RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254781082|ref|YP_003065495.1| hypothetical protein CLIBASIA_04920 [Candidatus Liberibacter asiaticus str. psy62] (108 letters) >gnl|CDD|178486 PLN02898, PLN02898, HMP-P kinase/thiamin-monophosphate pyrophosphorylase. Length = 502 Score = 30.1 bits (68), Expect = 0.13 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 6/55 (10%) Query: 21 SIVEALRKAKPSMSDLAMLSVEERDAILDDLEKNGSSDYSFVNDLWERLKYLRDL 75 SI+ ALR+ ++ + +V+E A+L V D+ K L L Sbjct: 126 SILSALREELLPLATIVTPNVKEASALLGGDPLE------TVADMRSAAKELHKL 174 >gnl|CDD|183311 PRK11780, PRK11780, isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional. Length = 217 Score = 27.8 bits (63), Expect = 0.57 Identities = 12/30 (40%), Positives = 19/30 (63%) Query: 19 RNSIVEALRKAKPSMSDLAMLSVEERDAIL 48 RN +VE+ R A+ + DLA E+ DA++ Sbjct: 61 RNVLVESARIARGEIKDLAEADAEDFDALI 90 >gnl|CDD|177604 PHA03367, PHA03367, single-stranded DNA binding protein; Provisional. Length = 1115 Score = 27.7 bits (62), Expect = 0.77 Identities = 10/50 (20%), Positives = 18/50 (36%), Gaps = 1/50 (2%) Query: 39 LSVEERDAILDDLEKNGSSDYSFVNDLWERLKYLRDLPVYNFSLDYVSRF 88 L DD+ + + E+L+ L D V ++SL+ Sbjct: 1018 LGDRCASLTSDDVLFYLGGYEILADSVMEKLQTLADSGV-DWSLENARSV 1066 >gnl|CDD|162267 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733 Score = 26.8 bits (59), Expect = 1.4 Identities = 14/35 (40%), Positives = 21/35 (60%) Query: 9 REFIEYWRLERNSIVEALRKAKPSMSDLAMLSVEE 43 EF++ ++E +EAL+K KPS+S ML E Sbjct: 690 EEFLKDLKVEMRHFLEALKKVKPSVSKEDMLRYER 724 >gnl|CDD|182853 PRK10939, PRK10939, autoinducer-2 (AI-2) kinase; Provisional. Length = 520 Score = 26.5 bits (59), Expect = 1.7 Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 6/40 (15%) Query: 1 MNTDVSRNREFIEYWRLERNSIVEALRKAKPSMSDLAMLS 40 M D+ +N W+L I +AL+KA SD+A +S Sbjct: 46 MEFDLEKN------WQLACQCIRQALQKAGIPASDIAAVS 79 >gnl|CDD|134335 PRK00625, PRK00625, shikimate kinase; Provisional. Length = 173 Score = 26.3 bits (58), Expect = 1.7 Identities = 18/83 (21%), Positives = 32/83 (38%), Gaps = 31/83 (37%) Query: 14 YWRLERNSIVEALRKAKPSMSDLAMLSVEERDAILDDLEKNGSSDYSFVNDLWERLKYLR 73 Y RL++ + E L+ A PS+ ++ L +R+ +R Sbjct: 110 YQRLQKRGLPERLKHA-PSLEEI----------------------------LSQRIDRMR 140 Query: 74 DLPVYNFSLDYVSRF--HSFVSD 94 + Y FSLD+V+ S + Sbjct: 141 SIADYIFSLDHVAETSSESLMRA 163 >gnl|CDD|179957 PRK05183, hscA, chaperone protein HscA; Provisional. Length = 616 Score = 26.3 bits (59), Expect = 1.9 Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 3/39 (7%) Query: 9 REFIEYWRLERNSIVEALRKAKPSMSDLAMLSVEERDAI 47 R E ++E ++EAL+ A +D +LS ER AI Sbjct: 527 RALAE-QKVEAERVLEALQAA--LAADGDLLSAAERAAI 562 >gnl|CDD|178924 PRK00197, proA, gamma-glutamyl phosphate reductase; Provisional. Length = 417 Score = 26.2 bits (59), Expect = 2.1 Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 4/40 (10%) Query: 19 RNSIVEALRKAKPSMSDLAMLSVEERDAIL----DDLEKN 54 + E R+AK + LA LS +++ L D LE N Sbjct: 3 MEYLEELGRRAKAASRKLAQLSTAQKNRALLAIADALEAN 42 >gnl|CDD|132460 TIGR03419, NifU_clost, FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not. Length = 121 Score = 25.9 bits (57), Expect = 2.3 Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 1/56 (1%) Query: 1 MNTDVSRNREFIEYWRLERNSIVEALRKAKPSMSDLAMLSVEE-RDAILDDLEKNG 55 M T++ + + E W L ++ EAL P ++L+ E AI D EKNG Sbjct: 66 MATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYREKNG 121 >gnl|CDD|149673 pfam08691, Nse5, DNA repair protein Nse5. Nse5 is a non essential nuclear protein that is critical for chromosome segregation in fission yeast. Nse5 forms a dimer with Nse6 and facilitates DNA repair as part of the Smc5-Smc6 holocomplex. Length = 344 Score = 25.5 bits (56), Expect = 3.5 Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 2/62 (3%) Query: 44 RDAILDDLEKNGSSDYSFVNDLWERLKYLRDLPVYNFSLDYVSRFHSFVSDEVAVWYEVT 103 I KN S + + ++L + LD +++ VSD+ W+ +T Sbjct: 55 EKDINASPRKNKSIVTTPHEERQKQLSKKFTNSIPTRLLDELAK--DRVSDKYKDWHFIT 112 Query: 104 KE 105 + Sbjct: 113 