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)