RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780496|ref|YP_003064909.1| integration host factor
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
         (114 letters)



>gnl|CDD|178961 PRK00285, ihfA, integration host factor subunit alpha; Reviewed.
          Length = 99

 Score =  112 bits (282), Expect = 2e-26
 Identities = 35/99 (35%), Positives = 60/99 (60%)

Query: 3   KTITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSR 62
            T+T++DL +++ ++ GLS++++   V   F EI D+   GE +K+S F  F ++ K  R
Sbjct: 1   MTLTKADLAEALFEKVGLSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQR 60

Query: 63  VGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDDMRGRK 101
            GRN +T +E+ I  RRVV F+ S  LK R+ +    ++
Sbjct: 61  PGRNPKTGEEIPISARRVVTFRPSQKLKSRVENAAPKKQ 99


>gnl|CDD|130060 TIGR00987, himA, integration host factor, alpha subunit.  This
          protein forms a site-specific DNA-binding heterodimer
          with the integration host factor beta subunit. It is
          closely related to the DNA-binding protein HU.
          Length = 96

 Score = 84.2 bits (208), Expect = 6e-18
 Identities = 31/90 (34%), Positives = 52/90 (57%)

Query: 4  TITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRV 63
           +T++++ + +  E GLS++++   V   F EI  +   GE +K+S F  F ++ K  R 
Sbjct: 1  ALTKAEMSEYLFDELGLSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRP 60

Query: 64 GRNLQTNQEVKIDPRRVVVFKASSILKKRI 93
          GRN +T +E+ I  RRVV F+    LK R+
Sbjct: 61 GRNPKTGEEIPITARRVVTFRPGQKLKSRV 90


>gnl|CDD|128689 smart00411, BHL, bacterial (prokaryotic) histone like domain. 
          Length = 90

 Score = 81.8 bits (203), Expect = 4e-17
 Identities = 29/89 (32%), Positives = 56/89 (62%)

Query: 5  ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64
          +T+S+L+ +I+++ GLS+KD+   V      I ++  +GE +++  F TF V+++ +R G
Sbjct: 1  MTKSELIDAIAEKAGLSKKDAKAAVDAFLEIITEALKKGEKVELRGFGTFEVRERKAREG 60

Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93
          RN +T +E++I  ++V  FK    LK  +
Sbjct: 61 RNPKTGEEIEIPAKKVPKFKPGKALKDAV 89


>gnl|CDD|178925 PRK00199, ihfB, integration host factor subunit beta; Reviewed.
          Length = 94

 Score = 58.7 bits (143), Expect = 3e-10
 Identities = 28/89 (31%), Positives = 52/89 (58%), Gaps = 1/89 (1%)

Query: 6  TRSDLVKSISKEFG-LSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64
          T+S+L++ ++     LS KD    V  +  E+ D+  RG+ I+I  F +F +  +  RVG
Sbjct: 2  TKSELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFSLHYRPPRVG 61

Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93
          RN +T ++V+++ + V  FK    L++R+
Sbjct: 62 RNPKTGEKVELEEKYVPHFKPGKELRERV 90


>gnl|CDD|130061 TIGR00988, hip, integration host factor, beta subunit.  This
          protein forms a site-specific DNA-binding heterodimer
          with the homologous integration host factor alpha
          subunit. It is closely related to the DNA-binding
          protein HU.
          Length = 94

 Score = 57.6 bits (139), Expect = 8e-10
 Identities = 26/90 (28%), Positives = 47/90 (52%), Gaps = 1/90 (1%)

Query: 5  ITRSDLVKSISKEFG-LSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRV 63
          +T+S+L++ I+ +   L  KD    V T+   +  +  +G+ I+I  F +F +  +  R 
Sbjct: 1  MTKSELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRT 60

Query: 64 GRNLQTNQEVKIDPRRVVVFKASSILKKRI 93
          GRN +T   V++D + V  FK    L+ R 
Sbjct: 61 GRNPKTGDSVELDGKYVPHFKPGKELRDRA 90


>gnl|CDD|170612 PRK10664, PRK10664, transcriptional regulator HU subunit beta;
          Provisional.
          Length = 90

 Score = 47.7 bits (113), Expect = 6e-07
 Identities = 25/89 (28%), Positives = 47/89 (52%)

Query: 5  ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64
          + +S L+  I+    +S+  + R +  +   + +S   G+ + +  F TF VK++ +R G
Sbjct: 1  MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTG 60

Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93
          RN QT +E+ I   +V  F+A   LK  +
Sbjct: 61 RNPQTGKEITIAAAKVPSFRAGKALKDAV 89


>gnl|CDD|138142 PRK10753, PRK10753, transcriptional regulator HU subunit alpha;
          Provisional.
          Length = 90

 Score = 45.2 bits (106), Expect = 4e-06
 Identities = 25/89 (28%), Positives = 45/89 (50%)

Query: 5  ITRSDLVKSISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKGSRVG 64
          + ++ L+  I+ +  LS+  +   + +    I +S   G+A+++  F TF V  +  R G
Sbjct: 1  MNKTQLIDVIADKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTG 60

Query: 65 RNLQTNQEVKIDPRRVVVFKASSILKKRI 93
          RN QT +E+KI    V  F +   LK  +
Sbjct: 61 RNPQTGKEIKIAAANVPAFVSGKALKDAV 89


>gnl|CDD|151379 pfam10932, DUF2783, Protein of unknown function (DUF2783).  This
          is a bacterial family of uncharacterized protein.
          Length = 60