EN 114 >gnl|CDD|163351 TIGR03607, TIGR03607, patatin-related protein. This bacterial protein family contains an N-terminal patatin domain, where patatins are plant storage proteins capable of phospholipase activity (see pfam01734). Regions of strong sequence conservation are separated by regions of significant sequence and length variability. Members of the family are distributed sporadically among bacteria. The function is unknown. Length = 739 Score = 25.5 bits (56), Expect = 3.5 Identities = 10/30 (33%), Positives = 13/30 (43%) Query: 1 MNTDVSRNREFIEYWRLERNSIVEALRKAK 30 N V R R ++ R E +VEAL Sbjct: 357 HNRRVRRLRAIVDARRPEVARLVEALFGRT 386 >gnl|CDD|181873 PRK09457, astD, succinylglutamic semialdehyde dehydrogenase; Reviewed. Length = 487 Score = 25.3 bits (56), Expect = 3.5 Identities = 13/29 (44%), Positives = 16/29 (55%), Gaps = 3/29 (10%) Query: 20 NSIVEALRKAKPSMSDLAMLSVEERDAIL 48 ++ V A R A P A LS EER AI+ Sbjct: 40 DAAVRAARAAFP---AWARLSFEERQAIV 65 >gnl|CDD|132128 TIGR03084, TIGR03084, conserved hypothetical protein TIGR03084. This family, like Pfam family pfam07398, belongs to the larger set of probable enzymes modeled by TIGRFAMs family TIGR03083. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family is uncharacterized. Length = 253 Score = 25.0 bits (55), Expect = 4.7 Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 9/41 (21%) Query: 9 REFIEYWRLERNSIVEALRKAK---------PSMSDLAMLS 40 E + WR R ++ EALR A P MS +M + Sbjct: 89 AELLARWRAGRAALAEALRAAPPGARVPWFGPPMSAASMAT 129 >gnl|CDD|180205 PRK05691, PRK05691, peptide synthase; Validated. Length = 4334 Score = 24.7 bits (54), Expect = 4.7 Identities = 8/18 (44%), Positives = 13/18 (72%) Query: 33 MSDLAMLSVEERDAILDD 50 +S+L +L +ERD +LD Sbjct: 3691 LSELPLLGEQERDFLLDG 3708 >gnl|CDD|181878 PRK09463, fadE, acyl-CoA dehydrogenase; Reviewed. Length = 777 Score = 24.8 bits (55), Expect = 5.1 Identities = 8/28 (28%), Positives = 13/28 (46%), Gaps = 6/28 (21%) Query: 20 NSIVEALRKAKPSMSDLAMLSVEERDAI 47 +++ RK P MS ER+A+ Sbjct: 29 APLLKWFRKVLPPMSQ------TEREAL 50 >gnl|CDD|163284 TIGR03480, HpnN, hopanoid biosynthesis associated RND transporter like protein HpnN. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921. Length = 862 Score = 24.6 bits (54), Expect = 5.8 Identities = 7/27 (25%), Positives = 13/27 (48%) Query: 23 VEALRKAKPSMSDLAMLSVEERDAILD 49 V A+RK P + + +E D ++ Sbjct: 686 VRAVRKVAPDATGAPVSILESGDTVVG 712 >gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift. Length = 360 Score = 24.3 bits (53), Expect = 7.2 Identities = 13/49 (26%), Positives = 27/49 (55%), Gaps = 4/49 (8%) Query: 8 NREFIEYWRLERNSIVEA---LRKAKPSMSDLAMLSVEERDAILDDLEK 53 + EY + + + I EA L ++ P M ++A +EE + +++LE+ Sbjct: 49 VDCYREYQQAQED-IKEAKEILEESDPEMREMAKEELEELEEKIEELEE 96 >gnl|CDD|179778 PRK04195, PRK04195, replication factor C large subunit; Provisional. Length = 482 Score = 24.1 bits (53), Expect = 7.7 Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 1/23 (4%) Query: 7 RNR-EFIEYWRLERNSIVEALRK 28 RN IE+ RL SIV L++ Sbjct: 149 RNACLMIEFKRLSTRSIVPVLKR 171 >gnl|CDD|173383 PTZ00089, PTZ00089, transketolase; Provisional. Length = 661 Score = 23.9 bits (52), Expect = 8.6 Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 2/30 (6%) Query: 79 NFSLDYVSRFHSFVSDEVAVWYEVTKEKKK 108 F LD +FH VS+EV ++E EKKK Sbjct: 278 LFGLDPEKKFH--VSEEVRQFFEQHVEKKK 305 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 0.317 0.132 0.383 Gapped Lambda K H 0.267 0.0668 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,806,104 Number of extensions: 104107 Number of successful extensions: 279 Number of sequences better than 10.0: 1 Number of HSP's gapped: 279 Number of HSP's successfully gapped: 42 Length of query: 108 Length of database: 5,994,473 Length adjustment: 74 Effective length of query: 34 Effective length of database: 4,395,481 Effective search space: 149446354 Effective search space used: 149446354 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 (23.2 bits)