn finger domain [DNA replication,
           recombination, and repair].
          Length = 715

 Score = 29.9 bits (67), Expect = 0.17
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 15  PKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLARAPLAQKVISVE 73
                 D+ +IV  L EE+ +A  +GG  E  G   F    R   L     A+K+ +++
Sbjct: 658 ATDAVFDLNRIVKELEEELPEAGVDGGGHETAGSIKFVEGLRKEVLGA--FAEKIAALK 714


>gnl|CDD|33156 COG3347, COG3347, Uncharacterized conserved protein [Function
           unknown].
          Length = 404

 Score = 26.1 bits (57), Expect = 2.2
 Identities = 21/82 (25%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 15  PKLNYQDVEKIVNMLLEEMTQALANGGRVEIRGFGSFSVRKRAARLAR-APLAQKVISVE 73
            K  Y+ +  IVN   E +      GG+V      S +   R A  A  AP+ +  +S +
Sbjct: 200 AKEAYERMISIVNEAEEYLA---RRGGKV----AKSLARPVRLAIAADLAPVIRGAVSEK 252

Query: 74  EKMVPFFRAGKNLKERLNSPDS 95
           +K +        + E  NS D 
Sbjct: 253 KKKIYRLDDSDAVLEFANSLDL 274


>gnl|CDD|38992 KOG3788, KOG3788, KOG3788, Predicted divalent cation transporter
           [Inorganic ion transport and metabolism].
          Length = 441

 Score = 25.2 bits (55), Expect = 3.4
 Identities = 17/57 (29%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 45  IRGFGSFSVRKRAARLARAPLAQKVISVEEKMVPFFRAGK-NLKERLNSPDSTLSNS 100
           + G G  S     A   +  L ++V  +   +VP     K NL+  L S  STL+N 
Sbjct: 39  LAGLGLISAGLVLAIAEKWELFKEVPEIL-ILVPALLGLKGNLEMTLASRLSTLANL 94


>gnl|CDD|29678 cd01916, ACS_1, Acetyl-CoA synthase (ACS), also known as acetyl-CoA
           decarbonylase, is found in acetogenic and methanogenic
           organisms and is responsible for the synthesis and
           breakdown of acetyl-CoA.  ACS forms a heterotetramer
           with carbon monoxide dehydrogenase (CODH) consisting of
           two ACS and two CODH subunits. CODH reduces carbon
           dioxide to carbon monoxide and ACS then synthesizes
           acetyl-CoA from carbon monoxide, CoA, and a methyl group
           donated by another protein (CoFeSP).  ACS has three
           structural domains, an N-terminal rossman fold domain
           with a helical region at its N-terminus which interacts
           with CODH, and two alpha + beta fold domains.  A Ni-Fe-S
           center referred to as the A-cluster is located in the
           C-terminal domain. A large cavity exists between the
           three domains which may bind CoA..
          Length = 731

 Score = 24.8 bits (54), Expect = 4.7
 Identities = 9/37 (24%), Positives = 20/37 (54%), Gaps = 1/37 (2%)

Query: 2   IKSSLIGTIAKKNPKLNYQDVEKIVNMLLEEMTQALA 38
           +++ +I T+    PK    D+E+ +    E++ Q L+
Sbjct: 103 VEAPIIRTVVGIKPK-TLGDLEEALEYAEEQIVQLLS 138


>gnl|CDD|30417 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
           modification, protein turnover, chaperones].
          Length = 750

 Score = 24.9 bits (54), Expect = 5.4
 Identities = 10/41 (24%), Positives = 15/41 (36%), Gaps = 4/41 (9%)

Query: 15  PKLNYQD----VEKIVNMLLEEMTQALANGGRVEIRGFGSF 51
           P L   +         N  + +  + L  G  V I+G G F
Sbjct: 181 PHLFLVNHDGEAIAEANEAIRKAAKLLKVGKIVAIKGIGGF 221