 Score = 26.1 bits (58), Expect = 2.1
 Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 4/34 (11%)

Query: 19 GLSRKDS----TRFVTTLFNEICDSAVRGEAIKI 48
          GLS + S     R +  L N I D AV  EAI +
Sbjct: 23 GLSDEQSAALNARLILLLANHIGDRAVLREAIAL 56


>gnl|CDD|148935 pfam07591, DUF1557, Protein of unknown function (DUF1557).  A
           cluster of homologous proteins identified in Leptospira
           interrogans. One member has been predicted to be a
           phenazine biosynthesis family protein.
          Length = 130

 Score = 25.2 bits (55), Expect = 4.2
 Identities = 10/41 (24%), Positives = 19/41 (46%)

Query: 20  LSRKDSTRFVTTLFNEICDSAVRGEAIKISSFATFHVKQKG 60
           L    + + V  +  EI D  ++   +K++ F T+ V   G
Sbjct: 84  LDSSGNVQTVENIKLEITDKPLKVYNLKVADFHTYFVGTNG 124


>gnl|CDD|162848 TIGR02414, pepN_proteo, aminopeptidase N, Escherichia coli type.
           The M1 family of zinc metallopeptidases contains a
           number of distinct, well-separated clades of proteins
           with aminopeptidase activity. Several are designated
           aminopeptidase N, EC 3.4.11.2, after the Escherichia
           coli enzyme, suggesting a similar activity profile. This
           family consists of all aminopeptidases closely related
           to E. coli PepN and presumed to have similar (not
           identical) function. Nearly all are found in
           Proteobacteria, but members are found also in
           Cyanobacteria, plants, and apicomplexan parasites. This
           family differs greatly in sequence from the family of
           aminopeptidases typified by Streptomyces lividans PepN
           (TIGR02412), from the membrane bound aminopeptidase N
           family in animals, etc.
          Length = 863

 Score = 25.0 bits (55), Expect = 5.0
 Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)

Query: 41  VRGEA-IKISSFATFHVKQKGSRVGRNLQT 69
           VR E+ ++I++F T  V +KG+ V R L T
Sbjct: 356 VRPESYVEINNFYTATVYEKGAEVIRMLHT 385


>gnl|CDD|180637 PRK06599, PRK06599, DNA topoisomerase I; Validated.
          Length = 675

 Score = 24.4 bits (54), Expect = 6.3
 Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)

Query: 14  ISKEFGLSRKDSTRFVTTLFNEICDSAVRGEAIK 47
           I++    ++         +FNEI   AV+ EAI+
Sbjct: 94  IAEVLKEAKLKDKNVKRVVFNEITKKAVQ-EAIE 126


>gnl|CDD|163565 TIGR03853, matur_matur, probable metal-binding protein.  This
          protein family was identified by searching with a
          phylogenetic profile based on an anaerobic
          sulfatase-maturase enzyme, which contains multiple
          4Fe-4S clusters. The linkages by phylogenetic profiling
          and by iron-sulfur cluster-related motifs together
          suggest this protein may be an accessory protein to
          certain maturases in sulfatase/maturase systems.
          Length = 77

 Score = 24.1 bits (53), Expect = 7.6
 Identities = 9/28 (32%), Positives = 14/28 (50%), Gaps = 4/28 (14%)

Query: 3  KTITRSDLVKSISKEFGLSRKDSTRFVT 30
          +  TR  L  +I ++FG    +  RF T
Sbjct: 16 EPYTRESLKAAIEQKFG----EDARFHT 39


>gnl|CDD|165170 PHA02820, PHA02820, phospholipase-D-like protein; Provisional.
          Length = 424

 Score = 24.2 bits (52), Expect = 7.8
 Identities = 11/31 (35%), Positives = 16/31 (51%)

Query: 18 FGLSRKDSTRFVTTLFNEICDSAVRGEAIKI 48
          + LS +  T F T + NEI     RG  ++I
Sbjct: 49 WSLSDEVGTNFGTMILNEIIQLPKRGVRVRI 79


>gnl|CDD|173427 PTZ00137, PTZ00137, 2-Cys peroxiredoxin; Provisional.
          Length = 261

 Score = 24.1 bits (52), Expect = 8.1
 Identities = 8/17 (47%), Positives = 12/17 (70%)

Query: 8   SDLVKSISKEFGLSRKD 24
           SD+ + +SK FGL R +
Sbjct: 168 SDISREVSKSFGLLRDE 184


>gnl|CDD|181196 PRK08010, PRK08010, pyridine nucleotide-disulfide oxidoreductase;
           Provisional.
          Length = 441

 Score = 23.8 bits (51), Expect = 9.8
 Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)

Query: 61  SRVGRNLQTNQEVKIDPRRVVVFKASSILKKRIMDDMRG 99
           SRVG   +  +E   D + VV    ++I + R+M+D RG
Sbjct: 339 SRVGMTEEQARESGADIQ-VVTLPVAAIPRARVMNDTRG 376


  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
   0.318    0.131    0.355 

Gapped
Lambda     K      H
   0.267   0.0781    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,652,133
Number of extensions: 87096
Number of successful extensions: 189
Number of sequences better than 10.0: 1
Number of HSP's gapped: 189
Number of HSP's successfully gapped: 25
Length of query: 114
Length of database: 5,994,473
Length adjustment: 79
Effective length of query: 35
Effective length of database: 4,287,441
Effective search space: 150060435
Effective search space used: 150060435
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 (21.7 bits)
S2: 50 (22.9 bits)