>gnl|CDD|173966 cd08047, TAF7, TATA Binding Protein (TBP) Associated Factor 7
           (TAF7) is one of several TAFs that bind TBP and is
           involved in forming Transcription Factor IID (TFIID)
           complex.  The TATA Binding Protein (TBP) Associated
           Factor 7 (TAF7) is one of several TAFs that bind TBP and
           are involved in forming the Transcription Factor IID
           (TFIID) complex. TFIID is one of seven General
           Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE,
           TFIIF, and TFIID) that are involved in accurate
           initiation of transcription by RNA polymerase II in
           eukaryotes. TFIID plays an important role in the
           recognition of promoter DNA and assembly of the
           preinitiation complex. TFIID complex is composed of the
           TBP and at least 13 TAFs. TAFs are named after their
           electrophoretic mobility in polyacrylamide gels in
           different species. A new, unified nomenclature has been
           suggested for the pol II TAFs to show the relationship
           between TAF orthologs and paralogs. Several hypotheses
           are proposed for TAFs functions such as serving as
           activator-binding sites, core-promoter recognition or a
           role in essential catalytic activity. Each TAF, with the
           help of a specific activator, is required only for
           expression of subset of genes and is not universally
           involved for transcription as are GTFs. TAF7 is involved
           in the regulation of the transition from PIC assembly to
           initiation and elongation. In yeast and human cells,
           TAFs have been found as components of other complexes
           besides TFIID. Several TAFs interact via histone-fold
           (HFD) motifs; the HFD is the interaction motif involved
           in heterodimerization of the core histones and their
           assembly into nucleosome octamers.
          Length = 162

 Score = 24.5 bits (54), Expect = 6.4
 Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 3/28 (10%)

Query: 12  KKNPKLNY---QDVEKIVNMLLEEMTQA 36
           +K P       ++VEK V  LL+E T+A
Sbjct: 127 RKTPSKKIAEIEEVEKEVKRLLKEDTEA 154


>gnl|CDD|39361 KOG4159, KOG4159, KOG4159, Predicted E3 ubiquitin ligase
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 398

 Score = 24.6 bits (53), Expect = 6.9
 Identities = 9/31 (29%), Positives = 17/31 (54%)

Query: 69  VISVEEKMVPFFRAGKNLKERLNSPDSTLSN 99
           ++  E ++   F A ++LK RL + D  L+ 
Sbjct: 352 LLPSEARLKSEFLAMRSLKNRLTAIDRELTL 382


>gnl|CDD|112537 pfam03727, Hexokinase_2, Hexokinase.  Hexokinase (EC:2.7.1.1)
           contains two structurally similar domains represented by
           this family and pfam00349. Some members of the family
           have two copies of each of these domains.
          Length = 238

 Score = 24.2 bits (53), Expect = 7.8
 Identities = 10/25 (40%), Positives = 13/25 (52%)

Query: 52  SVRKRAARLARAPLAQKVISVEEKM 76
           +V  RAARL  A LA  +  + E  
Sbjct: 155 AVSTRAARLCAAGLAAILQKIRENR 179


>gnl|CDD|36355 KOG1140, KOG1140, KOG1140, N-end rule pathway, recognition
           component UBR1 [Posttranslational modification, protein
           turnover, chaperones].
          Length = 1738

 Score = 23.8 bits (51), Expect = 9.5
 Identities = 4/23 (17%), Positives = 9/23 (39%)

Query: 15  PKLNYQDVEKIVNMLLEEMTQAL 37
                 D E  ++ ++EE    +
Sbjct: 738 VDYQSNDTEDTISFMIEEFLALI 760


  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
   0.315    0.130    0.344 

Gapped
Lambda     K      H
   0.267   0.0726    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,107,818
Number of extensions: 50968
Number of successful extensions: 179
Number of sequences better than 10.0: 1
Number of HSP's gapped: 178
Number of HSP's successfully gapped: 24
Length of query: 100
Length of database: 6,263,737
Length adjustment: 68
Effective length of query: 32
Effective length of database: 4,794,325
Effective search space: 153418400
Effective search space used: 153418400
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: 51 (23.4 bits)